Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

• Published in: Ecology and evolution Vol. 9; no. 4; pp. 2106 - 2120
• Main Authors: Lemopoulos, Alexandre, Prokkola, Jenni M., Uusi‐Heikkilä, Silva, Vasemägi, Anti, Huusko, Ari, Hyvärinen, Pekka, Koljonen, Marja‐Liisa, Koskiniemi, Jarmo, Vainikka, Anssi
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.02.2019; John Wiley and Sons Inc
• Subjects: Biodiversity; Conservation; Costs; ddRADseq; Deoxyribonucleic acid; Differentiation; DNA; DNA sequencing; Endangered & extinct species; Endangered species; Estimates; Estimation; Evolutionary Biology; Evolutionsbiologi; Fish hatcheries; Fish populations; fisheries; Gene pool; Genetic diversity; Genetic markers; Genetic structure; Genomes; Heterozygosity; Low level; Microsatellites; Mutation; Natural Sciences; Naturvetenskap; Nucleotides; Original Research; Phylogenetics; Population; Population genetics; Population statistics; Population structure; relatedness; Salmo trutta; salmonids; Single-nucleotide polymorphism; Studies; Trout; Wildlife conservation; Finland; population genetics; relatedness; fisheries; salmonids; ddRADseq
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.4905

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction‐site‐associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as FST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half‐ and full‐siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual‐level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual‐level genotype information, such as quantifying relatedness and individual‐level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity. We compared the performance of restriction‐site‐associated DNA sequencing (RADseq) and DNA microsatellite markers for estimating genetic diversity, relatedness, and genetic differentiation in brown trout (Salmo trutta) populations. The results indicate that moderately polymorphic microsatellites and SNPs from RADseq found similar genetic structure of moderately diverged, small populations, but RADseq outperformed microsatellites for quantifying relatedness and individual‐level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.