Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐PCR SNP Panel for Individual Identification From Faeces

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

ABSTRACT In recent years, numerous single nucleotide polymorphism (SNP) panel methods to genotype non‐invasive faecal samples have been developed. However, none of these existing fit all the criteria necessary make a SNP broadly usable for conservation projects in any country—cost effective, streamlined lab protocol and user‐friendly open‐source bioinformatics protocols design analysis. Here, we present such method display its utility by developing multiplex PCR conducting individual ID snow leopards, Panthera uncia , from samples. The consists 144 SNPs utilises next‐generation sequencing technology. We validate our with paired tissue zoo individuals, showing minimum 96.7% accuracy allele calls per run. then generate data 235 field‐collected across Pakistan show that can reliably identify individuals low‐quality unknown age is robust contamination. also has capability first‐order relatives among sampled provides insights into geographic origin This will empower leopard research community their efforts assess local global population sizes. More broadly, development be used species interest which adequate genomic reference available.

Language: Английский

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Topcats and underdogs: intraguild interactions among three apex carnivores across Asia's forestscapes

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2023, Volume and Issue: 98(6), P. 2114 - 2135

Published: July 14, 2023

ABSTRACT Intraguild interactions among carnivores have long held the fascination of ecologists. Ranging from competition to facilitation and coexistence, these their complex interplay influence everything species persistence ecosystem functioning. Yet, patterns pathways such are far understood in tropical forest systems, particularly across countries Global South. Here, we examined determinants consequences competitive between dholes Cuon alpinus two large felids (leopards Panthera pardus tigers tigris ) with which they most commonly co‐occur Asia. Using a combination traditional novel data sources ( N = 118), integrate information spatial, temporal, dietary niche dimensions. These three faced catastrophic declines extent co‐occurrence over past century; source populations now confined Protected Areas. Analysis dyadic pairs showed clear social hierarchy. Tigers were dominant dholes, although pack strength helped ameliorate some effects; leopards subordinate dholes. Population‐level spatio‐temporal assessed at 25 locations Asia did not show pattern overlap or avoidance pairs. Diet‐profile assessments indicated that wild ungulate biomass consumption by was highest, while consumed more primate livestock prey as compared co‐predators. In terms offtake (ratio available), together harvested 0.4–30.2% available prey, highest recorded location where reach very high densities. When re‐examined context availability offtake, low spatial temporal carnivore pairs, segregation. Based on observations, make predictions for 40 Areas India temporally synchronous estimates predator densities available. We expect will lead higher competition, extreme cases, complete exclusion one species. availability, intraguild coexistence conspecific carnivores, spill‐over forest‐edge habitats subsequent prey‐switching livestock. stress dhole–leopard–tiger range is facilitated through an intricate yet fragile balance competition. Data gaps limitations notwithstanding, our study shows how insights fundamental ecology can be immense utility applied aspects like conservation management human–carnivore interactions. Our findings also highlight potential avenues future research broaden current understanding systems beyond.

Language: Английский

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Chasms in charismatic species research: Seventy years of carnivore science and its implications for conservation and policy in India

Biological Conservation, Journal Year: 2022, Volume and Issue: 273, P. 109694 - 109694

Published: Aug. 11, 2022

Language: Английский

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Considerations for Initiating a Wildlife Genomics Research Project in South and South-East Asia

Journal of the Indian Institute of Science, Journal Year: 2021, Volume and Issue: 101(2), P. 243 - 256

Published: April 1, 2021

Language: Английский

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Similarity learning networks uniquely identify individuals of four marine and terrestrial species

Ecosphere, Journal Year: 2024, Volume and Issue: 15(10)

Published: Oct. 1, 2024

Abstract Estimating the size of animal populations plays an important role in evidence‐based conservation and management. Some methods for estimating population rely on animals being individually identifiable. Traditionally, this has been done by marking physically captured animals, but increasingly, with distinctive natural markings are surveyed noninvasively using cameras. Animal reidentification from photographs is usually manually, which expensive, laborious, requires considerable skill. An alternative to develop computer vision that can support or replace manual identification task. We developed automated approach deep learning identify whether a pair same individual not. The core similarity network uses paired convolutional neural networks triplet loss function summarize image pairs decide they individual. Prior main matching step, two additional perform segmentation, cropping object within image, orientation prediction, deciding side was photographed. applied four species, images often spanning several years: systematic surveys bottlenose dolphins ( Tursiops truncatus , 2008–2019) harbor seals Phoca vitulina 2015–2019), citizen science dataset western leopard toads Sclerophrys pantherina unknown dates), publicly available repository humpback whale Megaptera novaeangliae dates). For these our best‐performing models were able different individuals 95.8%, 94.6%, 88.2%, 83.8% cases, respectively. found functions outperformed binary cross‐entropy data augmentation curation training provided small consistent improvements performance. These results demonstrate potential or, more likely, facilitate efforts.

