Time is of the essence: using archived samples to develop a GT-seq panel to preserve continuity of ongoing genetic monitoring

For the past 25 years, genetic monitoring of Rio Grande silvery minnow (Hybognathus amarus) has been conducted annually. The monitoring program has been carried out using nine microsatellite loci. Recently a temporal genome-wide microhaplotype dataset obtained from nextRAD-seq (a reduced representation sequencing approach) was obtained from archived samples spanning 20 years and allowed to compare results from both datasets (Osborne et al. 2022). To develop a GT-seq panel that was able to track past genomic changes across the time-series, ensuring this way the continuity of the ongoing genetic monitoring, we first identified loci from that nextRAD-seq but using a new conspecific reference genome. The final dataset included 2,983 loci and 379 individuals (nextRAD_complete dataset). From those, we selected a subset of 500 loci with the highest power to track the changes identified with the genome-wide data for GT-seq PCR multiplex optimization. We also included the sex-linked marker HAM06..., Genome-wide SNP identification was performed using Nextera-tagmented reductively-amplified DNA sequencing (nextRAD-seq; Russello et al., 2015) data from 379 individuals reported in Osborne et al. (2023), comprising 12 temporal collections that spanned 20 years. Microhaplotypes were identified using the methods also described in Osborne et al. (2023), but with four modifications. First, NextRAD loci were identified using the draft genome sequenced for this study; no depth of coverage filter was applied to nextRAD loci before variant calling; loci were discarded if mean depth of coverage was lower than 20; and only individuals with less than 25% missing data were retained. Microhaplotypes and individuals retained after all filtering steps are referred to as nextRAD_complete dataset. The nextRAD_complete is provided as a VCF containing single SNPs and as GENEPOP file containing the haplotyped SNPs (microhaplotypes).
The optimized GT-seq panel excluding the sex-linked marker (GT-seq_283) wa..., , # Data from: Time is of the essence: using archived samples to develop a GT-seq panel to preserve continuity of ongoing genetic monitoring

[https://doi.org/10.5061/dryad.4mw6m90mv](https://doi.org/10.5061/dryad.4mw6m90mv)

## Description of the data and file structure

Filtered genotype data obtained from Rio Grande silvery minnow nextRAD-seq time-series and genotypes from an optimized GT-seq panel developed from that nextRAD-seq data. 

### Files and variables

#### File: GT-seq\_283loc\_72ind.gen

**Description:** GENEPOP file containing genotype (microhaplotypes) data from 283 loci for 72 Rio Grande silvery minnow samples from five temporal collections (1999, 2002, 2004, 2017,2018; separated as populations in this order).

#### File: nextRAD\_complete\_2983loc\_373ind.gen

**Description:** GENEPOP file containing genotype (microhaplotypes) data from 2983 loci for 373 Rio Grande silvery minnow samples from 12 temporal collections (1999, 2000, 2002, 2004, 2006, 2008, 2009, 2010, 2012,...,