Strategic Sampling of Eurasian Otter Spraints for Genetic Research in South Korea: Enhancing PCR Success and Data Accuracy

Animals, Journal Year: 2025, Volume and Issue: 15(4), P. 574 - 574

Published: Feb. 17, 2025

Non-invasive genetic approaches, particularly using fecal samples, are commonly used to study endangered and elusive species, as they easy collect with minimal permission cause little disturbance the subject population. However, such studies face limitations due poor DNA yield, which affects overall utilization of collected samples increases data errors. Here, we evaluated impact sample age collection season on performance extracted from feces (spraints) Eurasian otter (Lutra lutra), a semi-aquatic apex predator in South Korean freshwater ecosystems. We found that PCR amplification success rates decreased more rapidly summer (79.3-58.2%) compared winter (99.2-84.8%) extended environmental exposure. Genotyping error were higher during summer, rate increase over time being significantly greater than winter. The hot humid fosters microbial growth degradation, negatively impacts reducing increasing genotyping recommend collecting for better quality. If sampling is unavoidable, it crucial fresh can be facilitated by conducting frequent surveys latrine sites.

Language: Английский

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From blow to DNA: citizen science advancing genetic research on southern right whales

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

Published: Feb. 24, 2025

Language: Английский

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Integrating systematic and targeted scat collection approaches to estimate the abundance of a culturally significant threatened species on Indigenous lands

Conservation Science and Practice, Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Abstract Estimating the abundance of threatened species can be extremely difficult. This is particularly true in remote regions, where surveys are often expensive and subject to logistical challenges. Where occur on Indigenous lands, collaborative work between people ecologists who share an interest conservation management these may resolve some challenges while also meeting additional local objectives. Here, we show value integrating two on‐ground methods for non‐invasive genetic sampling scat estimate greater bilby ( Macrotis lagotis ), a highly significant central Australia that with extinction. We compared methods: (1) systematic surveys, designed repeatable, stratified, standardized, (2) targeted which focused areas sign was present involved more flexible intuitive search technique undertaken collaboratively informed by their knowledge skills. different combinations intensities explore how they affected modeled estimates abundance, derived combining information individual identities (from DNA extracted from scat) spatially explicit capture–recapture modeling. found collection provided best improved lower overall effort than increasing sampling. approach allowed inclusion diverse knowledges approaches detecting (scat) presence. By weaving multiple find identify scat, knowledge‐sharing practices deliver benefits science partners.

Language: Английский

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Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 30, 2023

Abstract Genetic non‐invasive sampling (gNIS) is a critical tool for population genetics studies, supporting conservation efforts while imposing minimal impacts on wildlife. However, gNIS often presents variable levels of DNA degradation and non‐endogenous contamination, which can incur considerable processing costs. Furthermore, the use restriction‐site‐associated sequencing methods (RADseq) assessing thousands genetic markers introduces challenge obtaining large sets shared loci with similar coverage across multiple individuals. Here, we present an approach to handling large‐scale gNIS‐based datasets using data from spotted hyena inhabiting Ngorongoro Crater in Tanzania. We generated 3RADseq more than thousand individuals, mostly faecal mucus samples collected non‐invasively varying contamination level. Using small‐scale sequencing, screened endogenous content, removed highly contaminated samples, confirmed overlap fragment length between libraries, balanced individual representation pool. evaluated impact (1) (2) PCR duplicates (3) different SNP filters genotype accuracy based Mendelian error estimated parent–offspring trio datasets. Our results showed that when depth, presented rates those non‐contaminated samples. also accuracy. In summary, potential monitoring SNPs demonstrated how improve control over library preparation by weighted re‐pooling strategy considers content.

Language: Английский

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Testing the effectiveness of genetic monitoring using genetic non‐invasive sampling

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 12(1)

Published: Dec. 27, 2021

Abstract Effective conservation requires accurate data on population genetic diversity, inbreeding, and structure. Increasingly, scientists are adopting non‐invasive sampling (gNIS) as a cost‐effective population‐wide monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream analyses. Here, using high‐quality single nucleotide polymorphism (SNP) from blood/tissue free‐ranging koala ( n = 430), we investigated how reduced SNP panel size call rate typical samples (derived experimental field trials) impacts measures, also effect intensity these measures. We found that at small sample sizes (14% population) can provide diversity but slightly underestimated inbreeding coefficients. Accurate measures internal relatedness required least 33% to be sampled. geographic spatial autocorrelation analysis between 28% 51% show low powerful tool aid decision‐making recommendations for researchers looking apply techniques systems.

