DOI: 10.5061/dryad.bk3j9kdfj
title: Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programs: lessons from a 20-year time series of paired data.

description: 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.
description: 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. 
description: 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".