Data from: 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
from Caeiro-Dias et al. (2023) in the panel optimization. After four
rounds of panel optimization, we retained 284 loci. The optimized panel
was used to genotype 118 samples from eight temporal collections (a subset
of the nextRAD_complete) for validation of the 283 loci in the GT-seq
panel; other 20 samples of known sex were used for sex assignment accuracy
using the sex-marker genotyped with the GT-seq panel. The nextRAD_complete
is provided as a VCF (single SNPs) and GENEPOP file (microhaplotypes). The
GT-seq_283 is provided as a GENEPOP file (microhaplotypes).