ORCID Profile
0000-0001-8441-5075
Current Organisation
CNRS
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Publisher: Wiley
Date: 03-02-2021
Abstract: We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and ergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N , m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a ergence continuum composed by 28 pairs of Mytilus mussel populations/species.
Publisher: Wiley
Date: 09-10-2019
DOI: 10.1111/NPH.16180
Publisher: Wiley
Date: 04-2019
DOI: 10.1111/MEC.15048
Publisher: Cold Spring Harbor Laboratory
Date: 27-12-2017
DOI: 10.1101/239244
Abstract: Reticulated evolution -i.e. secondary introgression / admixture between sister taxa-is increasingly recognized as playing a key role in structuring infra-specific genetic variation and revealing cryptic genetic connectivity patterns. When admixture zones coincide with ecological transitions, the connectivity patterns often follow environmental variations better than distance and introgression clines may easily be confounded with local adaptation signatures. The Kerguelen mussels is an ideal system to investigate the potential role of admixture in enhancing micro-geographic structure, as they inhabit a small isolated island in the Southern Ocean characterized by a highly heterogeneous environment. Furthermore, genomic reticulation between Northern species ( M. edulis, M. galloprovincialis and M. trossulus ) and Southern species ( M. platensis : South America and the Kerguelen Islands and M. planulatus : Australasia) has been suspected. Here, we extended a previous analysis by using targeted-sequencing data (51,878 SNPs) across the three Northern species and the Kerguelen population. Spatial structure in the Kerguelen was then analyzed with a panel of 33 SNPs, including SNPs that were more differentiated than the genomic average between Northern species (i.e., ancestry-informative SNPs). We first showed that the Kerguelen lineage splitted very shortly after M. edulis and M. galloprovincialis initiated speciation, and it subsequently experienced admixture with the three Northern taxa. We then demonstrated that the Kerguelen mussels were significantly differentiated over small spatial distance, and that this local genetic structure was associated with environmental variations and mostly revealed by ancestry-informative markers. Simulations of admixture in the island highlight that genetic-environment associations can be better explained by introgression clines between heterogeneously differentiated genomes than by adaptation.
Location: France
No related grants have been discovered for Christelle Fraïsse.