Data from: Canis STR-seq: A universal approach for non-invasive genetic monitoring of wolves and coyotes

Population genetic studies have traditionally relied on data from short
tandem repeat (STR) markers, known as microsatellites, to produce
individual genotypes used in population genetics research. However, size
fragment analysis from traditional capillary electrophoresis presents
scoring challenges and limits data comparisons among labs. Here, we
present a new cost-effective, universal microsatellite
genotype-by-sequencing assay for Canis species that allows for unambiguous
allele calls, flags homoplasy for more accurate assignment tests and
estimates of diversity, and improves genotyping output from low-template
DNA. We note size homoplasy in 18 of 26 loci, with the number of alleles
being 32% higher in the dataset that included sequence mutations
(Namut=334) compared to the dataset based on size alone (Nalen=253).
Bayesian cluster analysis was similar for both datasets, although 63 of 83
samples had higher assignment values to their primary cluster when
mutations were considered. We document and code a list of sequence
mutations associated with each locus and propose a framework for building
an accessible, universal STR dataset for wolves, coyotes, and dogs that
improves cluster assignments and admixture estimates in a system with
complex demography and hybridization patterns. Overall, the assay provides
an improved method of genetic monitoring for improved conservation of wolf
populations.