Transitioning from microsatellites to SNP‐based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years

Abstract

Genetic monitoring quantifies trajectories of individual-and population-level metrics that include heterozygosity, gene diversity and genetic effective population size (N e ) over contemporary time series (Schwartz et al., 2007). Tracking these metrics facilitates adaptive and evolutionary-cognizant management. For the past three decades, microsatellites were the workhorse for genetic monitoring programmes (e.g., Beatty et al., 2014;Dowling et al., 2014;Koelewijn et al., 2010). Long-term monitoring programmes are now transitioning to next-generation high-throughput genomic approaches based on single-nucleotide polymorphisms (SNPs) and microhaplotypes (i.e., multiple SNPs haplotyped at the same locus); raising questions about continuity and consistency across the time series as well as

Ex situ conservation of two rare oak species using microsatellite and SNP markers

“…Generally, results support the conclusion that larger numbers of SNP loci provide greater power to resolve finer-scale spatial resolution in the genetic differences between individuals (Putman & Carbone, 2014;Thrasher et al, 2018;Osborne et al, 2022). This is particularly noticeable in STRUCTURE analysis of garden and wild Q. acerifolia individuals, where 10 garden samples are erroneously clustered using microsatellites.…”

“…Genetic marker comparisons have largely demonstrated that broad measures of population differentiation generally correspond between microsatellites and SNPs, but the increased resolution of SNPs often allows for a more nuanced interpretation of population demography (Osborne et al., 2022; Putman & Carbone, 2014; Thrasher et al., 2018). The large number of SNP loci generated by RADseq approaches also allow for detection of subtle genetic distinctions even when only a few individuals are sampled (Jeffries et al., 2016).…”

Genetic erosion in an endangered desert fish during a megadrought despite long‐term supportive breeding

“…A subtle, but progressive, shift in allele frequencies was also detected by DAPC in the period following the demographic bottleneck, particularly after 2016. This shift is corroborated by genome-wide single nucleotide polymorphism (SNP) data (Osborne et al, 2022). The recent reduction in allelic diversity highlights the need for adaptive management that capitalizes on years with favorable environmental conditions and high wild abundance (Table 3).…”

“…We used NeEstimator (Do et al., 2014) to estimate linkage disequilibrium effective population size (LD N e ) with the single sample method (Hill, 1981) as described in Osborne et al. (2022). This method assumes a closed population.…”

“…Temporal genetic structure was evaluated with discriminant analysis of principal components (DAPC), which summarizes genotypes in principal components (PCs) used to construct linear functions maximizing among-group variation while minimizing within-group variation, in the R package adegenet v.1.3-1 (Jombart & Ahmed, 2011) as described in Osborne et al (2022). We calculated pairwise F ST among consecutive temporal samples and the stocks used to augment the population each year with the R package diveRsity 1.9 (Keenan et al 2013, Keenan 2017.…”