Phylogenomics and the rise of the angiosperms.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

A Taxonomically-verified and Vouchered Checklist of the Vascular Plants of the Republic of Guinea.

The Checklist of the Vascular Plants of the Republic of Guinea (CVPRG) is a specimen-based, expert-validated knowledge product, which provides a concise synthesis and overview of current knowledge on 3901 vascular plant species documented from Guinea (Conakry), West Africa, including their accepted names and synonyms, as well as their distribution and status within Guinea (indigenous or introduced, endemic or not). The CVPRG is generated automatically from the Guinea Collections Database and the Guinea Names Backbone Database, both developed and maintained at the Royal Botanic Gardens, Kew, in collaboration with the staff of the National Herbarium of Guinea. A total of 3505 indigenous vascular plant species are reported of which 3328 are flowering plants (angiosperms); this represents a 26% increase in known indigenous angiosperms since the last floristic overview. Intended as a reference for scientists documenting the diversity and distribution of the Guinea flora, the CVPRG will also inform those seeking to safeguard the rich plant diversity of Guinea and the societal, ecological and economic benefits accruing from these biological resources.

Phylogenomics sheds new light on the drivers behind a long-lasting systematic riddle: the figwort family Scrophulariaceae.

The figwort family, Scrophulariaceae, comprises c. 2000 species whose evolutionary relationships at the tribal level have proven difficult to resolve, hindering our ability to understand their origin and diversification. We designed a specific probe kit for Scrophulariaceae, targeting 849 nuclear loci and obtaining plastid regions as by-products. We sampled c. 87% of the genera described in the family and use the nuclear dataset to estimate evolutionary relationships, timing of diversification, and biogeographic patterns. Ten tribes, including two new tribes, Androyeae and Camptolomeae, are supported, and the phylogenetic positions of Androya, Camptoloma, and Phygelius are unveiled. Our study reveals a major diversification at c. 60 million yr ago in some Gondwanan landmasses, where two different lineages diversified, one of which gave rise to nearly 81% of extant species. A Southern African origin is estimated for most modern-day tribes, with two exceptions, the American Leucophylleae, and the mainly Australian Myoporeae. The rapid mid-Eocene diversification is aligned with geographic expansion within southern Africa in most tribes, followed by range expansion to tropical Africa and multiple dispersals out of Africa. Our robust phylogeny provides a framework for future studies aimed at understanding the role of macroevolutionary patterns and processes that generated Scrophulariaceae diversity.

Plastid phylogenomics of the Sansevieria Clade of Dracaena (Asparagaceae) resolves a recent radiation.

Best known as low maintenance houseplants, sansevierias are a diverse group of flowering plants native to Africa, Madagascar, the Arabian Peninsula, and the Indian subcontinent. Traditionally recognised as a distinct genus, Sansevieria was recently merged with the larger genus Dracaena based on molecular phylogenetic data. Within the Sansevieria Clade of Dracaena, taxonomic uncertainties remain despite attempts to unravel the relationships between the species. To investigate the evolutionary relationships, morphological evolution and biogeographical history in the group, we aim to reconstruct a robust dated phylogenetic hypothesis. Using genome skimming, a chloroplast genome (cpDNA) dataset and a nuclear ribosomal (nrDNA) dataset were generated. The sampling included representatives of all sections and informal groups previously described in Sansevieria based on morphology. Analysis of the cpDNA dataset using a maximum likelihood approach resulted in a well-supported phylogeny. The time-calibrated phylogeny indicated a recent radiation with five main clades emerging in the Pliocene. Two strongly supported clades align with previously defined groups, i.e., Sansevieria section Dracomima, characterised by the Dracomima-type inflorescence, and the Zeylanica informal group, native to the Indian subcontinent. Other previously defined groups were shown to be polyphyletic; a result of convergent evolution of the identifying characters. Switches between flat and cylindrical leaves occurred multiple times in the evolution of the Sansevieria Clade. Similarly, the Cephalantha-type inflorescence has originated multiple times from an ancestor with a Sansevieria-type inflorescence. Analysis of the nrDNA dataset resulted in a phylogenetic hypothesis with low resolution, yet it supported the same two groups confirmed by the cpDNA dataset. This study furthers our understanding of the evolution of the Sansevieria Clade, which will benefit taxonomic and applied research, and aid conservation efforts.

Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits.

PREMISE: Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. METHODS: We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. RESULTS: For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. CONCLUSIONS: The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.

The endemic plants of Mozambique: diversity and conservation status.

