Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus)

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

The management and conservation of large mammals, such as black bears (Ursus americanus), have long been informed by genetic estimates population size individual dispersal. Amplicon sequencing methods, also known 'genotyping-in-thousands-by sequencing' (GT-seq), now enable the efficient cost-effective genotyping hundreds loci individuals in same run. Here, we develop a GT-seq panel for identification kinship inference Alaska bears. Using genomic data from restriction site-associated DNA hunter-harvested Southcentral (n = 85), identified 170 microhaplotype single nucleotide polymorphism (SNP) that were highly heterozygous local populations. To sexing individuals, included previously published sex-linked locus panel. We empirically validated using samples collected at different spatial scales. These tissues 82) obtained within small geographic area Anchorage, Alaska, which likely to be relatives well geographically widespread locations throughout Alaska. Empirical validation indicated high success genotype reproducibility across replicate subsamples. Computer simulations demonstrated had ample statistical power distinguishing distinct first-order (parent-offspring full-sibling pairs) unrelated individuals. As final proof concept, was used identify close kin sampled urban wild habitats anticipate will useful resource monitoring bear

Language: Английский

Development of a Noninvasive Genotyping‐In‐Thousands (GTseq) Panel for Long‐Term Conservation of Western Great Lakes Gray Wolves (Canis lupus)

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT The application of noninvasive genetic methods toward the field conservation has increased our understanding many wildlife populations that are difficult to sample, allowing for better management. In molecular ecology, use sampling became widely feasible with advent microsatellites, a highly polymorphic, short‐length marker could be genotyped from low‐quality DNA sources. Despite decades use, microsatellite panels continue suffer high genotyping error rates, allelic dropout, and limited reproducibility across laboratories. To address these issues, single nucleotide polymorphisms (SNPs) offer advantages such as lower avoidance dropout due consistent allele length, automated calling through bioinformatic pipelines, reducing human subjectivity error. Given SNPs provide relative microsatellites marker, SNP specifically, method genotyping‐in‐thousands by sequencing (GTseq) gained popularity. Here, we developed GTseq panel western Great Lakes canids comprised 196 loci, capable species identification, accurately inferring sex (97.2%), identifying unique individuals (probability identity = 6.71e −41 ), assigning relationships (false positive rate 9.34e −14 genotypes low (0.39%). an attempt improve success samples, found while increasing number PCR cycles yielded higher percentage it also on‐target reads in negative controls. We suggest approaching this manipulation caution emphasize importance including reporting Further, quantitative was powerful estimate host‐specific concentrations, enabling conservative sample selection library preparation respect affordability.

Language: Английский

Evaluating genotyping‐in‐thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non‐invasive and archival samples

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(2)

Published: Feb. 1, 2024

Abstract Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Multiplexed targeted amplicon sequencing techniques, such as genotyping‐in‐thousands by (GT‐seq), cost‐effective approaches collecting genetic data from low‐quality quantity DNA samples, making them potentially useful long‐term using non‐invasive archival samples. Here, we developed a GT‐seq panel potential tool the American pika ( Ochotona princeps ) evaluated its performance when applied to traditional, non‐invasive, respectively. Specifically, optimized (307 single nucleotide polymorphisms (SNPs)) that included neutral, sex‐associated, putatively adaptive SNPs contemporary tissue samples n = 77) Northern Rocky Mountains lineage of pikas. The demonstrated high genotyping success (94.7%), low error (0.001%), excellent identifying individuals, sex, relatedness, structure. We subsequently 17) fecal pellet 129) collected within Canadian evaluate effectiveness. Although efficacy with (90.5% success, 0.0% error), this was not case (79.7% 28.4% error) likely due exceptionally quality/quantity recovered implemented. Overall, our study reinforced an effective providing future opportunities temporal applications historical specimens. Our results further highlight need additional optimization sample collection techniques prior broader‐scale implementation

Language: Английский