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Molecular Phylogeny and Divergence Time of Harpalyce (Leguminosae, Papilionoideae), a Lineage with Disjunct Amphitropical Diversification in Seasonally Dry Forests and Savannas
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Two new species of Harpalyce are described from Cuba, H. revoluta sp. nov. from a serpentine area in the northern part of E. Cuba and H. marianensis sp. nov. from calcareous areas in the southern part of E. Cuba. Both have relatively small flowers, with an up to 6 mm long standard, and 2–3 mm long wings. Harpalyce marianensis is further characterized by strongly suberous (corky) young branches of a spongy consistence, deeply furrowed longitudinally, and by leaflets covered with a particular type of orange, apparently disk-shaped, sessile glands abaxially. Harpalyce revoluta , moreover, has suborbicular or broadly elliptic leaflets with a strongly recurved or sometimes revolute margin, secondary veins inconspicuous on either side; the foliar glands, by their morphology and anatomy, are of a different type. An epitype is designated for the name Harpalyce and its type, H. formosa ; the distribution of both new species and their close relatives is mapped, and an updated identification key is offered, to cater for all 16 currently recognised Cuban species.
The evolution of hummingbird pollination is common across angiosperms throughout the Americas, presenting an opportunity to examine convergence in both traits and environments to better understand how complex phenotypes arise. Here we examine independent shifts from bee to hummingbird pollination in the Neotropical spiral gingers (Costus) and address common explanations for the prevalence of transitions from bee to hummingbird pollination.
We use floral traits of species with observed pollinators to predict pollinators of unobserved species and reconstruct ancestral pollination states on a well‐resolved phylogeny. We examine whether independent transitions evolve towards the same phenotypic optimum and whether shifts to hummingbird pollination correlate with elevation or climate.
Traits predicting hummingbird pollination include small flower size, brightly colored floral bracts and the absence of nectar guides. We find many shifts to hummingbird pollination and no reversals, a single shared phenotypic optimum across hummingbird flowers, and no association between pollination and elevation or climate.
Evolutionary shifts to hummingbird pollination in Costus are highly convergent and directional, involve a surprising set of traits when compared with other plants with analogous transitions and refute the generality of several common explanations for the prevalence of transitions from bee to hummingbird pollination.
Nitrogen‐fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2‐fixing clade retained nodulation and diversified as stable nodulators, while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades.
We characterize two nodule anatomy types across 128 species in 56 of the 152 genera of the legume subfamily Caesalpinioideae: fixation thread nodules (FTs), where nitrogen‐fixing bacteroids are retained within the apoplast in modified infection threads, and symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane‐bound symbiosomes (SYMs).
Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, we show that losses of nodulation are more prevalent in lineages with FTs than those with SYMs.
We propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through tighter compartmentalization of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species‐rich pantropical legume clade.
Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.
Premise:
Understanding the evolutionary history of flowering plants has been enriched by the integration of molecular phylogenies and evidence from the fossil record. Fossil fruits and leaves from the late Paleocene and Eocene of Wyoming and Eocene of Kentucky and Tennessee are described as extinct genera in the tropical American Bowdichia clade of the legume subfamily Papilionoideae. Recent phylogenetic study and taxonomic revision of the Bowdichia clade have facilitated understanding of relationships of the fossil taxa and their evolutionary implications and paleoenvironmental significance.
Methods:
The fossils were studied using standard methods of specimen preparation and light microscopy and compared to fruits and leaves from extant legume taxa using herbarium collections. Phylogenetic relationships of the fossil taxa were assessed using morphology and DNA sequence data.
Results:
Two new fossil genera are described and their phylogenetic relationships are established. Paleobowdichia lamarensis is placed as sister to the extant genus Bowdichia and Tobya claibornensis is placed with the extant genera Guianodendron and Staminodianthus.
Conclusions:
These fossils demonstrate that the tropical American Bowdichia clade was present in North America during a period when tropical or subtropical conditions prevailed in the northern Rocky Mountains during the late Paleocene and the Mississippi Embayment during the middle Eocene. These fossils also document that the Bowdichia clade had diversified by the late Paleocene when the fossil record of the family is relatively sparse. This result suggests that future work on early fossil legumes should focus on tropical and subtropical climatic zones, wherever they may occur latitudinally.
Harpalyce greuteri is described as a new species from the serpentine outcrops of Holguín in eastern Cuba. It differs from other Cuban species of the genus by having leaflets alternate along the rachis, an elliptic, rounded or slightly acuminate standard petal, mostly black keel petals and broadly linear wing petals. An illustration and a distribution map of the new species are presented, as well as a synopsis of and an identification key to all 14 recognized species of H. sect. Cubenses. Lectotypes are designated for nine species names in Harpalyce.
