Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

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.