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Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programs: lessons from a 20-year time series of paired data.


Osborne, Megan; Caeiro Dias, Guilherme; Turner, Thomas (2022), Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programs: lessons from a 20-year time series of paired data., Dryad, Dataset,


Many long-term genetic monitoring programs began before next-generation sequencing became widely available. Older programs can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programs should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population, and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild, and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.


Microsatellite data from nine loci previously genotyped in samples spanning the period 1999 – 2010 (Osborne et al. 2012) were used in this study for comparative analysis. In addition, we genotyped these microsatellites from 1,570 individuals collected in 2012, 2015, 2017, and 2018 from the Rio Grande as described previously. 

Raw DNA sequences obtained from nextRAD sequencing from 379 individuals were received from SNPSaurus and demultiplexed by sequencing lane and unique DNA barcode combinations that identified individuals. Raw reads were trimmed and aligned to a female Rio Grande silvery minnow reference genome. Resulting nextRAD loci were used to call variants that were subsequently filtered to obtain a biallelic SNP dataset. Variable positions in each locus were haplotyped using the dDocent pipeline (Willis et al. 2017). Loci deviating from Hardy-Weinberg equilibrium (HWE) and those in linkage disequilibrium (LD) were removed. A detailed description of each step to obtain the final dataset is presented in Table S2 of the manuscript, including the software, references, filters applied, and options used at each step. 

Usage Notes

Samples are listed by individual and collection year and collection river reach (AN-Angostura, IS- Isleta, SA- San Acacia). Missing values are coded as "0".


U.S. Bureau of Reclamation, Award: R18AP00130