Content uploaded by Mel Duvall
Author content
All content in this area was uploaded by Mel Duvall on Feb 04, 2015
Content may be subject to copyright.
Molecular phylogenetics of Lilianae
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.
Background and aims:
Asparagaceae subfamily Nolinoideae is an economically important plant group, however, the deep relationships and evolutionary history of the lineage remains poorly understood. Based on a large data set including 37 newly sequenced samples and publicly available plastomes, this study aims to better resolve the inter-tribal relationships of Nolinoideae, and to rigorously examine the tribe level monophyly of Convallarieae, Ophiopogoneae, and Polygonateae.
Methods:
Maximum likelihood (ML) and Bayesian inference (BI) methods were employed to infer phylogenetic relationships of Nolinoideae at the genus level and above. The diversification history of Nolinoideae was explored using molecular dating.
Key results:
Both ML and BI analyses identically recovered five clades within Nolinoideae, respectively corresponding to Dracaeneae + Rusceae, Polygonateae + Theropogon, Ophiopogoneae, Nolineae, and Convallarieae excluding Theropogon, and most deep nodes were well supported. As Theropogon was embedded in Polygonateae, the plastome phylogeny failed to resolve Convallarieae and Polygonateae as reciprocally monophyletic. Divergence time estimation showed that the origins of most Nolinoideae genera were dated to the Miocene and Pliocene. The youthfulness of Nolinoideae genera is well-represented in the three herbaceous tribes (Convallarieae, Ophiopogoneae, and Polygonateae) chiefly distributed in the temperate areas of the Northern Hemisphere, as the median stem ages of all the 14 genera currently belonging to them were estimated less than 12.37 Ma.
Conclusions:
This study recovered a robust backbone phylogeny, providing new insights for better understanding the evolution and classification of Nolinoideae. Compared with the deep relationships recovered by a previous study based on transcriptomic data, our data suggest that ancient hybridization or incomplete lineage sorting may have occurred in the early diversification of Nolinoideae. Our findings will provide important reference for further study of the evolutionary complexity of Nolinoideae using nuclear genomic data. The recent origin of these herbaceous genera currently belonging to Convallarieae, Ophiopogoneae, and Polygonateae provides new evidence to support the hypothesis that the global expansion of temperate habitats caused by the climate cooling over the past 15 Ma may have dramatically driven lineage diversification and speciation in the Northern Hemisphere temperate flora.
The genera Gloriosa L. and Sandersonia Hook. (Colchicaceae: Colchiceae) are revised for southern Africa, with full nomenclature, descriptions, distribution data and updated conservation assessments. All species are illustrated in colour. Both genera have a similar habit, with mostly cirrhose foliage and yellow (rarely greenish) to orange flowers nodding on slender extra-axillary pedicels, with a well-developed style longer than the branches. Despite their similar morphology, existing phylogenetic analyses indicate that they are not immediately related. Three species of Gloriosa are recognised from the region, distinguished by the shape and size of their flowers, and the orientation and relative length of the style. Gloriosa superba L., which is widespread through Africa and southeast Asia, is recognised by its relatively large flowers with recurved or reflexed tepals that are narrowed and ± clawed at the base, and a sharply flexed style. Capsule dehiscence is septicidal. Typical plants have a bicoloured red and yellow perianth but populations from the north-eastern parts of the subcontinent and also elsewhere in tropical Africa are predominantly plain yellow. The overlooked G. sect. Gloriola Chiov. is lectotypified against G. aurea Chiov., currently treated as a synonym of G. superba. A full nomenclator and synonymy of all names included in G. superba is provided for the first time, including the nomenclatural status of the names and their types. The two remaining species in the region share similar cup-shaped flowers with suberect, lanceolate tepals and erect style. The locally endemic G. rigidifolia (Bredell) J.C.Manning & Vinn. from the Waterberg in Limpopo, South Africa, has been confused with G. modesta (Hook.) J.C.Manning & Vinn. from eastern South Africa, Eswatini and Mozambique but it differs consistently from that species in its erect, mostly more floriferous habit and in its slightly smaller, greenish (vs mostly yellow or orange) flowers with slightly longer perianth tube and much longer style, and evidently also in its septicidal (vs loculicidal) capsule dehiscence. The two taxa constitute a species pair that differs from florally similar species from tropical Africa by the mostly whorled foliage and unusual nectaries with an auricle-like distal lobe on the lateral ridges. The monotypic genus Sandersonia is distinguished by its 3(5)-veined leaves, urceolate or lantern-shaped flowers with small, pouched or shortly spurred nectary, and verrucose seeds. The single species S. aurantiaca Hook. is endemic to temperate grasslands in South Africa and adjacent Eswatini.
