Comparative assessment of range-wide patterns of genetic diversity and
structure with SNPs and microsatellites: a case study with Iberian
amphibians
Abstract
Reduced representation genome sequencing has popularized the application
of single nucleotide polymorphisms (SNPs) to address evolutionary and
conservation questions in non-model organisms. Patterns of genetic
structure and diversity based on SNPs often diverge from those obtained
with microsatellites to different degrees, but few studies have
explicitly compared their performance under similar sampling regimes in
a shared analytical framework. We compared range-wide patterns of
genetic structure and diversity in two amphibians endemic to the Iberian
Peninsula: Hyla molleri and Pelobates cultripes, based on
microsatellite (18 and 14 loci) and SNP (15,412 and 33,140 loci)
datasets of comparable sample size and spatial extent. Model-based
clustering analyses with STRUCTURE revealed minor differences in genetic
structure between marker types, but inconsistent values of the optimal
number of populations (K) inferred. SNPs yielded more repeatable and
less admixed ancestries with increasing K compared to microsatellites.
Genetic diversity was weakly correlated between marker types, with SNPs
providing a better representation of southern refugia and of gradients
of genetic diversity congruent with the demographic history of both
species. Our results suggest that the larger number of loci in a SNP
dataset can provide more reliable inferences of patterns of genetic
structure and diversity than a typical microsatellite dataset, at least
at the spatial and temporal scales investigated.