Development of a high-throughput single nucleotide polymorphism panel for genetic stock identification of Striped Bass

Transactions of the American Fisheries Society, Journal Year: 2025, Volume and Issue: unknown

Published: April 29, 2025

ABSTRACT Objective The Striped Bass Morone saxatilis is an anadromous fish that has experienced population declines and recoveries throughout its range from the 1960s to present day. While many United States fisheries have reopened since most recent declines, ongoing monitoring required ensure numbers remain stable in long term. Central this need determine extent which major spawning locations contribute coastal stocks. next-generation genomic sequencing can discriminate among closely related breeding aggregations within native range, cost per sample of methods currently used too high be applied large-scale long-term projects moving forward. Methods We developed, optimized, evaluated a GT-Seq panel—a small panel highly informative single nucleotide polymorphisms—capable assigning large six genetically distinct regions across at much lower than previous methods. Results final 233 loci was able assign 95% reference individuals region origin had <5% error all simulations when estimating mixing proportion any stock. Conclusions This being characterizations along Massachusetts coast eastern Nova Scotia. For researchers tracking migration their provides low-cost method characterizing stocks specific times easily modified or updated as additional, new genetic data become available.

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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Standardization of a High‐Quality Methodological Framework for Long‐Term Genetic Monitoring of the French Wolf Population

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

Published: April 1, 2025

ABSTRACT Since the gray wolf was eradicated from large parts of Europe, this species has been recolonizing much its former distribution, particularly since past 30 years. Wolves benefit European legal protection through Habitats Directive and Bern Convention, reporting on evolution their populations in each country Europe is mandatory. To monitor French over long term, a standardized high‐quality methodological framework developed to analyze data noninvasively collected samples assess population diversity. We delineated step implemented laboratory control procedure 8733 harvested within distribution range between 2006 2022, provided key quality diversity indicators. Of these samples, 82.8% were successfully amplified sequenced for mitochondrial region. Subsequently, genotyped at 22 microsatellite autosomal loci sex locus displayed two independent multiplexes using multitube approach. The average success rate polymerase chain reaction per 64.2% across all replicates. residual genotyping error rates low compared those other studies non‐invasively with mean allelic dropout 5.8% false allele 1.0% locus. dataset identified 1735 individuals total last 15 years, which 99.9% exhibited single Italo–Alpine mitotype. Genetic relatively low, observed heterozygosity 0.482 expected 0.519. This supports natural colonization Alps by few originating remaining Italian populations, started approximately years ago. By generating standards processes, protocol enhances cost‐efficiency ratio monitoring holds high value managers tasked management conservation term.

Language: Английский

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Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field

Journal of Heredity, Journal Year: 2021, Volume and Issue: 112(4), P. 313 - 327

Published: April 14, 2021

Abstract A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production large-scale datasets with additional training often required to handle such datasets. Thus, there an increasing need for geneticists continually learn train stay up-to-date through avenues as symposia, meetings, workshops. The ConGen meeting a near-annual workshop that strives guide participants understanding population genetics principles, study design, data processing, analysis, interpretation, applications real-world issues. Each year gathers diverse set instructors, students, resulting lectures, hands-on sessions, discussions. Here, we summarize key lessons learned from 2019 more recent updates field focus on big genomics. First, highlight classical contemporary issues design are especially relevant working datasets, including intricacies filtering. We next emphasize importance building analytical skills simulating data, how these have within outside careers. also technological advances novel wild populations. Finally, provide recommendations support ongoing efforts by organizers instructors—and beyond—to increase participation underrepresented minorities eco-evolutionary sciences. future success requires both continual handling group people approaches tackle issues, global biodiversity-loss crisis.

Language: Английский

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Evaluating and integrating spatial capture–recapture models with data of variable individual identifiability

Ecological Applications, Journal Year: 2021, Volume and Issue: 31(7)

Published: July 10, 2021

Abstract Spatial capture–recapture (SCR) models have become the preferred tool for estimating densities of carnivores. Within this family are variants requiring identification all individuals in each encounter (SCR), a subset only (generalized spatial mark–resight, gSMR), or no individual (spatial count presence–absence). Although technique has been shown through simulation to yield unbiased results, consistency and relative precision estimates across methods real‐world settings seldom considered. We tested suite ranging from those detections unmarked others that integrate remote camera, physical capture, genetic, global positioning system (GPS) data into hybrid model, estimate population black bears, bobcats, cougars, coyotes. For species, we genotyped fecal DNA collected with detection dogs during 20‐d period. A species was affixed GPS collars bearing unique markings resighted by cameras over 140 d contemporaneous scat collection. Camera‐based gSMR produced density differed <10% genetic SCR coyotes once important sources variation (sex behavioral status) were controlled for. 33% higher than gSMR. The cause discrepancies likely attributable challenges designing study compatible disparate home range sizes difficulty collecting sufficient timeframe which demographic closure could be assumed. Unmarked estimated varied greatly SCR, but became more consistent wherein identifiable. Hybrid containing exhibited most precise species. studies sparse can obtained strictest model assumptions unlikely met, suggest researchers use caution making inference lacking identity. best further recommend at least is marked multiple sets incorporated when possible.

