10.5061/DRYAD.HM23P
Wang, Le
National University of Singapore
Wan, Zi YI
National University of Singapore
Lim, Huan Sein
Temasek Life Sciences Laboratory
Yue, Gen Hua
Nanyang Technological University
National University of Singapore
Data from: Genetic variability, local selection and demographic history:
genomic evidence of evolving towards allopatric speciation in Asian
seabass
Dryad
dataset
2016
Lates calcarifer
Holocene
2016-06-01T14:52:55Z
2016-06-01T14:52:55Z
en
https://doi.org/10.1111/mec.13714
30084114 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Genomewide analysis of genetic divergence is critically important in
understanding the genetic processes of allopatric speciation. We sequenced
RAD tags of 131 Asian seabass individuals of six populations from
South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we
examined the genetic diversity and patterns of population differentiation
across all the populations. We found significant evidence of genetic
heterogeneity between South-East Asian and Australian/Papua New Guinean
populations. The Australian/Papua New Guinean populations showed a rather
lower level of genetic diversity. FST and principal components analysis
revealed striking divergence between South-East Asian and Australian/Papua
New Guinean populations. Interestingly, no evidence of contemporary gene
flow was observed. The demographic history was further tested based on the
folded joint site frequency spectrum. The scenario of ancient migration
with historical population size changes was suggested to be the best fit
model to explain the genetic divergence of Asian seabass between
South-East Asia and Australia/Papua New Guinea. This scenario also
revealed that Australian/Papua New Guinean populations were founded by
ancestors from South-East Asia during mid-Pleistocene and were completely
isolated from the ancestral population after the last glacial retreat. We
also detected footprints of local selection, which might be related to
differential ecological adaptation. The ancient gene flow was examined and
deemed likely insufficient to counteract the genetic differentiation
caused by genetic drift. The observed genomic pattern of divergence
conflicted with the ‘genomic islands’ scenario. Altogether, Asian seabass
have likely been evolving towards allopatric speciation since the split
from the ancestral population during mid-Pleistocene.
SNP genotypes of Asian seabassThe genotype dataset contains 32433
ddRAD-based SNP loci for 131 individuals across 6 wild populations of
Asian seabass.All_genotypes.txt
Southeast Asia
Australia