The Galactia clade is one of three major lineages of the papilionoid legume tribe Diocleae. It comprises eight genera and approximately 140 species almost entirely restricted to the Americas. Establishing stable generic boundaries within this clade has been a challenge because of its tortuous taxonomic history and the broad polyphyly of the genera of the so-called Galactia-Camptosema-Collaea complex. Previous molecular phylogenetic studies revealed some well-supported lineages, but did not advance towards any new taxonomic arrangements. We carried out maximum parsimony and Bayesian phylogenetic analyses of a combined dataset including our previously published multilocus molecular data (nrITS and ETS and plastid trnK/matK and trnT-Y regions) and 82 morphological characters. The resulting topologies largely concur with those previously reported based on molecular data only, where Camptosema and Galactia appear as broadly polyphyletic, with species scattered among five (Camptosema) and seven (Galactia) of the twelve lineages that are newly recognized here at genus level. We are therefore proposing the following new taxonomic rearrangements within the Galactia clade: descriptions of the new genera Caetangil, Cerradicola, Mantiqueira, and Nanogalactia; resurrection of Betencourtia; and the subsuming of Neorudolphia into Rhodopis and of Camptosema sect. Macropetalum into Cratylia.
Mountains are among the most biodiverse areas on the globe. In young moun- tain ranges, exceptional plant species richness is often associated with recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analysing plant diversification dynamics in the campo rupestre, an ecosystem associated with pre-Cambrian mountaintops and highlands of eastern South America, areas where plant species richness and endemism are among the highest in the world. Analyses of 15 angiosperm clades show that radiations of endemics exhibit fastest rates of diversification during the last 5 Myr, a climatically unstable period. However, results from ancestral range estimations using different models disagree on the age of the earliest in situ speciation events and point to a complex floristic assembly. There is a general trend for higher diversification rates associated with these areas, but endemism may also increase or reduce extinction rates, depending on the group. Montane habitats, regardless of their geological age, may lead to boosts in speciation rates by accelerating population isolation in archipelago-like systems, circum- stances that can also result in higher extinction rates and fast species turnover, misleading the age estimates of endemic lineages.
Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate leaves distinguishing forest‐associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the evolutionary history of the family. We also estimated the ancestral habitat of Poaceae and tested whether forest margins served as transitional zones for shifts between forests and grasslands. We found that grass leaf shape is converging towards different shape optima in the forest understory, forest margins and open habitats. Leaf size also varies with habitat. Grasses have smaller leaves in open and drier areas, and in areas with high solar irradiance. Direct transitions between linear and ovate leaves are rare as are direct shifts between forest and open habitats. The most likely ancestral habitat of the family was the forest understory and forest margins along with an intermediate leaf shape served as important transitional habitat and morphology respectively for subsequent shifts across forest‐grassland biome boundaries.
This article is protected by copyright. All rights reserved
The extent to which phylogenetic biome conservatism vs biome shifting determines global patterns of biodiversity remains poorly understood. To address this question, we investigated the biogeography and trajectories of biome and growth form evolution across the Caesalpinia Group (Leguminosae), a clade of 225 species of trees, shrubs and lianas distributed across the Rainforest, Succulent, Temperate and Savanna Biomes. We focused especially on the little‐known Succulent Biome, an assemblage of succulent‐rich, grass‐poor, seasonally dry tropical vegetation distributed disjunctly across the Neotropics, Africa, Arabia and Madagascar.
We reconstructed a time‐calibrated phylogeny, assembled species occurrence data and assigned species to areas, biomes and growth forms. These data are used to estimate the frequency of transcontinental disjunctions, biome shifts and evolutionary transitions between growth forms and test for phylogenetic biome conservatism and correlated evolution of growth forms and biome shifts.
We uncovered a pattern of strong phylogenetic Succulent Biome conservatism. We showed that transcontinental disjunctions confined within the Succulent Biome are frequent and that biome shifts to the Savanna, Rainforest and Temperate Biomes are infrequent and closely associated with shifts in plant growth forms.
Our results suggest that the Succulent Biome comprises an ecologically constrained evolutionary arena spanning large geographical disjunctions across the tropics.
Two new Mesoamerican species of the papilionoid legume genus Harpalyce are described and illustrated. Harpalyce torresii São-Mateus & M. Sousa occurs in Belize and Mexico, whereas Harpalyce yucatanense Miranda ex São-Mateus & M. Sousa seems to be narrowly endemic to the Yucatan Peninsula. The discovery of these two new species highlights the diversity of Harpalyce in Mesoamerica.
PREMISE OF THE STUDY
Historical patterns and processes of plants with an American amphitropical disjunct (AAD) distribution have long interested botanists and biogeographers. Here we update examples of AAD vascular plants, their biogeographic history, and aspects of their biology elucidated by recent studies to make inferences about common patterns of AAD plants and formulate future research questions.
