Comparative assessment of range-wide patterns of genetic diversity and structure with SNPs and microsatellites: A case study with Iberian amphibians.

Adam Marques,Ana Veríssimo,Jeffrey O. Hanson,Guillermo Velo‐Antón,Craig Moritz,Íñigo Martínez‐Solano,Miguel Camacho‐Sanchez,Sílvia B. Carvalho

doi:10.1002/ece3.6670

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.

Highlights

Nuclear microsatellites became popular during the 1990s as a powerful tool to assess patterns of genetic variation in populations (Allendorf, 2017; Ellegren, 2004)
Our comparative assessment revealed that a typical microsatellite dataset (18 loci in H. molleri and 14 in P. cultripes) can yield similar rangewide patterns of genetic structure than those inferred with a few thousand single nucleotide polymorphisms (SNPs) (15,412 and 33,140, respectively)
We found overall concordance between markers in recovering the same major genetic clusters in STRUCTURE analyses (Figure 1), the model-free clustering approach based on NJ yielded poorly supported clustering for microsatellites compared with SNPs (File S1)

Summary

| INTRODUCTION

Nuclear microsatellites became popular during the 1990s as a powerful tool to assess patterns of genetic variation in populations (Allendorf, 2017; Ellegren, 2004) While they are still widely used, the development of Genotyping-by-Sequencing techniques, like RADseq (Baird et al, 2008; Miller, Dunham, Amores, Cresko, & Johnson, 2007) and similar techniques of genome complexity reduction (e.g., ddRAD and bestRAD), coupled with the decreasing costs of massive parallel sequencing, have extended the reach of massive single nucleotide polymorphism (SNP) genotyping to the study of nonmodel organisms (Allendorf, 2017; Andrews, Good, Miller, Luikart, & Hohenlohe, 2016; Baird et al, 2008; Davey et al, 2011; Peterson, Weber, Kay, Fisher, & Hoekstra, 2012; Putman & Carbone, 2014).

| MATERIALS AND METHODS

Findings

| DISCUSSION