10.5061/DRYAD.5P5C0
Rougemont, Quentin
French National Institute for Agricultural Research
Gagnaire, Pierre-Alexandre
INRA; UMR 985 Ecologie et Santé des Ecosystèmes; 35042 Rennes France
Perrier, Charles
INRA; UMR 985 Ecologie et Santé des Ecosystèmes; 35042 Rennes France
Genthon, Clémence
French National Institute for Agricultural Research
Besnard, Anne-Laure
French National Institute for Agricultural Research
Launey, Sophie
French National Institute for Agricultural Research
Evanno, Guillaume
French National Institute for Agricultural Research
Data from: Inferring the demographic history underlying parallel genomic
divergence among pairs of parasitic and nonparasitic lamprey ecotypes
Dryad
dataset
2016
Genetic parallelism
Lampetra planeri
ecotypic divergence
Lampetra fluviatilis
Allele surfing
heterogeneous differentiation
2016-04-21T19:21:52Z
2016-04-21T19:21:52Z
en
https://doi.org/10.1111/mec.13664
20902136 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Understanding the evolutionary mechanisms generating parallel genomic
divergence patterns among replicate ecotype pairs remains an important
challenge in speciation research. We investigated the genomic divergence
between the anadromous parasitic river lamprey (Lampetra fluviatilis) and
the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in
nine population pairs displaying variable levels of geographic
connectivity. We genotyped 338 individuals with RAD sequencing and
inferred the demographic divergence history of each population pair using
a diffusion approximation method. Divergence patterns in geographically
connected population pairs were better explained by introgression after
secondary contact, whereas disconnected population pairs have retained a
signal of ancient migration. In all ecotype pairs, models accounting for
differential introgression among loci outperformed homogeneous migration
models. Generating neutral predictions from the inferred divergence
scenarios to detect highly differentiated markers identified greater
proportions of outliers in disconnected population pairs than in connected
pairs. However, increased similarity in the most divergent genomic regions
was found among connected ecotype pairs, indicating that gene flow was
instrumental in generating parallelism at the molecular level. These
results suggest that heterogeneous genomic differentiation and parallelism
among replicate ecotype pairs have partly emerged through restricted
introgression in genomic islands.
DatasetRougemontRAD.tarContains the main file from Rougemont et al. study
. 9 pairwise vcf used to compute diversity analysis, Fst, perform genome
scan, etc..1 main genepop file containing data from the 9 populations
pairs (8962 SNPs) 1 files containing the 40 more relevant SNPs used for
hybrid identification Folded and Unfolded JSFS for diffusion
approximation. Note: information on dadi are available at:
https://github.com/QuentinRougemont/DemographicInferenceDatasetRougemontRAD2016.tar.gz