10.5061/DRYAD.23HS1
Papadopoulou, Anna
University of Michigan-Ann Arbor
Knowles, L. Lacey
University of Michigan-Ann Arbor
Data from: Genomic tests of the species-pump hypothesis: recent island
connectivity cycles drive population divergence but not speciation in
Caribbean crickets across the Virgin Islands
Dryad
dataset
2015
Amphiacusta sanctaecrucis
Holocene
2015-04-20T15:43:13Z
2015-04-20T15:43:13Z
en
https://doi.org/10.1111/evo.12667
21370013 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Harnessing the power of genomic scans, we test the debated ‘species pump’
hypothesis that implicates repeated cycles of island connectivity and
isolation as drivers of divergence. This question has gone understudied
given the limited resolution of past molecular markers for studying such
dynamic phenomena. With an average of 32000 SNPs from the genome of 136
individuals from ten populations of a Caribbean flightless ground cricket
species (Amphiacusta sanctaecrucis) and a complementary set of statistical
approaches, we infer a stepping-stone colonization model and high levels
of genetic differentiation across the Virgin Islands, which have been
periodically inter-connected until 8 ka. Estimates of divergence times
from models based on the site frequency spectrum coincide with a period of
repeated connection and fragmentation of the islands at 75–130 ka. These
results are consistent with a role of island connectivity cycles in
promoting genomic divergence and indicate that the genetic distinctiveness
of island populations has persisted despite subsequent and extended
interisland connections identified from bathymetric data. We discuss these
findings in the broader context of Caribbean biogeography, and more
specifically why high levels of genomic divergence across the Virgin
Islands associated with repeated connectivity cycles do not actually
translate into species diversification.
Amphiacusta_5558SNPs_StructureFile.txtA structure format file containing
5,558 single bi-allelic SNPs that were used for assessing population
structure and genetic differentiation (for STRUCTURE, PCA and procrustes
analyses, IBD and estimation of genetic diversity
statistics).Amphiacusta10pops5558SNPsStructure.txtAmphiacusta_82443SNPs_ForQuartets.txtA phylip file containing 82,443 single bi-allelic SNPs that were used for the quartet analysis (in SVDquartets).Amphiacusta82443SNPsForQuartets.txtsampleDownMSFS.pyPython script that downsamples the population sizes and calculates the joint folded Site Frequency Spectrum (for the minor allele frequency) of two populations based on a vcf file. Includes an example vcf input file and population map.sampleDownMSFSWithExampleInputFiles.zipInputFilesForFastsimcoal.zipA set of folders containing the input files for analyses with fastsimcoal2, including the calculated joint Site Frequency Spectrum for each of the focal population pairs. Folder and file names follow the population codes used consistently throughout the manuscript.
Virgin Islands