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AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonia Araucaria species (Araucariaceae)
Abstract
Premise of the study:
Despite its small size, New Caledonia is characterized by a very diverse flora and striking environmental gradients, which make it an ideal setting to study species diversification. Thirteen of the 19 Araucaria species are endemic to the territory and form a monophyletic group, but patterns and processes that lead to such a high species richness are largely unexplored.
Methods:
We used 142 polymorphic AFLP markers and performed analyses based on Bayesian clustering algorithms, genetic distances, and cladistics on 71 samples representing all New Caledonian Araucaria species. We examined correlations between the inferred evolutionary relationships and shared morphological, ecological, or geographic parameters among species, to investigate evolutionary processes that may have driven speciation.
Key results:
We showed that genetic divergence among the present New Caledonian Araucaria species is low, suggesting recent diversification rather than pre-existence on Gondwana. We identified three genetic groups that included small-leaved, large-leaved, and coastal species, but detected no association with soil preference, ecological habitat, or rainfall. The observed patterns suggested that speciation events resulted from both differential adaptation and vicariance. Last, we hypothesize that speciation is ongoing and/or there are cryptic species in some genetically (sometimes also morphologically) divergent populations.
Conclusions:
Further data are required to provide better resolution and understanding of the diversification of New Caledonian Araucaria species. Nevertheless, our study allowed insights into their evolutionary relationships and provides a framework for future investigations on the evolution of this emblematic group of plants in one of the world's biodiversity hotspots.
... Результатами палеонтологических и сравнительно-морфологических исследований (ксилотомических, в первую очередь) обосновывали древность рода Araucaria (и семейства Araucariaceae в целом), а дизъюнктивный ареал, по мнению большинства авторов XX в., бесспорно указывал на реликтовость рода (Pilger, 1926;Gaussen, 1970;Page, 1990). Однако современные молекулярно-генетические исследования показали, например, что среди 13 эндемичных новокаледонских видов Araucaria генетическая диверсификация довольно низкая, что говорит о недавней (в масштабах геологического времени) дивергенции исследованных таксонов (Gaudeul et al., 2012). Это ставит под сомнение классическую идею о том, что семейство Araucariaceae является реликтовым. ...
... Это ставит под сомнение классическую идею о том, что семейство Araucariaceae является реликтовым. В цитируемой работе (Gaudeul et al., 2012) были определены и основные «генетические группы» видов, которые также отличаются друг от друга морфологическими и/или экологическими признаками (Laubenfels, 1972 (Gaudeul et al., 2012). Очевидно, что традиционные взгляды на эволюцию рода Araucaria во времени и пространстве, как минимум, нуждаются в ревизии (Gilmore, Hill, 1997;Setoguchi et al., 1998). ...
... Это ставит под сомнение классическую идею о том, что семейство Araucariaceae является реликтовым. В цитируемой работе (Gaudeul et al., 2012) были определены и основные «генетические группы» видов, которые также отличаются друг от друга морфологическими и/или экологическими признаками (Laubenfels, 1972 (Gaudeul et al., 2012). Очевидно, что традиционные взгляды на эволюцию рода Araucaria во времени и пространстве, как минимум, нуждаются в ревизии (Gilmore, Hill, 1997;Setoguchi et al., 1998). ...
The analysis of molecular data of all 19 recent species of the genus Araucaria Juss. (Araucariaceae) wascarried out and original cladogramm was build. Based on the cladogramm, the map of correlations of the phylogeneticrelationships and the distribution of all recent Araucaria species is proposed.
... This suggests a considerable contraction through the Cenozoic of both the genus and the sections it contains. Section Eutacta has the highest extant species diversity in the genus by far, but today the majority of these species occur in New Caledonia, and this appears to represent relatively recent speciation (Gaudeul et al. 2012;Kranitz et al. 2014). However, the fossil record indicates a more widespread past distribution of section Eutacta, including recent records of leafy shoots of certain affinity with section Eutacta from the late Eocene Loreto Formation in southern Chile (Ohsawa et al. 2016) and a record of a bract-scale complex and associated foliage, tentatively assigned to section Eutacta, from the early-middle Eocene of King George Island in the Antarctic Peninsula (Shi et al. 2018). ...
... Leaves of section Eutacta are easily distinguished from the other extant sections by their stomatal orientation, since their stomata are typically aligned at random or at high angles approaching 907, while in all other extant sections, the stomata are aligned predominantly parallel to the long axis of the leaf. Section Eutacta is by far the most species-diverse section and has probably speciated profusely on New Caledonia since its apparent arrival there in the Neogene (Hill and Brodribb 1999;Gaudeul et al. 2012;Kranitz et al. 2014). Farjon (2001) recognized 19 living species (plus one variety) of Araucaria section Eutacta, and Mill et al. (2017) have recently described another New Caledonian species in that section. ...
... Similarly, the leaves of A. balfourensis appear to be quite two-dimensional and flattened compared with A. biramulata, and the cuticle at the margins of the guard cell is not thickened at all in the fossil, but it is clearly thickened in A. biramulata. In more general terms, the extant New Caledonian species appear to be the result of a relatively recent radiation of the genus on that land mass (Gaudeul et al. 2012;Kranitz et al. 2014). Hence, finding a close morphological match between a New Caledonian extant species and a Paleogene fossil is more likely to be an example of reradiation and convergence than to represent a true nearest living relative. ...
... Similarly, various combinations of seven plastid DNA barcodes only had about 30% species discrimination success at best (Hollingsworth et al. 2009a). More recent attempts to resolve the evolutionary relationships within the New Caledonian clade using AFLPs (Gaudeul et al. 2012), a combination of eight plastid genes and morphological characters (Escapa & Catalano 2013), and a study of 11 plastid genes plus the nuclear ribosomal internal transcribed spacer ITS2 (Kranitz et al. 2014), all recovered three major clades ('coastal', 'small leaved' and 'large leaved'). However, depending on the study, there was little or no bootstrap support for most of these clades and relationships among clades were ambiguous. ...
... However, depending on the study, there was little or no bootstrap support for most of these clades and relationships among clades were ambiguous. With few exceptions, species resolution within clades was poor (Gaudeul et al. 2012;Escapa & Catalano 2013;Kranitz et al. 2014). Therefore, despite recent insights into the evolutionary relationships of New Caledonian Araucaria species, a fully resolved and well-supported phylogeny remains elusive, as does effective DNA barcode discrimination of individual species. ...
... All 13 New Caledonian Araucaria species and their sister species, A. heterophylla, endemic to Norfolk Island (Setoguchi et al. 1998;Gaudeul et al. 2012;Escapa & Catalano 2013) were included in the study (Table 1, Table S3, Supporting information). We included multiple individuals per species from 11 of 13 New Caledonian species. ...
Obtaining accurate phylogenies and effective species discrimination using a small standardised set of plastid genes is challenging in evolutionarily young lineages. Complete plastid genome sequencing offers an increasingly easy-to-access source of characters that helps address this. The usefulness of this approach, however, depends on the extent to which plastid haplotypes track morphological species boundaries. We have tested the power of complete plastid genomes to discriminate among multiple accessions of 11 out of 13 New Caledonian Araucaria species, an evolutionary young lineage where the standard DNA barcoding approach has so far failed and phylogenetic relationships have remained elusive. Additionally, 11 nuclear gene regions were Sanger sequenced for all accessions to ascertain the success of species discrimination using a moderate number of nuclear genes. Overall, fewer than half of the New Caledonian Araucaria species with multiple accessions were monophyletic in the plastid or nuclear trees. However, the plastid data retrieved a phylogeny with a higher resolution compared to any previously published tree of this clade and supported the monophyly of about twice as many species and nodes compared to the nuclear data set. Modest gains in discrimination thus are possible, but using complete plastid genomes or a small number of nuclear genes in DNA barcoding may not substantially raise species discriminatory power in many evolutionarily young lineages. The big challenge therefore remains to develop techniques that allow routine access to large numbers of nuclear markers scaleable to thousands of individuals from phylogenetically disparate sample sets.This article is protected by copyright. All rights reserved.
... The conifer genus Araucaria Juss. (Araucariaceae) provides a good model to explore alternative hypotheses regarding the age, origins and diversification of the New Caledonian biota [7,8]. Araucaria has been considered an old lineage [9] and for instance, fossil data from both the Northern and Southern Hemisphere of the early Mesozoic (Jurassic, c. 190 Ma, or earlier) have been taken to indicate that at least some of the extant sections of Araucaria had begun to diversify and were widespread by this time. ...
... In this study, however, the morphological species were characterised by very low levels of DNA sequence divergence suggestive of a recent radiation. Gaudeul et al. [7] also argued for a recent diversification of the New Caledonian Araucaria based on a low ratio of among versus within species genetic divergence using AFLP markers. In the context of these findings it has been proposed that the origin of this lineage may be maximally constrained by the age of Norfolk Island (c. ...
... These are generally consistent regarding relationships among genera and among the major lineages within Araucaria. While the New Caledonian species of Araucaria section Eutacta consistently form a clade, establishing a robust understanding of interspecific relationships has proven difficult [7,8,37]. AFLP markers resolved three main genetic groups including a small leaved, large leaved and a coastal species group [7]. Escapa and Catalano [11] presented an analysis of a combined morphological and molecular data set, and found reasonable agreement with these interspecific groupings but their hypothesis differed from Gaudeul et al. [7] in the resolution of group inter-relationships. ...
New Caledonia is a global biodiversity hotspot. Hypotheses for its biotic richness suggest either that the island is a 'museum' for an old Gondwana biota or alternatively it has developed following relatively recent long distance dispersal and in situ radiation. The conifer genus Araucaria (Araucariaceae) comprises 19 species globally with 13 endemic to this island. With a typically Gondwanan distribution, Araucaria is particularly well suited to testing alternative biogeographic hypotheses concerning the origins of New Caledonian biota. We derived phylogenetic estimates using 11 plastid and rDNA ITS2 sequence data for a complete sampling of Araucaria (including multiple accessions of each of the 13 New Caledonian Araucaria species). In addition, we developed a dataset comprising 4 plastid regions for a wider taxon sample to facilitate fossil based molecular dating. Following statistical analyses to identify a credible and internally consistent set of fossil constraints, divergence times estimated using a Bayesian relaxed clock approach were contrasted with geological scenarios to explore the biogeographic history of Araucaria. The phylogenetic data resolve relationships within Araucariaceae and among the main lineages in Araucaria, but provide limited resolution within the monophyletic New Caledonian species group. Divergence time estimates suggest a Late Cretaceous-Cenozoic radiation of extant Araucaria and a Neogene radiation of the New Caledonian lineage. A molecular timescale for the evolution of Araucariaceae supports a relatively recent radiation, and suggests that earlier (pre-Cenozoic) fossil types assigned to Araucaria may have affinities elsewhere in Araucariaceae. While additional data will be required to adequately resolve relationships among the New Caledonian species, their recent origin is consistent with overwater dispersal following Eocene emersion of New Caledonia but is too old to support a single dispersal from Australia to Norfolk Island for the radiation of the Pacific Araucaria sect. Eutacta clade.
... The genus Araucaria comprises a total of 19 species worldwide, 13 of which are endemic to the archipelago. They usually occur as large populations, in a variety of ecological habitats (most often humid forest or maquis; [34]). Importantly, all species are confined to ultramafic soils -characterized by low fertility (low N, P, K), high concentrations of heavy metals (e.g., Co, Cr, Ni) and low water-holding capacity [35]-except A. montana Brongn. ...
... Based on rbcL sequencing, Setoguchi et al. [37] showed that New Caledonian Araucaria species form a monophyletic group and, using AFLP markers, Gaudeul et al. [34] delineated three clades within this group: the large-leaved, small-leaved and coastal clades. Nevertheless, the exact relationships among species remain unresolved, especially within the large-leaved group that includes six species: A. montana, A. laubenfelsii Corbasson, A. rulei F.Muell., A. biramulata J. Buchholz, A. muelleri (Carrière) Brong. ...
... In total, we studied 711 samples from 32 populations and five species for nDNA (Table 1). For cpDNA, we added a few samples of A. muelleri and A. humboldtensis, as well as of A. columnaris and A. nemorosa that belong to the third Araucaria clade ( [34]; Table 1). In total, the cpDNA dataset included 617 individuals from 45 populations and nine species. ...
Background
New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nuclear microsatellites and chloroplast DNA sequencing, we focused on five closely related Araucaria species to investigate among-species relationships and the distribution of within-species genetic diversity across New Caledonia.ResultsThe species could be clearly distinguished here, except A. montana and A. laubenfelsii that were not differentiated and, at most, form a genetic cline. Given their apparent morphological and ecological similarity, we suggested that these two species may be considered as a single evolutionary unit. We observed cases of nuclear admixture and incongruence between nuclear and chloroplast data, probably explained by introgression and shared ancestral polymorphism. Ancient hybridization was evidenced between A. biramulata and A. laubenfelsii in Mt Do, and is strongly suspected between A. biramulata and A. rulei in Mt Tonta. In both cases, extensive asymmetrical backcrossing eliminated the influence of one parent in the nuclear DNA composition. Shared ancestral polymorphism was also observed for cpDNA, suggesting that species diverged recently, have large effective sizes and/or that cpDNA experienced slow rates of molecular evolution. Within-species genetic structure was pronounced, probably because of low gene flow and significant inbreeding, and appeared clearly influenced by geography. This may be due to survival in distinct refugia during Quaternary climatic oscillations.Conclusions
The study species probably diverged recently and/or are characterized by a slow rate of cpDNA sequence evolution, and introgression is strongly suspected. Within-species genetic structure is tightly linked with geography. We underline the conservation implications of our results, and highlight several perspectives.
... Amplified fragment length polymorphism (AFLP; [14]) is a fingerprinting technique that has proven to be useful for revealing phylogenetic relationship among closely related taxa (e.g. Hypochaeris, [15]; Lactuca, [16]; Phylica, [17]; Trollius, [18]; Ranunculus alpestris, [19]; Puya, [20,21]; Araucaria, [22]). In contrast to standard phylogenetic markers, AFLP variation is spread across the whole genome, spanning both coding and non-coding DNA regions and may therefore be more representative of overall genetic patterns present as well as being highly informative for phylogenetic analyses at the low phylogenetic level [23,24]. ...
... Intra-specific variation was greater (~80%) than that found at inter-specific level (~20%). This low ratio of among-versus within-species divergence in the context of considerable morphological and ecological divergence is indicative of a recent diversification [22]. Such a process can explain why we were able to get clear species boundaries for most species but were unable to clearly resolve phylogenetic relationships between them. ...
... After climatic conditions became more favourable, the two groups probably expanded rapidly into newly suitable habitats where they overlapped; the time scale of these fluctuations (ca. 0.02 -0.1 myr; [37]) was probably not enough to allow woody species with long generation time such as Diospyros to diverge and become permanently reproductively isolated [22]. There are a few admixed individuals in the STRUCTURE analysis (Figure 4), which implies that hybridization might have played a role in evolution of this group. ...
Radiation in some plant groups has occurred on islands and due to the characteristic rapid pace of phenotypic evolution, standard molecular markers often provide insufficient variation for phylogenetic reconstruction. To resolve relationships within a clade of 21 closely related New Caledonian Diospyros species and evaluate species boundaries we analysed genome-wide DNA variation via amplified fragment length polymorphisms (AFLP).
A neighbour-joining (NJ) dendrogram based on Dice distances shows all species except D. minimifolia, D. parviflora and D. vieillardii to form unique clusters of genetically similar accessions. However, there was little variation between these species clusters, resulting in unresolved species relationships and a star-like general NJ topology. Correspondingly, analyses of molecular variance showed more variation within species than between them. A Bayesian analysis with BEAST produced a similar result. Another Bayesian method, this time a clustering method, Structure, demonstrated the presence of two groups, highly congruent with those observed in a principal coordinate analysis (PCO). Molecular divergence between the two groups is low and does not correspond to any hypothesised taxonomic, ecological or geographical patterns.
We hypothesise that such a pattern could have been produced by rapid and complex evolution involving a widespread progenitor for which an initial split into two groups was followed by subsequent fragmentation into many diverging populations, which was followed by range expansion of then divergent entities. Overall, this process resulted in an opportunistic pattern of phenotypic diversification. The time since divergence was probably insufficient for some species to become genetically well-differentiated, resulting in progenitor/derivative relationships being exhibited in a few cases. In other cases, our analyses may have revealed evidence for the existence of cryptic species, for which more study of morphology and ecology are now required.
... the evolution, paleobiodiversity, and phylogenetic radiations within the family. Evolutionary diversification of Araucaria in particular, has been the subject of scrutiny because of the hidden diversity and threatened status of Araucaria species, especially the 13 closely related New Caledonian taxa (Stefenon et al., 2006;Martín et al., 2012;Gaudeul et al., 2012Gaudeul et al., , 2014Kranitz et al., 2014;Ruhsam et al., 2016). ...
... As systematic analyses of the Araucariaceae have accumulated over the past half century, our understanding of relationships, both of the family (see Leslie et al., 2018) and within the family has increased steadily, but relationships among the species of Araucaria remain uncertain. The 13 New Caledonian species of Araucaria Section Eutacta appear to be more closely related to one another than to other species of the genus, and to have been the result of a relatively recent radiation (or radiations) among species that are both geographically clustered and closely related genetically (Gaudeul et al., 2012;Martín et al., 2012;Zonneveld, 2012;Gaudeul et al., 2014;Kranitz et al., 2014;Liu, et al., 2009;Ruhsam et al., 2016), but their genetic relationships to other species of Section Eutacta remain uncertain. ...
Premise:
Exceptional anatomical preservation of a fossil araucarian seed cone from a marine carbonate concretion from Vancouver Island, British Columbia, Canada provides unusually complete evidence for cone structure including seeds, megagametophytes, microgametophytes, and embryos of an Upper Cretaceous (Campanian) species of Araucaria, providing important new insights into the structure and relationships of Cretaceous Northern Hemisphere Araucariaceae.
