Biology subjects

Haevermans, T.

Publications and source records attributed to Haevermans, T..

3 recordsLinked to original sources

bioRxiv2024

Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation

O_LIGrasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. C_LIO_LIWe inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1,153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a 910-tip plastome tree. C_LIO_LIThe nuclear phylogeny matches that of the plastome at most deep branches, with only a few instances of incongruence. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly in the history of grasses. C_LIO_LIWe provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture. C_LI

plant biology↗

bioRxiv2021

Global Plant Extinction Risk Assessment Informs Novel Biodiversity Hotspots

Curbing biodiversity loss and its impact on ecosystem services, resilience and Natures Contributions to People is one of the main challenges of our generation (IPBES, 2019b, 2019a; Secretariat of the United Nations Convention on Biological Diversity, 2020). A global baseline assessment of the threat status of all of biodiversity is crucial to monitor the progress of conservation policies worldwide (Mace & al., 2000; Secretariat of the United Nations Convention on Biological Diversity, 2021) and target priority areas for conservation (Walker & al., 2021). However, the magnitude of the task seems insurmountable, as even listing the organisms already known to science is a challenge (Nic Lughadha & al., 2016; Borsch & al., 2020; Govaerts & al., 2021). A new approach is needed to overcome this stumbling block and scale-up the assessment of extinction risk. Here we show that analyses of natural history mega-datasets using artificial intelligence allows us to predict a baseline conservation status for all vascular plants and identify target areas for conservation corresponding to hotspots optimally capturing different aspects of biodiversity. We illustrate the strong potential of AI-based methods to reliably predict extinction risk on a global scale. Our approach not only retrieved recognized biodiversity hotspots but identified new areas that may guide future global conservation action (Myers & al., 2000; Brooks & al., 2006). To further work in this area and guide the targets of the post-2020 biodiversity framework (Diaz & al., 2020a; Secretariat of the United Nations Convention on Biological Diversity, 2020; Mair & al., 2021), it will be necessary to accelerate the acquisition of fundamental data and allow inclusion of social and economic factors (Possingham & Wilson, 2005).

plant biology↗

bioRxiv2019

Tracking the origin of island diversity: insights from divergence with the continental pool in monocots

At their early age, a large proportion of island pools were a partial sampling of mainland pools whatever islands are oceanic or fragments of the mainland. Through time, colonization, diversification, extinctions, have deeply transformed insular and continental communities and therefore the degree to which they share species. We studied the relative importance of these mechanisms by looking at the shared evolutionary history between species pools on islands and continents. Indeed, most of these mechanisms are not neutral regarding phylogeny but are linked to species evolutionary relationships. We measured the phylogenetic divergence between continental and insular monocot communities through metrics of beta Mean Pairwise Distance and beta Mean Nearest Taxon Distance. We first tested the influence of spatial and environmental distance to the continent, two main factors of divergence, but whose explanatory power in a phylogenetic context was still unclear. We showed that both dispersal and enviromental filtering were important to explain divergence, although species that could pass these filters were not phylogenetically clustered. There was however a clear distinction between oceanic and continental islands: a stable climate in the latters was key to the survival of the original biota leading to a high proportion of shared lineages between the mainland and islands. But distance to the continent was only part of the story, we investigated additionnal mechanisms of phylogenetic divergence through their relation to island features and community structure. This showed that the most divergent islands occurred in the tropics and that processes of persistence of original species, diversification in remote archipelagos, neutral colonization on easy-to-reach islands, turnover, and high speciation rates may have driven phylogenetic divergence at a world scale. This study showed how phylogenetic approaches may explain how divergence, or similarity may have arisen and provide new insights in the continental origin of plant diversity on islands.

ecology↗