METHODS
All known examples of AAD vascular plants were tabulated, along with data on plant duration and habit, chromosome number, dispersal direction, and divergence time. The data were then compared with regard to taxonomic categories, AAD bioregions, and character evolution.
KEY RESULTS
We clarify the definition of amphitropical and summarize features of AAD plants. We identify 237 AAD plant divergence events. Timing of these events generally corresponds with taxonomic category. Plant duration and habit are associated with AAD bioregions. Increases in chromosome number mostly occurred in members of the recipient area. The AAD plants of bipolar or temperate bioregions entirely or largely dispersed from North to South America, whereas almost half of desert plants dispersed from South to North America.
CONCLUSIONS
Tabulating AAD plants by taxonomic group and bioregion yields insight into character evolution and processes of divergence. Phylogenetic studies provide information on the timing and direction of dispersal. However, more research on AAD plants is needed to draw inferences regarding general patterns and processes, especially those at the clade level. Our AAD Working Group website provides current information on AAD vascular plants to aid workers doing research in this field.
While specialized interactions, including those involving plants and their pollinators, are often invoked to explain high species diversity, they are rarely explored at macroevolutionary scales. We investigate the dynamic evolution of hummingbird and bat pollination syndromes in the centropogonid clade (Lobelioideae: Campanulaceae), an Andean-centered group of ∼550 angiosperm species. We demonstrate that flowers hypothesized to be adapted to different pollinators based on flower color fall into distinct regions of morphospace, and this is validated by morphology of species with known pollinators. This supports the existence of pollination syndromes in centropogonids, an idea corroborated by ecological studies. We further demonstrate that hummingbird pollination is ancestral, and that bat pollination has evolved ∼13 times independently, with ∼11 reversals. This convergence is associated with correlated evolution of floral traits within selective regimes corresponding to pollination syndrome. Collectively, our results suggest that floral morphological diversity is extremely labile, likely resulting from selection imposed by pollinators. Finally, even though this clade's rapid diversification is partially attributed to their association with vertebrate pollinators, we detect no difference in diversification rates between hummingbird- and bat-pollinated lineages. Our study demonstrates the utility of pollination syndromes as a proxy for ecological relationships in macroevolutionary studies of certain species-rich clades. This article is protected by copyright. All rights reserved.
The effects of specific functional groups of pollinators in the diversification of angiosperms are still to be elucidated. We investigated whether the pollination shifts or the specific association with hummingbirds affected the diversification of a highly diverse angiosperm lineage in the Neotropics. We reconstructed a phylogeny of 583 species from the Gesneriaceae family and detected diversification shifts through time, inferred the timing and amount of transitions among pollinator functional groups, and tested the association between hummingbird pollination and speciation and extinction rates. We identified a high frequency of pollinator transitions, including reversals to insect-pollination. Diversification rates of the group increased through time since 25 Mya, coinciding with the evolution of hummingbird-like flowers and the arrival of hummingbirds in South America. We showed that plants pollinated by hummingbirds have a two-fold higher speciation rate compared to plants pollinated by insects, and that transitions among functional groups of pollinators had a little impact on the diversification process. We demonstrated that floral specialization on hummingbirds for pollination has triggered rapid diversification in the Gesneriaceae family since the early Miocene, and that it represents one of the oldest identified plant-hummingbird associations. Biotic drivers of plant diversification in the Neotropics could be more related to this specific type of pollinator (hummingbirds), than to shifts among different functional groups of pollinators.
Significance
The Amazon is largely covered by contiguous rain forest. Nevertheless, previous studies have suggested that past geological and climatic events, as well as limited seed dispersal, may have restricted the movement of tree lineages across the Amazon. Using a phylogenetic approach, we show that dispersal into local communities and larger regions in the Amazon appears to not have been limited on evolutionary timescales, but instead, local communities have been assembled by lineages from across the Amazon. These results contrast with those from seasonally dry tropical forests, where closely related species are clustered in geographic space. Furthermore, our results suggest a role for dispersal as an initiator for geographic isolation that might lead to speciation in Amazonian trees.
We present an r package, ggtree , which provides programmable visualization and annotation of phylogenetic trees.
ggtree can read more tree file formats than other softwares, including newick , nexus , NHX , phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node‐specific and other data from the analysis outputs of beast , epa , hyphy , paml , phylodog , pplacer , r8s , raxml and revbayes software, and allows using these data to annotate the tree.
The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion.
A two‐dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images.
The package ggtree is released under the artistic‐2.0 license . The source code and documents are freely available through bioconductor ( http://www.bioconductor.org/packages/ggtree ).
Harpalyce magnibracteata is described and illustrated as a new species of the tribe Brongniartieae (Papilionoideae, Leguminosae). It is chiefly diagnosed by the unique combination of persistently attached, large leaf-like amplexicaul bracts measuring 1.2‒2.3 × 1.2‒2.3 cm, features that do not match with any other species of the genus. The new species grows as a small shrub in upland patches of savanna vegetation on gravelly soils of the mountains of Chapada Diamantina.
