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

---

Conservation and the Genomics of Populations

Oxford University Press eBooks, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 10, 2022

Abstract Loss of biodiversity is among the greatest problems facing world today. Conservation and Genomics Populations gives a comprehensive overview essential background, concepts, tools needed to understand how genetic information can be used conserve species threatened with extinction, manage ecological or commercial importance. New molecular techniques, statistical methods, computer programs, principles, methods are becoming increasingly useful in conservation biological diversity. Using balance data theory, coupled basic applied research examples, this book examines phenotypic variation natural populations, principles mechanisms evolutionary change, interpretation from these conservation. The includes examples plants, animals, microbes wild captive populations. This third edition has been thoroughly revised include advances genomics contains new chapters on population genomics, monitoring, genetics practice, as well sections climate emerging diseases, metagenomics, more. More than one-third references were published after previous edition. Each 24 Appendix end Guest Box written by an expert who provides example presented chapter their own work. for advanced undergraduate graduate students genetics, resource management, biology, professional biologists policy-makers working wildlife habitat management agencies. Much will also interest nonprofessionals curious about role

Language: Английский

---

Maintaining tiger connectivity and minimizing extinction into the next century: Insights from landscape genetics and spatially-explicit simulations

Biological Conservation, Journal Year: 2017, Volume and Issue: 218, P. 181 - 191

Published: Dec. 30, 2017

Language: Английский

---

Protected areas and biodiversity conservation in India

Biological Conservation, Journal Year: 2019, Volume and Issue: 237, P. 114 - 124

Published: July 3, 2019

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

---

Empowering conservation practice with efficient and economical genotyping from poor quality samples

Methods in Ecology and Evolution, Journal Year: 2019, Volume and Issue: 10(6), P. 853 - 859

Published: April 10, 2019

Abstract Moderate‐ to high‐density genotyping (100 + SNPs) is widely used determine and measure individual identity, relatedness, fitness, population structure migration in wild populations. However, these important tools are difficult apply when high‐quality genetic material unavailable. Most genomic developed for DNA sources from laboratory or medical settings. As a result, most data market field settings limited easily amplified mitochondrial few microsatellites. To enable conservation contexts, we next‐generation sequencing of multiplex PCR products very low‐quality extracted faeces, hair cooked samples. We demonstrated utility wide‐ranging potential application endangered tigers tracking commercial trade Caribbean queen conch. genotyped 100 SNPs degraded tiger samples identify individuals, discern close relatives detect differentiation. Co‐occurring carnivores do not amplify (e.g. Indian dog/dhole) monomorphic leopard). Sixty‐two conch fritters field‐collected were test relatedness structure. provide proof concept rapid, simple, cost‐effective scalable method (for both number loci), framework that can be applied other scenarios previously by These approaches critical advance wildlife monitoring forensics, open the door field‐ready testing, will strengthen use science policy decisions trade.

Language: Английский

---

Evolutionary principles and genetic considerations for guiding conservation interventions under climate change

Global Change Biology, Journal Year: 2020, Volume and Issue: 27(3), P. 475 - 488

Published: Sept. 26, 2020

Abstract Impacts of climate change are apparent in natural systems around the world. Many species and will continue to struggle persist their current location as preferred environment changes. Traditional conservation efforts aiming prevent local extinctions have focused on two aspects that theoretically enhance genetic diversity—population connectivity population size—through ‘passive interventions’ (such protected areas corridors). However, exceptionally rapid loss biodiversity we experiencing result anthropogenic has shifted approaches more ‘active rewilding, assisted gene flow, evolution, artificial selection, engineering). We integrate genetic/genomic into an evolutionary biology framework order discuss with scientists, managers decision makers about opportunities risks interventions need careful consideration avoid unwanted outcomes.

Language: Английский

---

Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(11)

Published: Sept. 15, 2023

Conservation genetic analyses of many endangered species have been based on genotyping microsatellite loci and sequencing short fragments mtDNA. The increase in power resolution afforded by whole genome approaches may challenge conclusions made limited numbers maternally inherited haploid markers. Here, we provide a matched comparison versus control region (CR) for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated "stronghold" populations otter Britain, derived from regional that survived the population crash 1950s-1980s. Using resequencing data 45 samples across British stronghold populations, confirmed some aspects structure previous marker-driven studies. Importantly, showed genomic signals bottlenecks evidence surveys. Unexpectedly, two strongly divergent mitochondrial lineages were undetectable using CR fragments, east England distinct surprisingly variable. We hypothesize this previously unsuspected variability derive past releases other, non-British source around time bottleneck. Our highlights even reasonably well-studied harbor surprises, if studied modern high-throughput methods.

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

---

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

---