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

Molecular Ecology Resources, Год журнала: 2024, Номер 24(7)

Опубликована: Июль 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

Язык: Английский

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FecalSeq enrichment with RAD Sequencing from non-invasive environmental samples holds promise for genetic monitoring of an imperiled lagomorph

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Июль 30, 2024

Despite advances in genomic sequencing and bioinformatics, conservation genomics is still often hindered by a reliance on non-invasive samples. The presence of exogenous DNA the low quantity poor quality samples have been roadblock to sequencing, thereby limiting potential for monitoring endangered species. Recent molecular advances, such as host enrichment, hold promise facilitating from We used FecalSeq method enrich extracted wild-collected fecal pellets imperiled New England cottontail identified SNPs 3RAD Sequencing. obtained rabbit pellets, including that were collected environmental conditions performed poorly with microsatellites. Measures success improved greater amounts starting 32% generated SNP genotypes passed control filtering. Genotyping error rates high, however, approach was unable consistently distinguish unique individuals or matching genotypes, while it suitable recovering expected population structure. Pairing enrichment RADseq promising low-cost wild populations using an context, but may be better suited informing through genomics.

Язык: 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), Год журнала: 2024, Номер unknown

Опубликована: Сен. 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.

Язык: Английский

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From single species to communities: microsatellite amplicon sequencing to monitor felids using Feliplex

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 23, 2024

Abstract The current biodiversity crisis demands a shift from single-species to multispecies approaches in conservation, particularly for rare and endangered species. However, this transition requires tools optimised research, which are currently limited. Recent advances high-throughput sequencing (HTS) technologies bioinformatics have enabled efficient robust acquisition of genetic data. Amplicon approaches, particular, demonstrated potential enhancing non-invasive studies species, but their application has been mostly limited single To enable we introduce cost-effective HTS-based amplicon approach genotyping multiple species simultaneously, designed population monitoring, including individual identification ascertaining patterns structure. We developed Feliplex, multiplex panel 85 co-amplifying tetranucleotide microsatellite markers cross-genotyping Felidae demonstrate the utility our approach. Feliplex was validated on known samples nine Indian felid across genera Panthera, Prionailurus , Felis . applied it invasive (blood tissue) (hair faeces) DNA extracts 173 wild individuals obtaining respectively 70% 56% multilocus success rates. accurately identified clusters tigers ( Panthera tigris n=19) revealed hitherto unknown structure fishing cats viverrinus n=40). Feliplex’s wide applicability allows reliable low-quality/quantity samples, while supporting conservation monitoring lesser-known like small cats. Our broad can be adapted develop similar panels closely related groups.

Язык: Английский

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