Aldina (Leguminosae) is among the very few ecologically successful ectomycorrhizal lineages in a family largely marked by the evolution of nodulating symbiosis. The genus comprises 20 species exclusively distributed in Amazonia and has been traditionally classified in the tribe Swartzieae because of its radial flowers with an entire calyx and numerous free stamens. The taxonomy of Aldina is complicated due to its poor representation in herbaria and the lack of a robust phylogenetic hypothesis of relationship. Recent phylogenetic analyses of matK and trnL sequences confirmed the placement of Aldina in the 50-kb inversion clade, although the genus remained phylogenetically isolated or unresolved in the context of the evolutionary history of the main early-branching papilionoid lineages. We performed maximum likelihood and Bayesian analyses of combined chloroplast datasets (matK, rbcL, and trnL) and explored the effect of incomplete taxa or missing data in order to shed light on the enigmatic phylogenetic position of Aldina. Unexpectedly, a sister relationship of Aldina with the Andira clade (Andira and Hymenolobium) is revealed. We suggest that a new tribal phylogenetic classification of the papilionoid legumes should place Aldina along with Andira and Hymenolobium. These results highlight yet another example of the independent evolution of radial floral symmetry within the early-branching Papilionoideae, a large collection of florally heterogeneous lineages dominated by papilionate or bilaterally symmetric flower morphology.
Open-access digital resources: http://www.earthbyte.org/ocean-basin-evolution-and-global-scale-plate-reorganization-events-since-pangea-breakup/
ftp://ftp.earthbyte.org/Data_Collections/Muller_etal_2016_AREPS
We present a revised global plate motion model with continuously closing plate boundaries ranging from the Triassic at 230 Ma to the present day, assess differences between alternative absolute plate motion models, and review global tectonic events. Relatively high mean absolute plate motion rates around 9–10 cm yr-1 between 140 and 120 Ma may be related to transient plate motion accelerations driven by the successive emplacement of a sequence of large igneous provinces during that time. A ~100 Ma event is most clearly expressed in the Indian Ocean and may reflect the initiation of Andean-style subduction along southern continental Eurasia, while an ~80 Ma acceleration of mean rates from 6 to 8 cm yr-1 reflects the initial northward acceleration of India and simultaneous speedups of plates in the Pacific. An event at ~50 Ma expressed in relative, and some absolute plate motion changes around the globe and in a reduction of global mean velocities from about 6 to 4–5 cm yr-1, indicates that an increase in collisional forces (such as the India-Eurasia collision) and ridge subduction events in the Pacific (such as the Izanagi-Pacific Ridge) play a significant role in modulating plate velocities.
Premise of the study:
Floral development can help to shed light on puzzling features across flowering plants. The enigmatic Amazonian monospecific genus Petaladenium of the legume family (Leguminosae) had rarely been collected and only recently became available for ontogenetic studies. The fimbriate-glandular wing petals of P. urceoliferum are unique among the more than 19000 legume species. Ontogenetic data illuminate the systematic position of the genus and foster our understanding on floral evolution during the early diversification of the papilionoid legumes.
Methods:
Flower buds were collected in the field, fixed in 70% ethanol, and investigated using scanning electron microscopy (SEM). Results were compared with existing material from early-diverging papilionoid legumes.
Key results:
Formation of sepals and petals shows bidirectional tendencies. Stamens arise in two whorls, and the single carpel arises concomitantly with the outer stamen whorl. Gland formation starts early on the edges of the wing petals. The carpel reopens for a short time when the initiation of ovules is visible. Stomata at the base of the hypanthium indicate that the flower functions like other standard flag blossoms.
Conclusions:
The floral ontogeny confirms the close affinity of P. urceoliferum with the florally heterogeneous, early-diverging papilionoid Amburaneae clade. The results strengthen the theory of a distinct experimental phase among early-branching papilionoid legumes during which a wider range of floral morphologies arose. Polysymmetry, monosymmetry, variable organ numbers, and a wide range of ontogenetic patterns laid the foundation for a successful canalization toward the more restricted but well-adapted dorsiventral papilionoid flag blossom.
