Swatting Flies: Biting Insects as Non‐Invasive Samplers for Mammalian Population Genomics

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 22, 2025

ABSTRACT Advances in next‐generation sequencing have allowed the use of DNA obtained from unusual sources for wildlife studies. However, these samples been used predominantly to sequence mitochondrial species identification while population genetics analyses rare. Since allows indiscriminate detection all fragments a sample, technically it should be possible whole genomes animals environmental samples. Here we blood‐feeding insect, tsetse fly, target genome sequences wild animals. Using pools flies, compared ability recover genomic data hosts using short‐read (Illumina) and adaptive sampling long‐read generated Oxford nanopore technology (ONT). We found that most (85%–99%) was dominated by fly on ONT platform did not substantially reduce this proportion. once reads were removed, remaining both platforms tended belong dominant host expected blood meal. Reads mapping elephants, warthogs giraffes recovered more reliably than buffalo, there high variance contribution individual flies pools, suggesting are specific biases. For able identify over 300,000 unfiltered SNPs, which estimate allele frequencies heterozygosity population. Overall, our results show at least certain mammals, is genome‐wide insects.

Язык: Английский

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On the road to losing connectivity: Faecal samples provide genome‐wide insights into anthropogenic impacts on two large herbivore species in central India

Molecular Ecology, Год журнала: 2024, Номер 33(16)

Опубликована: Июль 3, 2024

Abstract Humans have impacted most of the planet, and ensuing fragmentation results in small, isolated habitat patches posing a risk genetic diversity loss, inbreeding, load. Understanding how natural anthropogenic landscape features affect gene flow among is critical for maintaining connectivity. Genome‐wide data are required to comprehend impacts recent fragmentation, which can be challenging when only non‐invasive samples available. Here, we build upon advancements conservation genomics address connectivity two large herbivores, gaur ( Bos gaurus ) sambar Rusa unicolor central India. Given their associations, expected these species respond similarly fragmentation. We used faecal‐DNA methylation‐based host‐DNA enrichment with modified ddRAD protocol generate genome‐wide single‐nucleotide polymorphism (SNP) 124 99 individuals. Our findings reveal that populations India fragmented, displaying high differentiation, drift significantly affecting small like Umred Karhandla Wildlife Sanctuary. Although shows low structure, another population, Bor Tiger Reserve genetically differentiated. suggest although land cover change roads restrict animal movement, extent this impact varies across species. show different differently features, even similar associations. highlight requiring urgent intervention. Such multi‐species approaches enhance our understanding cross‐species patterns. shifting from single‐species holistic approach rapidly developing landscapes better manage co‐occurring endangered

Язык: Английский

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Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencing

Oryx, Год журнала: 2025, Номер unknown, С. 1 - 6

Опубликована: Янв. 23, 2025

Abstract Big cats are of conservation concern throughout their range, and genetic tools often employed to study them for various purposes. However, there several difficulties in using big cat that could be resolved by modern methods DNA sequencing. Recent reports the sighting a putative Javan tiger Panthera tigris sondaica West Java, Indonesia, highlight some studying genetics cats. We reanalysed data original found conclusions were drawn based on incorrect copies genes. Specifically, nuclear copy mitochondrial gene was analysed with sequence, leading discordance results. re-sequencing remaining confirms have been tiger, but subspecies cannot confirmed. This work highlights urgency developing high-throughput sequencing infrastructure tropics need reliable databases

Язык: Английский

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Scat DNA Applications for Low‐Density Carnivore Survey: Techniques, Efficiency and Future Directions

Mammal Review, Год журнала: 2025, Номер unknown

Опубликована: Май 12, 2025

ABSTRACT Background Large and mesocarnivores often occur at low densities due to both natural factors human activities. Consequently, the noninvasive collection of carnivore data, such as scats for genetic analyses, provides a robust alternative capture‐based data. Aims In this review, we focussed on low‐density carnivores answer following questions: What are applications scat‐derived DNA samples? is sampling effort required how efficient scat detecting species compared other methods? methodological advances in analyses? Material & Methods We systematicaly compiled results 338 studies applying reliable source material myriad applications. Most were conducted Asia Europe, encompassing mainly Felidae, Canidae Mustelidae species. Results Discussion general, recommend allowing enough time accumulate field, but collecting before significant degradation occurs. Storage extraction can be successfully achieved using various methods, although commercial kits have become more widely used over time. However, samples show an inherent high variability amplification success rate. Considering transects, average distance travelled encounter molecularly identified was 6.9 km. Faecal found equally number individuals present, respectively, methods. Conclusion The information presented here should guide new focussing carnivores, providing basis cost‐effective surveys improving data quality conservation.