Language: Английский

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That’s not the Mona Lisa! How to interpret spatial capture-recapture density surface estimates

Biometrics, Journal Year: 2024, Volume and Issue: 80(1)

Published: Jan. 29, 2024

ABSTRACT Spatial capture-recapture methods are often used to produce density surfaces, and these surfaces misinterpreted. In particular, spatial change in is confused with uncertainty about density. We illustrate correct incorrect inference visually by treating a grayscale image of the Mona Lisa as an activity center intensity or surface simulating survey data from it. Inferences can be drawn point process generating centers, likely locations centers associated capture histories obtained single realization this process. show that probabilistic predictions estimates results invalid misleading ecological inferences, highly dependent on where detectors placed how much effort used. Estimates should estimating model for centers. Practitioners state explicitly whether they making location, not intensity.

Language: 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, Journal Year: 2023, Volume and Issue: 13(9)

Published: Sept. 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 (

Language: Английский

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Development of a Panel of Genotyping-in-Thousands by Sequencing in Capsicum

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: Oct. 26, 2021

Genotyping by sequencing (GBS) enables genotyping of multiple loci at low cost. However, the single nucleotide polymorphisms (SNPs) revealed GBS tend to be randomly distributed between individuals, limiting their direct comparisons without applying various filter options obtain a comparable dataset SNPs. Here, we developed panel multiplex targeted method, genotyping-in-thousands (GT-seq), genotype SNPs in Capsicum spp. Previously Fluidigm® SNP markers were converted GT-seq and combined with new using information obtained through GBS. We then optimized PCR conditions: highest rate when first consisted 25 cycles. In addition, determined that 101 primer pairs performed best amplifying target sequences 79 bp. minimized interference dimer formation PrimerPooler program. Using our pipeline on Illumina Miseq Nextseq platforms, genotyped up 1,500 (Miseq) 1,300 (Nextseq) samples for optimum size 100 loci. To allow species, designed 332 informative from Fluidigm GBS-derived This study illustrates application crop plants. The marker set here will useful tool molecular breeding peppers future.

Language: Английский

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Methodological approaches for estimating populations of the endangered dhole Cuon alpinus

PeerJ, Journal Year: 2022, Volume and Issue: 10, P. e12905 - e12905

Published: Feb. 22, 2022

Large carnivores are important for maintaining ecosystem integrity and attract much research conservation interest. For most carnivore species, estimating population density or abundance is challenging because they do not have unique markings individual identification. This hinders status assessments many threatened calls testing new methodological approaches. We examined past efforts to assess the of endangered dhole ( Cuon alpinus ), explored application a suite recently developed models their populations using camera-trap data from India’s Western Ghats. compared performance Site-Based Abundance (SBA), Space-to-Event (STE), Time-to-Event (TTE) against current knowledge size in area. also applied two these (TTE STE) co-occurring leopard Panthera pardus which estimates were available Spatially Explicit Capture–Recapture (SECR) models, so as simultaneously validate accuracy one marked unmarked species. Our review literature n = 38) showed that involved crude indices (relative index; RAI) occupancy area suitable habitat; very few studies attempted estimate populations. Based on empirical our field surveys, TTE SBA overestimated beyond ecologically plausible limits, but STE model produced reliable both findings suggest it difficult sizes species when assumptions fully met sparse, commonplace ecological surveys tropics. assessment, we propose practitioners who access photo-encounter dholes across Asia test old analytical approaches increase overall knowledge-base contribute towards monitoring this carnivore.

Language: Английский

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Population genetics of animals in the wild to aid conservation: Uma Ramakrishnan—Recipient of the 2023 Molecular Ecology Prize

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(5)