The taxonomic composition of three principal and distantly related groups of the former tribe Millettieae, which were first identified from nuclear phytochrome and chloroplast trnK/matK sequences, was more extensively investigated with a phylogenetic analysis of nuclear ribosomal DNA ITS/5.8S sequences. The first of these groups includes the neotropical genera Poecilanthe and Cyclolobium, which are resolved as basal lineages in a clade that otherwise includes the neotropical genera Brongniartia and Harpalyce and the Australian Templetonia and Hovea. The second group includes the large millettioid genera, Millettia, Lonchocarpus, Derris, and Tephrosia, which are referred to as the “core Millettieae” group. Phylogenetic analysis of nuclear ribosomal DNA ITS/5.8S sequences reveals that Millettia is polyphyletic, and that subclades of the core Millettieae group, such as the New World Lonchocarpus or the pantropical Tephrosia and segregate genera (e.g., Chadsia and Mundulea), each form well supported monophyletic subgroups. The third lineage includes the genera Afgekia, Callerya, and Wisteria. These genera are resolved as a basal subclade in the inverted-repeat-lacking clade, which is a large legume group that includes the many well known temperate and herbaceous legumes, such as Astragalus, Medicago and Pisum, but not any other Millettieae. Communicating Editor: Jerrold I. Davis
Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal–Extinction–Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC + J, which adds founder-event speciation, the importance of which is governed by a new free parameter, j. The identifiability of DEC and DEC + J is tested on data sets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC + J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes + J. DEC and DEC + J are compared on 13 empirical data sets drawn from studies of island clades. Likelihood-ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC + J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC + J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods.
Cryptic species are organisms which look identical, but which represent distinct evolutionary lineages. They are an emerging trend in organismal biology across all groups, from flatworms, insects, amphibians, primates, to vascular plants. This book critically evaluates the phenomenon of cryptic species and demonstrates how they can play a valuable role in improving our understanding of evolution, in particular of morphological stasis. It also explores how the recognition of cryptic species is intrinsically linked to the so-called 'species problem', the lack of a unifying species concept in biology, and suggests alternative approaches. Bringing together a range of perspectives from practicing taxonomists, the book presents case studies of cryptic species across a range of animal and plant groups. It will be an invaluable text for all biologists interested in species and their delimitation, definition, and purpose, including undergraduate and graduate students and researchers.
The papilionoid legume genus Ormosia (Fabaceae) comprises about 150 species of trees and exhibits a striking disjunct geographical distribution between the New World- and Asian and Australasian wet tropics and subtropics. Modern classifications of Ormosia are not grounded on a well-substantiated phylogenetic hypothesis and have been limited to just portions of the geographical range of the genus. The lack of an evolutionarily-based foundation for systematic studies has hindered taxonomic work on the genus and prevented the testing of biogeographical hypotheses related to the origin of the Old World/New World disjunction and the individual dispersal histories within both areas. Here, we present the most comprehensively sampled molecular phylogeny of Ormosia to date, based on analysis of both nuclear (ITS) and plastid (matK and trnL–F) DNA sequences from 82 species of the genus. Phylogenetically-based divergence times and ancestral range estimations are employed to test hypotheses related to the biogeographical history of the genus. We find strong support for the monophyly of Ormosia and the grouping of all sampled Asian species of the genus into two comparably sized clades, one of which is sister to another large clade containing all sampled New World species. Within the New World clade, additional resolution supports the grouping of most species into three mutually exclusive subordinate clades. The remaining New World species form a fourth well-supported clade in the analyses of plastid sequences, but that result is contradicted by the analysis of ITS. With few exceptions the supported clades have not been previously recognized as taxonomic groups. The biogeographical analysis suggests that Ormosia originated in continental Asia and dispersed to the New World in the Oligocene or early Miocene via long-distance trans-oceanic dispersal. We reject the hypothesis that the inter-hemispheric disjunction in Ormosia resulted from fragmentation of a more continuous “Boreotropical” distribution since the dispersal post-dates Eocene climatic maxima. Both of the Old World clades appear to have originated in mainland Asia and subsequently dispersed into the Malay Archipelago and beyond, at least two lineages dispersing across Wallace’s Line as far as the Solomon Islands and northeastern Australia. In the New World, the major clades all originated in Amazonia. Dispersal from Amazonia into peripheral areas in Central America, the Caribbean, and Extra-Amazonian Brazil occurred multiple times over varying time scales, the earliest beginning in the late Miocene. In a few cases, these dispersals were followed by local diversification, but not by reverse migration back to Amazonia. Within each of the two main areas of distribution, multiple modest bouts of oceanic dispersal were required to achieve the modern distributions.
Premise:
Pollinators are thought to exert selective pressures on plants, mediating the evolution of convergent floral shape often recognized as pollination syndromes. However, little is known about the accuracy of using petal shape for inferring convergence in pollination mode without a priori pollination information. Here we studied the genus Erythrina L. as a test case to assess whether ornithophyllous pollination modes (hummingbirds, passerines, sunbirds, or mixed pollination) can be inferred based on the evolutionary analysis of petal shape.
Methods:
We characterized the two-dimensional dissected shape of standard, keel, and wing petals from 106 Erythrina species using geometric morphometrics and reconstructed a phylogenetic tree of 83 Erythrina species based on plastid trnL-F and nuclear ribosomal ITS sequences. We then used two phylogenetic comparative methods based on Ornstein-Uhlenbeck models, SURFACE and l1OU, to infer distinct morphological groups using petal shape and identify instances of convergent evolution. The effectiveness of these methods was evaluated by comparing the groups inferred to known pollinators.
