Whole‐genome resequencing improves the utility of otoliths as a critical source of DNA for fish stock research and monitoring

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(8)

Published: Sept. 5, 2024

Fish ear bones, known as otoliths, are often collected in fisheries to assist management, and a common sample type museum national archives. Beyond their utility for ageing, morphological trace element analysis, otoliths repository of valuable genomic information. Previous work has shown that DNA can be extracted from the quantities tissue remaining on surface despite fact they stored dry at room temperature. However, much this used reduced representation sequencing methods clean lab conditions, achieve adequate yields DNA, libraries ultimately single-nucleotide polymorphisms (SNPs). Here, we pioneer use small-scale (spike-in) screen contemporary otolith samples prepared regular molecular biology (in contrast clean) laboratories contamination quality levels, submitting whole-genome resequencing only above defined endogenous threshold. Despite typically low quantity able produce sets filtered, unlinked even putatively adaptive SNPs ample numbers downstream uses population, climate conservation genomics. By comparing with set same species, highlight efficacy extraction library preparation, bioinformatic preprocessing SNP calling. We provide detailed schematics, protocols scripts our approach, such it adopted widely by community, improving source data.

Language: Английский

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Koala conservation in South East Queensland: A grey literature review analysis

Conservation Science and Practice, Journal Year: 2023, Volume and Issue: 5(3)

Published: Jan. 29, 2023

Abstract This grey literature review documents koala ( Phascolarctos cinereus ) conservation initiatives applied across 12 local government areas in South East Queensland, Australia. To overcome threats to koalas' survival, the indicates that governments this region focus on wildlife management solutions, signage, habitat restoration projects and awareness campaigns. Despite these measures, land clearing of cater for urban population growth combined with recent bushfires floods have contributed decline koalas region. Recommendations enhance progress include greater usage peer work further application social marketing encourage residents uptake behaviors can mitigate koalas, including slowing down when driving zones, participating citizen science, leashing dogs walking native bush areas. The need collaborative efforts aimed at conserving from potential extinction is indicated. paper provides an approach be track coordinated conserve koalas.

Language: Английский

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Southern marsh deer (Blastocerus dichotomus) populations assessed using Amplicon Sequencing on fecal samples

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

Published: July 13, 2024

Abstract Populations in isolated and small fragments lose genetic variability very fast are usually of conservation concern because they at greater risk local extinction. The largest native deer South America, Blastocerus dichotomus (Illiger, 1815) , is a Vulnerable species according to the IUCN categorization, which inhabits tropical subtropical swampy areas. In Argentina, its presence has been restricted four fragments. Here we examine diversity differentiation among three them, including different patches that form southernmost population, using 18 microsatellite markers genotyped by Amplicon Sequencing DNA extracted from fecal samples. Genetic was low (H E < 0.45) all populations studied. We found clusters compatible with geographic location also metapopulation dynamics involves make up evidence barrier gene flow between two them. Our results point creation corridor as necessary urgent management action. This first study, population level, employing genotyping non-invasive samples an endangered species.

Language: Английский

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Genotyping Error Detection and Customised Filtration for SNP Datasets

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 22, 2024

ABSTRACT A major challenge in analysing single‐nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses misinterpret ecological evolutionary processes. Here, we present a comprehensive method to estimate minimise genotyping error rates (deviations from the ‘true’ genotype) any SNP using triplicates (three repeats of same sample) four‐step filtration pipeline. The approach involves: (1) by missing data; (2) rates; (3) sample data (4) detection recaptured individuals estimated rates. modular pipeline provided an R script allows customised adjustments. We demonstrate applicability non‐invasive sampling Asiatic wild ass ( Equus hemionus ) population Israel. genotyped 756 samples 625 SNPs, which 255 were 85 samples. average rate, calculated based on number mismatching genotypes across before filtration, was 0.0034 reduced 0.00174 following filtration. Evaluating genetic distance (GD) relatedness r between after (expected be at minimum maximum respectively) showed significant reduction GD, 58.1 25.3 p = 0.0002) increase relatedness, 0.98 0.991 0.00587). how rate estimation enhances recapture improves quality.

Language: Английский

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Non-invasive sampling reveals low mitochondrial genetic diversity for a Critically Endangered island endemic species

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: June 12, 2023

As an island endemic with a decreasing population, the Critically Endangered Grenada DoveLeptotila wellsiis threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed first assessment Dove a) assessing mtDNA only two areas occupancy on Grenada, b) defining number haplotypes present at each site and c) evaluating evidence isolation between sites. used non-invasively collected locations: Mt Hartman (n = 18) Perseverance 12). DNA extraction PCR were amplify 1,751 bps mitochondrial markers: NADH dehydrogenase 2 (ND2) Cytochrome b (Cyt b). Haplotype (h) 0.4, nucleotide (π) 0.4 unique identified within theND2sequences; one haplotype was theCyt bsequences. Of identified; most common (haplotype A 73.9%) observed both sites other B 26.1%) Perseverance. Our results show low diversity, non-expanding population clear for genetically isolated populations. The needs urgent conservation action, including protection potentially augmentation gene flow translocation order increase resilience ultimate aim securing long-term survival this species.

Language: Английский

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Influence of scat ageing on the gut microbiome: how old is too old?

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: July 31, 2023

Abstract Background The study of the host-microbiome by collection non-invasive samples has potential to become a powerful tool for conservation monitoring and surveillance wildlife. However, multiple factors can bias quality data recovered from scats, particularly when field-collected are used given that time defecation is unknown. Previous studies using scats have shown impact aerobic exposure on microbial composition species-specific, leading different rates change in communities. this aging process relationship between bacterial fungal yet be explored. In study, we measured effects post-defecation compositions controlled experiment scat endangered koala ( Phascolarctos cinereus ). Results We found remained stable through process, while did not. absence an increase facultative anaerobes population obligate anaerobic bacteria were likely due our sampling inner portion scat. report cluster taxa colonises after which dilute genetic material autochthonous mycoflora inhibit recovery. Conclusion emphasize need preserve integrity collected wild combat provide strategies doing so.

Language: Английский

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Non‐invasive sampling reveals low mitochondrial genetic diversity for an island endemic species: The critically endangered Grenada Dove Leptotila wellsi

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(11)

Published: Nov. 1, 2023

Abstract As an island endemic with a decreasing population, the critically endangered Grenada Dove Leptotila wellsi is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, populations are difficult to sample directly but advances in molecular methods mean that non‐invasive samples can be used. We performed first assessment (a) assessing mtDNA only two areas occupancy on Grenada, (b) defining number haplotypes present at each site and (c) evaluating evidence isolation between sites. used non‐invasively collected locations: Mt Hartman ( n = 18) Perseverance 12). DNA extraction PCR were amplify 1751 bps mitochondrial markers: NADH dehydrogenase 2 ND2 ) Cytochrome b Cyt ). Haplotype h 0.4, nucleotide π 0.00023 unique identified within sequences; single haplotype was sequences. Of identified, most common (haplotype A 73.9%) observed both sites other B 26.1%) Perseverance. Our results show low clear for genetically isolated populations. The needs urgent conservation action, including protection potentially augmentation gene flow translocation order increase resilience ultimate aim securing long‐term survival this species.

Language: Английский

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