10.5061/DRYAD.P928V
Chan, Kin Onn
University of Kansas
Alexander, Alana M.
University of Kansas
Grismer, Jesse L.
University of California Los Angeles
Su, Yong-Chao
Kaohsiung Medical University
Quah, Evan S.H.
University of Kansas
Brown, Rafe M.
University of Kansas
Quah, Evan S. H.
Universiti Sains Malaysia
Grismer, L. Lee
La Sierra University
Data from: Species delimitation with gene flow: a methodological
comparison and population genomics approach to elucidate cryptic species
boundaries in Malaysian Torrent Frogs
Dryad
dataset
2017
Amolops
2017-08-09T19:46:01Z
2017-08-09T19:46:01Z
en
https://doi.org/10.1111/mec.14296
151838136 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Accurately delimiting species boundaries is a non-trivial undertaking that
can have significant effects on downstream inferences. We compared the
efficacy of commonly-used species delimitation methods (SDMs) and a
population genomics approach based on genome-wide single nucleotide
polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent
Frog Complex currently recognized as a single species (Amolops
larutensis). First, we used morphological, mitochondrial DNA and
genome-wide SNPs to identify putative species boundaries by implementing
non-coalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then
tested the validity of putative boundaries by estimating spatiotemporal
gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic
isolation among putative species. Our results show that the A. larutensis
complex runs the gamut of the speciation continuum from highly divergent,
genetically isolated lineages (mean Fst = 0.9) to differentiating
populations involving recent gene flow (mean Fst = 0.05; Nm > 5).
As expected, SDMs were effective at delimiting divergent lineages in the
absence of gene flow but overestimated species in the presence of marked
population structure and gene flow. However, using a population genomics
approach and the concept of species as separately evolving metapopulation
lineages as the only necessary property of a species, we were able to
objectively elucidate cryptic species boundaries in the presence of past
and present gene flow. This study does not discount the utility of SDMs
but highlights the danger of violating model assumptions and the
importance of carefully considering methods that appropriately fit the
diversification history of a particular system.
md5mc48p10STRUCTURE file for sNMF analysis and GENODIVE. Filtered using
min. depth = 5; missing data = 50%md5mc48p.10.strmd5mc68p.10STRUCTURE file
for sNMF analysis and GENODIVE. Filtered using min. depth = 5; missing
data = 30%md10mc48p.10STRUCTURE file for sNMF analysis and GENODIVE.
Filtered using min. depth = 10; missing data = 50%md10mc68p.10STRUCTURE
file for sNMF analysis and GENODIVE. Filtered using min. depth = 10;
missing data = 30%16S.ND1.concatenated.nexconcatenated mitochondrial
sequence matrix for MrBayes.Concatenated.mrbayes2.nexsNMF analysisExample
R script for the sNMF analysisLEA.Rmd5mc48_final_noinvariantSNP input file
for maximum likelihood phylogenetic analysis after filtering for invariant
and non-binary sitesmd5mc48p.10Input file for ABBA-BABA analysis. Min
depth = 5; missing data = 50%snapp.7spInput file for SNAPP
Malaysia