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Comparative assessment of range-wide patterns of genetic diversity and structure with SNPs and microsatellites: a case study with Iberian amphibians
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  • Miguel Camacho-Sanchez,
  • Guillermo Velo-Antón,
  • Jeffrey Hanson,
  • Ana Verissimo,
  • Inigo Martinez-Solano,
  • Adam Marques,
  • Craig Moritz,
  • Silvia Carvalho
Miguel Camacho-Sanchez
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Guillermo Velo-Antón
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Jeffrey Hanson
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Ana Verissimo
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Inigo Martinez-Solano
Museo Nacional de Ciencias Naturales
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Adam Marques
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Craig Moritz
Australian National University
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Silvia Carvalho
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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.

Peer review status:ACCEPTED

21 Jul 2020Submitted to Ecology and Evolution
22 Jul 2020Assigned to Editor
22 Jul 2020Submission Checks Completed
22 Jul 2020Review(s) Completed, Editorial Evaluation Pending
22 Jul 2020Editorial Decision: Accept