Язык: Английский

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India: Hotspot of Connectivity Research and Conservation in Central India

Опубликована: Янв. 1, 2025

Abstract The persistence of wildlife in human-dominated landscapes is a challenge. Fragmentation natural ecosystems one the major threats to biodiversity conservation, especially densely populated and developing regions. Connectivity among remaining habitats can mitigate negative ecological evolutionary effects fragmentation great extent. Central India has been hotspot landscape connectivity research South Asia. We reviewed published on identify prominent trends patterns literature. overarching pattern we found that most region conducted terrestrial ecosystems, forests, single species—usually tiger—by independent groups applying singular methods. However, recent tending more toward multi-species approaches within collaborative frameworks. There need integrate multiple methods, social acceptance towards wildlife, collective action ensure Indian landscape.

Язык: Английский

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Review of small cat ecology and status within India

Mammal Review, Год журнала: 2024, Номер 54(4), С. 341 - 356

Опубликована: Март 1, 2024

Abstract Small felids play pivotal roles in India's ecosystems, regulating prey populations, facilitating nutrient transfer, and safeguarding critical habitats. Despite their ecological significance, these species receive inadequate conservation attention, contrasting sharply with the focus on larger carnivores. Our review assesses status of nine native Indian small felids, aiming to consolidate data for improved draw connections global carnivore efforts. Over last 50 years, scarcity has impeded comprehensive understanding, hindering assessment crucial dynamics. We delve into factors influencing distribution abundance cats across India, identifying climate, human disturbances, presence large carnivores, topography, vegetation cover as influential determinants. Notably, trade records reveal a decline wild felid since 1997, suggesting potentially positive outcomes from enhanced law‐enforcement measures. Highlighting necessity robust data, particularly pertaining demographic parameters, prey–predator relationships, responses human‐induced habitat alterations, we advocate integrating insights strategies. stress urgency collaborative efforts supported by unwavering political commitment sustained financial backing ensure successful globally. This underscores imperative filling knowledge gaps, findings frameworks, fostering international collaborations preserve terrestrial ecosystems worldwide.

Язык: Английский

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Citizen science facilitates first ever genetic detection of wolf‐dog hybridization in Indian savannahs

Ecology and Evolution, Год журнала: 2023, Номер 13(5)

Опубликована: Май 1, 2023

Abstract Human demographic expansion has confined wildlife to fragmented habitats, often in proximity human‐modified landscapes. Such interfaces facilitate increased interactions between feral or domesticated animals and wildlife, posing a high risk wild species. This is especially relevant for free‐ranging dogs ( Canis lupus familiaris ) canids like gray wolves golden jackals aureus ). Wolf–dog hybridization may lead significant reduction of specific adaptations that could result the decline wolf populations. Detection genetic discrimination hybrids are challenging because their complex history close ancestry. Citizen scientists identified two phenotypically different‐looking individuals subsequently collected non‐invasive samples were used by geneticists test wolf‐dog hybridization. Genomic data from shed hair suspected hybrid using double‐digest restriction‐site‐associated DNA (ddRAD) sequencing resulted 698 single nucleotide polymorphism (SNP) markers. We investigated origin these analyzed with genetically known dogs, wolves, other canid species including dholes Cuon alpinus Our results provide first evidence one F2 individual be wolves. re‐iterate power next‐generation (NGS) as an efficient tool detecting hybrids. suggest need more robust monitoring populations highlight tremendous potential collaborative approaches citizens conservation detect monitor threats biodiversity.

Язык: Английский

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Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink

Ecology and Evolution, Год журнала: 2023, Номер 13(9)

Опубликована: Сен. 1, 2023

The application of next-generation sequencing (NGS) to non-invasive samples is one the most promising methods in conservation genomics, but these types present significant challenges for NGS. European mink (

Язык: Английский

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On the road to losing connectivity: Fecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Окт. 30, 2023

Abstract Humans have impacted most of the planet, and ensuing fragmentation results in small, isolated habitat patches posing a risk genetic diversity loss, inbreeding load. Understanding how natural anthropogenic landscape features affect gene flow among is critical for maintaining connectivity. Genome-wide data required to comprehend impacts recent fragmentation, which can be challenging when only non-invasive samples are available. Here, we build upon advancements conservation genomics address connectivity two large herbivores, gaur ( Bos gaurus ) sambar Rusa unicolor central India. Given their associations, expected these species respond similarly fragmentation. We used fecal-DNA methylation-based host-DNA enrichment with modified ddRAD protocol generate genome-wide single nucleotide polymorphism (SNP) 124 Gaur 99 Sambar individuals. Our findings reveal that populations India fragmented, displaying high differentiation, drift significantly affecting small like Umred-Karhandala Wildlife Sanctuary. Although shows low structure, another population, Bor Tiger Reserve genetically differentiated. suggest although landcover change roads restrict animal movement, extent this impact varies across species. show different species, differently features, even similar associations. highlight requiring urgent intervention. Such multi-species approaches enhance our understanding cross-species patterns. shifting from single-species holistic approach rapidly developing landscapes better manage co-occurring endangered

Язык: Английский

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Past population control biases interpretations of contemporary genetic data: implications for future invasive Sitka black-tailed deer management in Haida Gwaii

Biological Invasions, Год журнала: 2023, Номер 25(12), С. 3871 - 3886

Опубликована: Авг. 12, 2023

Язык: Английский

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