Improved estimation of aquaculture associated European introgression in a captive breeding program for endangered Atlantic salmon

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 16, 2025

Abstract The rapid, range-wide decline in Atlantic salmon, Salmo salar , populations is well documented and has led to establishment of captive rearing breeding programs order preserve populations. However, recovery potential may be limited by the inclusion non-local genotypes, which can both difficult detect quantify. In genetically unique Inner Bay Fundy population located Canada, three Live Gene Bank have been established aid this endangered conservation unit. Evidence aquaculture associated (i.e., European) introgression had previously detected using small panels microsatellite markers with power. Here we show how advances sequencing machine learning technologies support a program. We used corresponding panel 301 SNPs estimate individual-level proportions European ancestry. To assess degree each program changes over time, fish were randomly selected across several generations. Estimates validated genotyping subset individuals on 220 K SNP array admixture methods. Of 1741 analyzed, only 48 found ancestry greater than detection threshold. amount was overestimated, that very few wild-collected founder large Moreover, because introduced via from escapees, these values represent minimum

Language: Английский

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Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐PCR SNP Panel for Individual Identification From Faeces

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

ABSTRACT In recent years, numerous single nucleotide polymorphism (SNP) panel methods to genotype non‐invasive faecal samples have been developed. However, none of these existing fit all the criteria necessary make a SNP broadly usable for conservation projects in any country—cost effective, streamlined lab protocol and user‐friendly open‐source bioinformatics protocols design analysis. Here, we present such method display its utility by developing multiplex PCR conducting individual ID snow leopards, Panthera uncia , from samples. The consists 144 SNPs utilises next‐generation sequencing technology. We validate our with paired tissue zoo individuals, showing minimum 96.7% accuracy allele calls per run. then generate data 235 field‐collected across Pakistan show that can reliably identify individuals low‐quality unknown age is robust contamination. also has capability first‐order relatives among sampled provides insights into geographic origin This will empower leopard research community their efforts assess local global population sizes. More broadly, development be used species interest which adequate genomic reference available.

Language: Английский

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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

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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

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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

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From fear to food: predation risk shapes deer behaviour, their resources and forest vegetation

Peer Community Journal, Journal Year: 2025, Volume and Issue: 5

Published: Jan. 6, 2025

The "ecology of fear" posits that predation risk shapes the behaviour large herbivores, their foraging patterns, habitat selection and consequent effect on forest ecology. To test some these predictions we used extensive empirical experimental data vegetation cover composition, deer anti-predator behaviour, collected at study sites with different histories hunting natural in Haida Gwaii archipelago nearby areas coastal British Columbia (Canada). Because also forage intertidal, a hypothetically more exposed to risk, analysed how affected intertidal by measuring proportion marine versus terrestrial stable isotopes bone collagen. In absence had strong negative understory plant composition. populations remarkable tolerance human presence (short flight initiation travel distances when disturbed), willingness consume foreign bait or investigate baited traps, propensity be active daytime. Where faced long-term predators, understories were denser diverse resembled those forests never deer. Severe culling initially without dramatically increased vegetation, although composition from one predators hunting, Deer born after exhibited longer fleeing, reluctance night-time foraging. translocation unwary population island where culls partially restored showed was not significantly modified abundant higher-quality forage. This contrasted wary observed local culls. Finally, hunters and/or less likely this trend might be, extent, resources understory. We interpreted our results as evidence is key shaping, potentially selecting for, lasting behavioural contrasts between populations, intimately connected effects diversity, ecological networks, ecosystem complexity.