To prioritise conservation actions and management strategies for threatened forest deer species at the Atlantic forest, we aimed to identify and describe the most suitable habitat areas for forest deer species and to indicate conservation measures for state agents and local communities. We adopt an approach based on ecological niche modelling, key variable thresholds and spatial analyses. In addition, we associated our approach with a human influence index, an invasive species dataset of occurrences, protected area cover and IUCN category. We indicate 2% (484 km²) of the Atlantic forest cover as conservation priority areas (CPAs). Of these, 56.8% are outside protected areas, 20.7% are inside IUCN categories i, ii and iii protected areas, 19.9% are inside IUCN categories iv, v, and vi protected areas, and 2.6% are inside indigenous areas. Also, we indicate the most relevant protected areas for deer conservation in the Atlantic forest. The CPAs were classified into more human-influenced areas (MHIA) and less human-influenced areas (LHIA), and we identified 21 significant (>120 km²) continuous CPAs outside protected areas. We highlight actions in several perspectives of human influence, governance levels and law protection that would rationalise the use of funds and human resources.
Cyanobacteria are considered to be among the first microorganisms to settle in hot springs where they form a favourable environment for further biological establishment. Nevertheless, the exact pioneer species and how early they start participating in the biomineralisation processes remain unknown. The aim of the present study was twofold, i.e. to identify the pioneer Cyanobacteria in hot springs (i.e. Aedipsos area, Greece) and to record their early biomineralisation processes. The in situ experimental approach included the setup of sterile glass and/or plexiglass slides in several locations to facilitate colonisation by Cyanobacteria, and removal of slides for study after 48 to 202 hours. Synechococcales (37%) and Oscillatoriales (33%) were the dominant orders, followed by Chroococcales (15%) and Spirulinales (11%); whereas Chroococcidiopsidales (4%) was found only in a few sites. The order Nostocales was not observed at the early stages of colonisation although it was present in mature stages. Forty‐three species of Cyanobacteria were identified as pioneer microorganisms, with Spirulina subtilissima being the most frequently found. The most common pioneers were multicellular filamentous Cyanobacteria, i.e. organisms with a large surface area able to form significant amounts of extracellular polymeric substances. Among the pioneers, thermophilic species of Cyanobacteria were typical such as Chroococcidiopsis thermalis, Chroococcus thermalis, Leptolyngbya thermalis, Spirulina subtilissima and Symploca thermalis, as well as typical limestone substrate species such as Chroococcus lithophilus and Leptolyngbya laminosa. Temperature seems to affect biodiversity. Also, pioneers were found to contribute to the biomineralisation processes from their first appearance. In the studied samples, three biomineralisation processes were identified, i.e. i) calcification of cyanobacterial sheaths, ii) trapping of carbonate crystals on a crystal retention lattice formed by extracellular polymeric substances and filaments, and iii) trapping and confinement of carbonate crystals around filamentous Cyanobacteria.
Tribe Lilieae, encompassing Lilium, Notholirion, Cardiocrinum, and Fritillaria, includes economically important crops with a horticultural and medicinal value. It is considered to be a core lineage of Liliaceae, but phylogenetic relationships within it, and the timing of the origin of individual clades, remain incompletely resolved. To address these issues, we reconstructed the evolutionary history of the tribe. We sequenced 45 Liliaceae plastomes and combined them with publicly available data (for a total of 139 plastomes) to explore the systematics, origin, divergence, and evolution of Lilieae. Our taxon sampling covers all ten sections of Lilium, all Cardiocrinum species, three Notholirion species, and major phylogenetic clades of Fritillaria. Our phylogenetic analysis confirms the monophyly of major sections/subgenera of Lilium and Fritillaria with strong support. We dated the origin of Lilieae to the Eocene, with genera and species radiations inferred to have occurred in the Miocene. The reconstruction of the ancestral area implies that Lilieae may have originated from the Qinghai-Tibet Plateau (QTP): the Himalayas and Hengduan Mountains and uplifting of the QTP likely promoted divergence within the tribe. Ancestral-state reconstructions of the bulb component number (including bulblets and scales) show a strong correlation with the genus-level phylogenetic diversity in Lilieae. They also predict that the most recent common ancestor of Lilieae had bulbs with numerous bulblets. Based on these observations, we predicted that climatic oscillations associated with the QTP uplift played an important role in the evolution of the Lilieae bulb. Our findings provide a well-supported picture of evolutionary relationships and a useful framework for understanding the pathway of bulb evolution within Lilieae, contributing to a better understanding of the evolutionary history of lilies.