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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The origin, connectivity, and individual specialization of island wolves after deer extirpation

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(4)

Published: April 1, 2024

Wolves are assumed to be ungulate obligates, however, a recently described pack on Pleasant Island, Alaska USA, is persisting sea otters and other marine resources without prey, violating this long-held assumption. We address questions about these wolves regarding their origin fate, degree of isolation, risk inbreeding depression, diet specialization by individual sex. applied DNA metabarcoding genotyping amplicon sequencing using 957 scats collected from 2016 2022, reduced representation tissue samples establish detailed understanding Island wolf ecology compare them with adjacent mainland wolves. Dietary overlap was higher among (Pianka's index mean 0.95 ± 0.03) compared (0.70 0.21). The diets island were dominated otter, ranging 40.6% 63.2% weighted percent occurrence (wPOO) (mean 55.5 8.7). In contrast, primarily fed ungulates (42.2 21.3) or voles during population outbreak (31.2 23.2). traced the pair that colonized around 2013 produced several litters. After breeding killed, female offspring an immigrant male became new breeders in 2019. detected 20 individuals which 8 (40%) trapped killed while two died natural causes 6-year study. Except for male, pedigree analysis genotype results showed no additional movement island, indicating limited dispersal but evidence inbreeding. Our findings suggest exhibit more flexible foraging behavior than previously believed, hunting strategies can substantially differ between within packs. Nevertheless, anthropogenic mortality combined connectivity may inhibit continued persistence

Language: Английский

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The truth about scats and dogs: Next-generation sequencing and spatial capture–recapture models offer opportunities for conservation monitoring of an endangered social canid

Biological Conservation, Journal Year: 2021, Volume and Issue: 256, P. 109028 - 109028

Published: Feb. 27, 2021

Language: Английский

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An efficient method for simultaneous species, individual, and sex identification via in‐solution single nucleotide polymorphism capture from low‐quality scat samples

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(4), P. 1345 - 1361

Published: Nov. 15, 2021

Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful study like canids that can be difficult to capture or directly observe. Here, we introduce FAECES* method (Fast and Accurate Enrichment Canid Excrement Species* other analyses) which expands toolbox canid researchers conservationists by using in-solution hybridization sequence produce single nucleotide polymorphism (SNP) genotypes multiple species from scat-derived DNA a enrichment. We designed set probes genotype both coyotes (Canis latrans) kit foxes (Vulpes macrotis) at hundreds polymorphic SNP loci tested on tissues field-collected scat samples. enriched genotyped sequencing 52 coyote 70 fox scats collected in around easement Nevada Mojave Desert. demonstrate produces capable differentiating foxes, identifying individuals their sex, estimating diversity effective sizes, even highly degraded, low-quantity extracted scat. found area harbours large diverse relatively smaller coyotes. By replicating our future, assess impacts decisions populations. The also adapted applied more broadly enrich any interest noninvasive

Language: Английский

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ISSRseq: An extensible method for reduced representation sequencing

Methods in Ecology and Evolution, Journal Year: 2021, Volume and Issue: 13(3), P. 668 - 681

Published: Dec. 10, 2021

Abstract The capability to generate densely sampled single nucleotide polymorphism (SNP) data is essential in diverse subdisciplines of biology, including crop breeding, pathology, forensics, forestry, ecology, evolution and conservation. However, the wet‐laboratory expertise bioinformatics training required conduct genome‐scale variant discovery remain limiting factors for investigators with limited resources. Here we present ISSRseq, a PCR‐based method reduced representation genomic variation using simple sequence repeats as priming sites inter repeat (ISSR) regions. Briefly, ISSR regions are amplified primers, pooled, used construct sequencing libraries commercially available kit, sequenced on Illumina platform. We also flexible bioinformatic pipeline that assembles loci, calls hard filters variants, outputs matrices common formats, conducts population analyses R. Using three angiosperm species case studies, demonstrate ISSRseq highly repeatable, necessitates only skills commonplace instrumentation, terms number primers used, can genomic‐scale par existing RRS methods which require more complex procedures. represents straightforward approach SNP genotyping any organism, predict this will be particularly useful those studying genomics phylogeography non‐model organisms. Furthermore, ease relative other should prove lacking advanced or bioinformatics.

Language: Английский

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