Language: Английский

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A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(6)

Published: June 1, 2022

Abstract Studies in ecology, evolution, and conservation often rely on noninvasive samples, making it challenging to generate large amounts of high‐quality genetic data for many elusive at‐risk species. We developed optimized a Genotyping‐in‐Thousands by sequencing (GT‐seq) panel using samples inform the management invasive Sitka black‐tailed deer ( Odocoileus hemionus sitkensis ) Haida Gwaii (Canada). validated our paired tissue fecal hair simultaneously distinguish individuals, identify sex, reconstruct kinship among sampled across archipelago, then provided proof‐of‐concept application field‐collected feces SGang Gwaay, an island high ecological cultural value. Genotyping success 244 loci was (90.3%) comparable that genotyped restriction‐site associated DNA (92.4%), while genotyping discordance between low (0.50%). The will be used future species operations providing individual population information management. More broadly, GT‐seq workflow includes quality control analyses targeted SNP selection modified protocol may wider utility other studies systems where sampling is employed.

Language: Английский

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Development and validation of a GT‐seq panel for genetic monitoring in a threatened species using minimally invasive sampling

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(5)

Published: May 1, 2024

Abstract Minimally invasive samples are often the best option for collecting genetic material from species of conservation concern, but they perform poorly in many genomic sequencing methods due to their tendency yield low DNA quality and quantity. Genotyping‐in‐thousands by (GT‐seq) is a powerful amplicon method that can genotype large numbers variable‐quality at standardized set single nucleotide polymorphism (SNP) loci. Here, we develop, optimize, validate GT‐seq panel federally threatened northern Idaho ground squirrel ( Urocitellus brunneus ) provide approach future monitoring assessment recovery goals using minimally samples. The optimized consists 224 neutral 81 putatively adaptive SNPs. collected buccal swabs 2016 2020 had 73% genotyping success, while hair 2002 2006 little no remaining did not successfully. We evaluated our measuring discordance rates compared RADseq whole‐genome sequencing. other similar population diversity F ST estimates, consistently called more heterozygotes than expected, resulting negative IS values level. Genetic ancestry assignment was consistent when estimated with different Our an effective efficient tool will aid this species, results insights applying sampling techniques rare animals.

Language: Английский

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Generation of genome‐wide SNP markers from minimally invasive sampling in endangered animals and applications in species ecology and conservation

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(7)

Published: July 26, 2024

Abstract High‐density genotyping methods have revolutionized the field of population and conservation genetics in past decade. To exploit technological analytical advances field, access to high‐quality genetic material is a key component. However, such samples endangered rare animals often challenging or even impossible. Here, we used minimally invasive sampling method (MIS) cave salamander Proteus anguinus , olm, generate thousands markers using ddRADseq for genomic analyses. Using tail clips MIS skin swabs taken from same individual, investigated data properties two different types. We found that sufficient DNA can be extracted swab up 200,000 polymorphic SNPs divergent lineages. Swab tissue were highly reproducible exhibiting low SNP error rates. most frequently (~50%) located within genic regions, while rest mapped mostly flanking regions repetitive DNA. The vast majority recovered swabbing was host fraction contained additional ecological information on species, including eDNA surrounding environment bacterial fauna. Most exogenous bacteria (~80%), followed by vertebrates (~20%). Our results demonstrate (i) tens analyses (ii) inform species health status ecology

Language: Английский

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Next-generation snow leopard population assessment tool: multiplex-PCR SNP panel for individual identification from feces

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 24, 2024

Abstract Snow leopards, Panthera uncia , are under threat from numerous pressures and the focus of a great deal conservation efforts. However, their elusive nature makes it difficult to estimate population sizes. Current methods used monitor local sizes include visually identifying individuals camera trap photos genetically fecal samples using microsatellite loci. Here, we present new method for snow leopard multiplex PCR single nucleotide polymorphism (SNP) panel method. The SNP consists 144 SNPs utilizes next-generation sequencing technology, making cheaper easier than current methods. We validate our with paired tissue zoo individuals, showing minimum 96.7% accuracy in allele calls per run. then generate data 235 field-collected across Pakistan show that can reliably identify low-quality unknown age is robust contamination. also has capability first-order relatives provides insights into geographic origin samples. This will empower research community efforts assess global More broadly, developing open source software selection primer design, Illumina streamlined lab bioinformatics protocol which be create similar panels any species interest adequate genomic reference available.

Language: Английский

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