Results:
We found significant petal shape differences between hummingbird- and passerine-pollinated Erythrina species. Our analyses also revealed that petal combinations generally provided better inferences of pollinator types than individual petals and that the method and optimization criterion can affect the results.
Conclusions:
We show that model-based approaches using petal shape can detect convergent evolution of floral shape and relatively accurately infer pollination modes in Erythrina. The inference power of the keel petals argues for a deeper investigation of their role in the pollination biology of Erythrina and other bird-pollinated legumes.
Camoensia scandens is a papilionoid legume inserted in the core genistoid clade. It has large, crepuscular, scented flowers but the corolla is non-papilionaceous, which deviates from the pattern found in the subfamily. The vexillum has a folded claw, forming a tube, which is opposed to the androecium opening; all petals have yellow-gold crinkled margins. In addition, there is a long hypanthium, which stores a translucid liquid. The goal of this study is to elucidate the ontogenetic pathways that result in such a peculiar flower and the glands responsible for the sweet fragrance of the petals. Floral buds and flowers were processed for SEM, TEM and light microscopy analyses. Five sepals arise unidirectionally followed by five petals that initiate simultaneously. After the petals, 11 stamens emerge unidirectionally; a pair of adaxial stamens is opposite to the vexillum. In the intermediate developmental stages the sepals unite basally; the two adaxial sepals unite with each other to a greater extent than with the other sepals. The filaments are basally connate, forming a tube with an adaxial opening at the base. The carpel emerges concomitantly with the two abaxial antepetalous stamens. The long hypanthium forms from the outer floral organs (base of the sepals, petals, filaments) and is attached to the base of the stipe. The corolla is noticeable in the intermediate stages of development. The crinkled golden margins house scent glands formed of a secretory epidermis with secretory trichomes and secretory subepidermal cells. The odor is composed of neutral polysaccharides, nitrogenous substances and essential oils. An extensive nectariferous region is found on the inner surface of the hypanthial tube. The nectar is translucent, viscous and released through large pores. The comparison of our data with that of other genistoid flowers enabled discussions about the pollination and systematics of the group.
Changes in floral traits across evolutionary time are expected in response to selective pressures imposed by pollinators. Stamen dimetrism (here defined as size differences between stamens within the same flower) represents an important strategy to decrease pollen loss during bee-flower interactions in pollen flowers. However, the evolutionary history of stamen dimetrism, and the links between this and other reproductive traits across long periods of time are still poorly understood. Here we investigate the evolution of stamens dimetrism and the evolutionary correlation of this trait and other floral structures and reproductive strategies in Melastomataceae. Floral traits were scored from 336 species and reproductive biology data was gathered for 81 species. Stamen dimetrism is a labile trait, appeared several times throughout the evolutionary history of this clade and is evolutionarily correlated to floral size. Among the 81 species analyzed, we observed that the lineages that depend on pollinators to reproduce correspond to those that evolved the highest stamen dimetrism. The evolutionary lability of stamen dimetrism has probably contributed to the maintenance of the buzz pollination adaptive plateau in possibly the largest radiation of pollen flowers in angiosperms.
With extraordinary levels of plant diversity and endemism, the Brazilian campos rupestres across the Espinhaço Range have a species/area ratio 40 times higher than the lowland Amazon. Although diversification drivers in campos rupestres remain a matter of debate, the Pleistocene refugium hypothesis (PRH) is often adopted as the most plausible explanation for their high diversity. The PRH has two main postulates: highland interglacial refugia and a species pump mechanism catalysed by climatic changes. We critically assessed studies on campos rupestres diversification at different evolutionary levels and conclude that most of them are affected by sampling biases, unrealistic assumptions or inaccurate results that do not support the PRH. By modelling the palaeo-range of campos rupestres based on the distribution of 1123 species of vascular plants endemic to the Espinhaço Range and using climate and edaphic variables, we projected a virtually constant suitable area for campos rupestres across the last glacial cycle. We challenge the great importance placed on Pleistocene climatic oscillations in campos rupestres plant diversification and offer an alternative explanation named escape-to-radiate model, which emphasizes niche shifts. Under this biogeographic model of diversification, the long-term fragmentation of campos rupestres combined with recurrent extinctions after genetic drift and sporadic events of adaptive radiation may provide an explanation for the current diversity and endemism in the Espinhaço Range. We conclude that long-term diversification dynamics in campos rupestres are mainly driven by selection, while most endemic diversity is ephemeral, extremely fragile and mainly driven by drift.
