Contexte scientifique – The outstanding biodiversity of Amazonia is progressively unveiled by the accumulation of studies delimiting species and unraveling the tempo of their diversification, notably in frogs. Nevertheless, vast knowledge gaps remain such as for the Rhinella margaritifera species group, a prominent component of anuran communities of the region (abundant and large sized) in which species boundaries and taxonomy are notoriously complex. A preliminary using an unprecedentedly large sampling (>800 individuals) throughout the distribution of the clade and comprising all but one described species, delimited 54 species-level mtDNA lineages among which 27 are confirmed by acoustic and/or morphological data. A time-calibrated phylogenetic tree from a mitogenomic matrix suggests a relatively recent (10 Ma) western Amazonian origin of the group and subsequent and later dispersals throughout Amazonia after the demise of the Acre system, thus throughout the modern amazonian hydrographic system, i.e., during the last 6 Ma. However, some incongruences among mtDNA, nuDNA, acoustic and morphological data suggest several introgression events which blur parts of the mtDNA-based species boundaries and question the reliability of the diversification scenario based on mitogenomic data.
Thanks to (1) rapid advance in the production of massive amount of genomic data, (2) the design of new genomic tools especially designed for anurans (> 8k genomic markers FrogCap – MyBaits) and (3) preliminary results (mtDNA) allowing a complete and optimized sampling within Rhinella gr. margaritifera throughout its distribution, we have an opportunity to accurately delimit species and investigate the historical biogeography of this important group of neotropical toads.
Objectifs du stage – This project thus aims at investigating the process of diversification within Amazonia using phylogenomics focusing on a prominent component of anuran communities of the region. The project will be articulated over three main objectives (1) accurately delimit species; (2) investigate the timing of diversification and the directionality of dispersals and (3) the existence of historical introgressions. More specifically, we will test the expectations based on previous mtDNA based investigation that these toads (a) represent a highly diversified clade of more than 30 species, that (b) emerged from Andean ancestors, (c) started to diversify some 9 Ma in Western Amazonia, (d) dispersed eastward some 6 Ma after the demise of the Acre system, (e) entered in secondary contact along the Rio Negro and the Andean foothills during the Pleistocene, (f) forming hybrid zones producing incongruent mtDNA – nuDNA-morphology-bioacoustic patterns.
Compétences recherchées et/ou Environnement & programmes principaux :
Raw data (illumina reads) cleaning, assembling and annotating on the genotoul cluster using an array of bioinformatic tools.
Phylogenomic analyses (IQ-tree, SVD quartets, ..) testing conflicting tree topologies and hybridization (Phyparts, ..)
Modalités des candidatures :
Merci de faire parvenir un CV et une lettre de motivation à Antoine Fouquet
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