Methods:
The cone was studied from serial thin sections prepared by the coal ball peel technique. Phylogenetic analysis using a modified morphological matrix with both discrete and continuous characters was performed using TNT version 1.5.
Results:
The nearly spherical cone, 6 × 6 cm in diameter, has helically arranged cone-scale complexes, consisting of a large bract with an upturned tip and a small, fleshy ovuliferous scale. Vascularization of the cone-scale complex is single at its origin. Widely winged bracts, with a bulging base, contain numerous vascular bundles, interspersed with transfusion tissue, and a large number of resin canals. Seeds are ovoid, 1.2 cm long, 1.2 cm in diameter. Nucellus is free from the integument, except at its base, with a convoluted apex, containing possible pollen tubes. Megagametophytes and mature cellular embryos occur in several seeds.
Conclusions:
This small cone with attached, imbricate leaves, wide bracts, and unusually large seeds, most closely resembles those of Araucaria Section Eutacta. Width and continuity of secondary xylem in the cone axis, and intact cone-scale complexes indicate that this cone probably did not disarticulate readily at maturity. When added to a modified, previously published phylogenetic analysis, Araucaria famii sp. nov. enhances our understanding of the Cretaceous radiation of Northern Hemisphere Araucaria Section Eutacta.
... The addition of fossils to the analyses introduced uncoded characters, including the missing genetic data and many morphological characters that are not preserved in fossils, all of which lowered the overall support of the tree. Within the problematic New Caledonian Eutacta clade, low support values are expected even without the addition of fossils, due to the known genetic and morphologic similarities within the clade (e.g., Setoguchi et al., 1998;Stefenon et al., 2006;Gaudeul et al., 2012Gaudeul et al., , 2014Ruhsam et al., 2015). Despite the low support values, including the fossils in the analysis resulted in the same topology for Araucaria and Araucariaceae that was found for the molecular-only phylogeny. ...
... Asterisk (*), fossil taxa. The extant species from New Caledonia are color-coded according to the systematic treatments of Gaudeul et al. (2012) and Escapa and Catalano (2013): "large-leaved" species = red; "small-leaved" species with an interior distribution = light blue; "small-leaved" species with a coastal distribution = dark blue. Interestingly, Araucaria huncoensis is found among the "large-leaved" clade, although the fossils from Laguna del Hunco have some of the smallest leaves compared with any of the extant species (Fig. 12A); however, support values are low. ...
The iconic genus Araucaria, distributed worldwide during the Mesozoic, now has a relict, disjunct distribution between South America (2 species) and Australasia (18 species). Australasian Araucaria Section Eutacta is the most diverse clade with 16 species, all but two of them endemic to New Caledonia. Fossils assigned to Sect. Eutacta usually are based on single dispersed organs, making it difficult to diagnose the section and test molecular estimates of its crown age, which are generally near 20-25 Ma. Araucaria fossils thought to belong to Sect. Eutacta are abundant in early and middle Eocene Patagonian caldera-lake deposits from Laguna del Hunco (LH; ~52.2 Ma; Early Eocene Climatic Optimum) and Rio Pichileufu (RP; ~47.7 Ma; earliest middle Eocene, when initial opening of the Drake Passage had begun, and climatic cooling was underway). Araucaria pichileufensis Berry 1938 was described from the type locality RP and has been reported from LH. Although there is increasing evidence of angiosperm species turnover between these floras via loss of some rainforest taxa, the diverse conifers found at LH and RP are thought to represent the same set of species. However, the relationship of A. pichileufensis to Sect. Eutacta and the conspecificity of the Araucaria material in these floras have not been rigorously tested. Large new fossil collections from LH and RP include the multi-organ preservation of Araucaria leafy branches, cuticle, bract-scales, and pollen cones, which allows for the development of a more complete plant concept for Araucaria pichileufensis at RP and for the recognition of a new species from LH. Analysis of characters, including those of an attached terminal pollen cone discovered from RP, establishes a relationship of both species to Eutacta, suggesting presence and survival in Patagonia of this group during initial separation from Antarctica. A total evidence phylogenetic analysis places both Eocene species within the crown group of Sec. Eutacta, confirming the taxonomic treatment and adding to the Gondwanan connection of Patagonian fossil floras to Australasia. Furthermore, these Araucaria fossils comprise one of the most complete representations of fossil Eutacta in the world, and they predate the molecular age estimates for the crown of Eutacta by ~30 million years. The differentiation of two Araucaria species is the first documentation of a change in the conifer species composition between LH and RP, adding to the evidence for turnover between the two floras during the climate change and movement of landmasses of the earliest middle Eocene.
... The addition of fossils to the analyses introduced uncoded characters, including the missing genetic data and many morphological characters that are not preserved in fossils, all of which lowered the overall support of the tree. Within the problematic New Caledonian Eutacta clade, low support values are expected even without the addition of fossils, due to the known genetic and morphologic similarities within the clade (e.g., Setoguchi et al., 1998;Stefenon et al., 2006;Gaudeul et al., 2012Gaudeul et al., , 2014Ruhsam et al., 2015). Despite the low support values, including the fossils in the analysis resulted in the same topology for Araucaria and Araucariaceae that was found for the molecular-only phylogeny. ...
... Asterisk (*), fossil taxa. The extant species from New Caledonia are color-coded according to the systematic treatments of Gaudeul et al. (2012) and Escapa and Catalano (2013): "large-leaved" species = red; "small-leaved" species with an interior distribution = light blue; "small-leaved" species with a coastal distribution = dark blue. Interestingly, Araucaria huncoensis is found among the "large-leaved" clade, although the fossils from Laguna del Hunco have some of the smallest leaves compared with any of the extant species (Fig. 12A); however, support values are low. ...
Premise:
Eocene floras of Patagonia document biotic response to the final separation of Gondwana. The conifer genus Araucaria, distributed worldwide during the Mesozoic, has a disjunct extant distribution between South America and Australasia. Fossils assigned to Australasian Araucaria Sect. Eutacta usually are represented by isolated organs, making diagnosis difficult. Araucaria pichileufensis E.W. Berry, from the middle Eocene Río Pichileufú (RP) site in Argentine Patagonia, was originally placed in Sect. Eutacta and later reported from the early Eocene Laguna del Hunco (LH) locality. However, the relationship of A. pichileufensis to Sect. Eutacta and the conspecificity of the Araucaria material among these Patagonian floras have not been tested using modern methods.
Methods:
We review the type material of A. pichileufensis alongside large (n = 192) new fossil collections of Araucaria from LH and RP, including multi-organ preservation of leafy branches, ovuliferous complexes, and pollen cones. We use a total evidence phylogenetic analysis to analyze relationships of the fossils to Sect. Eutacta.
Results:
We describe Araucaria huncoensis sp. nov. from LH and improve the whole-plant concept for Araucaria pichileufensis from RP. The two species respectively resolve in the crown and stem of Sect. Eutacta.
Conclusions:
Our results confirm the presence and indicate the survival of Sect. Eutacta in South America during early Antarctic separation. The exceptionally complete fossils significantly predate several molecular age estimates for crown Eutacta. The differentiation of two Araucaria species demonstrates conifer turnover during climate change and initial South American isolation from the early to middle Eocene.
... Among the molecular markers used in genetic diversity studies, those generated by Amplified Fragment Length Polymorphism (AFLP) analysis, described by Vos et al. (1995), are widely used to evaluate genetic diversity in plant species (EHRICH et al., 2009;SUDHEER PAMIDIAMARRI et al., 2009;TATIKONDA et al., 2009;GARCÍA-PEREIRA et al., 2010;MENDELSON et al., 2010;GAUDEUL et al., 2012). ...
... Entre os marcadores moleculares utilizados em estudos de diversidade genética destacam-se os marcadores gerados pela análise de polimorfismo de comprimento de fragmento amplificado (Amplified Fragment Length Polymorphism -AFLP), descrito por Vos et al. (1995), que são amplamente utilizados para avaliar diversidade genética em espécies vegetais (EHRICH et al., 2009;SUDHEER PAMIDIAMARRI et al., 2009;TATIKONDA et al., 2009;GARCÍA-PEREIRA et al., 2010;MENDELSON et al., 2010;GAUDEUL et al., 2012). In a study of lettuce, Jansen and Van Hintum (2007), used AFLP markers to develop a new sampling method for obtaining core collections. ...
The efficient use of genetic resources- stored in germplasm collections can be maximized if morphoagronomic and molecular information on the accessions is made available. To achieve this, a collection that is well-structured, well-curated and easily accessible (the core collection) is required. Consequently, the
objective of the current study was to characterize 80 landrace accessions from the maize core collection of the Federal University of Viçosa (UFV), and assay thenngenetic diversity of the various landraces, considering grain type and ecogeographic origin. For this, AFLP analysis was performed using 12 primer combinations. Genetic diversity of the collection was quantified with the UPGMA method, using the Jaccard Index to quantify dissimilarity. The core collection was divided into four sub-populations by grain type, and into six sub-populations based on ecogeographic origin. Genetic diversity analysis was performed both within and between sub-populations. A high level of genetic variability was found among the landrace accessions of UFV
Core Collection, principally among those accessions with dentate type grains.Classification by grain type and ecogeographic origin allowed genetically divergent groups to be distinguished.
... angustifolia and A. araucana) in South America; and Section Eutacta with 15 species in New Caledonia, New Guinea, Queensland, New South Wales, Norfolk Island and Philip Island (Figure 2;Farjon 2010). New Caledonia is the center of extant Araucaria diversity, with 13 endemic species (Jaffré 1995;Farjon 2010;Gaudeul et al. 2012). The monophyly of Araucaria and of its four sections is well supported by molecular and morphological phylogenetic studies (Setoguchi et al. 1998;Biffin et al. 2010;Leslie et al. 2012;Escapa and Catalano 2013). ...
... Araucariaceous fossils are not reported from South America after the Eocene-early Oligocene (flora from Rio de Las Minas, southern Chile, see Ohsawa et al. 2016), and the latest fossil occurrences of Eutacta species in New Zealand (Pole 1992a), Tasmania (Hill 1990), and southeastern Australia (Hill 1990;Hill and Brodribb 1999) are in the early Miocene ( Figure 2). Global climate changes are therefore likely responsible for the present restricted distribution of the Eutacta clade, with its diversity in New Caledonia resulting from a more recent tropical radiation, as suggested by molecular phylogenies (Gaudeul et al. 2012;Leslie et al. 2012) and the relatively recent emergence of the island of New Caledonia itself in the Oligocene (Aitchison et al. 1995;Schellart et al. 2006;Neall and Trewick 2008) The finding of Araucaria bract-scale complex similar to those of the Section Eutacta in the Eocene of Antarctica provides important direct evidence for the trans-Antarctic dispersal of conifers between southern South America and southern Australia during the warm early-middle Eocene. The presence of Araucaria is consistent with the previous interpretation of the Fossil Hill flora that it was a diverse, humid, and temperate Nothofagus and conifer dominated forest (Li 1994b;Li and Zhou 2007;Jacques et al. 2014). ...
The early-middle Eocene Fossil Hill flora from King George Island in the Antarctic Peninsula regions is one of the most diverse Cenozoic plant assemblages in Antarctica. It represents a rich Nothofagus and conifer dominated vegetation. These plant fossils, especially conifers are of crucial importance for understanding the biogeographic history of the Gondwanan plants. Here we describe the first Araucaria bract-scale complex, A. fildesensis sp. nov., and associated foliage from the Fossil Hill flora and tentatively assigned them to the Section Eutacta, which is today restricted to Australasia, based on comparison with extant material. This study confirms that Araucaria species with small bract-scale complexes, small scale-like mature leaves and awl-shaped juvenile leaves like those of extant Section Eutacta, lived in Antarctica in the Eocene. These fossils provide potential evidence for the trans-Antarctic floristic changes of Araucaria species in the Section Eutacta between southern Australia and southern South America during the Eocene, when Antarctica was ice-free and forested.
... Presently the island of Grande Terre in New Caledonia has 19 Araucariaceae species of which 13 are endemic (Jaffré 1995;Gaudeul et al. 2012), and it has often been termed a Gondwanan refuge (Holloway 1979;Morat 1993a, b). However, recent studies suggest that the species richness of New Caledonia's araucarians is rather a result of adaptive radiation in the post-Eocene era, mainly forced by unusual edaphic conditions, i.e. the widespread occurrence of ultramafic soils (Setoguchi et al. 1998;Gaudeul et al. 2012;Escapa and Catalano 2013;Kranitz et al. 2014;Grandcolas et al. 2015). ...
... Presently the island of Grande Terre in New Caledonia has 19 Araucariaceae species of which 13 are endemic (Jaffré 1995;Gaudeul et al. 2012), and it has often been termed a Gondwanan refuge (Holloway 1979;Morat 1993a, b). However, recent studies suggest that the species richness of New Caledonia's araucarians is rather a result of adaptive radiation in the post-Eocene era, mainly forced by unusual edaphic conditions, i.e. the widespread occurrence of ultramafic soils (Setoguchi et al. 1998;Gaudeul et al. 2012;Escapa and Catalano 2013;Kranitz et al. 2014;Grandcolas et al. 2015). Nevertheless, with an evolutionary history of more than 200 million years, Araucariaceae are among the oldest extant conifers (Kunzmann 2007). ...
Conifers of the endemic species Araucaria humboldtensis on Mont Humboldt in New Caledonia exhibit extensive resin exudation. The resin flows of these threatened trees are here shown to be induced by two beetle species, which bore into branches and branchlets, leading to abundant outpouring of resin, which gradually solidifies into often drop-shaped resin bodies. The exudate is colonized by a resinicolous and likely insect-vectored ascomycete, Resinogalea humboldtensis, which is only known from Mont Humboldt. The fungus grows into fresh resin and eventually develops ascomata on the surface of solidifying resin. The solidified resin is also colonized by another fungus, a dematiaceous hyphomycete. Based on protein coding (CO1, CAD, ArgK) and ribosomal (LSU) genes, the larger branch-boring beetle is a weevil of the tribe Araucariini, which represents the sister group of all other cossonine weevils. The smaller beetle species belongs to the longhorn beetles (Cerambycidae). The strong host specificity of the Araucariini, along with the occurrence of two unique fungi, suggests that the resin-associated community is native and has evolved on the endemic conifer host. The formation of large amber deposits indicates massive resin production in the past, but the environmental triggers of exudation in Mesozoic and Cenozoic ecosystems remain unclear. Our observations from Mont Humboldt support the notion that the occurrences of small drop-shaped amber pieces in Triassic to Miocene amber deposits were linked to ancient insect infestations.
... The AFLP technique provides numerous genetic markers that are distributed across the whole genome and usually exhibit moderate to high rates of variability. AFLPs require no prior knowledge of the genome analyzed, and have been proven to be a time and cost efficient tool in assessing interspecific relationships in complex plant groups (Gaudeul et al., 2012;Meudt and Clarke, 2007). ...
... AMOVA analysis revealed that only 10.4% of the genetic variation found in the data set is due to species-level differences whereas 75.7% was found within populations. This low ratio of among-versus within-species differentiation in the context of considerable morphological and ecological divergence is indicative of a recent diversification (Gaudeul et al., 2012;Turner et al., 2013). In fact, Aechmea subgenus Ortgiesia diversification started as recent as 2.5 Ma . ...
... The use of amplified fragment length polymorphism (AFLP) provides an alternative to direct sequencing for species-level phylogenetics particularly for recent and rapidly radiating groups (Albertson et al., 1999;Després et al., 2003;Richardson et al., 2003;Koopman, 2005;Spooner, Peralta & Knapp, 2005;Pellmyr et al., 2007;McKinnon et al., 2008;Dasmahapatra, Hoffman & Amos, 2009;Kropf, Comes & Kadereit, 2009;Arrigo et al., 2011;Bacon et al., 2011;Gaudeul et al., 2012). Despite the often mentioned advantages and limitations of using AFLP in phylogenetic analyses (see recent review by Gaudeul et al., 2012), few studies have explicitly assessed congruence between phylogenetic analyses based on AFLP and DNA sequence data or provide a theoretical basis for using or not using AFLP. ...
... The use of amplified fragment length polymorphism (AFLP) provides an alternative to direct sequencing for species-level phylogenetics particularly for recent and rapidly radiating groups (Albertson et al., 1999;Després et al., 2003;Richardson et al., 2003;Koopman, 2005;Spooner, Peralta & Knapp, 2005;Pellmyr et al., 2007;McKinnon et al., 2008;Dasmahapatra, Hoffman & Amos, 2009;Kropf, Comes & Kadereit, 2009;Arrigo et al., 2011;Bacon et al., 2011;Gaudeul et al., 2012). Despite the often mentioned advantages and limitations of using AFLP in phylogenetic analyses (see recent review by Gaudeul et al., 2012), few studies have explicitly assessed congruence between phylogenetic analyses based on AFLP and DNA sequence data or provide a theoretical basis for using or not using AFLP. Importantly, recent theoretical studies indicate that the major drawback of this technique is the low information content of AFLP markers (Simmons et al., 2007;García-Pereira, Caballero & Quesada, 2010, 2011 and not the other commonly invoked limitations such as the lack of homology of co-migrating fragments (García-Pereira et al., 2010), the dominant nature of AFLP characters (Simmons et al., 2007) and correlation with genome size (Fay, Cowan & Leitch, 2005;Althoff, Gitzendanner & Segraves, 2007;. ...