Ecology, geography, morphology, and a combined phylogenetic analysis of DNA sequence variation support the recognition of the new species Luetzelburgia jacana (Leguminosae, Papilionoideae, vataireoid clade). This species is found in the inter-Andean Rio Cauca Valley in Colombia. Phylogenetic analyses of nine plastid and nuclear DNA sequences from 44 accessions representing all known Luetzelburgia species show that L. jacana is sister to the rest of the genus and has a mean estimated stem age of ca. 4 Ma, much older than other Luetzelburgia species. Luetzelburgia jacana is distinguished by a combination of mostly 7–9-foliolate, glabrous leaves with leaflets obtuse to shortly acute at the apex, flowers up to 9.6 mm long, and samaras bearing two small lateral wings on the seed chamber. Luetzelburgia jacana, along with two other earliestbranching species in the genus, L. guaissara and L. trialata, are geographical outliers in the genus, with L. jacana having the northernmost distribution and L. guaissara and L. trialata having the southernmost distributions. These three earliest-branching species are also ecological outliers within Luetzelburgia by occurring in wetter and less seasonal settings than other species.
The discovery of L. jacana resolves these three earliest-branching species in Luetzelburgia as ecologically transitional between most species of the vataireoid clade that inhabit wet forests and most species of Luetzelburgia that inhabit highly seasonal dry forests and woodlands.
The pollen brush commonly is referred to as a “bearded” or “pubescent” style in taxonomic literature and traditionally is taken to be an aggregation of trichomes on the distal end of the style, and occasionally including the stigma. We present data that support the taxonomic utility of the pollen brush but define it more specifically as a dense aggregation of erect trichomes emanating from the style (not stigma or ovary) and functioning in secondary pollen presentation. We recommend avoiding such vague terminology as bearded or pubescent styles as these refer not only to the pollen brush but also to ciliate and penicillate stigmas and ciliate styles. The latter three conditions have some taxonomic use, and since their occurrence is not necessarily correlated with the presence of a pollen brush, they should be distinguished from it. We estimate that the pollen brush has arisen independently in the following eight taxa: 1) Crotalaria and Bolusia (Crotalaraieae), 2) subtribe Coluteinae (Galegeae), 3) Tephrosia subgenus Barbistyla (Millettieae), 4) Adenodolichos (Phaseoleae subtribe Cajaninae), 5) Clitoria (Phaseoleae subtribe Clitoriinae), 6) the subtribe Phaseolinae (Phaseoleae), 7) the Robinia group (Robinieae), and 8) the tribe Vicieae. Its hypothesized homology within each of these groups is supported by a cooccurrence with other taxonomic characters, both morphological and molecular.
The Caatinga Domain (CD) in northeastern Brazil harbors the largest and most continuous expanse of the seasonally dry tropical forest and woodland biome (SDTFW) in the New World. Phytogeographical data collected over the past 10 years support previous hypotheses that recognized two major biotas in Caatinga SDTFW: the Crystalline Caatinga, mostly associated with medium to highly fertile soils in the wide Sertaneja Depression; and the Sedimentary Caatinga, mostly associated with poor sandy soils derived from patchy sedimentary surfaces. A third floristic set is represented by tall Caatinga forests. The CD is the richest SDTFW area in the New World, with 3150 species in 930 genera and 152 families of flowering plants. About 23% of the species and 31 genera are endemic to the CD. We performed phylogenetic meta-analyses to estimate times of divergence and ancestral areas for SDTFW lineages, which indicated that plant diversity in the Caatinga arose mostly by in situ speciation following Mid to Late Miocene vicariance events with two major SDTFW nuclei: (1) the northwestern Caribbean dry coast of Colombia and Venezuela; and (2) the southwestern South American dry forests of southern Bolivia and northwestern Argentina. Phylogenetic analyses also uncovered unexpected patterns of recent radiations, with evolutionarily new species and incomplete lineage sorting that sharply contrast with the most common phylogenetic patterns found in SDTFW clades. Recent, mostly Pleistocene, ecological speciation better explains the emergence of distinct biotas on sandy and karstic surfaces.
Nuclear DNA sequence data (Internal Transcribed Spacer 1 of the 45S rDNA cistron) and morphological data were used for phylogenetic studies of the tribe Brongniartieae (Fabaceae), a tribe of four Australian and two tropical American genera. Alignment of the ITS-1 region was largely unambiguous and the phylogeny produced using parsimony methods had a high consistency index. Morphological data were mostly congruent with the molecular data and were informative for some nodes where molecular data were lacking. Combining molecular and morphological data resulted in a well-resolved phylogeny, Analyses confirm the monophyly of the tribe and show that the American genus Brongniartia is more closely related to Australian genera than to Harpalyce, the other American genus in the tribe. There is evidence that the Australian genus Plagiocarpus is related to Brongniartia. Templetonia is polyphyletic. Templetonia biloba, T incana, and Lamprolobium form a monphyletic group. Analyses also support the recognition of three groups within the Australian endemic genus Hovea.
