Conservation and the Genomics of Populations

Oxford University Press eBooks, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 10, 2022

Abstract Loss of biodiversity is among the greatest problems facing world today. Conservation and Genomics Populations gives a comprehensive overview essential background, concepts, tools needed to understand how genetic information can be used conserve species threatened with extinction, manage ecological or commercial importance. New molecular techniques, statistical methods, computer programs, principles, methods are becoming increasingly useful in conservation biological diversity. Using balance data theory, coupled basic applied research examples, this book examines phenotypic variation natural populations, principles mechanisms evolutionary change, interpretation from these conservation. The includes examples plants, animals, microbes wild captive populations. This third edition has been thoroughly revised include advances genomics contains new chapters on population genomics, monitoring, genetics practice, as well sections climate emerging diseases, metagenomics, more. More than one-third references were published after previous edition. Each 24 Appendix end Guest Box written by an expert who provides example presented chapter their own work. for advanced undergraduate graduate students genetics, resource management, biology, professional biologists policy-makers working wildlife habitat management agencies. Much will also interest nonprofessionals curious about role

Language: Английский

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Genetic and genomic monitoring with minimally invasive sampling methods

Evolutionary Applications, Journal Year: 2018, Volume and Issue: 11(7), P. 1094 - 1119

Published: Feb. 2, 2018

Abstract The decreasing cost and increasing scope power of emerging genomic technologies are reshaping the field molecular ecology. However, many modern approaches (e.g., RAD ‐seq) require large amounts high‐quality template DNA . This poses a problem for an active branch conservation biology: genetic monitoring using minimally invasive sampling ( MIS ) methods. Without handling or even observing animal, methods collection hair, skin, faeces) can provide information on individuals populations. Such samples typically yield low‐quality and/or quantities , restricting type that be used. Despite this limitation, is effective tool estimating population demographic parameters diversity in natural Genetic likely to become more important future as populations undergoing anthropogenically driven declines, which unlikely abate without intensive adaptive management efforts often include approaches. Here, we profile expanding suite platforms compatible with producing genotypes from considering factors such development costs error rates. We evaluate how powerful new will enhance our ability investigate questions answered monitoring, abundance, structure relatedness. As period unusually rapid transition, also highlight importance legacy data sets recommend address challenges moving between traditional next‐generation platforms. Finally, consider could move beyond future. For example, assessing microbiomes epigenetic markers greater understanding relationship their environment.

Language: Английский

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Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 20(3), P. 662 - 680

Published: Jan. 11, 2020

Abstract The genomic era has led to an unprecedented increase in the availability of genome‐wide data for a broad range taxa. Wildlife management strives make use these vast resources enable refined genetic assessments that enhance biodiversity conservation. However, as new platforms emerge, problems remain adapting usually complex approaches genotyping noninvasively collected wildlife samples. Here, we provide practical guidelines standardized development reduced single nucleotide polymorphism (SNP) panels applicable microfluidic degraded DNA samples, such faeces or hairs. We demonstrate how SNP can be optimized efficiently monitor European wildcat ( Felis silvestris S.) populations. show set up modular fashion accommodate informative markers relevant population genetics questions, individual identification, hybridization assessment and detection structure. discuss various aspects regarding implementation framework will allow both molecular ecologists practitioners help bridge gap between genomics applied

Language: Английский

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More affordable and effective noninvasive single nucleotide polymorphism genotyping using high‐throughput amplicon sequencing

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 20(6), P. 1505 - 1516

Published: June 10, 2020

Abstract Noninvasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates and error rates. The information lost when may lead to decreased precision in animal population densities, which could misguide conservation management actions. Single nucleotide polymorphisms (SNPs) provide a promising alternative traditionally used microsatellites as SNPs allow amplification shorter DNA fragments, are less prone errors produce results that easily shared among laboratories. Here, we outline detailed protocol for cost‐effective accurate noninvasive SNP using multiplexed amplicon sequencing optimized degraded DNA. We validated this method individual identification 216 scats, 18 hairs 15 tissues from coyotes ( Canis latrans ) 26 SNPs. Our rate scat samples was 93%, 100% hair tissue, representing substantial increase compared previous microsatellite‐based studies while remaining at cost under $5 per PCR replicate (excluding labour). accuracy genotypes further corroborated scats matching known, GPS‐collared were always located within territory known individual. also show different levels multiplexing produced similar results, product cleanup strategies can effects on success. By making more affordable, efficient, use monitor conserve free‐ranging populations.

