Biology subjects

Sauquet, H.

Publications and source records attributed to Sauquet, H..

22 records · Page 2Linked to original sources

bioRxiv2020

Phylogenomics of Brosimum Sw. (Moraceae) and allied genera, including a revised subgeneric system

We present a phylogenomic study of Brosimum and the allied genera Trymatococcus and Helianthostylis, with near-complete taxon sampling. Distributed from Mexico and the Greater Antilles to the Amazon, this clade contains the underutilized crop ramon (bread nut) (Brosimum alicastrum) as well as other species valued for timber or medicinal uses. Target enrichment for 333 genes produced a well-resolved phylogenetic tree and showed that Trymatoccocus and Helianthostylis are nested within Brosimum. We present a revised subgeneric classification of Brosimum based on phylogenetic and morphological considerations, including the reduction of Trymatococcus and Helianthostylis to subgenera. The monophyletic subgenera can be diagnosed based on stipule, pistillode, and cotyledon synapomorphies. Divergence date estimates suggest a Miocene origin for Brosimum, and ancestral area reconstruction indicated that all four subgenera originated and initially diversified in Amazonia before dispersing into other parts of South and Central America. ResumenPresentamos un estudio filogenomico del genero Brosimum y sus aliados, Trymatococcus y Helianthostylis, y que incluye practicamente todas las especies descritas. Su distribucion va desde Mexico y las Antillas Mayores hasta el Amazonas y comprende especies como el ramon (B. alicastrum), un cultivo infrautilizado, y otras especies empleadas como madera o en medicina. La secuenciacion masiva dirigida de 333 marcadores nucleares de copia unica permitio la reconstruccion de una filogenia bien resuelta, en la que se demuestra que Trymatococcus y Helianthostylis estan anidados en Brosimum. Presentamos, por lo tanto, una clasificacion revisada a nivel de especies, teniendo en cuenta los resultados moleculares y las caracteristicas morfologicas, y donde Trymatococcus y Helianthostylis pasan a ser subgeneros de Brosimum. Estos subgeneros monofileticos pueden ser identificados por caracteres de las estipulas y de los pistilodios.

plant biology↗

bioRxiv2019

The soursop genome and comparative genomics of basalangiosperms provide new insights on evolutionaryincongruence

Deep relationships and the sequence of divergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used. Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver further conflicting signals. To disentangle key angiosperm relationships, we report a high-quality draft genome for the soursop (Annona muricata, Annonaceae). We reconstructed phylogenomic trees and show that the soursop represents a genomic mosaic supporting different histories, with scaffolds almost exclusively supporting single topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previous whole genome-based studies remained inconclusive. This result is clear and consistent with recent studies using plastomes. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history.

evolutionary biology↗

bioRxiv2019

Long-distance dispersal shaped the diversity of tribe Dorstenieae (Moraceae)

AimThe Neotropics have the highest terrestrial biodiversity on earth. Investigating the relationships between the floras of the Neotropics and other tropical areas is critical to understanding the origin and evolution of this mega-diverse region. Tribe Dorstenieae (Moraceae) has a pantropical distribution and almost equal number of species on both sides of the Atlantic. In this study, we investigate the relationship between the African and Neotropical floras using Dorstenieae (15 genera, 156 species, Moraceae) as a model clade. Locationthe Neotropics and Africa. MethodsWe used a targeted enrichment strategy with herbarium samples and a nuclear bait set to assemble a data set of 102 genes sampled from 83 (53%) species and fifteen genera (100%) of Dorstenieae, and five outgroup species. Phylogenetic relationships were reconstructed with maximum likelihood and coalescent approaches. This phylogeny was dated with a Bayesian relaxed clock model and four fossil calibrations. The biogeographic history of the group was then reconstructed with several dispersal-extinction-cladogenesis models (incl. DEC and DEC+J). ResultsThe crown-group ages of Dorstenieae and Dorstenia were estimated in the Cretaceous (65.8-79.8 Ma) and the Paleocene (50.8-67.3 Ma), respectively. Tribe Dorstenieae as a whole appears to have originated in the joint area of continental Africa, Madagascar and Asia-Oceania area. The Neotropical species of Dorstenia diversified in the Eocene (29.8-44.7 Ma) and formed a clade nested within the African lineages in the genus. Brosimum s.l., with a crown-group age at the period of the Oligocene and Miocene (14.9-31.1 Ma), represents another Neotropical clade in Dorstenieae. Main conclusionsTribe Dorstenieae originated in the joint area of continental Africa, Madagascar and Asia-Oceania area in the Cretaceous and then dispersed into Neotropics twice. Neotropical diversification after long-distance dispersal across the Atlantic is the most plausible explanation for the extant distribution pattern of Dorstenieae.

evolutionary biology↗

bioRxiv2018

Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 109 genera and ca. 2450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364 653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked eaually well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

evolutionary biology↗