Puya (Bromeliaceae), with > 200 species, is a classic example of a recent, rapid species-level radiation in the Andes. To assess the biogeographical history of this primarily Andean species group and the evolution of different life histories, amplified fragment length polymorphism (AFLP) data were generated for 75 species from throughout the geographical range of the genus. Distribution data for latitudinal and elevational ranges were compiled for almost all species. The greatest number of species is found at mid-elevations and mid-latitudes south of the equator. The genus originated in central Chile and first moved into the Cordillera Oriental of the central Andes via inter-Andean valleys. Cladogenesis progressed in a general south to north direction tracking the final uplift of the Andes. All taxa north of the Western Andean Portal form a monophyletic group implying a single colonization of the northern Andes, with no subsequent transitions back south from the Northern Andes. Repeated evolutionary transitions of lineages up and down in elevation are suggestive of allopatric speciation driven by Pleistocene glaciation cycles. True semelparity evolved once in P. raimondii, with similar semi-semelparity evolving repeatedly in páramos of the northern Andes. Fieldwork and phylogenetic characterization of high-elevation Puya are priorities for future efforts.
... In this regard, groups that have undergone adaptive radiation usually show a high rate of morphological differentiation (with or without obvious sequence level DNA divergence), which makes interpretation of their phylogenetics and evolution challenging (Glor, 2010;Knope et al., 2020). The roles of genetic, geographic and environmental isolation, alone and variously combined, in promoting divergence of ILS associated plant clades have often been recognized (Hughes & Eastwood, 2006;Givnish et al., 2009;Gaudeul et al., 2012;Turner et al., 2013;Wanderley et al., 2018). In this sense, endemic ILS species can be excellent models to test whether this environment provides evolutionary trends similar to those described for insular clades. ...
... Therefore, we must consider the diversity and rarity of all population species (Ciofi & Bruford, 1999;Ryder, 1986). AFLP data have been used to analyze genetic diversity in various threatened or rare gymnosperm taxa, such as Picea ziyuanensis , Araucaria species (Gaudeul et al., 2012), Abies chensiensis, A. fargesii (Zhan et al., 2014), and Pinus monticola (Kim et al., 2011), among others. The RGUCs sampling strategy allows us to determine which and how many populations to choose for conservation purposes (Peñas et al., 2016;Pérez-Collazos et al., 2008). ...
Preserving the genetic diversity of forest species is critical for maintaining their adaptive potential and allowing for generation turnover in forest ecosystems. Considering an uncertain future, it is necessary to establish reliable genetic conservation strategies to optimize the genetic variation preserved within populations in a spatially explicit context to assist decision-makers. Hence, we aimed to incorporate genetic information into spatially designed conservation actions. Cedrus atlantica is a large, long-lived conifer native to the mountains of North Africa, threatened by extinction. The relevant genetic units for conservation were selected using Bayesian analysis. The relative contribution of the populations to the genetic pool that maximized the species' genetic diversity was calculated to design an optimal seed bank. Finally, the relationship between the genetic composition and bioclimatic variables was estimated and projected throughout the study area under current and future climatic conditions. Three relevant genetic units were found for C. atlantica conservation that maximizes genetic diversity in a spatial context. Bioclimatic variables with the highest influence on genetic composition were closely related to climate warming and decreased soil water availability. We identified the role of genetic markers in designing a reliable conservation strategy for forest trees considering climate change, increased deforestation, and aridity. Projections of genetic composition due to the climate in the study region of North Africa provide spatially explicit guidance for optimizing the selection and preservation of seed banks.
... In Pinus tabulaeformis, Di and Wang (2013) studied the population genetic diversity and structure. In Araucaria species, Gaudeul et al. (2012) provided insights into protecting genetic resources and exploring mechanisms of adaptability and evolution. ...
As a dynamic ex situ conservation strategy, a clonal seed orchard was started in a nursery in Pomaio (POM) in central Italy in 1993 for an assisted migration experiment of Abies nebrodensis (Lojac.) Mattei. Two artificial ex situ populations were planted with this gene pool: a seedling arboretum in Pieve Santo Stefano (PSS) and a small dendrological collection in Papiano (PAP), both originating from the Sicilian relict population. Here, using AFLP markers, we estimated the relatedness among the relocated genotypes of the three collections to check whether the three collections had sufficient genetic variability to be considered as additional sources of variability to the original gene pool for the assisted migration strategy. High individual genetic variability was found in the collections; each plant had a different genotype and was confirmed to belong to its population of origin. PAP and PSS trees were shown to be only from the original population of A. nebrodensis species and were derived from a limited set of maternal fertile genotypes. Based on the Sicilian fir population inventory, nursery production in Sicily, and structure clustering analysis, close genetic relationships among POM, PAP and several PSS trees (1–35) were evident. Similarly, the PSS group (36–78) was genetically close to tree 1 of POM and in a lesser proportion to plants 7 and 9 of POM. The sampling of seedlings used to form batches in the nursery might have influenced the structure of the resultant plantations. All genotypes will be useful for enriching the original gene pool.
... Therefore, it seems that differentiation could have been driven by ecotypic variation. Failure in seedling establishment due to a unique environment could also have affected allele frequencies and survival of possibly associated to speciation to local environmental conditions, as this is the only population of the species growing on acid soils, instead of ultramafic soils (Gaudeul et al. 2012). ...
The Bahaman archipelago contains large expanses of pine forests, where the endemic Caribbean pine Pinus caribaea var. bahamensis is the dominant species. This pine forest ecosystem is rich in species and also a valuable resource for the local economy. Small areas of old-growth forest still remain in the Turks and Caicos islands (TCI) and in some of the islands in the Bahamas; despite on-going severe infestation by pine tortoise scale insect Toumeyella parvicornis and high pine mortality in the former and intensive past commercial logging activities in the latter. For the first time integrated research on the genetics, morphology, ecology and biogeography of this variety was carried out throughout its whole distribution range. Past and present forest areas were mapped using historical physical maps and modern satellite imagery, showing forest loss due to urbanisation, pests and storm surges and expansions resulting mainly from dry-season human induced fires. Population genetic analysis using plastid and nuclear microsatellites revealed high ancient gene flow and recent genetic distance between populations of the Bahamas and the TCI; in addition to genetic structure within regions. Morphological differences were also observed and discussed. The variety showed high individual genetic and morphological variance and high plasticity. Despite the observation of good forest regeneration in normal circumstances, stochastic events did cause severe reductions in forest area and effective population size. A predominantly random and outcrossing breeding system was also inferred from the data, despite detection of some inbreeding in the smaller populations. Suggestions for the future conservation and management of the species included fire management and the creation or extension of in-situ conservation areas and ex-situ collections.
Available online: http://bbktheses.da.ulcc.ac.uk/18/
... L'auteur de ce travail a mis l'accent sur la possibilité d'émettre des priorités de conservation sur ces résultats, soulignant la nécessité de conserver les espèces parentales des espèces hybrides mais aussi les zones de contact dans lesquelles elles se retrouvent (Pillon et al., 2009a (Gaudeul et al., 2011). Malheureusement aucune mesure précise n'a été prise à ce jour et un rapprochement entre le monde scientifique et les gestionnaires est plus que recommandé dans ce genre de situation. ...
Les milieux naturels de la Nouvelle-Calédonie, Hotspot de biodiversité, ont subi de nombreuses dégradations par l’action simultanée de différentes menaces telles que les incendies, les extractions minières, l’urbanisation et l’introduction d’espèces envahissantes. A cela s’ajouteront probablement à court terme les impacts des changements climatiques. Afin de proposer un consensus entre la nécessité de protéger cette importante biodiversité néo-calédonienne et l’accroissement rapide des activités anthropiques à l’origine de ces menaces, une étude comprenant une approche à une échelle macroscopique et une approche comparative de la flore micro-endémique est proposée. La première s’attache à appréhender le micro-endémisme sur l’ensemble de la flore vasculaire du territoire. Les espèces micro-endémiques(EME), séparées en trois groupes, ont été identifiées à partir de la littérature et des échantillons d’herbiers. De nombreuses espèces se sont révélées être micro-endémiques (309 restreintes à une localité, 193 à deux localités, 133 à trois localités). Parmi celles-ci, de nombreuses n’ont pas de statut UICN (76%) et de ce fait ne sont pas protégées par la règlementation locale. Cependant, une corrélation significative a été mise en évidence entre les EME inscrites à l’UICN et les EME à une et à deux localités, conduisant à l’établissement d’une liste d’espèces extrêmement menacées, non protégées par la réglementation, l’objectif étant de favoriser la mise en place d’études pour leur inscription et de fait leur protection. Aussi, grâce à la localisation de ces espèces, il a été possible d’identifier des Hotspots de Micro-Endémisme Végétal (HMEV), zones présentant de fortes densités en EME. La distribution de ces HMEV a été comparée à celle des aires protégées, mettant en évidence de nombreux espaces d’une exceptionnelle diversité micro-endémique non encore protégés et qu’il conviendrait de prendre en compte dans les politiques actuelles de conservation. Le recueil par ce travail de la liste des nombreuses localités abritant des EME et la spatialisation sur l’ensemble du territoire de variables environnementales, ont permis de séparer les EME en fonction de leurs exigences écologiques et de modéliser, par utilisation de MaxEnt, la distribution potentielle de micro-habitats susceptibles d’en héberger d’autres. De nombreuses nouvelles zones se sont ajoutées aux HMEV déjà identifiés, permettant d’orienter les opérations futures de prospection et de conservation à mettre en place rapidement sur l’ensemble du territoire au regard des menaces grandissantes. La seconde approche utilisée pour étudier le micro-endémisme avait pour objectif de comprendre pourquoi au sein d’un même genre, certaines espèces proches phylogénétiquement présentent des distributions larges et d’autres plus restreintes. Pour cela, une étude comparative a été menée entre Scaevola montana, espèce indigène à large répartition, et S. coccinea, espèce micro-endémique de la vallée de la Tontouta. L’espèce commune s’est révélée très tolérante en terme de climats et de sols, à l’inverse de S. coccinea limitée aux seuls sols bruns hypermagnésiens. Au niveau de leur biologie de la reproduction, l’espèce commune est pollinisée par une guilde d’insectes et dispersée par les oiseaux, alors que l’espèce micro-endémique est pollinisée par des oiseaux territoriaux et ses fruits ne sont pas dispersés par des animaux. Ces modes de reproduction bien distincts laissaient envisager de forts impacts sur les flux de gènes entre les individus et les populations. Cet élément a été confirmé par l’étude de la diversité et de la structuration génétiques des populations à partir de marqueurs microsatellites. Les populations de S. montanas ont organisées en deux grands groupes, celui des massifs ultramafiques de la côte ouest et celui du Grand Sud (deux populations particulières ont été retrouvées à l’Ile des Pins et au Col d’Amoss). A l’opposé les populations de S. coccinea apparaissent très différenciées alors même qu’elles sont proches géographiquement (<2km). Ceci met en évidence l’absence de flux de gènes sur de très courtes distances chez cette espèce. S. coccinea a donc une distribution restreinte principalement due à son incapacité à se disperser sur de longues distances et à une niche écologique relativement restreinte. Ces observations vont permettre de mieux gérer ces deux espèces. S. montana étant utilisée dans des programmes de revégétalisation, il conviendra d’utiliser des semences du groupe correspondant à la zone d’implantation. Quant à S. coccinea, sa conservation apparaît incontournable car représentée par quelques populations situées dans une vallée fortement impactée par les activités minières.
... Molecular phylogenetics suggest that (a) Araucaria heterophylla, the host plant of P. novozelandicus n. sp., is sister to the complex of the endemic New Caledonian Araucaria spp. (Gaudeul et al. 2012), and that (b) divergence between the South American and New Caledonian araucarians + A. heterophylla happened about 60 mya (estimates range from c. 103-29 mya) (Kranitz et al. 2014). Surprisingly, our molecular phylogenetic analyses suggest a sister relationship between P. novozelandicus n. sp. and P. araucariae, although a sister relationship between the two South American Pentasetacus species (P. ...
A new vagrant eriophyoid mite species of the archaic genus Pentasetacus (Schliesske 1985), P. novozelandicus n. sp., is described with the aid of conventional microscopy, confocal laser scanning microscopy and scanning electron microscopy. It was found on Araucaria heterophylla, which is an araucarian that is endemic to Norfolk Island and introduced to New Zealand. Partial sequences of mitochondrial barcode COI gene and D1–D2 domains of nuclear rDNA of two pentasetacid mites, P. araucariae (MK903025 and MK898944) and P. novozelandicus n. sp. (MK903024 and MK898943) are provided. Molecular phylogenetic analyses of full-length D1–D2 eriophyoid sequences, including GenBank sequences and newly generated sequences of pentasetacids, confirmed the monophyly of Pentasetacidae but failed to resolve the basal phylogeny of Eriophyoidea. This may be because the D1–D2 domains of 28S are hypervariable in Eriophyoidea. Moreover, in pentasetacids D1–D2 sequences are about 20% shorter than in other eriophyoids, and thus harder to align. Two types of anal lobes are described in Eriophyoidea: (1) Eriophyidae s.l. and Phytoptidae s.l. have bilaterally symmetric lobes; (2) pentasetacids have non-divided lobes. The presence of an anal secretory apparatus, comprising internal structures that have previously been described in Eriophyidae s.l. and Phytoptidae s.l., is confirmed in pentasetacid genera. The phylogeny of pentasetacids is also discussed in the context of the paleobiography of Araucariaceae.
... However, this does not necessarily mean the taxon has reached a dead end. The majority of Gymnostoma species occur on New Caledonia and it is likely that the genus may have undergone radiation on the island along with many other taxa such as Araucaria (Gaudeul et al. 2012) and Beauprea (He et al. 2016) as just two examples. ...
Key message
The phylogenetically basal genus of the Casuarinaceae, Gymnostoma, from relatively mesic environments, shows morphological and anatomical structures that are precursors to xeromorphic modifications in the derived genera Casuarina and Allocasuarina.
Abstract
Gymnostoma is the basal genus of the Casuarinaceae with a long evolutionary history and a morphology that has changed little over many millions of years. From a wide distribution in the Tertiary of the southern hemisphere, it is now restricted to islands in the Pacific Ocean, the Malesian region and one small area of northeastern Queensland where it occurs in mesic climates, often on poor soils. The unique vegetative morphology it shares with other more derived genera in the family appears to be xeromorphic. Its distribution combined with the fossil evidence that early Tertiary Gymnostoma occurred with other taxa whose morphology indicated they grew in mesic environments implies that the reduction in the photosynthetic organs was not specifically related to growing in xeric environments. It may be related to evolutionary adaptation to growing on nutrient poor substrates that may also suffer from seasonal water deficit. The foliage reduction then served as a pre-adaptation for derived species to help them cope with the aridity that developed on the Australian continent through the later part of the Tertiary. The fusion of the leaves to the stem to form phyllichnia was a precursor which enabled the development of specific adaptations in the derived genera Casuarina and Allocasuarina to improve water conservation, such as stomata restricted to furrows between the phyllichnia and proliferation of structural sclerenchyma that helps prevent cell collapse under drought conditions.
... As with other organisms, molecular phylogenetics has reshaped our understanding of conifer evolution (e.g., Bowe et al., 2000;Chaw et al., 2000;Rai et al., 2008). Many parts of the conifer tree remain difficult to resolve, especially among closely related species (e.g., Gernandt et al., 2001Gernandt et al., , 2009Campbell et al., 2005;Parks et al., 2012;Gaudeul et al., 2012;Ruhsam et al., 2015), but results from molecular datasets are consistent with respect to backbone relationships among major extant conifer clades (Stefanović et al., 1998;Gugerli et al., 2001;Rai et al., 2008;Leslie et al., 2012;Wickett et al., 2014). Some analyses have also used fossil-calibrated molecular clocks to estimate divergence ages in various conifer clades (Wang et al., 2000;Gernandt et al., 2008;Biffin et al., 2012, Leslie et al., 2012Mao et al., 2012), and more recent dating techniques promise better (or at least new; see Bapst et al., 2016) ways in which to integrate fossils into molecular phylogenies by analyzing morphological and molecular data together in a single model (Ronquist et al., 2012;Heath et al., 2014;O'Reilly et al., 2015;Zhang et al., 2015). ...
Premise of the Study
Conifers are an important living seed plant lineage with an extensive fossil record spanning more than 300 million years. The group therefore provides an excellent opportunity to explore congruence and conflict between dated molecular phylogenies and the fossil record.
Methods
We surveyed the current state of knowledge in conifer phylogenetics to present a new time‐calibrated molecular tree that samples ~90% of extant species diversity. We compared phylogenetic relationships and estimated divergence ages in this new phylogeny with the paleobotanical record, focusing on clades that are species‐rich and well known from fossils.
Key Results
Molecular topologies and estimated divergence ages largely agree with the fossil record in Cupressaceae, conflict with it in Araucariaceae, and are ambiguous in Pinaceae and Podocarpaceae. Molecular phylogenies provide insights into some fundamental questions in conifer evolution, such as the origin of their seed cones, but using them to reconstruct the evolutionary history of specific traits can be challenging.
Conclusions
Molecular phylogenies are useful for answering deep questions in conifer evolution if they depend on understanding relationships among extant lineages. Because of extinction, however, molecular datasets poorly sample diversity from periods much earlier than the Late Cretaceous. This fundamentally limits their utility for understanding deep patterns of character evolution and resolving the overall pattern of conifer phylogeny.
... A similar problem has been mentioned for Araucaria section Eutacta, which is the most diverse section for the genus and also has extinct relatives in Patagonia (Berry, 1938;Florin, 1940;Ohsawa et al., 2016). Relationships among the species of section Eutacta that are endemic to New Caledonia, which are thought to have diverged during the Neogene (Kranitz et al., 2014), are debated on the basis of various sets of molecular data (e.g., AFLP markers, Gaudel et al., 2012;nuclear and chloroplast markers, Gaudel et al., 2014;complete plastid genome, Ruhsam et al., 2015). Also, section Eutacta has been considered as a complex of closely related taxa, among which hybridization and introgression are suspected (Gaudeul et al., 2014). ...