To determine the evolutionary relationships among some members of geophytes collected from their natural habitat in Kulp-Diyarbakır we carried out molecular phylogenetic analysis of one nuclear DNA (nrDNA) region (internal transcribed spacer, ITS) and one chloroplast DNA (cpDNA) region (intergenic spacer region of trnL-F). Despite phylogenetic analysis using maximum likelihood done by two different DNA source show some differences it was identified that monocotyl petaloid taxa differ from dicotyledone geophyte ones. Also both phylogenetic trees reveal that Serapias, Anacamptis, Cephalanthera, Himanthoglossum and Dactylorhiza are nested in Orchis. Therefore the infraspecific relationships of these genera should be re-evaluated according to our molecular phylogenetic study results. Dicotyl geophyts show molecular phylogeny in accordance with the classical systematic order in Flora of Turkey and reveal the accuracy of interspecific and infraspecific distinctions of these taxa.
The subfamily Nolinoideae of Asparagaceae is an extremely morphologically heterogeneous group, which is comprised of seven lineages, formerly known as Eriospermaceae, Polygonateae, Ophiopogoneae, Convallarieae, Ruscaceae s.s., Dracaenaceae, and Nolinaceae from different families or even orders. Their drastically divergent morphologies and low level of molecular resolution have hindered our understanding on their evolutionary history. To resolve reliable and clear phylogenetic relationships of the Nolinoideae, a phylogenetic study was conducted based on transcriptomic sequencing of 15 species representing all the seven lineages. A dataset containing up to 2,850,331 sites across 2,126 genes was analyzed using both concatenated and coalescent methods. Except for Eriospermum as outgroup, the transcriptomic data strongly resolved the remaining six lineages into two groups, one is a paraphyletic grade including the woody lineages of dracaenoids, ruscoids, and nolinoids and a monophyletic herbaceous clade. Within the herbaceous group, the Ophiopogoneae + Theropogon is sister to a clade that is composed of Convallarieae and the monophyletic Polygonateae. Our work provides a first robust deep relationship of the highly heterogeneous Nolinoideae and paves the way for further investigations of its complex evolution.
Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.
Asparagaceae: Lomandroideae are a species-rich and economically important subfamily in the monocot order Asparagales, with a center of diversity in Australia. Lomandroideae are ecologically diverse, occupying mesic and arid biomes in Australia possessing an array of key traits, including sexual dimorphism, storage organs and polyploidy potentially adaptive for survival in seasonally arid and fire-dependent habitats. The Lomandroideae phylogeny was reconstructed using maximum likelihood and Bayesian inferences criteria, based on plastome data from genome-skimming to infer generic and specific relationships. A fossil-calibrated chronogram provided a temporal framework for understanding directional and transitions of traits. Ancestral state reconstructions and phylogenetic comparative trait correlations analyses provided insights for evolutionary and ecological drivers associated with Lomandroideae diversification. Lomandroideae diverged from the other Asparagaceae ca 56 Ma and the major lineages diversified since Oligocene-Miocene. The Most Recent Common Ancestor of the clade likely occupied the mesic biome, was hermaphroditic and geophytic. The probability of biome occupancy transition was increased by 1. evolution of polyploidy, and 2. the presence of storage roots. Polyploidy potentially serves as an “enabler” trait, generating novel phenotypes, which may confer tolerance to climatic ranges and soil conditions putatively required for expansion into and occupation of new arid biomes. Storage roots, as a key factor driving biome transitions, may have been associated with fire rather than with aridification events in the Australian flora. This study contributes significantly to our understanding of biome evolution by identifying polyploidy and storage organs as key factors associated with transitions in biome occupancy in this lineage.
ResearchGate has not been able to resolve any references for this publication.