Canis STR-Seq: A Universal Approach for Non-Invasive Genetic Monitoring of Wolves and Coyotes

Area of Science:

• Population genetics
• Genomics
• Conservation biology

Background:

• Traditional population genetic studies rely on short tandem repeat (STR) markers, also known as microsatellites.
• Capillary electrophoresis for STR analysis presents scoring challenges and limits inter-laboratory data comparison.

Purpose of the Study:

• To develop a cost-effective, universal genotype-by-sequencing (GBS) assay for Canis species.
• To improve the accuracy of allele calls, homoplasy detection, and genotyping from low-template DNA.
• To enhance population assignment and admixture estimates in complex Canis populations.

Main Methods:

• Development of a universal microsatellite GBS assay for Canis species.
• Comparison of allele data based on size alone versus sequence mutations.
• Application of Bayesian cluster analysis for population assignment tests.

Main Results:

• The GBS assay provides unambiguous allele calls and flags homoplasy.
• Including sequence mutations increased the number of observed alleles by 32% (Na_mut = 334) compared to size alone (Na_len = 253).
• Population assignment values were higher for 64 of 84 samples when sequence mutations were considered.

Conclusions:

• The new GBS assay offers an improved method for microsatellite genotyping in Canis species.
• It enhances the accuracy of genetic monitoring, aiding conservation efforts for wolf populations.
• The proposed framework supports a universal STR dataset for improved population structure analysis in Canis.