Premise of the Study
The fossil record of Agathis historically has been restricted to Australasia. Recently described fossils from the Eocene of Patagonian Argentina showed a broader distribution than found previously, which is reinforced here with a new early Paleocene Agathis species from Patagonia. No previous phylogenetic analyses have included fossil Agathis species.
Methods
We describe macrofossils from Patagonia of Agathis vegetative and reproductive organs from the early Danian, as well as leaves with Agathis affinities from the latest Maastrichtian. A total evidence phylogenetic analysis is performed, including the new Danian species together with other fossil species having agathioid affinities.
Key Results
Early Danian Agathis immortalis sp. nov. is the oldest definite occurrence of Agathis and one of the most complete Agathis species in the fossil record. Leafy twigs, leaves, pollen cones, pollen, ovuliferous complexes, and seeds show features that are extremely similar to the living genus. Dilwynites pollen grains, associated today with both Wollemia and Agathis and known since the Turonian, were found in situ within the pollen cones.
Conclusions
Agathis was present in Patagonia ca. 2 million years after the K‐Pg boundary, and the putative latest Cretaceous fossils suggest that the genus survived the K–Pg extinction. Agathis immortalis sp nov. is recovered in a stem position for the genus, while A. zamunerae (Eocene, Patagonia) is recovered as part of the crown. A Mesozoic divergence for the Araucariaceae crown group, previously challenged by molecular divergence estimates, is supported by the combined phylogenetic analyses including the fossil taxa.
... Other DNA-based method such as amplified fragment length polymorphisms (AFLP) has been suggested to tackle this problem (Després et al. 2003, Gaudeul et al. 2012). However, for agarwood, which is often traded in wood or wood products, the only other option is through wood anatomy. ...
Indonesia is home to several tree taxa that are harvested for agarwood. This highly valuable oleoresin ironically was the cause for some species to become vulnerable due to gluttonous human activity. However, information on the genetic diversity of these endangered trees is limited. In this study, 28 specimens representing eight species from two genera, Aquilaria and Gyrinops, were collected from ex-situ and in-situ populations in Indonesia. Phylogenetic analysis conducted on DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS) and the trnL-trnF intergenic spacer regions, revealed that Aquilaria and Gyrinops are paraphyletic when Aquilaria cumingiana is excluded. The phylogenetic analysis for ITS and trnL-trnF showed capability to categorise agarwood-producing species based on their regions: East Indonesia and West Indonesia, using Wallace's Line as the divider. In addition, we discuss challenges in species identification and taxonomy of agarwood-producing genera, and their conservation efforts in Indonesia.
... Speciation has influenced the diversification of presentday species (Barraclough and Nee 2001) and a comprehensive understanding of population genetic differentiation along environmental gradients is therefore important when investigating speciation mechanisms of taxa (Gaudeul et al. 2012). Genetic variation within a species often has a geographic basis since the processes of adaptation, gene flow, and genetic drift act differentially across heterogeneous landscapes and may be strongly influenced by the demography and spatial distributions of populations (Eckert et al. 2008). ...
Speciation is a complex process that is fundamental to the origins of biological diversity. While there has been considerable progress in our understanding of speciation, there are still many unanswered questions, especially regarding barriers to gene flow in diverging populations. Eucalyptus is an appropriate system for investigating speciation mechanisms since it comprises species that are rapidly evolving across heterogeneous environments. We examined patterns of genetic variation within and among six closely related Eucalyptus species in subgenus Eucalyptus section Eucalyptus in south-eastern Australia (commonly known as the “green ashes”). We used reduced representation genome sequencing to genotype samples from populations across altitudinal and latitudinal gradients. We found one species, Eucalyptus cunninghamii, to be highly genetically differentiated from the others, and a population of mallees from Mount Banks to be genetically distinct and therefore likely to be a new undescribed species. Only modest levels of differentiation were found between all other species in the study. There was population structure within some species (e.g., E. obstans) corresponding to geographical factors, indicating that vicariance may have played a role in the evolution of the group. Overall, we found that lineages within the green ashes are differentiated to varying extents, from strongly diverged to much earlier stages of the speciation continuum. Furthermore, our results suggest the green ashes represent a group where a range of mechanisms (e.g., reticulate evolution and vicariance) have been operating in concert. These findings not only offer insights into recent speciation mechanisms in Eucalyptus, but also other species complexes.
... (Araliaceae; Eibl & al., 2001), Psychotria L. (Rubiaceae; Barrabé & al., 2013), Santalum L. (Santalaceae; Harbaugh & Baldwin, 2007), Sapotaceae (Swenson & al., 2014) and Winteraceae (Thomas & al., 2014). After colonization, species diversification in NC was probably favoured by the island's pronounced topological complexity and its many strong environmental gradients (e.g., precipitation and soils; Eibl & al., 2001;Pillon & al., 2009a, b;Espeland & Johanson, 2010;Gaudeul & al., 2012). ...
Based on a worldwide dataset of molecular sequence data from three plastid DNA markers (rbcL, rbcL-accD-accD, rps4-trnS) obtained from 109 species of Hymenophyllum (Hymenophyllaceae), we investigated the systematics and bioge- ographic origins of the New Caledonian (NC) members of this fern genus, which were thought to include 16 species with 10 endemics. Located in the southwest Pacific, NC is a continental Gondwanan island that was long supposed to harbour phylogenetic relicts. However, molecular and geological data suggest that the current flora and fauna are the result of recent colonizations that occurred after total submersion (during the Eocene) and subsequent re-emersion of NC ca. 37 Ma. Our molecular phylogenetic results, complemented by morphological observations of herbarium specimens, show the existence of a new species that was as yet undescribed, and suggest that a previously recognized variety should be elevated to the rank of species to avoid species polyphyly. These two species, which are recognizable based on several morphological features, are endemic to NC: (i) Hymenophyllum soriemersum sp. nov. is sister to the other NC endemic H. dimidiatum; and (ii) H. neo- caledonicum comb. & stat. nov, previously described as a variety within H. lyallii, was retrieved as a distinct lineage. We also confirmed the synonymy of H. streptophyllum and H. subdimidiatum (both previously considered as endemic to NC) with the more widely distributed H. javanicum and H. holochilum, respectively. These synonymies were previously hypothesised based on morphology alone. New Caledonia thus has as total of 17 Hymenophyllum species, 12 (71%) of which are endemics. Biogeographic inferences based on the results of our phylogenetic analyses suggest that Hymenophyllum originated in New Zealand ca. 49.8 Ma (95% HPD: 40.7–59.5 Ma). Its spatio-temporal history may in part have been influenced by vicariance (with potential exchange via the Antarctica land bridge that persisted between Australia and South America until 34 Ma), but long-distance dispersal (LDD) appears as the predominant process leading to the present-day distribution of species. At least eight LDD events are needed to explain the presence of the 10 NC endemics analysed here (H. francii and H. humboldtianum were not included), each of which occurred < 22.1 Ma and originated from a surrounding territory: Southeast Asia was probably the dispersal source for the NC endemic clade comprising H. soriemersum, H. dimidiatum, and H. rolandi-principis while the ancestors of the other NC endemics most likely dispersed from New Zealand, Australia or other Pacific Islands. Such a regional pattern is congruent with the distribution of non-endemic species, which are mostly shared among neighbouring territories. Lastly, we found evidence for only two cases of diversification within NC, yielding two and three species each (H. soriemersum, H. dimidiatum and H. rolandi-principis; and H. lyallii and the ancestor of H. braithwaitei and H. tomaniiviense). Such a low level of in situ diversification may be explained by the high dispersal abilities of ferns in general (via dust-like spores), which slow down the differentiation process among populations and make a newly available niche likely to be filled by an immigrant before a new species might evolve locally.
... A similar pattern was observed with New Caledonian species of Araucaria Juss. (Gaudeul et al., 2012). The clusters revealed by PCoA and Bayesian clustering were consistent with the well-supported relationships in the phylogenetic analyses. ...
Differences in habitat, geographical distribution and minor details related to floral and vegetative structures of Petunia spp. have led to many changes in the taxonomy of the genus. In the face of controversy relating to species circumscription in the genus and insufficient variation to identify the evolutionary relationships among Petunia spp. using conventional molecular phylogenetic markers, the purpose of this work was to investigate the potential and limitations of amplified fragment length polymorphism (AFLP) data analyses for delimiting species and inferring evolutionary relationships in a young group, providing the bases for future studies. We analysed 152 individuals distributed randomly across the geographical range of 14 Petunia taxa. AFLP analysis resulted in 1259 polymorphic fragments that proved to be efficient in identifying high numbers of polymorphisms in recently diverged plant species. The phylogenetic approach using AFLP allowed a high level of correct assignment of individuals to their corresponding morphological groups. The results of the genetic clustering analyses were consistent with respect to the main groups and the well-supported relationships in phylogenetic analyses. In this study, we demonstrated the efficiency of AFLP to identify polymorphisms in recently diverged lineages of Petunia. We report that this approach was also valuable in species delimitation for species status of difficult taxa and indicating new species.
... In groups in which sequence analyses revealed only insufficiently resolved phylogenetic trees like Dyckia, the AFLP method (amplified fragment length polymorphism; Vos et al., 1995) has proved to be an alternative and viable option for analysing closely related species, particularly in groups that have undergone a recent radiation (Albertson et al., 1999;Despr es et al., 2003;Mechanda et al., 2004;Jacobs et al., 2008;Koopman et al., 2008;Gaudeul et al., 2012). The AFLP method can be adopted for molecular systematic and population genetic analyses in most organisms and has been successfully applied in Bromeliaceae (Rex et al., 2007;Schulte et al., 2010). ...
Dyckia is a xeromorphic bromeliad genus with 168 species distributed throughout south-eastern South America, with the centre of diversity in Brazil. Previous phylogenetic studies based on sequence data revealed, in general, poor resolution among species. To improve our understanding of infrageneric relationships, here we present a molecular phylogenetic analysis of Dyckia based on amplified fragment length polymorphism (AFLP) markers. We also discuss the evolution of floral characters and their implications for the life-history of the genus. Dyckia proved to be well supported as a monophyletic group, although showing a poor resolution in the backbone of the tree. In accordance with previous data, our results suggest that hybridization and introgression have played a significant role in the evolution of the genus. However, the AFLP data showed stronger support for terminal nodes. The results provided deeper insights into the infrageneric relationships, the correlation between species groups, morphological aspects and geographical distribution. Additionally, the character reconstruction corroborates the geographical association found, in which a pattern could generally be observed for species stated as early diverging. Analysing the genus at a population level and taxonomic revision are crucial to understanding the evolutionary dynamics of the clade.
... Our study was motivated by the presence of (relatively) widespread, patchily distributed species, and species with broad ecological amplitude-both of which we considered as holding the potential for cryptic taxa (i.e., overlooked discrete biologically meaningful entities showing evidence of divergent evolutionary trajectories). Our study focuses on a pair of closely related species, A. rulei and A. muelleri, which belong to the same clade ( Gaudeul et al., 2012 ;Kranitz et al., 2014 ;Ruhsam et al., 2015 ). Specifi cally, we establish whether there is strong regional genetic structure that may warrant consideration in conservation programs, and whether there is evidence for cryptic species in this fl agship group. ...
Premise of the study:
Cryptic species represent a conservation challenge, because distributions and threats cannot be accurately assessed until species are recognized and defined. Cryptic species are common in diminutive and morphologically simple organisms, but are rare in charismatic and/or highly visible groups such as conifers. New Caledonia, a small island in the southern Pacific is a hotspot of diversity for the emblematic conifer genus Araucaria (Araucariaceae, Monkey Puzzle trees) where 13 of the 19 recognized species are endemic.
Methods:
We sampled across the entire geographical distribution of two closely related species (Araucaria rulei and A. muelleri) and screened them for genetic variation at 12 nuclear and 14 plastid microsatellites and one plastid minisatellite; a subset of the samples was also examined using leaf morphometrics.
Key results:
The genetic data show that populations of the endangered A. muelleri fall into two clearly distinct genetic groups: one corresponding to montane populations, the other corresponding to trees from lower elevation populations from around the Goro plateau. These Goro plateau populations are more closely related to A. rulei, but are sufficiently genetically and morphological distinct to warrant recognition as a new species.
Conclusions:
Our study shows the presence of a previously unrecognized species in this flagship group, and that A. muelleri has 30% fewer individuals than previously thought. Combined, this clarification of species diversity and distributions provides important information to aid conservation planning for New Caledonian Araucaria.
... AFLP markers are typically used at low taxonomic level in closely related species and population analyses (e.g. Despré et al., 2003;Tremetsberger et al., 2006;Gaudeul et al., 2012). In the case of the New Caledonian Diospyros species, we used AFLPs to evaluate species limits (Turner et al., 2013b), and in most cases we found congruence with the species concepts of White (1993). ...
Background and aims:
Some plant groups, especially on islands, have been shaped by strong ancestral bottlenecks and rapid, recent radiation of phenotypic characters. Single molecular markers are often not informative enough for phylogenetic reconstruction in such plant groups. Whole plastid genomes and nuclear ribosomal DNA (nrDNA) are viewed by many researchers as sources of information for phylogenetic reconstruction of groups in which expected levels of divergence in standard markers are low. Here we evaluate the usefulness of these data types to resolve phylogenetic relationships among closely relatedDiospyrosspecies.
Methods:
Twenty-two closely relatedDiospyrosspecies from New Caledonia were investigated using whole plastid genomes and nrDNA data from low-coverage next-generation sequencing (NGS). Phylogenetic trees were inferred using maximum parsimony, maximum likelihood and Bayesian inference on separate plastid and nrDNA and combined matrices.
Key results:
The plastid and nrDNA sequences were, singly and together, unable to provide well supported phylogenetic relationships among the closely related New CaledonianDiospyrosspecies. In the nrDNA, a 6-fold greater percentage of parsimony-informative characters compared with plastid DNA was found, but the total number of informative sites was greater for the much larger plastid DNA genomes. Combining the plastid and nuclear data improved resolution. Plastid results showed a trend towards geographical clustering of accessions rather than following taxonomic species.
Conclusions:
In plant groups in which multiple plastid markers are not sufficiently informative, an investigation at the level of the entire plastid genome may also not be sufficient for detailed phylogenetic reconstruction. Sequencing of complete plastid genomes and nrDNA repeats seems to clarify some relationships among the New CaledonianDiospyrosspecies, but the higher percentage of parsimony-informative characters in nrDNA compared with plastid DNA did not help to resolve the phylogenetic tree because the total number of variable sites was much lower than in the entire plastid genome. The geographical clustering of the individuals against a background of overall low sequence divergence could indicate transfer of plastid genomes due to hybridization and introgression following secondary contact.
... Cryptic species are probably common in many groups of organisms and will be detected with increasing frequency as sensitive molecular methods, such as sequence analysis, are applied to systematic problems. Cryptic species identification has become the subject of extensive research due to its importance for such research fields as for example population genetics or biogeography (Dilon and Quipuscoa, 2014;Gomez et al., 2002;Heinrichs et al., 2010;Gaudel et al., 2012;Niwa et al., 2014;Saunders and Lehmkuhl, 2005;Yu et al., 2013). ...
Carpological and molecular variation among the 14 species of Erysimum distributed in Central Europe was examined. Special attention was paid to the group of six wallflowers (E. hungaricum, E. pieninicum, E. wahlenbergii, E. virgatum, E. durum and E. hieracifolium) that are morphologically difficult to distinguish forming a complex taxonomic group. It was found that the sculpturing of seed testa and the micromorphological patterns regarding the surface of silique septum obviously vary among the studied wallflowers while seed dimensions and shapes overlap and are not adequately informative. The highest carpological dissimilarity was noted between E. cheiri and E. crepidifolium, whereas the taxa in the mentioned taxonomic complex were carpologically very similar, only E. virgatum was slightly different. The molecular techniques used here including SSCP and restriction endonuclease-digested rDNA amplified by PCR and combined with RAPD, strongly support the genetic distinctiveness of all Erysimum species studied. Moreover, the results obtained here indicate that the group of five out of six taxonomically problematic Erysimum species consist of distinct, closely related species and may constitute a complex of cryptic species.
... The Jaccard similarity index is defined as the fraction of fragments shared by two individuals (Kosman and Leonard 2005). It considers only shared presence as contributing to the similarity of individuals and disregards shared absence, which is more prone to homoplasy (Gaudeul et al. 2012). PCoA based on the Jaccard distance matrix was computed and visualized using the R CRAN package ade4 (Dray et al. 2007; R Development Core Team 2011). ...
Premise of research. Determination of species boundaries is essential for understanding and preserving biological diversity, yet it remains a difficult task for many plant lineages. Population genetics approaches explicitly taking into account the geographic context of processes driving population divergence and speciation may help to identify species boundaries in complex groups. Here, we adopt this approach to investigate genetic boundaries in an endemic group of trumpet daffodils (Narcissus, section Pseudonarcissi) whose taxonomic distinctiveness remains controversial.
Methodology. We analyzed amplified fragment length polymorphism markers from a total of 36 populations (526 individuals) spanning the group’s entire distribution range in the southern Iberian Peninsula. To identify the most likely number of distinct genetic groups, model- and nonmodel-based methods (Bayesian, principal coordinates, and neighbor-joining classification) were applied. Effects of long-term historical divergence were dissected from more recent or local differentiation processes using simple and partial Mantel tests.
Pivotal results. A major genetic split, consistently supported by the three analytical methods used, differentiated all populations generally ascribed to Narcissus bujei in traditional taxonomic treatments from the rest, which included all populations generally designated as Narcissus longispathus and Narcissus nevadensis. The two groups exhibited contrasting levels of within-population genetic diversity and rarity. Comparative analyses of the relationship between genetic differentiation and geographic distance in these two main genetic lineages suggested that they have remained isolated through a long time period. Separate analyses of genetic and geographic patterns within each major lineage suggested contrasting evolutionary histories.