Language: Английский

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Inbreeding and cognition in wild populations: a relationship that remains unnoticed

Oikos, Journal Year: 2024, Volume and Issue: 2024(9)

Published: July 18, 2024

Anthropogenic activities are causing a steep decline of wildlife populations. Increased inbreeding in shrinking populations can substantially curb individual fitness and population viability. One potentially important but largely ignored component depression may be cognitive decline. Cognition affects an animal's capacity to respond environmental disturbance, which, the face global change, make difference between persistence extinction. While effects on performance have been relatively well documented humans, they remain unexplored natural Here we review current (limited) knowledge whether how impinges animals' abilities. Insights into relationship cognition could prove valuable not only for comprehending development evolution also conservation.

Language: Английский

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Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(9), P. 2174 - 2185

Published: Feb. 9, 2023

The genetic consequences of the subdivision populations are regarded as significant to long-term evolution, and research has shown that scale speed at which this is now occurring critically reducing adaptive potential most species inhabit human-impacted landscapes. Here, we provide a rare and, our knowledge, first analysis process while it happening demonstrate method evaluating effect mitigation measures such fauna crossings. We did by using an extensive data set collected from koala population was intensely monitored during construction linear transport infrastructure resulted in their population. First, found both allelic richness effective size decreased through subdivision. Second, predicted extent drift could impact diversity over time showed after only 10 generations resulting two subdivided experience between 12% 69% loss diversity. Lastly, forward simulations estimated minimum eight koalas would need disperse each side per generation maintain connectivity close zero but 16 ensure remained unchanged. These results have important for management landscapes showing metrics best identify immediate how evaluate effectiveness any measures.

Language: Английский

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The effects of fire on large‐ and medium‐sized mammal communities: what do we know? A review

Mammal Review, Journal Year: 2024, Volume and Issue: 54(4), P. 357 - 372

Published: March 22, 2024

Abstract Large‐ and medium‐sized mammals play a unique role in ecosystem dynamics. They can change the physical biotic landscape by altering flow of resources among trophic levels, thereby affecting functioning. Although effects fire on some ungulates have been well studied, data gaps exist for many species, including canids, felids, mustelids ursids others. To address this knowledge gap, we conducted literature review to synthesize what is known about large medium mammal responses fire, communities, species richness interactions connection with fire. Twenty‐seven were studied. Fifty percent studies examined ungulates, far exceeding other levels. Eighty‐six significantly fewer mammals. Only four multiple Results indicated that had largely positive effect large‐ However, considerable heterogeneity exists within taxa. Most research has focal rather than biodiversity, gap or Forest management focus changing from suppression reinstating natural regimes. Effectiveness monitoring programmes will be needed test efficacy restoration strategies mammalian communities.

Language: Английский

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Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(21), P. 5455 - 5467

Published: Aug. 31, 2022

The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some well known and have clear methods prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others less easily addressed. One major current to koalas chlamydial disease, which impacts on individual survival reproduction rates translate into Effective management strategies for disease in wild currently lacking, and, date, we know little about determinants susceptibility disease. Here, investigated genetic basis variation chlamydia using intensively studied koala populations. We combined data from veterinary examinations, testing, sampling movement monitoring. Out our sample 342 koalas, 60 were found chlamydia. Using genotype information 5007 SNPs investigate role determining status, no evidence inbreeding depression, but a heritability 0.11 (95% CI: 0.06-0.23) probability had Heritability could relevant future management, as it suggests adaptive potential population.

Language: Английский

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Technological advances have enhanced and expanded conservation genomics research but are yet to be integrated fully into biodiversity management

Biological Conservation, Journal Year: 2024, Volume and Issue: 299, P. 110788 - 110788

Published: Sept. 16, 2024

Language: Английский

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