An annotated checklist of the 271 strict-endemic taxa (235 species) and 387 near-endemic taxa (337 species) of vascular plants in Mozambique is provided. Together, these taxa constitute c. 9.3% of the total currently known flora of Mozambique and include five strict-endemic genera (Baptorhachis, Emicocarpus, Gyrodoma, Icuria and Micklethwaitia) and two near-endemic genera (Triceratella and Oligophyton). The mean year of first publication of these taxa is 1959, with a marked increase in description noted following the onset of the two major regional floristic programmes, the "Flora of Tropical East Africa" and "Flora Zambesiaca", and an associated increase in botanical collecting effort. New taxa from Mozambique continue to be described at a significant rate, with 20 novelties described in 2018. Important plant families for endemic and near-endemic taxa include Fabaceae, Rubiaceae and Euphorbiaceae s.s. There is a high congruence between species-rich plant families and endemism with the notable exceptions of the Poaceae, which is the second-most species rich plant family, but outside of the top ten families in terms of endemism, and the Euphorbiaceae, which is the seventh-most species rich plant family, but third in terms of endemism. A wide range of life-forms are represented in the endemic and near-endemic flora, with 49% being herbaceous or having herbaceous forms and 55% being woody or having woody forms. Manica Province is by far the richest locality for near-endemic taxa, highlighting the importance of the cross-border Chimanimani-Nyanga (Manica) Highlands shared with Zimbabwe. A total of 69% of taxa can be assigned to one of four cross-border Centres of Endemism: the Rovuma Centre, the Maputaland Centre sensu lato, and the two mountain blocks, Chimanimani-Nyanga and Mulanje-Namuli-Ribaue. Approximately 50% of taxa have been assessed for their extinction risk and, of these, just over half are globally threatened (57% for strict-endemics), with a further 10% (17% for strict-endemics) currently considered to be Data Deficient, highlighting the urgent need for targeted conservation of Mozambique's unique flora. This dataset will be a key resource for ongoing efforts to identify "Important Plant Areas - IPAs" in Mozambique, and to promote the conservation and sustainable management of these critical sites and species, thus enabling Mozambique to meet its commitments under the Convention on Biological Diversity (CBD).

ResumoApresenta-se a lista das plantas vasculares de Moçambique, que compreende 271 taxa endémicos (235 espécies) e 387 taxa quase-endémicos (337 espécies). Estes taxa constituem cerca de 9,3% da flora total actualmente conhecida em Moçambique e incluem cinco géneros estritamente endémicos (Baptorhachis, Emicocarpus, Gyrodoma, Icuria e Micklethwaitia) e dois géneros quase-endémicos (Triceratella e Oligophyton). O ano médio das primeiras publicações destes taxa é 1959. Um aumento significativo na descrição de espécies novas foi verificado, relacionado com o início de dois projectos regionais, a "Flora of Tropical East Africa" e a "Flora Zambesiaca", permitindo um esforço maior de colheitas botânicas. Novos taxa têm vindo a ser descritos a um ritmo significativo, com 20 novas espécies descritas em 2018 para a flora de Moçambique. As famílias Fabaceae, Rubiaceae e Euphorbiaceae, incluem importantes taxa endémicos e quase-endémicos. Existe uma estreita relação entre as famílias de plantas com elevado número de espécies e o grau de endemismo, excepção feita às Poaceae, que embora seja a segunda família mais rica em espécies não se posiciona no grupo das dez principais famílias em termos de endemismo. Por outro lado a família Euphorbiaceae, que é a sétima mais rica em espécies, posiciona-se em terceiro lugar quanto ao número de endemismo. A flora endémica apresenta diferentes formas de vida, sendo 49% das espécies herbáceas e 55% lenhosas. A Província de Manica é o local mais rico em taxa quase-endémicos, realçando assim a importância da área transfronteiriça Chimanimani-Nyanga (Manica) entre Moçambique e Zimbabwe. Refira-se ainda que 69% dos taxa encontra-se num dos quatro centros de endemismo transfronteiriços: o Centro do Rovuma, o Centro de Maputaland sensu lato e nas regiões montanhosas de Chimanimani-Nyanga e Mulanje-Namuli-Ribáuè. Cerca de 50% dos taxa foram avaliados quanto ao risco de extinção, estando mais da metade ameaçados globalmente (57% de endemismos) e 10% (17% de endemismos) foram incluídos na categoria Informação Insuficiente (DD), revelando que a maioria das plantas endémicas de Moçambique necessitam de conservação urgente. Este estudo fornece novos dados indispensáveis à identificação das "Áreas Importantes de Plantas ­ IPAs" em Moçambique, contribuindo ainda para implementar as estratégias de conservação anteriormente estabelecidas pela Convenção sobre a Diversidade Biológica (CBD).