Conclusions. Genetically, geographically, and ecologically well-defined lineages of the Pseudonarcissi section occur throughout the southern mountains of the Iberian Peninsula, generally supporting the traditional taxonomical delimitation of this lineage and qualifying as separate units of conservation. Our findings emphasize the usefulness of molecular data and population genetics approaches in a geographic context to delineate morphologically cryptic species in complex lineages.
... Indeed, several authors have suggested that this technique can be especially useful in reconstructing phylogenetic relationships among species that have diverged or radiated recently [50][51][52][53]. Although some considerations must be taken into account for its use, AFLP are currently widely employed in molecular ecology and evolution research [54][55][56][57][58][59]. In fact, this DNA fingerprinting approach has proven to be particularly suitable for evaluating the genetic structure of plant species in different oceanic archipelagos, and hence elucidating the potential evolutionary forces -such as gene flow or genetic driftthat influence the distribution of genetic diversity among individuals, populations, and species [60][61][62]. ...
The radiation of the genus Cheirolophus (Asteraceae) in Macaronesia constitutes a spectacular case of rapid diversification on oceanic islands. Twenty species - nine of them included in the IUCN Red List of Threatened Species - have been described to date inhabiting the Madeiran and Canarian archipelagos. A previous phylogenetic study revealed that the diversification of Cheirolophus in Macaronesia started less than 2 Ma. As a result of such an explosive speciation process, limited phylogenetic resolution was reported, mainly due to the low variability of the employed molecular markers. In the present study, we used highly polymorphic AFLP markers to i) evaluate species' boundaries, ii) infer their evolutionary relationships and iii) investigate the patterns of genetic diversity in relation to the potential processes likely involved in the radiation of Cheirolophus. One hundred and seventy-two individuals representing all Macaronesian Cheirolophus species were analysed using 249 AFLP loci. Our results suggest that geographic isolation played an important role in this radiation process. This was likely driven by the combination of poor gene flow capacity and a good ability for sporadic long-distance colonisations. In addition, we also found some traces of introgression and incipient ecological adaptation, which could have further enhanced the extraordinary diversification of Cheirolophus in Macaronesia. Last, we hypothesize that current threat categories assigned to Macaronesian Cheirolophus species do not reflect their respective evolutionary relevance, so future evaluations of their conservation status should take into account the results presented here.
... The AFLP fingerprinting method has been widely used to provide genetic polymorphisms for phylogenetic, phylogeographical, and microevolutionary questions. Therefore, this approach is extensively used to disentangle evolutionary relationships in hybridising and polyploid complexes (e.g., Guo & al., 2005Guo & al., , 2008Pleines & Blattner, 2008;Weiss-Schneeweiss & Tremetsberger, 2008;Perrie & Shepherd, 2009;Culumber & al., 2011;Gaudeul & al., 2011;Safer & al., 2011;Greiner & al., 2013). ...
AFLP fingerprinting for 236 individuals from 75 populations and 31 taxa of the Southern Hemisphere genus Leptinella (Compositae: Anthemideae) was carried out in order to infer the evolutionary relationships among the New Zealand representatives of the genus and to compare the
results with sequence-based phylogenetic reconstructions for the genus. The New Zealand–based clade of the genus is characterised by the formation of an impressive polyploid complex with ploidy levels reaching from 4x to 24x. We observe a tripartition of taxa into species
groups that correspond to species assemblages also found in the sequence-based reconstructions: A basal, presumably paraphyletic stock of tetraploid species (AFLP cluster A) corresponding to the morphologically defined Leptinella subg. Radiata is connected through one of its
sub-clusters (A1, the L. minor group) with a monophyletic group of two clusters (B and C) with a sister-group relationship. While AFLP cluster B remained on the tetraploid level, clusters A and C form ploidy series reaching the levels of 16x and 24x, respectively. The
lack of intermediate AFLP genotypes demonstrates that polyploidisation has occurred independently in the two clusters forming the L. pectinata/L. pyrethrifolia assemblage (cluster A2) in L. subg. Radiata and the L. dioica assemblage (clusters C1 and C2) in
L. subg. Leptinella. The joint consideration of sequence-based reconstructions and AFLP fingerprint patterns further allows the formulation of an evolutionary hypothesis for the genus that tries to explain differentiation processes in a temporal and geographic framework: The
available data argue for a Late Miocene (ca. 5–10 Ma) establishment of Leptinella in New Zealand and its further differentiation on the tetraploid level throughout the Pliocene and the Early Pleistocene, followed by extensive polyploidisation cycles caused by the climatic oscillations
of the Pleistocene.
... Myr, Biffin, Hill & Lowe, 2010). AFLP data (Gaudeul et al., 2012) ...
New Caledonia is well known for its rich and unique flora. Many studies have focused on the biogeographical origins of New Caledonian plants but rates of diversification on the island have scarcely been investigated. Here, dated phylogenetic trees from selected published studies were used to evaluate the time and tempo of diversification in New Caledonia. The 12 plant lineages investigated all appear to have colonized the island <?37?Mya, when New Caledonia re-emerged after a period of inundation, and the timing of these arrivals is spread across the second half of the Cenozoic. Diversification rates are not particularly high and are negatively correlated with lineage age. The palms have the fastest diversification rates and also the most recent arrival times. The lineage ages of rainforest plants suggest that this ecosystem has been present for at least 6.9?Myr. The New Caledonian flora is apparently a relatively old community that may have reached a dynamic equilibrium. Colonization by new immigrants has been possible until relatively recently and diversity-dependent processes may still be affecting the diversification rates of the earlier colonizers. Further studies on the diversification of large plant clades with exhaustive sampling should help to clarify this.
... In addition, estimated the ages and diversification rates of gymnosperm lineages, and found that living gymnosperm groups are not ancient, occupy diverse habitats and some probably survived after making adaptive shifts. Actually, the radiative speciation in the middle to late Cenozoic with a very low interspecific genetic differentiation has been reported in most of the studied gymnospermous genera with multiple species, such as Agathis, Araucaria, Cycas, Ephedra, Gnetum, Juniperus, Picea, Pinus, and Podocarpus (Hill, 1995;Wagstaff, 2004;Ran et al., 2006;Won and Renner, 2006;Willyard et al., 2007;Ickert-Bond et al., 2009;Biffin et al., 2010;Mao et al., 2010;Nagalingum et al., 2011;Gaudeul et al., 2012;Leslie et al., 2012). The low species diversity of extant gymnosperms could be attributed to the Cenozoic extinctions, although recent radiations have occurred in some lineages such as cycads Nagalingum et al., 2011). ...
... In general, the likelihood of homoplasy among AFLP, RAPD, or ISSR fragments should increase with genetic distance of the species studied, so that they should be useful for phylogenetic inference if sequence divergence among the ingroup taxa is low [29,41,42]. Indeed fragment-based markers have been successfully to reconstruct phylogenies for a number of recent and rapidly radiating groups [29,31,33,35,3839404142434445464748, including implementation of an AFLP clock in at least one case [46]. Plastid sequence data. ...
Previous studies based on DNA restriction-site and sequence variation have shown that the Hawaiian lobeliads are monophyletic and that the two largest genera, Cyanea and Clermontia, diverged from each other ca. 9.7 Mya. Sequence divergence among species of Clermontia is quite limited, however, and extensive hybridization is suspected, which has interfered with production of a well-resolved molecular phylogeny for the genus. Clermontia is of considerable interest because several species posses petal-like sepals, raising the question of whether such a homeotic mutation has arisen once or several times. In addition, morphological and molecular studies have implied different patterns of inter-island dispersal within the genus. Here we use nuclear ISSRs (inter-simple sequence repeat polymorphisms) and five plastid non-coding sequences to derive biparental and maternal phylogenies for Clermontia. Our findings imply that (1) Clermontia is not monophyletic, with Cl. pyrularia nested within Cyanea and apparently an intergeneric hybrid; (2) the earliest divergent clades within Clermontia are native to Kauài, then Òahu, then Maui, supporting the progression rule of dispersal down the chain toward progressively younger islands, although that rule is violated in later-evolving taxa in the ISSR tree; (3) almost no sequence divergence among several Clermontia species in 4.5 kb of rapidly evolving plastid DNA; (4) several apparent cases of hybridization/introgression or incomplete lineage sorting (i.e., Cl. oblongifolia, peleana, persicifolia, pyrularia, samuelii, tuberculata), based on extensive conflict between the ISSR and plastid phylogenies; and (5) two origins and two losses of petaloid sepals, or-perhaps more plausibly-a single origin and two losses of this homeotic mutation, with its introgression into Cl. persicifolia. Our phylogenies are better resolved and geographically more informative than others based on ITS and 5S-NTS sequences and nuclear SNPs, but agree with them in supporting Clermontia's origin on Kauài or some older island and dispersal down the chain subsequently.
This chapter explores the main characteristics of New Caledonian plant biodiversity, and provides a condensed picture of the major unique elements of its flora. We present the results of recent research conducted in a territory that has much to contribute to science and society. We explore the original and unique representation of some plant lineages and functional groups, as well as the rich and diversified vegetation.
Our understanding of the natural world is constantly evolving and strengthening as more observations are made and experiments are performed. For example, we understand that tree stems grow toward the light (positive phototropism; Darwin 1880, Loehle 1986, Christie et al. 2013) and against gravity (negative gravitropism; Knight 1806, Hashiguchi et al. 2013). We also know that plants respond to mechanical stimulus and perturbation (thigmotropism; Braam 2005). Genes and their resulting proteins have been described to uncover some of the mechanisms for these environmental responses, but relatively speaking, we have just scratched the surface (Wyatt et al. 2013). While the discovery of the molecular mechanisms responsible for these behaviors is certainly dependent on the ever-improving lab technology available, every molecular discovery is dependent on a macroscopic observation. In this manuscript I present the two novel macroscopic observations I made on members of Araucaria in the urban forest. The first describes a hemisphere-dependent lean in A. columnaris, and the second provides genetic and morphological evidence that hybrids exist between A. columnaris and A. heterophylla. Araucaria columnaris (J.R. Forst.) Hooker, or the Cook Pine is a conifer with a narrow native range that has been cultivated worldwide and grows unlike any other tree known. The initial observation we made was that trees in California and Hawaii lean south, and trees in California lean to a greater extent than trees in Hawaii. Measuring 250 trees in 16 regions worldwide, however, produced statistically significant evidence for a hemisphere dependent directional leaning pattern. Trees in the northern hemisphere lean south, and trees in the southern hemisphere lean north. Additionally, the lean becomes more pronounced at greater distances from the equator. We also gathered morphological and genetic evidence in the California urban forest that A. columnaris and A. heterophylla (Salisb.) Franco are hybridizing. Many individuals have intermediate characteristics of both species, which originally led me to believe that hybrids exist in cultivation. After analyzing several individuals with microsatellite genetic markers, I have enough evidence to conclude that hybrids between A. columnaris and A. heterophylla exist. This is an important observation mainly for municipalities and arborists interested in properly identifying trees in the urban forest. Knowing the proper identity of trees is imperative to informing decisions about their protection or removal. As we continue to ask questions about the inner workings of nature we will continue to gain a better appreciation for what we still do not know. The evidence provided in this manuscript better informs our future questions about a leaning pattern in A. columnaris and about the history of the cultivation of Araucaria.
Araucaria goroensis R.R.Mill & Ruhsam sp. nov., a new monkey puzzle species from New Caledonia, is described and illustrated with photographs from the field and from herbarium specimens. Previously confused with Araucaria muelleri , it is more similar to A. rulei . It is distinguished from the latter species by its larger leaves, microsporophylls without a shouldered base, and shorter female cone bracts. It occurs in a very limited area of south-east New Caledonia, where its existence is threatened by nickel mining. Using the guidelines of the International Union for Conservation of Nature, we propose an assessment of Endangered for the new species and reassess Araucaria muelleri also as Endangered. A key to the seven species in the ‘large-leaved clade’ of New Caledonian species of Araucaria is given. The name Eutassa latifolia de Laub. is synonymised with Araucaria muelleri , and the recent typification of the latter name by Vieillard 1276 is rejected. Detailed reasoning is given for these nomenclatural acts.
In the Australia-Pacific Region ultramafic outcrops are both widespread and extensive, covering thousands of km(2). Soils derived from ultramafic bedrock impose edaphic challenges and are widely known to host highly distinctive floras with high levels of endemism. In the Australia-Pacific Region, the ultramafics of the island of New Caledonia are famed for harbouring 2150 species of vascular plants of which 83% are endemic. Although the ultramafic outcrops in Western Australia are also extensive and harbour 1355 taxa, only 14 species are known to be endemic or have distributions centred on ultramafics. The ultramafic outcrops in New Zealand and Tasmania are small and relatively species-poor. The ultramafic outcrops in Queensland are much larger and host 553 species of which 18 (or possibly 21) species are endemic. Although New Caledonia has a high concentration of Ni hyperaccumulator species (65), only one species from Western Australia and two species from Queensland have so far been found. No Ni hyperaccumulator species are known from Tasmania and New Zealand. Habitat destruction due to forest clearing, uncontrolled fires and nickel mining in New Caledonia impacts on the plant species restricted to ultramafic soils there. In comparison with the nearby floras of New Guinea and South-east Asia, the flora of the Australia-Pacific Region is relatively well studied through the collection of a large number of herbarium specimens. However, there is a need for studies on the evolution of plant lineages on ultramafic soils especially regarding their distinctive morphological characteristics and in relation to hyperaccumulation.
A novel species of ascomycetes is described from resin of Araucaria humboldtensis on Mont Humboldt in New Caledonia. The fungus is placed in the new genus Resinogalea Rikkinen & A.R. Schmidt, with the species name R. humboldtensis Rikkinen & A.R. Schmidt. It has only been found growing on semi-hardened resin flows on branches of its endemic and endangered conifer host. The morphology and anatomy of the new fungus are compared with those of ecologically similar taxa, including Bruceomyces castoris. The new family Bruceomycetaceae Rikkinen & A.R. Schmidt is described to accommodate Resinogalea and Bruceomyces.
Premise of research. Phylogenetic relationships of Araucariaceae (Coniferophyta, Araucariales) are revised
on the basis of the first combined data matrix for the family.
Methodology. Taxon sampling includes 39 ingroup species (31 extant, 8 fossils) and outgroup species of
all the remaining conifer families. Five fossil Araucaria species, one species of the genus Araucarites, and two
species of the extinct genera Wairarapaia and Emwadea were included in the analyses. Character sampling
includes 23 genomic regions (19 plastid, 2 nuclear, and 2 mitochondrial) and 62 morphological characters
(52 discrete and 10 continuous). The phylogenetic analyses were conducted with equally weighted parsimony.
Additionally, several analyses under different taxon- and gene-sampling regimes were analyzed for identifying
the causes of the long-lasting controversies in the interrelationships of the three extant genera of Araucariaceeae.
Pivotal results. Monophyletic Araucariaceae is the sister group of Podocarpaceae, forming the order
Araucariales. Monophyly of Araucaria and Agathis is also strongly supported by the data. The results of both
molecular and combined analyses indicate that Wollemia and Agathis form a clade (pagathioid clade) sister
to Araucaria. Within Araucaria, the analyses support the monophyly of the four currently recognized sections:
Araucaria, Bunya, Intermedia, and Eutacta. Results support the monophyly of living and fossil Araucaria
(including Araucarites), whereas the remaining extinct genera are placed as the stem of the agathioid clade.
In terms of the sensitivity analyses performed, results suggest that inconsistencies among previous results would
be related to ingroup sampling.
Conclusions. By means of a combined phylogenetic analysis, we have been able to obtain a strongly
supported and well-resolved phylogeny of Araucariaceae that includes both living species and fossil species
for the group. This study shows the feasibility and usefulness of phylogenetic analyses that incorporate multiple
sources of evidence (molecules/morphology, living/fossil species, discrete/continuous characters).
To clarify phylogenetic relationships among New Caledonian species of Diospyros, sequences of four plastid markers (atpB, rbcL, trnK-matK and trnS-trnG) and two low-copy nuclear markers (ncpGS and PHYA) were analysed. New Caledonian Diospyros species fall into three clades, two of which have only a few members (1 or 5 species); the third has 21 closely related species for which relationships among species have been mostly unresolved in a previous study. Although species of the third group (NC clade III) are morphologically distinct and largely occupy different habitats, they exhibit little molecular variability. Diospyros vieillardii is sister to the rest of the NC clade III, followed by D. umbrosa and D. flavocarpa, which are sister to the rest of this clade. Species from coastal habitats of western Grande Terre (D. cherrieri and D. veillonii) and some found on coralline substrates (D. calciphila and D. inexplorata) form two well-supported subgroups. The species of NC clade III have significantly larger genomes than found in diploid species of Diospyros from other parts of the world, but they all appear to be diploids. By applying a molecular clock, we infer that the ancestor of the NC clade III arrived in New Caledonia around nine million years ago. The oldest species are around seven million years old and the youngest ones probably much less than one million years.
Premise of the study:
Anagenesis (or phyletic evolution) is one mode of speciation that occurs in the evolution of plants on oceanic islands. Of two endemic species on the Juan Fernández Islands (Chile), Myrceugenia fernandeziana and M. schulzei (Myrtaceae), believed to have originated anagenetically from different continental progenitors, the first is endemic to Robinson Crusoe Island and has no clear tie to continental relatives; the last is endemic to the younger island, Alejandro Selkirk Island, and has close affinity to M. colchaguensis in mainland Chile.
Methods:
Using AFLPs and six nuclear microsatellites from 381 individuals representing 33 populations, we determined patterns of genetic variation within and among populations on both islands and between those of the islands and mainland.
Key results:
Considerable genetic variation was found within populations on both islands. The level of gene diversity within M. schulzei was equivalent to that of its close continental relative M. colchaguensis. Genetic diversity was not partitioned geographically in M. fernandeziana and was weakly so and nonsignificantly in M. schulzei.
