Comparative Analysis of Microsatellite and SNP Markers for Genetic Management of Red Deer

SIMPLE SUMMARY: Population genetic structure and individual multilocus heterozygosity are vital for wildlife management. Traditionally, microsatellite markers have been used to estimate population genetic parameters, but single-nucleotide polymorphisms (SNPs) have gained popularity due to their greater measurement precision. This study compared genetic estimates at the population and individual levels using microsatellite and SNP markers in red deer (Cervus elaphus). The findings revealed correlations between parameters estimated with both markers that were associated with the level of genetic diversity and genetic differentiation. However, microsatellites showed lower accuracy in representing the distribution of genetic diversity among individuals. ABSTRACT: The analysis of population genetic structure and individual multilocus heterozygosity are crucial for wildlife management and conservation. Microsatellite markers have traditionally been used to assess these genetic parameters. However, single-nucleotide polymorphisms (SNPs) are becoming increasingly popular. Our goal here was to determine to what extent SNPs can provide better insights than microsatellites into the overall genetic status and population genetic processes in the species. To this end, we genotyped 210 red deer (Cervus elaphus) in the Spanish wild population with both 11 microsatellites and 31,712 SNPs. We compared parameters related to population genetic structure and individual multilocus heterozygosity obtained with both types of markers. Our results showed correlations between parameters measured using both microsatellites and SNPs, particularly those related to the level of genetic diversity and genetic differentiation. However, we found notably lower precision of microsatellites in measuring the distribution of genetic diversity among individuals. We conclude that microsatellites can be used to monitor the overall genetic status and detect broad patterns in red deer populations. Nevertheless, the greater precision of SNPs in inferring genetic structure and multilocus heterozygosity leads us to encourage scientists and wildlife managers to prioritize their use whenever possible.