Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(49)

Published: Nov. 30, 2021

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small may be able purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing depression increasing population viability. We used whole-genome sequences from 57 tigers estimate individual mutation load a small-isolated two large-connected India. As expected, the had substantially higher average genomic (

Language: Английский

---

Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(6), P. 2366 - 2379

Published: Feb. 3, 2021

Abstract Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic endangered species garner significant attention. However, their history genomic variation remain poorly known, especially for Indian tigers. With 70% world’s wild tigers living in India, such is critical. We re-sequenced 65 individual tiger genomes representing extant subspecies with a specific focus on from India. As suggested earlier studies, we found strong differentiation between putative subspecies. Despite high total diversity host longer runs homozygosity, potentially suggesting recent inbreeding or founding events, possibly due to small fragmented protected areas. suggest impacts ongoing connectivity loss persistence closely monitored. Surprisingly, demographic models divergence (within last 20,000 years) population bottlenecks. Amur revealed strongest signals selection related metabolic adaptation cold, whereas Sumatran show evidence weak genes involved body size regulation. recommend detailed investigation local prior initiating rescue.

Language: Английский

---

Non-invasive real-time genomic monitoring of the critically endangered kākāpō

eLife, Journal Year: 2023, Volume and Issue: 12

Published: March 17, 2023

We used non-invasive real-time genomic approaches to monitor one of the last surviving populations critically endangered kākāpō ( Strigops habroptilus ). first established an environmental DNA metabarcoding protocol identify distribution and other vertebrate species in a highly localized manner using soil samples. Harnessing nanopore sequencing high-quality reference genome, we then extracted species-specific from soil. combined long read-based haplotype phasing with known individual variation population presence individuals, confirmed these genomically informed predictions through detailed metadata on distributions. This study shows that identification is feasible DNA, important implications for future efforts application genomics conservation rare species, potentially expanding research monitoring inferring fitness parameters such as diversity inbreeding.

Language: Английский

---

Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild?

Ecology and Evolution, Journal Year: 2020, Volume and Issue: 10(11), P. 4583 - 4594

Published: May 18, 2020

Abstract Knowledge of relationships in wild populations is critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies endangered species. To delineate pedigrees populations, study genetic connectivity, genotype‐phenotype associations, trace individuals, or track wildlife trade, many identified individuals need be genotyped at thousands loci, mostly from noninvasive samples. This requires us (a) identify the most common sample available (b) assess ability acquire genome‐wide data such samples, (c) evaluate quality data, its reconstruct between animals within a population. We followed tiger population found that shed hair samples were compared scat opportunistically carcasses, opportunistic invasive extracted DNA these prepared whole genome sequencing libraries, sequenced genomes these. Whole methods resulted 25%–98% five Exploratory analyses revealed free holistic biases could recover expected structure relatedness. Mitochondrial recovered matrilineages accordance with long‐term monitoring data. Even just we able uncover matrilineage three unknown ancestry. In summary, demonstrated yield adequate quantity conjunction sensitive library preparation methods, provide reliable hundreds SNPs across genome. makes an ideal resource studying individual‐based genetics elusive species wild.

Language: Английский

---

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, Journal Year: 2024, Volume and Issue: 33(16)

Published: July 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

Language: Английский

---

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

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

Published: Jan. 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.

Language: Английский

---

High frequency of an otherwise rare phenotype in a small and isolated tiger population

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(39)

Published: Sept. 13, 2021

Significance Small and isolated populations have low genetic variation due to founding bottlenecks drift. Few empirical studies demonstrate visible phenotypic change associated with drift using data in endangered species. We used genomic analyses of a captive tiger pedigree identify the basis for rare trait, pseudomelanism, tigers. Genome sequencing extensive genotyping noninvasive samples across range revealed unique spatial presence this allele Similipal Tiger Reserve, India. Population confirmed that is small population. Simulations suggest intense could result observed patterns, implicating Our study highlights ongoing evolution, potentially from human-induced fragmentation, large carnivore populations.

Language: Английский

---

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

Oryx, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 6

Published: Jan. 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

Language: Английский

---

Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples

Conservation Genetics Resources, Journal Year: 2021, Volume and Issue: 13(3), P. 261 - 274

Published: April 22, 2021

Abstract For conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such have instead mostly relied on analyses of traditional markers as microsatellites (SSRs). Recently, high throughput genotyping single nucleotide polymorphisms (SNPs) has become available, expanding the use genomic methods include non-model species concern. We developed a 96-marker SNP array for in applied monitoring Scandinavian wolverine ( Gulo gulo ) population. By more than thousand we were able obtain precise estimates different types errors and sample dropout rates. The panel significantly outperforms SSR (and DBY intron sexing) both terms precision genotyping, sex assignment individual identification, well proportion samples successfully genotyped. Furthermore, offers simplified laboratory analysis pipeline with fewer needed repeatedly genotyped order reliable consensus data. In addition, utilised unique opportunity demonstrate application genotype reconstructing pedigrees wild populations, by validating method from individuals known relatedness. offering workflow improved performance, anticipate this methodology will facilitate non-invasive improve management many populations that previously been challenging survey.

Language: Английский

---

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

---