Conclusions:
The high genetic variation in both taxa is most likely due to anagenetic speciation. Subsidence of the older island Robinson Crusoe, landscape erosion, and restructuring of communities have severely reduced the overall island population to a single panmictic system. On the younger and less modified Alejandro Selkirk Island, slightly stronger patterns of genetic divergence are seen in M. schulzei. Because both species are genetically diverse and number in the thousands of individuals, neither is presently endangered in the archipelago.
Fundamental differences in the distribution of oceans and landmasses in the Northern and Southern Hemispheres potentially impact patterns of biological diversity in the two areas. The evolutionary history of conifers provides an opportunity to explore these dynamics, because the majority of extant conifer species belong to lineages that have been broadly confined to the Northern or Southern Hemisphere during the Cenozoic. Incorporating genetic information with a critical review of fossil evidence, we developed an age-calibrated phylogeny sampling ∼80% of living conifer species. Most extant conifer species diverged recently during the Neogene within clades that generally were established during the later Mesozoic, but lineages that diversified mainly in the Southern Hemisphere show a significantly older distribution of divergence ages than their counterparts in the Northern Hemisphere. Our tree topology and divergence times also are best fit by diversification models in which Northern Hemisphere conifer lineages have higher rates of species turnover than Southern Hemisphere lineages. The abundance of recent divergences in northern clades may reflect complex patterns of migration and range shifts during climatic cycles over the later Neogene leading to elevated rates of speciation and extinction, whereas the scattered persistence of mild, wetter habitats in the Southern Hemisphere may have favored the survival of older lineages.
New Caledonia has generally been considered a continental island, the biota of which largely dates back to Gondwanan times owing to its geological origin and the presence of phylogenetic relicts. This view is contradicted by geological evidence indicating long Palaeocene and Eocene submersions and by recent biogeographic and phylogenetic studies, with molecular or geophysical dating placing the biota no older than the Oligocene. Phylogenetic relicts do not provide conclusive information in this respect, as their presence cannot be explained by simple hypotheses but requires assumption of many ad hoc extinction events. The implication of this new scenario is that all the New Caledonian biota colonized the island since 37 Ma Local richness can be explained by local radiation and adaptation after colonization but also by many dispersal events, often repeated within the same groups of organisms. Local microendemism is another remarkable feature of the biota. It seems to be related to recent speciation mediated by climate, orography, soil type and perhaps unbalanced biotic interactions created by colonization disharmonies. New Caledonia must be considered as a very old Darwinian island, a concept that offers many more fascinating opportunities of study.
Highly polymorphic AFLP markers were applied to analyse the phylogenetic relationships of seven species from three sections within genus Araucaria (Araucariaceae) with cladistic and phenetic approaches. The objectives of the study were to compare the intrageneric relationships within Araucaria assessed by AFLP markers with the classification according to chloroplast DNA sequences and morphological characters. The AMOVA revealed 48% of the variation among species. The results of the principal coordinate analysis revealed three distinct groups: (1) A. angustifolia and A. araucana (= section Araucaria), (2) A. bidwillii (= section Bunya) and (3) A. cunninghamii, A. heterophylla, A. rulei and A. scopulorum (= section Eutacta). In the cladistic and phenetic analyses, phylogenetic trees were subdivided into two sister clades, one comprising the samples from section Eutacta, the other one was divided again into two sister clades corresponding to sections Araucaria and Bunya. These results are congruent with a previous phylogenetic study of the family Araucariaceae based on rbcL sequences and with the classification of genus Araucaria based on morphological characters. Both rbcL sequence data and AFLP analyses do not support section Bunya as one of the oldest sections within genus Araucaria, as suggested by the fossil record. The utility of AFLP markers for phylogenetic analyses is discussed.
The three southern conifer families, Araucariaceae, Cupressaceae and Podocarpaceae, have a long history and continue to be an important part of the vegetation today. The Araucariaceae have the most extensive fossil record, occurring in both hemispheres, and with Araucaria in particular having an ancient origin. In the Southern Hemisphere Araucaria and Agathis have substantial macrofossil records, especially in Australasia, and Wollemia probably also has an important macrofossil record. At least one extinct genus of Araucariaceae is present as a macrofossil during the Cenozoic. Cupressaceae macrofossils are difficult to identify in older sediments, but the southern genera begin their record in the Cretaceous (Athrotaxis) and become more diverse and extensive during the Cenozoic. Several extinct genera of Cupressaceae also occur in Cretaceous and Cenozoic sediments in Australasia. The Podocarpaceae probably begin their macrofossil record in the Triassic, although the early history is still uncertain. Occasional Podocarpaceae macrofossils have been recorded in the Northern Hemisphere, but they are essentially a southern family. The Cenozoic macrofossil record of the Podocarpaceae is extensive, especially in south-eastern Australia, where the majority of the extant genera have been recorded. Some extinct genera have also been reported from across high southern latitudes, confirming an extremely diverse and widespread suite of Podocarpaceae during the Cenozoic in the region. In the Southern Hemisphere today conifers achieve greatest abundance in wet forests. Those which compete successfully with broad-leaved angiosperms in warmer forests produce broad, flat photosynthetic shoots. In the Araucariaceae this is achieved by the planation of multiveined leaves into large compound shoots. In the other two families leaves are now limited to a single vein (except Nageia), and to overcome this limitation many genera have resorted to re-orientation of leaves and two-dimensional flattening of shoots. The Podocarpaceae show greatest development of this strategy with 11 of 19 genera producing shoots analogous to compound leaves. The concentration of conifers in wet forest left them vulnerable to the climate change which occurred in the Cenozoic, and decreases in diversity have occurred since the Paleogene in all regions where fossil records are available. Information about the history of the dry forest conifers is extremely limited because of a lack of fossilisation in such environments. The southern conifers, past and present, demonstrate an ability to compete effectively with angiosperms in many habitats and should not be viewed as remnants which are ineffectual against angiosperm competitors.
The three southern conifer families, Araucariaceae, Cupressaceae and
Podocarpaceae, have a long history and continue to be an important part of the
vegetation today. The Araucariaceae have the most extensive fossil record,
occurring in both hemispheres, and with Araucaria in
particular having an ancient origin. In the Southern Hemisphere
Araucaria and Agathis have
substantial macrofossil records, especially in Australasia, and
Wollemia probably also has an important macrofossil
record. At least one extinct genus of Araucariaceae is present as a
macrofossil during the Cenozoic. Cupressaceae macrofossils are difficult to
identify in older sediments, but the southern genera begin their record in the
Cretaceous (Athrotaxis) and become more diverse and
extensive during the Cenozoic. Several extinct genera of Cupressaceae also
occur in Cretaceous and Cenozoic sediments in Australasia. The Podocarpaceae
probably begin their macrofossil record in the Triassic, although the early
history is still uncertain. Occasional Podocarpaceae macrofossils have been
recorded in the Northern Hemisphere, but they are essentially a southern
family. The Cenozoic macrofossil record of the Podocarpaceae is extensive,
especially in south-eastern Australia, where the majority of the extant genera
have been recorded. Some extinct genera have also been reported from across
high southern latitudes, confirming an extremely diverse and widespread suite
of Podocarpaceae during the Cenozoic in the region.
In the Southern Hemisphere today conifers achieve greatest abundance in wet
forests. Those which compete successfully with broad-leaved angiosperms in
warmer forests produce broad, flat photosynthetic shoots. In the Araucariaceae
this is achieved by the planation of multiveined leaves into large compound
shoots. In the other two families leaves are now limited to a single vein
(except Nageia), and to overcome this limitation many
genera have resorted to re-orientation of leaves and two-dimensional
flattening of shoots. The Podocarpaceae show greatest development of this
strategy with 11 of 19 genera producing shoots analogous to compound leaves.
The concentration of conifers in wet forest left them vulnerable to the
climate change which occurred in the Cenozoic, and decreases in diversity have
occurred since the Paleogene in all regions where fossil records are
available. Information about the history of the dry forest conifers is
extremely limited because of a lack of fossilisation in such environments. The
southern conifers, past and present, demonstrate an ability to compete
effectively with angiosperms in many habitats and should not be viewed as
remnants which are ineffectual against angiosperm competitors.
Introduction The New Caledonian exclusive economic zone is located in the Southwest Pacific between Australia and the Vanuatu archipelago (formerly New Hebrides). It extends over 1200 km from north to south and 1800 km from west to east, from the Chesterfield Islands up to the Matthew and Hunter Islands at the southern tip of the Vanuatu archipelago (Figure 1, page 8). The main islands of New Caledonia are located on two parallel NW-SE trending ridges. The largest island (the 400 km-long and 50 km-wide Grande Terre) and subordinate islands including the Belep islands in the north and the Isle of Pines in the south are supported by the New Caledonia Ridge. The Loyalty Islands are supported by the Loyalty Ridge. Geologically, the area is schematically composed of a series of NW-SE trending ridges and basins formed by i) stretching and spreading along the eastern margin of Australia during Late Cretaceous-Paleocene times and ii) Eocene convergence which was responsible for the emplacement of one of the largest ophiolitic complexes in the world: the New Caledonian ophiolitic nappe (a slice of oceanic lithospheric mantle) from which weathering formed one of the world's largest reservoirs of nickel. The ridges and basins are nowadays supported by the Australia plate that subducts beneath the Vanuatu active volcanic arc. The southernmost segment of the arc supports the active volcanic islands of Matthew and Hunter. These latter islands are thus on a plate (a micro-plate) that differs from the one supporting the main islands of New Caledonia territory. After reviewing the different morphostructural units and discussing the geological history of the New Caledonia area, I will point out some facts that may be relevant in the study and understanding of New Caledonia biodiversity. Geological of the morphostructural units of the New Caledonia region From west to east, the main geological units between Australia and Vanuatu include the Tasman Sea Basin, the Lord Howe Rise with subordinate basins, ridges and chains, the New Caledonia Basin, the New Caledonia Ridge, the South Loyalty Basin, the Loyalty Ridge, the North Loyalty Basin and the Vanuatu Ridge (Missègue et al., 1991; Smith and Sandwell, 1997; ZoNéCo 1998) (Fig. 1 plate 1/1 and Fig. 2 plate 2/1). The Tasman Sea Basin To the southeast of Australia the Tasman Sea Basin is a wide (up to 2000 km) and deep (4000 m) basin floored with oceanic crust formed by spreading from the Cretaceous (85 Ma: Santonian to Early Campanian) to Earliest Eocene (52 Ma) (Hayes et Ringis, 1973; Weissel and Hayes 1977; Gaina et al., 1998). In the central part of the basin, the N-S trending Tasmantid volcanic chain is an Oligocene to Late Miocene hot spot chain showing the northward drift of the Australia plate (Vogt and Conolly, 1971; Mc Dougall and Duncan, 1988).
Balke, M., Wewalka, G., Alarie, Y., Ribera, I. (2007). Molecular phylogeny of Pacific Island Colymbetinae: radiation of New Caledonian and Fijian species (Coleoptera, Dytiscidae). — Zoologica Scripta, 36, 173–200. We present a molecular phylogeny and taxonomic review of the Pacific island colymbetine diving beetles, focusing on the Fijian and New Caledonian faunas. Four new species are described: Rhantus monteithi and R. poellerbauerae from New Caledonia, and R. kini and R. bula from Fiji. We also describe the 3rd instar larvae of R. monteithi and R. poellerbauerae spp. nov., assigned to adults using mtDNA sequence data and discuss larval characters in the light of phylogeny. The phylogenetic hypotheses derived from both parsimony and Bayesian inference based on 3508 aligned nucleotides from a combination of mitochondrial (cox1, cob and rrnL-tRNALeu-Nad1) and nuclear genes (18S rRNA and H3) reveal a clade comprising R. novaecaledoniae, R. alutaceus, R. pseudopacificus, R. monteithi sp. nov. and R. poellerbauerae sp. nov., which agrees with the R. pacificus group sensu Balke (1993). Carabdytes upin was included within this clade, possibly indicating paraphyly of the genus Rhantus. Rhantus annectens, R. bacchusi, R. supranubicus, R. suturalis, R. simulans, and the Palearctic R. exsoletus, R. latitans and R. bistriatus formed a clade corresponding to the R. suturalis group sensu Balke (2001). Rhantus vitiensis, previously assigned to the R. pacificus group, was included in the R. suturalis clade. We find some support for a scenario where the Pacific was colonized out of the Northern hemisphere only during the past c. 12 million years, rejecting a Gondwanan origin of the morphologically isolated endemics. The new species are all characterized by mtDNA haplotype clusters, the degree of divergence between sister species pairs ranging from 1.3 to 7%, while R. novaecaledoniae individuals from all over New Caledonia apparently form one morphospecies, with moderate genetic diversity (up to 2.3% mtDNA divergence between populations). The sisters R. pollerbauerae sp. nov. + R. monteithi sp. nov. occur sympatrically on Mont Panié but appear ecologically segregated, while the sisters R. vitiensis + R. bula sp. nov. were encountered syntopically on Viti Levu. Comparing genetic and morphological data of Fijian Rhantus and Copelatus diving beetles, we here show that even in island radiations it is not per se possible to know if mitochondrial DNA barcoding would perform well (Rhantus: YES, Copelatus: NO). At the same time we show that fixed cutoff values, as sometimes used to discriminate between barcodes, thus species, might be meaningless. We underpin the importance of morphology for sustainable exploration of global diversity.
Response of populations to the climatic changes of Quaternary Milankovitch cycles can be taken as typical of the way populations have behaved throughout earth history. Any microevolutionary change that accumulates on a time scale of thousands of years is likely to be lost as communities are reorganized following climatic changes. A four-tier hierarchy of time scales for evolutionary processes can be constructed as follows: ecological time (thousands of years), Milankovitch cycles (20-100 k.y.), geological time (millions of years), mass extinctions (approximately 26 m.y.). "Ecological time' and "geological time' are defined temporally as the intervals between events of the second and fourth tiers, respectively. Gould's (1985) "paradox of the first tier' can be resolved, at least in part, through the undoing of Darwinian natural selection at the first tier by Milankovitch cycles at the second tier. -from Author
Farris, J. S. (Biol. Set., State Univ., Stony Brook, N.Y.) 1970. Methods for computing Wagner Trees. Syst. Zool., 19:83-92.—The article derives some properties of Wagner Trees and Networks and describes computational procedures for Prim Networks, the Wagner Method, Rootless Wagner Method and optimization of hypothetical intermediates (HTUs).
The relative commonness of a shift in soil preference (from non serpentine to
serpentine soils and vice versa) in the New Caledonian flora is examined. A
number of phanerogam genera occurring on the island of which modern phylogenies
are available are used in this study (Acianthus, Cupaniopsis, Guioa,
Morinda and in particular Oxera). It is concluded that the ability to grown on
serpentine soil is either a plesiomorphic or a very homoplasious character for
most groups in this study and that therefore the hypothesis that serpentine
soils preserve the indigenous flora against competition with immigrant species
can not be supported for these groups.
New Caledonia preserves evidence that constrains models for the tectonic evolution of the southwest Pacific region. Onland geology reflects four main tectonic phases: (1) early Mesozoic development of subduction-related terranes and their accretion to the Gondwana margin; (2) Cretaceous passive margin development and sea-floor spreading during the Gondwana breakup; (3) foundering of an oceanic basin and the Eocene arrival of thinned Gondwana margin crust at a southwest-facing subduction zone, resulting in collisional orogenesis and obduction of an ophiolitic nappe from the northeast; and (4) detachment faulting during extensional collapse, resulting in unroofing of metamorphic core complexes. The last phase explains supposedly anomalous metamorphic gradients in the northeast of the island.
Ecology affects each of the three principal processes leading to speciation: genetic differentiation among populations within species, acquisition of reproductive isolation among populations, and the rise of ecological differentiation among such populations, allowing them to coexist. Until recently, however, the ties between ecology and speciation in plants have received relatively little attention. This paper reviews some exciting new insights into the role of ecology in speciation, focusing on the angiosperms. I consider five main topics, including (1) the determinants of the spatial scale of genetic differentiation within species; (2) the role and limits of adaptive radiation in increasing net rates of plant diversification; (3) the potential role of ecological speciation; (4) the contributions of hybridization to speciation, adaptive radiation, and the ecological breadth of clades; and (5) the ecological determinants of net diversification rate for individual lineages, and of the species richness for regional floras. Limited dispersal, especially of seeds, favors genetic differentiation at small spatial scales and is likely to foster rapid speciation and narrow endemism. Meta-analyses show that the minimum area required for in situ speciation on islands increases with the spatial scale of gene flow in various organisms. In angiosperms, fleshy fruits dispersed by vertebrates often increase the distance over which seeds are dispersed, but can decrease it in forest understories. Nutrient-poor soils should work against the evolution of fleshy fruits and promote speciation and narrow endemism. Selection for adaptation to different conditions drives adaptive radiation, the rise of a diversity of ecological roles and attendant adaptations within a lineage. On islands, adaptive radiation often leads to woodiness, monocarpy, developmental heterophylly, and sexual dimorphism, as well as differences in habitat, growth form, and floral morphology. Adaptive radiation appears to accelerate speciation in only some plant clades. Extensive radiation in some lineages has been ascribed to early colonization, large amounts of heritable genetic variation, “genetic lines of least resistance upon which selection could act, absence of potential competitors, and possession of “key innovations that provide access to novel resources. To these should be added large island area, organismal abundance, saturation of ecological space, and the synergism action of limited dispersal and divergent selection producing parallel radiations in isolated regions. Data for Hawaiian lobeliads suggest that within-island species richness of Cyanea—involving divergence in elevation and flower tube length—saturates within 0.6 and 1.5 Ma. Adaptive radiation in pollinators is an important mechanism of ecological speciation: adaptation to different pollinators leads to pollinator partitioning and reproductive isolation. Selection for longer nectar spurs and pollinator mouth parts led to increased speciation in Aquilegia and other groups. A similar process may work once tubular flowers evolve from cup-shaped blossoms. Selection for floral divergence may be limited in forest understories illuminated by dim, greenish light, which may account for the predominance of small, visually inconspicuous flowers in temperate and tropical understory species. Hybridization can stimulate speciation by forming transgressive phenotypes that exceed the range seen in parental taxa, and by introgressing adaptive gene combinations. The likelihood of transgressive phenotypes increases with the genetic divergence between parental taxa, so speciation via transgressive hybridization may be most likely among taxa with intermediate amounts of divergence. Several large adaptive radiations appear to have occurred after hybridization, suggesting a special role for the extensive amount of genetic variation that can be supplied and refreshed by syngameons. Rates of net species diversification are greater in herbs (especially annuals) vs. woody plants; in animal- vs. wind-pollinated species; in plants with poorly dispersed seeds; in families with a greater diversity of growth forms, pollination and seed dispersal mechanisms, and species distributions; in families at lower latitudes; in families with higher rates of genetic evolution; in hermaphroditic or monoecious vs. dioecious clades; in earlier-maturing woody plants; in plants with bilateral vs. radial flowers; in plants with hummingbird-pollinated flowers; in epiphytic vs. terrestrial bromeliads and orchids; in bromeliads differentiating along geographically extensive cordilleras; and in young vs. old clades. Evidence for the last pattern may, however, be an artifact of (auto)regressing (ln N) / t vs. t.