A revision of the northern Australian genus Plagiocarpus Benth. (Fabaceae: Brongniartieae) is presented. Six new species are described in the formerly monotypic genus: Plagiocarpus arcuatus I.Thomps., P. arnhemicus I.Thomps., P. conduplicatus I.Thomps., P. dispermus I.Thomps., P. Ianatus I.Thomps. and P. longiflorus I.Thomps. Distribution maps and an identification key are presented.
A revision of the Western Australian genus Cristonia J.H.Ross (Fabaceae: Brongniartieae) is presented. The number of taxa is increased from one to three. Bossiaea biloba var. stenophylla Meisn. is resurrected and recombined at species rank to become Cristonia stenophylla (Meisn.) I.Thomps. and Cristonia biloba subsp. pubescens I.Thomps. is described as new. Distribution maps and identification keys are presented.
A revision of the leafless species of Templetonia R.Br. (Fabaceae: tribe Brongniartieae) is presented. Two new species are described, T. incrassata I.Thomps. and T. ceracea I.Thomps. In addition, Bossiaea rossii F.Muell. is resurrected and recombined as Templetonia rossii (F.Muell.) I.Thomps. Distribution maps and identification keys are presented.
The fossil history of plant life in Antarctica is central to our understanding of the evolution of vegetation through geological time and also plays a key role in reconstructing past configurations of the continents and associated climatic conditions. This book provides the only detailed overview of the development of Antarctic vegetation from the Devonian period to the present day, presenting Earth scientists with valuable insights into the break up of the ancient supercontinent of Gondwana. Details of specific floras and ecosystems are provided within the context of changing geological, geographical and environmental conditions, alongside comparisons with contemporaneous and modern ecosystems. The authors demonstrate how palaeobotany contributes to our understanding of the palaeoenvironmental changes in the southern hemisphere during this period of Earth history. The book is a complete and up-to-date reference for researchers and students in Antarctic palaeobotany and terrestrial palaeoecology.
Premise of research. Chamaecrista sect. Chamaecrista ser. Coriaceae comprises 22 species, mostly distributed in the highlands of Brazil in Cerrado (Neotropical savanna) and Campo Rupestre (upland rocky field) vegetation. Phylogenetic studies for plant taxa of these rich and endemic Brazilian floras are still scarce. In this context, the main objective of our study was to examine the phylogenetic history of a plant group diversified in the mountainous areas of central Brazil. Methodology. The phylogeny of Chamaecrista ser. Coriaceae was examined with combined data from two nuclear regions (ETS [external transcribed spacer] and ITS), two plastid regions (trnD-T and trnL-F), and morphological evidence from comprehensive sampling of the series. We used phylogenetic analyses to evaluate morphological-character evolution to identify putative synapomorphies, and we used Bayesian estimation to explore the timing of diversification of the group. Pivotal results. The series, as currently circumscribed, appears as polyphyletic in all of the analyses, but most of the species ascribed to it form a well-supported clade endemic to highland areas in the Brazilian Cerrado, referred to as the Coriaceae clade. The plastid regions provided high support for the monophyly of this clade, with the nuclear regions providing better resolution within the clade. In addition to molecular evidence, two putative morphological synapomorphies were found. The age-estimation analyses show a recent diversification in the group. Conclusions. Molecular and morphological data indicated that a narrower definition of Chamaecrista ser. Coriaceae as a monophyletic group is required. In addition to two clear deletions in the plastid sequences studied, the presence of a woody underground system and flowers with one stamen displaced to the same side as the gynoecium appear as putative morphological synapomorphies. The low resolution found among species within the clade may reflect a recent radiation that has occurred in the past 5 Myr-a common pattern in other groups restricted to highland areas in South America.
I. II. III. IV. V. VI. VII. VIII. References SUMMARY: A fundamental premise of this review is that distinctive phylogenetic and biogeographic patterns in clades endemic to different major biomes illuminate the evolutionary process. In seasonally dry tropical forests (SDTFs), phylogenies are geographically structured and multiple individuals representing single species coalesce. This pattern of monophyletic species, coupled with their old species stem ages, is indicative of maintenance of small effective population sizes over evolutionary timescales, which suggests that SDTF is difficult to immigrate into because of persistent resident lineages adapted to a stable, seasonally dry ecology. By contrast, lack of coalescence in conspecific accessions of abundant and often widespread species is more frequent in rain forests and is likely to reflect large effective population sizes maintained over huge areas by effective seed and pollen flow. Species nonmonophyly, young species stem ages and lack of geographical structure in rain forest phylogenies may reflect more widespread disturbance by drought and landscape evolution causing resident mortality that opens up greater opportunities for immigration and speciation. We recommend full species sampling and inclusion of multiple accessions representing individual species in phylogenies to highlight nonmonophyletic species, which we predict will be frequent in rain forest and savanna, and which represent excellent case studies of incipient speciation.