Published: Feb. 10, 2024

Uma Ramakrishnan grew up on an academic campus—the Indian Institute of Science (IISc)—where her father was a chemistry professor. Campus life provided early exposure to scientists, particularly the ecologists at Centre for Ecological Sciences (CES), IISc, where she hoped, one day, be faculty member herself. As luck would have it, returned after training become campus next door, National Biological (NCBS), Bengaluru. During high school, various ideas from ecologist Madhav Gadgil and his then-student, Ranjith Daniels, captivated her. She exposed biodiversity analytical approaches ecology. Her interest further sustained by tagging along field trips Western Ghat mountains conducting small school projects. simulated herbivory quantified its impacts some plants IISc campus; meanwhile, continued exploring quantitative The biggest break when had just finished went sabbatical Princeton University. took gap year decided join Princeton, audited undergraduate courses interned with working experimental biology. fascinated work being carried out Adina Merenlender genetic structure lemurs, which Uma's first brush PCRs gel electrophoresis. how data informed our understanding biology wild animals, bringing closer molecular graduated bachelor's degree Bangalore University, choosing stream that involved mathematics fuel in Meanwhile, connections interning Dr Raghavendra Gadagkar, feeding behaviour wasps learning computer programming. It clear this time interested animals examining their data-driven patterns. master's Biotechnology Pune University; choice motivated presence good statistics department there. also Cellular Molecular Biology (CCMB), only places India genetics time. project elephants (Ramakrishnan et al., 1998), reproductive success tuskless males. Here, became recovering DNA dung—a technique significantly developed, it backbone research later career (Mondol, Navya, 2009; Natesh 2019). pursued interests through PhD population David Woodruff University California San Diego. doctoral focused diversity composition (Nievergelt 2000; 2004; Storz 2001, 2002). as postdoctoral fellow Stanford two years, mentors. Joanna L Mountain Elizabeth Hadly are both dynamic women scientists who substantial focus approach science. With Mountain, used skills study aspects human African populations (Mountain & Ramakrishnan, 2005; Tishkoff 2007) while developing new tools simulations (Belle 2006; 2005). well, but climate environmental change (Hadly van Tuinen 2004) anthropogenic contributed statistical packages like SerialSimCoal (Anderson 2005 young Bengaluru, looking find niche. At time, even best-studied animal is arguably tiger (Jhala Karanth 2004). significant funding Government India, much conservation country has been centred around species 2021). Many global developments techniques driven studies ecology (Ullas Nichols, 2017). What missing otherwise well-studied populations. started fruitful collaboration Ullas Karanth, bridging tools. arrival coincided increase number members institutions, several trained leading institutions abroad. There motivation conduct globally relevant, cutting-edge research. NCBS facilitated ambition bring grounded India. initial years were largely exploratory. On hand, trying figure fit ecosystem. In contrast, others headed seek any since very few labs conducted such included describing species—a muntjac (James 2008), primate (Chakraborty birds (Robin 2010). given challenges materials (Madhusudan 2006), developed methods obtain faecal samples. Identifying samples other co-occurring step (Mukherjee 2007), led identifying individual tigers 2009) leopards 2009). Subsequently, group characterised variation across This large, endangered trajectory, continues day. described broad patterns cats, jungle cat leopard 2010) occurrence fishing cats (Shomita 2012). idea multiple factors impact distribution variation. insights came central landscape (Joshi 2013), larger specific factors. Thatte al. (2018) combination empirical collected hundreds landscape, simulations, show features roads implicated restriction geneflow landscape. Recent habitat fragmentation impacted already isolated sky islands Ghats (Robin, Gupta, 2015). A majority these implications conservation. support creation world's largest underpasses Pench Tiger Reserve—a major story. Recognition body Parker-Gentry Award Field Museum (Chicago) Uma. Himalayas, sites team member. bats got fairly detailed, mating systems (Garg 2015) coming captures bats, disease appeared inevitable step. Stories large-scale (thousands) bat consumption emerged, did stories mortalities possibilities zoonosis (Dovih, surveys humans consumed traditionally. They found Lyssavirus (Mani 2017), later, they evidence zoonotic spillover Filovirus (Dovih 2021) into harvesters. Most perhaps relative isolation public, results may appear another outcome. However, outbreak Covid-19 pandemic. under significant, sloppy public scrutiny (Ghosh, regulatory agencies mixed cause effect coincidence jostled target Not persist intense pressures expanded. recently documented Bartonella mammal communities (Ansil explored possible driver (Ansil, Viswanathan, 2023). Similar (Gupta pandemic surged, joined collaborators develop sampling (Sanyal 2022) use saliva source screening SARS-CoV2 George, 2023), staying committed social relevance past 5 roots. But able integrate considerable natural history knowledge protocols built foundations over 15 years. lab identified mutation associated rare phenotype—a pseudomelanistic large black stripes, (Sagar whole genome pedigree-based analyses captive alleles phenotype. reported frequency allele Odisha. genomic most populations—Ranthambore indicated inbreeding probable purging deleterious (Khan contemporary highlight populations, including potential rescues. Clearly, lead-up long, establishing connectivity, assess those build collaborations partnerships stakeholders. One themes development Apart tools, arguably, pioneered poor quality DNA, faeces. While sources previously extract microsatellite (Thatte 2020) rapidly progressing world genomics (Natesh Their changing differing (Aylward 2022; Sagar These now genome-wide SNP landscapes taxa herbivores (Tyagi, Yadav, 2023) dogs (Srivathsa Shed hair tested 2020; 2019) demonstrate hybridsation between wolf dog Godbole, Twenty-five starting attempt elephants, species, using modern examine signatures implications, tigers, lions clear. generates feeds efforts—a challenge colleagues decades, (Bawa 2020, evident publication profile student circulated lab, prominent mentorship role was, male-dominated area. broke glass ceiling adding unique value incorporating invested energy outreach capacity building workshops. awarded Homi Bhabha Education 2020 Education. research, provided, inspired students, especially field. so far revolved understudied wild. Some created part world. contributing growth field, outputs key strategies. Information rescue, certainly ahead current paradigm Still, will helpful managers come.

Language: Английский

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