Quercus ellipsoidalis (Hill's oak), an endemic of east-central North America, is morphologically similar to Q. coccinea (scarlet oak) and is subsumed into that species in several floristic treatments. This study uses data from more than 250 amplified fragment length polymorphism (AFLP) markers to investigate whether Q. coccinea and Q. ellipsoidalis are genetically distinct from one another. Whereas Q. coccinea and Q. ellipsoidalis separate from one another in all analyses, Q. velutina (black oak) populations collected from the geographic range of both Q. coccinea and Q. ellipsoidalis do not separate out by geographic region. This, combined with the strong differentiation between Q. coccinea and Q. velutina but weak differentiation between Q. ellipsoidalis and Q. velutina, supports the view that Q. coccinea and Q. ellipsoidalis are not simply regional variants of a single taxon. Moreover, while there is no evidence from the molecular data we collected of hybridization between Q. coccinea and Q. ellipsoidalis, the data suggest that there may be gene flow between Q. ellipsoidalis and Q. velutina. A clearer understanding of the relationships among these taxa is essential to understanding the taxonomy of Quercus section Lobate in eastern North America.
The genus Dracophyllum Labill. (Ericaceae) has a fragmented distribution in Australasia, but reaches the greatest level of species richness and morphological diversity in New Zealand. We investigated evolutionary processes that contribute to this disparity in species richness by comparing DNA sequences from members of Dracophyllum, its close relatives Richea Labill. and Sphenotoma R. Br. ex Sweet (together constituting tribe Richeeae Crayn & Quinn), along with more distant relatives in the Ericaceae. We created complementary data sets for the chloroplast-encoded genes matK and rbcL. Parsimony, Bayesian, and maximum likelihood analyses were conducted to assess the robustness of our phylogenetic inferences. The results were largely congruent and, when analyzed in combination, provided greater resolution. In our analyses, tribe Richeeae formed a monophyletic group that diverged during the Eocene (at least 33.3 million years ago [Ma]) with a crown radiation during the Early Miocene (at least 16.5 Ma) that resulted in two disjunct lineages. This date corresponds roughly to the onset of aridification in central Australia. The southern Western Australian genus Sphenotoma formed an isolated evolutionary lineage, while Dracophyllum and Richea together formed a second lineage restricted to eastern Australia, Lord Howe Island, New Caledonia, and New Zealand. The relationships of the Tasmanian endemic, D. milliganii Hook. f., remain an enigma. It was ambiguously placed as sister to Sphenotoma or to the Dracophyllum–Richea clade. We recovered two distinct lineages, traditionally recognized as Richea sect. Cystanthe (R. Br.) Benth. and Richea sect. Dracophylloides Benth., which were nested within Dracophyllum. The Lord Howe Island endemic, D. fitzgeraldii F. Muell., emerged as sister to an eastern Australian clade of Dracophyllum. Our evidence suggests that the New Caledonian and New Zealand species of Dracophyllum dispersed from Australia; we document two independent episodes of long-distance dispersal in the Late Miocene to Early Pliocene. Low levels of sequence divergence suggest a rapid and recent species radiation in these two island archipelagos largely within the last three to six million years. This radiation accompanied Pliocene uplift of the New Zealand Southern Alps and episodes of glaciation during the Pleistocene. Because Dracophyllum is paraphyletic and Richea is polyphyletic, the taxonomic circumscription of these genera requires revision.
Studies of a variety of phenomena, ranging from rates of molecular substitution to rates of diversification, draw on estimates of geological age. Studies incorporating estimates of timing from fossils or other geological evidence are largely of relatively young, Tertiary divergences, to which older systems may provide useful comparisons. One apparently old assemblage comprises the beetle groups associated with the ancient genus Araucaria that share comparable, ostensibly Gondwanan distributions with their host. Our previous studies suggested a possibly Cretaceous age for Araucaria associations in bark beetles. However, the absence of confirmed bark beetle fossils earlier than the Tertiary has been taken as evidence of Cretaceous absence, and their confirmed phylogenetic position within the primitively angiosperm-feeding weevil family rules out pre-angiosperm, Jurassic origins. Nevertheless, an early shift from angiosperms to Araucaria seemed plausible in the light of Araucaria fossil history which spans the Mesozoic since the Jurassic. To resolve the phylogenetic affinities and to estimate divergence times of the Australian and South American bark beetle genera affiliated with Araucaria we analysed DNA sequences of nuclear and mitochondrial genes: protein coding elongation factor alpha, enolase and cytochrome oxidase I. The most parsimonious reconstruction of the host relationships of Tomicini from the combined dataset corroborates the ancestral association with the genus Araucaria of both South American and Australian Tomicini. Bayesian estimation of divergence times indicates that the divergence between the Australian and the South American Araucaria-feeding taxa occurred at the very latest in the Cretaceous/Paleocene border and that the age of the first Scolytinae–Araucaria association would then be during the later stages of the Late Cretaceous, while other known beetle/Araucaria associations are Jurassic.
The Araucariaceae are important to biogeography because they have an ancient origin and are a distinctive and sometimes dominant component of southern hemisphere forest communities. This paper examines recent information on ecology and phylogeny and on pollen and macrofossil assemblages to assess the history and present-day status of the family and its potential for refinement of past environmental, particularly climatic, conditions. From an origin in the Triassic, the family expanded and diversified in both hemispheres in the Jurassic and Early Cretaceous and remained a significant component of Gondwanan vegetation until the latter part of the Cenozoic. The development of angiosperms in the Middle Cretaceous probably assisted in the demise of some araucarian components but there was also evolution of new genera. Recorded diversity in the early Cenozoic of Australia is as high as it was in the Early Cretaceous. Continental separation and associated climatic drying, cooling, and increased variability progressively reduced the ranges of conifers to moist, predominantly mesothermal climates on continents. However, tectonic and volcanic activity, partially associated with Australia's collision with Southeast Asia, provided new opportunities for some araucarian components on Asia-Pacific islands. Araucarians provide information on climatic conditions suitable for rainforest vegetation throughout their recorded period, even prior to the recognition or even existence of these forests in the fossil record. High pollen abundance is also indicative of marginal rainforest environments where these canopy emergents can compete effectively with angiosperm forest taxa. Despite their apparent relictual status in many areas, they provide precise paleoclimatic estimates in late Quaternary pollen records and have particular value in providing evidence of climatic variability that has otherwise been difficult to detect.
Aim: Continental disjunctions in pantropical taxa have been explained by vicariance or long-distance dispersal. The relative importance of these explanations in shaping current distributions may vary, depending on historical backgrounds or biological characteristics of particular taxa. We aimed to determine the geographical origin of the pantropical subfamily Chrysophylloideae (Sapotaceae) and the roles vicariance and dispersal have played in shaping its modern distribution.
Location: Tropical areas of Africa, Australasia and South America.
Methods: We utilized a recently published, comprehensive data set including 66 species and nine molecular markers. Bayesian phylogenetic trees were generated and dated using five fossils and the penalized likelihood approach. Distributional ranges of nodes were estimated using maximum likelihood and parsimony analyses. In both biogeographical and molecular dating analyses, phylogenetic and branch length uncertainty was taken into account by averaging the results over 2000 trees extracted from the Bayesian stationary sample.
Results: Our results indicate that the earliest diversification of Chrysophylloideae was in the Campanian of Africa c. 73–83 Ma. A narrow time interval for colonization from Africa to the Neotropics (one to three dispersals) and Australasia (a single migration) indicates a relatively rapid radiation of this subfamily in the latest Cretaceous to the earliest Palaeocene (c. 62–72 Ma). A single dispersal event from the Neotropics back to Africa during the Neogene was inferred. Long-distance dispersal between Australia and New Caledonia occurred at least four times, and between Africa and Madagascar on multiple occasions.
Main conclusions: Long-distance dispersal has been the dominant mechanism for range expansion in the subfamily Chrysophylloideae. Vicariance could explain South American–Australian disjunction via Antarctica, but not the exchanges between Africa and South America and between New Caledonia and Australia, or the presence of the subfamily in Madagascar. We find low support for the hypothesis that the North Atlantic land bridge facilitated range expansions at the Palaeocene/Eocene boundary.
Aim To test whether environmental diversification played a role in the diversification of the New Caledonian Hydropsychinae caddisflies.
Location New Caledonia, south-west Pacific.
Methods The phylogeny of the New Caledonian Hydropsychinae caddisflies was hypothesized using parsimony and Bayesian methods on molecular characters. The Bayesian analysis was the basis for a comparative analysis of the correlation between phylogeny and three environmental factors: geological substrate (ultrabasic, non-ultrabasic), elevation and precipitation. Phylogenetic divergence times were estimated using a relaxed clock method, and environmental factors were mapped onto a lineage-through-time plot to investigate the timing of environmental diversification in relation to species radiation. The correlation between rainfall and elevation was tested using independent contrasts, and the gamma statistic was calculated to infer the diversification pattern of the group.
Results The diversification of extant Orthopsyche–Caledopsyche species began in the Middle–Late Oligocene, when much of the island of New Caledonia was covered by ultrabasic substrate and mountain forming was prevalent. Most lineages originated in the Middle–Late Miocene, a period associated with long-term climate oscillation. Optimization of environmental factors on the phylogeny demonstrated that the New Caledonian Hydropsychinae group adapted to ultrabasic substrate early in its evolutionary history. The clade living mostly on ultrabasic substrate was far more species-rich than the clade living mostly on non-ultrabasic substrate. Elevation and rainfall were significantly correlated with each other. The lineage-through-time plot revealed that the main environmental diversification preceded species diversification. A constant speciation through time was rejected, and the negative gamma indicates that most of the diversification occurred early in the history of the clade. According to the inferred phylogeny, the genus Orthopsyche McFarlane is a synonym under Caledopsyche Kimmins, and Abacaria caledona Oláh & Barnard should also be included in Caledopsyche.
Main conclusions The age of the radiation does not support a vicariance origin of New Caledonian Hydropsychinae caddisflies. Environmental diversification pre-dates lineage diversification, and thus environmental heterogeneity potentially played a role in the diversification of the group, by providing a variety of fragmented habitats to disperse into, promoting speciation. The negative gamma indicates that the speciation rate slowed as niches started to fill.
With 76% of its 3063 native species of flora endemic, the New Caledonia biodiversity hotspot has long been recognized as having a high potential for conservation. Under the new IUCN Red List categories, 25% of the endemic plants are at risk (Conservation Dependent, Vulnerable, Endangered, Critically Endangered), and five species are already extinct. A review of their distribution demonstrates that 83% of the threatened species do not occur at all in a conservation area, and only 11% have their conservation status improved by a protected area. The protected area network is geographically and floristically very unbalanced, with the rainforest and high altitude maquis in the south concentrating most of the conservation effort. Conversely, the middle and northern segments of the island, as well as all of the dry west coast, are left without adequate conservation area. Two vegetation types, the sclerophyll forest and the unique low/middle altitude maquis, are virtually totally unprotected. We conclude that the current network of protected areas needs to be considerably expanded, in terms of both geographical/floristic subregions within New Caledonia and vegetation type covered. With only 54% of the conservation area covered by strict mining restrictions, existing reserves need to have their conservation efficiency improved by a more vigorous enforcement of their status, and by extending mining bans to all of them.
Forty-one endemic conifer species occur on New Caledonia’s ultramafic substrates (known locally as “terrains miniers”), the source of nickel ore deposits being exploited at a rapidly increasing rate. Impacts of the removal of native vegetation and its destruction by the deposition of mine wastes are compounded by fire, which has dramatically reduced and fragmented the original cover. A new threat evaluation of these conifers, now being incorporated into the IUCN Red List, is presented.
A conservation action plan is proposed to ensure their long term survival. Four species are classified as Critically Endangered
(CR), 13 Endangered (EN), 6 Vulnerable (VU), 7 Nearly Threatened (NT) and 11 Least Concern. Wetland habitats contain two threatened
species (i.e., CR, EN or VU), all inadequately protected in a single reserve. High altitude forest and maquis (a characteristic
scrub-like vegetation) have four threatened and three NT conifers only partially encompassed in protected areas, some open
to mining. Thirteen threatened species are restricted to low- and mid-elevation forests, and another three that can also occur
on non-ultramafic substrates have isolated, unprotected populations in small forest remnants. Fire and land clearing for mining
threaten two conifer species in low- to mid-elevation maquis along with subpopulations of five primarily forest species. Conserving
the threatened conifers on terrains miniers will require coordinated measures including: comprehensive protection of forest remnants by forbidding mine waste stockpiling;
establishment of new reserves, especially in key unprotected massifs; effective fire prevention; restoration of forest corridors
between forest remnants; and multiplication/transplanting of selected species.
KeywordsConifers-Conservation-Mining-New Caledonia-Threatened species-Ultramafic substrates
We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The climate elements considered were monthly precipitation and mean, minimum, and maximum temperature. Input data were gathered from a variety of sources and, where possible, were restricted to records from the 1950-2000 period. We used the thin-plate smoothing spline algorithm implemented in the ANUSPLIN package for interpolation, using latitude, longitude, and elevation as independent variables. We quantified uncertainty arising from the input data and the interpolation by mapping weather station density, elevation bias in the weather stations, and elevation variation within grid cells and through data partitioning and cross validation. Elevation bias tended to be negative (stations lower than expected) at high latitudes but positive in the tropics. Uncertainty is highest in mountainous and in poorly sampled areas. Data partitioning showed high uncertainty of the surfaces on isolated islands, e.g. in the Pacific. Aggregating the elevation and climate data to 10 arc min resolution showed an enormous variation within grid cells, illustrating the value of high-resolution surfaces. A comparison with an existing data set at 10 arc min resolution showed overall agreement, but with significant variation in some regions. A comparison with two high-resolution data sets for the United States also identified areas with large local differences, particularly in mountainous areas. Compared to previous global climatologies, ours has the following advantages: the data are at a higher spatial resolution (400 times greater or more); more weather station records were used; improved elevation data were used; and more information about spatial patterns of uncertainty in the data is available. Owing to the overall low density of available climate stations, our surfaces do not capture of all variation that may occur at a resolution of 1 km, particularly of precipitation in mountainous areas. In future work, such variation might be captured through knowledge-based methods and inclusion of additional co-variates, particularly layers obtained through remote sensing.
The phylogeny of a representative group of genera and species from the Sapotaceae tribe Chrysophylleae, mainly from Australia and New Caledonia, was studied by jackknife analyses of sequences of nuclear ribosomal DNA. The phylogeny conflicts with current opinions on generic delimitation in Sapotaceae. Pouteria and Niemeyera, as presently circumscribed, are both shown to be nonmonophyletic. In contrast, all species currently assigned to these and other segregate genera confined to Australia, New Caledonia, or neighboring islands, form a supported clade. Earlier classifications in which more genera are recognized may better reflect relationships among New Caledonian taxa. Hence, there is need for a revision of generic boundaries in Chrysophylleae, and particularly within the Pouteria complex, including Leptostylis, Niemeyera, Pichonia, Pouteria pro parte (the main part of section Oligotheca), and Pycnandra. Section Oligotheca have been recognized as the separate genus Planchonella, a monophyletic group that needs to be resurrected. Three clades with strong support in our jackknife analysis have one Australian species that is sister to a relatively large group of New Caledonian endemics, suggesting multiple dispersal events between this small and isolated tropical island and Australia. The phylogeny also suggests an interesting case of a relatively recent and rapid radiation of several lineages of Sapotaceae within New Caledonia.
Results of the first genus-wide phylogenetic analysis for Santalum (Santalaceae), using a combination of 18S-26S nuclear ribosomal (ITS, ETS) and chloroplast (3' trnK intron) DNA sequences, provide new perspectives on relationships and biogeographic patterns among the widespread and economically important sandalwoods. Congruent trees based on maximum parsimony, maximum likelihood, and Bayesian methods support an origin of Santalum in Australia and at least five putatively bird-mediated, long-distance dispersal events out of Australia, with two colonizations of Melanesia, two of the Hawaiian Islands, and one of the Juan Fernandez Islands. The phylogenetic data also provide the best available evidence for plant dispersal out of the Hawaiian Islands to the Bonin Islands and eastern Polynesia. Inability to reject rate constancy of Santalum ITS evolution and use of fossil-based calibrations yielded estimates for timing of speciation and colonization events in the Pacific, with dates of 1.0-1.5 million yr ago (Ma) and 0.4-0.6 Ma for onset of diversification of the two Hawaiian lineages. The results indicate that the previously recognized sections Polynesica, Santalum, and Solenantha, the widespread Australian species S. lanceolatum, and the Hawaiian species S. freycinetianum are not monophyletic and need taxonomic revision, which is currently being pursued.