Language: Английский

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Wildlife parasitology: sample collection and processing, diagnostic constraints, and methodological challenges in terrestrial carnivores

Parasites & Vectors, Journal Year: 2024, Volume and Issue: 17(1)

Published: March 13, 2024

Abstract Wild terrestrial carnivores play a crucial role as reservoir, maintenance, and spillover hosts for wide parasite variety. They may harbor, shed, transmit zoonotic parasites of veterinary importance domestic hosts. Although wild are globally distributed comprise many different species, some living in close proximity to human settlements, only few studies have investigated using non-specific techniques. Access samples be challenging species protected, others secretive, possibly explaining the data paucity. Considering carnivores’ health ecological role, combined with lack specific diagnostic methodologies, this review aims offer an overview methods investigation carnivores, providing precise techniques collection analysis fecal, blood, tissue samples, environmental impact on said limitations researchers currently face analyzing carnivores. In addition, paper offers information how factors affect detection postmortem insects can used estimate time death highlight insect larvae. The contains literature available procedures emphasizes need method standardization Graphical

Language: Английский

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Empowering conservation practice with efficient and economical genotyping from poor quality samples

Methods in Ecology and Evolution, Journal Year: 2019, Volume and Issue: 10(6), P. 853 - 859

Published: April 10, 2019

Abstract Moderate‐ to high‐density genotyping (100 + SNPs) is widely used determine and measure individual identity, relatedness, fitness, population structure migration in wild populations. However, these important tools are difficult apply when high‐quality genetic material unavailable. Most genomic developed for DNA sources from laboratory or medical settings. As a result, most data market field settings limited easily amplified mitochondrial few microsatellites. To enable conservation contexts, we next‐generation sequencing of multiplex PCR products very low‐quality extracted faeces, hair cooked samples. We demonstrated utility wide‐ranging potential application endangered tigers tracking commercial trade Caribbean queen conch. genotyped 100 SNPs degraded tiger samples identify individuals, discern close relatives detect differentiation. Co‐occurring carnivores do not amplify (e.g. Indian dog/dhole) monomorphic leopard). Sixty‐two conch fritters field‐collected were test relatedness structure. provide proof concept rapid, simple, cost‐effective scalable method (for both number loci), framework that can be applied other scenarios previously by These approaches critical advance wildlife monitoring forensics, open the door field‐ready testing, will strengthen use science policy decisions trade.

Language: Английский

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A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Jan. 22, 2024

Abstract The European bison was saved from the brink of extinction due to considerable conservation efforts since early twentieth century. current global population > 9500 individuals is result successful ex situ breeding based on a stock only 12 founders, resulting in an extremely low level genetic variability. Due allelic diversity, traditional molecular tools, such as microsatellites, fail provide sufficient resolution for accurate assessments bison, let alone non-invasive samples. Here, we present SNP panel high-resolution genotyping which suitable wide variety sample types. accommodates 96 markers allowing individual and parental assignment, sex determination, line discrimination, cross-species detection. Two applications were shown be utilisable further Bos species with potential significance. new will allow tackle crucial tasks conservation, including monitoring reintroduced populations, assessment pedigree data documented world’s first studbook threatened species.

Language: Английский

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Range-wide patterns of human-mediated hybridisation in European wildcats

Conservation Genetics, Journal Year: 2020, Volume and Issue: 21(2), P. 247 - 260

Published: Jan. 25, 2020

Abstract Hybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber relatives in population size distribution may therefore genetically swamp the native species. The European wildcat ( Felis silvestris ) has been shown to hybridise with cats catus ). Previously suggested spatially divergent introgression levels have not confirmed on scale due differences applied methods assess hybridisation of wildcat. We analysed 926 spp. samples from 13 countries, using set 86 selected ancestry-informative SNPs, 14 microsatellites, ten mitochondrial Y-chromosome markers study regional patterns differentiation. detected 51 hybrids (four F1 47 F2 or backcrosses) 521 pure wildcats throughout Europe. abundance varied considerably among studied populations. All Scotland were identified as backcrosses, supporting previous findings that genetic integrity seriously compromised. In other populations, low moderate found, lowest being Central Southeast occurrence distinct maternal paternal cat suggests there no severe episodes past. overall (< 1%) prevalence risk for long-term most However, regionally elevated rates confirm poses potential threat. propose in-depth monitoring identify factors driving so develop effective strategies conservation.

Language: Английский

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International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions

Forensic Science International Genetics, Journal Year: 2021, Volume and Issue: 54, P. 102551 - 102551

Published: June 8, 2021

Language: Английский

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Genotyping‐in‐thousands by sequencing (GT‐seq) of noninvasive faecal and degraded samples: A new panel to enable ongoing monitoring of Canadian polar bear populations

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(5), P. 1906 - 1918

Published: Jan. 10, 2022

Genetic monitoring using noninvasive samples provides a complement or alternative to traditional population methods. However, next-generation sequencing approaches typically require high quality DNA and the use of (e.g., scat) is often challenged by poor contamination nontarget species. One promising solution highly multiplexed approach called genotyping-in-thousands (GT-seq), which can enable cost-efficient genomics-based for populations based on noninvasively collected samples. Here, we develop validate GT-seq panel 324 single nucleotide polymorphisms (SNPs) optimized genotyping polar bears from faecal We demonstrate (1) successful range sample sources, including (>50% loci) 62.9% determined contain bear DNA; (2) that reliably differentiate individuals, ascertain sex, assess relatedness, resolve structure Canadian subpopulations SNPs. Our data reveal spatial-genetic patterns similar previous studies but at lesser cost per through samples, indicating potential this monitoring. This foundation toolkit contribute community-based programmes - framework may serve as model wildlife conservation management species worldwide.

Language: Английский

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