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 nonmodel 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.

Keywords: DArTseq; Hyla molleri; Iberian Peninsula; Pelobatescultripes; microsatellites; population genetics.

Figure 1

Genetic structure in Hyla molleri (left) and Pelobates cultripes (right) based on STRUCTURE analyses of the SNP and microsatellite datasets. Pies represent averaged proportion of inferred ancestries of the major mode in CLUMPAK, from K = 2 to K = 8. Shaded areas represent the species distributions. To facilitate visual comparison of spatial patterns of genetic structure between markers, Q‐matrices from both markers for any given K and species were aligned using CLUMPP before plotting

Figure 2

Comparison of STRUCTURE results in the SNP and microsatellite datasets for H. molleri (a) and P. cultripes (b). The horizontal axis shows Pairwise Symmetric Similarity Coefficients between Q‐matrices from STRUCTURE runs across K values (vertical axis) using averaged ancestries per locality in H. molleri and individual ancestries in P. cultripes. Comparisons involving the same marker type (microsatellite‐microsatellite: blue triangles, and SNP‐SNP: green circles) show higher similarity than those involving different marker types (red squares)

Figure 3

Genetic diversity measured as multilocus heterozygosity (sMLH) for H. molleri (a: SNPs, b: microsatellies) and P. cultripes (c: SNPs, d: microsatellites)