The genus Rosa has a complex evolutionary history caused by several factors, often in conjunction: extensive hybridization, recent radiation, incomplete lineage sorting, and multiple events of polyploidy. We examined the applicability of AFLP markers for reconstructing (species) relationships in Rosa, using UPGMA clustering, Wagner parsimony, and Bayesian inference. All trees were well resolved, but many of the deeper branches were weakly supported. The cluster analysis showed that the rose cultivars can be separated into a European and an Oriental cluster, each being related to different wild species. The phylogenetic analyses showed that (1) two of the four subgenera (Hulthemia and Platyrhodon) do not deserve subgeneric status; (2) section Carolinae should be merged with sect. Cinnamomeae; (3) subsection Rubigineae is a monophyletic group within sect. Caninae, making sect. Caninae paraphyletic; and (4) there is little support for the distinction of the five other subsections within sect. Caninae. Comparison of the trees with morphological classifications and with previous molecular studies showed that all methods yielded reliable trees. Bayesian inference proved to be a useful alternative to parsimony analysis of AFLP data. Because of their genome-wide sampling, AFLPs are the markers of choice to reconstruct (species) relationships in evolutionary complex groups.
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
Abstract The biota of Hawaiian Islands is derived entirely from long distance dispersal, often followed by in situ speciation. Species descended from each colonist constitute monophyletic lineages that have diverged to varying degrees under similar spatial and temporal constraints. We partitioned the Hawaiian angiosperm flora into lineages and assessed morphological, ecological, and biogeographic characteristics to examine their relationships to variation in species number (S). Lineages with external bird dispersal (through adhesion) were significantly more species-rich than those with abiotic dispersal, but only weakly more species-rich than lineages with internal bird dispersal (involving fleshy fruits). Pollination mode and growth form (woody vs. herbaceous) had no significant effect on S, in contrast to studies of angiosperm families. S relates positively to the geographic and ecological range size of whole lineages, but negatively to local abundance and mean range sizes of constituent species. Species-rich lineages represent a large proportion of major adaptive shifts, although this appears to be an artifact of having more species. Examination of 52 sister species pairs in numerous lineages provides evidence for allopatric (including peripheral isolates) and parapatric (ecological) modes, with 15 cases of each. Although postspeciational dispersal may obscure these modes in many of the remaining cases, instances of sympatric and hybrid speciation are also discussed. Because speciation is both a consequence and a cause of ecological and biogeographic traits, speciation mode may be integral to relationships between traits. We discuss the role of speciation in shaping the regional species pool.
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
The ecological hypothesis of speciation is that reproductive isolation evolves ultimately as a consequence of divergent natural selection on traits between environments. Ecological speciation is general and might occur in allopatry or sympatry, involve many agents of natural selection, and result from a combination of adaptive processes. The main difficulty of the ecological hypothesis has been the scarcity of examples from nature, but several potential cases have recently emerged. I review the mechanisms that give rise to new species by divergent selection, compare ecological speciation with its alternatives, summarize recent tests in nature, and highlight areas requiring research.
Studies of a variety of phenomena, ranging from rates of molecular substitution to rates of diversification, draw on estimates of geological age. Studies incorporating estimates of timing from fossils or other geological evidence are largely of relatively young, Tertiary divergences, to which older systems may provide useful comparisons. One apparently old assemblage comprises the beetle groups associated with the ancient genus Araucaria that share comparable, ostensibly Gondwanan distributions with their host. Our previous studies suggested a possibly Cretaceous age for Araucaria associations in bark beetles. However, the absence of confirmed bark beetle fossils earlier than the Tertiary has been taken as evidence of Cretaceous absence, and their confirmed phylogenetic position within the primitively angiosperm-feeding weevil family rules out pre-angiosperm, Jurassic origins. Nevertheless, an early shift from angiosperms to Araucaria seemed plausible in the light of Araucaria fossil history which spans the Mesozoic since the Jurassic. To resolve the phylogenetic affinities and to estimate divergence times of the Australian and South American bark beetle genera affiliated with Araucaria we analysed DNA sequences of nuclear and mitochondrial genes: protein coding elongation factor alpha, enolase and cytochrome oxidase I. The most parsimonious reconstruction of the host relationships of Tomicini from the combined dataset corroborates the ancestral association with the genus Araucaria of both South American and Australian Tomicini. Bayesian estimation of divergence times indicates that the divergence between the Australian and the South American Araucaria-feeding taxa occurred at the very latest in the Cretaceous/Paleocene border and that the age of the first Scolytinae-Araucaria association would then be during the later stages of the Late Cretaceous, while other known beetle/Araucaria associations are Jurassic.
One possible response of plant populations to heterogeneous environments is genetic adaptation resulting in the formation of distinct ecotypes. Genetic adaptation to stressful environments may affect both the limits to species boundaries and the potential for response to a changing environment. Reciprocal transplant experiments have frequently been used to describe ecotypic differentiation and to infer the role of natural selection when there is evidence for home site advantage. The demonstration of a home site advantage, however, does not reveal which plant characters are responsible for conferring increased fitness on populations planted in their native site. Here, we combine the classic reciprocal transplant experiment with multivariate regression analysis of selection to ask a series of questions relevant to understanding adaptive genetic differentiation in natural plant populations. Impatiens pallida plants from a mesic floodplain and a dry hillside site were reciprocally transplanted. We initially presumed the hillside to be a stressful site for Impatiens given its sparser population of consistently smaller individuals. This study describes the two environments from the perspective of the plant to ask whether it is stressful. In addition, we investigate genetic differentiation between populations and ask whether the two populations are distinctly adapted to their home sites. To identify traits that may be important for conferring home site advantage, we quantify present-day natural selection in these sites and ask whether the observed selective forces can explain genetic differences. Finally, because phenotypic correlations may play an important role in a population's response to its environment, we investigate relationships among traits to determine the extent to which they are genetically and/or environmentally controlled. The large reduction in total seed production when plants from both populations were grown on the hillside supported our initial bias that this site was stressful to Impatiens. In addition, the higher relative fitness of each population planted in its native site demonstrated that these populations represent distinct ecotypes. Genetic differences between populations were observed for several life history and morphological characters. In particular, plants from the hillside population were smaller and produced cleistogamous flowers earlier than floodplain plants. Selection analysis revealed that, while there is strong selection favoring early flowering on the hillside, there is no advantage to early flowering for plants grown on the floodplain. An increased developmental rate, which allows plants to produce seeds before they succumb to drought stress, appears to be the most important mechanism responsible for the greater relative fitness of the hillside population in its native site. While greater total plant leaf area is favored by selection on the floodplain, there is no evidence for selection on this trait on the hillside. Phenotypic covariances among traits differed between sites and populations, resulting in differences in the action of indirect selection. There is evidence that indirect selection on correlated traits is responsible for some of the observed genetic differences.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
The richness and originality of the New Caledonian flora (3200 species, of which 79% are endemic) are largely due to the territory's geological history After a brief review of relevant data and events, the current status and progress of our knowledge of this flora, including both phanerogams and cryptogams, is presented. The cryptogams are at present the least known component; with the exception of the algae, inventory work on these groups has hardly started The diversity and endemism of New Caledonia's flora varies considerably from one major plant group to another, and between the various vegetation types present The role substrate plays in this variation is highlighted
Broadening of the genetic base and systematic exploitation of heterosis in faba bean requires reliable information on the genetic diversity in the germ plasm. Three groups of faba bean inbred lines were examined by means of RAPDs (random amplified polymorphic DNAs) assays: 13 European small-seeded lines, 6 European large-seeded lines, and 9 Mediterranean lines. Out of 59 primers, 35 were informative and yielded 365 bands, 289 of which were polymorphic with a mean of 8.3 bands per primer. Monomorphic bands were omitted from the analyses and genetic distances (GD) were estimated via the coefficient of Jaccard. The mean GD among the European small-seeded lines was significantly greater than those among the lines of the other two groups. Repeatability of GD estimates was high. Cluster (UPGMA) and principal coordinate analyses identified European small-seeded lines and Mediterranean lines as distinct groups with European large-seeded lines located in between. The results are in harmony with published archaeobotanical findings. We conclude that RAPDs are useful for classification of germ plasm and identification of divergent heterotic groups in faba bean.
As a matter of fact, Araucaria angustifolia populations occur predominately in small and isolated stands; only a minor number of continuous natural forests of this dioecious
wind-pollinated coniferous tree species remain. To implement reasonable conservation, breeding and restorations program it
is necessary to have the knowledge of pollen dispersal distance and fine-scale genetic structure. In this paper, levels and
dispersion distance of pollen and spatial genetic structure of A. angustifolia were investigated in a 14 ha transect in a continuous forest in Paraná State, Brazil. Analyses have been performed by the
use of eight microsatellite loci, paternity and TwoGener approaches, and spatial autocorrelation analysis. In transect, 52 male and 56 female adult trees were mapped and genotyped,
together with 190 seeds. In the present transect, A. angustifolia show spatial genetic structure at distances up to 75 m. Paternity analysis indicated that 54% of seeds were fertilized by
pollen from trees outside the transect. The calculated average pollination distance within transect was 102 and 98 m based
on the paternity analysis and TwoGener analysis, respectively. We found a significant pollen gene pool structure across seed-trees (
$$\widehat\Phi _{ft} = 0.078$$, P 100 m) inside the continuous forest. However, the high
proportion occurs in short-distance producing biparental and correlated mating as well as reducing the variance effective
size.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
The spectacular diversity of the Cape flora has promoted wide speculation on the evolutionary processes behind its origins, but until recently these ideas could not be tested rigorously due to the almost complete absence of a fossil record for the region. Now, molecular phylogenetic approaches, combined with analyses of ecological and biogeographical information, offer the potential to test key hypotheses about speciation of so-called Cape clades of flowering plants. We outline the main theories and how they might be tested by phylogenetic approaches. One conclusion is that population level studies of particular species complexes are now needed to complement the growing volume of phylogenetic information for Cape clades and to provide better understanding of mechanisms of population divergence in the Cape. Another is that comparisons between Cape and non-Cape clades are needed to confirm whether speciation is indeed faster in the Cape region. An alternative possibility, that extinction rates are lower, should also be considered in these comparisons. By virtue of the ongoing, coordinated efforts by a global team of botanists, the Cape is now uniquely placed for exploring the origins and assembly of a regional assemblage or biome.
Tropical and subtropical forests once covered large areas of Central and South America. An important member of forests of the southern hemisphere is the genus Araucaria. Because of clear cutting only small remnants of Araucaria angustifolia forests still exist in Southern Brazil. Attempts at reforestation have had only limited success because of lack of knowledge about the environmental requirements of this species. This is especially true with respect to the root/fungus symbiosis (mycorrhiza) which is necessary for enhanced water and nutrient uptake and present in more than 90 % of land plants. Analysis of the root systems of Araucaria trees from forest and grassland (campo) sites revealed mycorrhizal structures (appressoria, penetration and coiled hyphae, vesicles, arbuscules, spores) which are characteristic for the arbuscular mycorrhiza (AM) type. The spores of AM fungi at both sites - forest and campo - were identified. The biodiversity at the forest site was much higher, with 13 species, whereas only 6 different species could be identified at the campo site. Glomus and Acaulospora were the only genera present at the campo. The forest, however, also contained spores of Entrophospora and Scutellospora. In addition to the greater biodiversity, the spore number in soil as well as the percent mycorrhizal colonization in roots were significantly higher at the forest site than at the campo site. Because of the low frequency of hyphal coils and the dominating intercellular growth of hyphae, these mycorrhizas can be classified as an Arum-type, which is the first report of this kind in gymnosperms.
The Oceanian plant genus Spiraeanthemum (Cunoniaceae) has a centre of diversity in New Caledonia, where it is represented by seven species. Its diversification was investigated using two low-copy nuclear genes, ncpGS and GapC, and phylogenetic analyses were based on maximum parsimony, maximum likelihood and recombination networks. We detected several cases of gene recombination in both datasets, and these have obscured the history within the genus. For S. ellipticum and S. pubescens, accessions from southern populations on ultramafic soils were genetically distinct from accessions from northern populations on non-ultramafic soils. Given that no obvious morphological characters distinguish northern and southern populations in either taxon, both may be considered as examples of cryptic species. Incongruence between gene trees and species' delimitation may be explained by the parallel evolution of similar morphology, differential lineage sorting leading to differential fixation of alleles or different introgression patterns in the north and south leading to allele displacement. In New Caledonia, some species with broad ecological preferences may thus be artificial concepts. This suggests that they should be treated more critically in monographs and that the species' richness of the New Caledonian flora may be underestimated. Problems associated with the typification of S. ellipticum and evidence of hybridization events in the history of Spiraeanthemum are also discussed. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161, 137–152.
The patterns of local endemism in New Caledonia were analysed in two endemic genera of Tingidae (Insecta, Heteroptera), Cephalidiosus and Nobarnus, through a phylogenetic analysis and species' distribution modelling. The aim was to determine the possible causes of diversification and endemism in New Caledonia. Our results show that environmental conditions are probably important for the distribution of the genus Cephalidiosus, in conjunction with other factors such as resource (host plant) distribution, but suggest that the same environmental conditions have not influenced the speciation processes and diversification in the genus. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 177–184.
New Caledonia is well known as a hot spot of biodiversity whose origin as a land mass can be traced back to the Gondwanan supercontinent. The local flora and fauna, in addition to being remarkably rich and endemic, comprise many supposedly relictual groups. Does the New Caledonian biota date back to Gondwanan times, building up its richness and endemism over 100 Myr or does it result from recent diversifications after Tertiary geological catastrophic events? Here we use a molecular phylogenetic approach to answer this question with the study of the Neocaledonian cockroach genus Angustonicus belonging to the subfamily Tryonicinae from Australia and New Caledonia. Both geological and molecular dating show that the diversification of this group is less than two million years old, whatever the date of its origin itself. This dating is not consistent with hypotheses of Gondwanan richness and endemism in New Caledonian biota. In other terms, local richness and endemism at the specific level are not necessarily related to an old Gondwanan origin of the Neocaledonian groups.
© The Willi Hennig Society 2005.
Conifers (the fast-growing softwoods of the world) occur as the dominant plants of most temperate rainforest communities. Almost all are tall forest trees, whose high commercial value creates conservation vulnerability for many local species in our increasingly resource-hungry world. Counting species, of an estimated 600 world total 362 would fall into this category and consequently appear on this list. This paper provides a preliminary analytical world census list of 416 conifer taxa (species, subspecies and varieties) considered to be of conservation concern.
The tropical Far East has many outcrops of ultramafic rock including very large areas in Sulawesi (c. 8000 km2) and New Caledonia (c. 5500 km2). The outcrops occur under several different climates, and give rise to a range of soils, the characteristics of which are reviewed. The vegetation on them is very varied. Under the same climate one can find grassland, scrub, and both short and tall rain forests. The variation in species richness on the ultramafics is difficult to explain. The degree of endemism varies too; it is probably less dependent on soil characteristics than on historical factors. The causes of the various unusual types of vegetation on ultramafic outcrops are discussed. It is possible that the somewhat dwarfed forests result from a shortage of one or more major nutrients or from very high soil Mg/Ca quotients or high Ni concentrations. The distinct ‘maquis’ vegetation of New Caledonia, and probably ultramafic scrub elsewhere, has evolved in relation to not only the soil chemical factors just listed but also periodic fire and varying degrees of drought. Fires are certainly more important than was once thought and the adverse soil factors may have a role in delaying recolonisation. The plant chemistry is notable for the presence of species which hyperaccumulate certain elements, notably Ni. This phenomenon is discussed in relation to its ecological importance, which may be protection of the hyperaccumulators against herbivores. The need for a conservation policy for the ultramafic areas is stressed, and mention is made of the restoration work on sites damaged by nickel mining in New Caledonia.
The ecological hypothesis of speciation is that reproductive isolation evolves ultimately as a consequence of divergent natural selection on traits between environments. Ecological speciation is general and might occur in allopatry or sympatry, involve many agents of natural selection, and result from a combination of adaptive processes. The main difficulty of the ecological hypothesis has been the scarcity of examples from nature, but several potential cases have recently emerged. I review the mechanisms that give rise to new species by divergent selection, compare ecological speciation with its alternatives, summarize recent tests in nature, and highlight areas requiring research.
Phylogenetic relationships were determined in the Araucariaceae, which are now found mainly in the Southern Hemisphere. This conifer family was well diversified and widely distributed in both hemispheres during the Mesozoic era. The sequence of 1322 bases of the rbcL gene of cpDNA was determined from 29 species of Araucariaceae, representing almost all the species of the family. Phylogenetic trees determined by the parsimony method indicate that Araucariaceae are well defined by rbcL sequences and also that the monophyly of Agathis or Araucaria is well supported by high bootstrap values. The topology of these trees revealed that Wollemia had derived prior to Agathis and Araucaria. The rbcL phylogeny agrees well with the present recognition of four sections within Araucaria: Araucaria, Bunya, Eutacta, and Intermedia. Morphological characteristics of the number of cotyledons, position of male cone, and cuticular micromorphologies were evaluated as being phylogenetically informative. Section Bunya was found to be derived rather than to be the oldest taxon. Infrageneric relationships of Agathis could not be well elucidated because there are few informative site changes in the rbcL gene, suggesting the more recent differentiation of the species as their fossil records indicate. The New Caledonian Araucaria and Agathis species each formed a monophyletic group with very low differentiation in rbcL sequences among them, indicating rapid adaptive radiation to new edaphic conditions, i.e., ultramafic soils, in the post-Eocene era.