Showing papers by "Thomas L. P. Couvreur published in 2021"

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Abstract: Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological spe-ciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology.

Abstract: The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata) We assembled the genome using 44432 Gb of DNA sequences (676× sequencing depth) from PacBio and Illumina short-reads, in combination with 10× Genomics and Bionano data (v1) A total of 949 scaffolds were assembled to a final size of 65677 Mb, with a scaffold N50 of 343 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 932 Mb, total size in chromosomes: 6396 Mb) Heterozygosity was very low (006%), while repeat sequences accounted for 5487% of the genome, and 23,375 protein-coding genes with an average of 479 exons per gene were annotated using de novo, RNA-seq and homology-based approaches Reconstruction of the historical population size showed a slow continuous contraction, probably related to Cenozoic climate changes The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry

Pulled Diversification Rates, Lineage-Through-Time Plots and Modern Macroevolutionary Modelling

Abstract: Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has lead to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we demonstrate the characteristics of newly-proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.

Three new species of Uvariodendron (Annonaceae) from coastal East Africa in Kenya and Tanzania.

Abstract: East Africa is a hotspot of biodiversity with many endemic plant species. We describe three new species of the genus Uvariodendron (Annonaceae) from the coastal forests of Kenya and Tanzania. Uvariodendron mbagoi Dagallier & Couvreur, sp. nov. is endemic to Tanzania and unique within the genus by its strong bergamot scent and its tomentose fruits having regular tufts of higher hair density. Uvariodendron dzomboense Dagallier, W.R.Q. Luke & Couvreur, sp. nov. is endemic to Dzombo Hill in Kenya and is rendered distinct by its small leaves and very densely pubescent carpels. Uvariodendron schmidtii W.R.Q. Luke, Dagallier & Couvreur, sp. nov. is endemic to Shimba Hills in Kenya and differs by its small flowers and fused sepals forming a ring. Following IUCN criteria we assessed U. mbagoi and U. dzomboense as endangered (EN) while U. schmidtii is assessed as Vulnerable (VU). We also propose a new combination: Polyceratocarpus oligocarpus (Verdc.) Dagallier, comb. nov. The description of these three new species underlines the richness in endemics in East Africa and that new discoveries might arise from further botanical exploration of this region.

Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species of Mauritiella

Abstract: The palm tribe Lepidocaryeae (Arecaceae) comprises seven genera and 51 currently accepted species that are distributed in lowland tropical forests and savannas across Africa and the Americas. Subtribal relationships within Lepidocaryeae have been a persistent challenge, limiting our understanding of its systematics, morphology, and biogeography. Several aspects make the tribe an ideal system to study plant evolution and diversity: it is well-represented in the fossil record as a prolific pollen producer, its continental diversity contradicts common biodiversity patterns of lower species richness in Africa in comparison to South America, and it contains one of the most abundant Amazonian tree species, Mauritia flexuosa. Here, we investigated the systematics of the tribe by sampling 122 individuals representing 42 species (82% of the tribe), using target sequence capture. We recovered nearly 10,000 single nucleotide polymorphisms from nuclear and plastid DNA across 146 target sequences to separately infer a phylogenomic tree. Our results strongly support inter-generic and inter-specific relationships, where a majority of nodes were resolved with over 90% bootstrap support. We also identify strong phylogenetic support for the recognition of a new species from central and south Amazonia, Mauritiella disticha. The distichous phyllotaxy is diagnostic of the species within the genus. Rare and currently only known from the middle-lower Madeira River basin in the state of Amazonas, Brazil, M. disticha is restricted to open vegetation and forest edges growing in white sand habitats with saturated or well-drained soils. Our preliminary red list assessment suggests its threatened status to be vulnerable (VU). We use our phylogenomic inference to define and contextualize systematic relationships in the tribe, and present a formal species description.