How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India DOI Creative Commons
Megan L. Aylward, Vinay Sagar, Meghana Natesh

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1852)

Published: April 18, 2022

Unprecedented advances in sequencing technology the past decade allow a better understanding of genetic variation and its partitioning natural populations. Such inference is critical to conservation: understand species biology identify isolated We review empirical population genetics studies Endangered Bengal tigers within India, where 60-70% wild live. assess how changes marker type sampling strategy have impacted inferences by reviewing studies, presenting three novel analyses including single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, whole-mitochondrial genome network. At broad spatial scale, less than 100 SNPs revealed same patterns clustering as whole genomes (with exception one additional sampled only panel). Mitochondrial DNA indicates strong structure between northeast other regions. Two with more populations further substructure Central India. Overall, comparison varied types sample sets allows rigorous structure. Yet some limited across all these should be focus future efforts. discuss challenges our structure, address relevant questions conservation genetics. This article part theme issue 'Celebrating 50 years since Lewontin's apportionment human diversity'.

Language: Английский

fastsimcoal2: demographic inference under complex evolutionary scenarios DOI Creative Commons
Laurent Excoffier, Nina Marchi, David A. Marques

et al.

Bioinformatics, Journal Year: 2021, Volume and Issue: 37(24), P. 4882 - 4885

Published: June 22, 2021

fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from site frequency spectrum maximum-likelihood framework.Other improvements include multi-threading, handling population inbreeding, extended input file syntax facilitating description scenarios, and more efficient simulations sparsely structured populations large chromosomes.fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows MacOS, additional scripts analysis visualization simulated estimated as well detailed documentation ready-to-use examples.

Language: Английский

Citations

268
Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers DOI Creative Commons
Anubhab Khan,

Kaushalkumar Patel,

Harsh Shukla

et al.

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

Citations

145
Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data DOI Creative Commons
Ellie E. Armstrong, Ryan W. Taylor, Danny E. Miller

et al.

BMC Biology, Journal Year: 2020, Volume and Issue: 18(1)

Published: Jan. 8, 2020

Abstract Background The lion ( Panthera leo ) is one of the most popular and iconic feline species on planet, yet in spite its popularity, last century has seen massive declines for populations worldwide. Genomic resources endangered represent an important way forward field conservation, enabling high-resolution studies demography, disease, population dynamics. Here, we present a chromosome-level assembly from captive African Exotic Feline Rescue Center (Center Point, IN) as resource current subsequent genetic work sole social clade. Results Our composed 10x Genomics Chromium data, Dovetail Hi-C, Oxford Nanopore long-read data. Synteny highly conserved between lion, other genomes, domestic cat. We find variability length runs homozygosity across indicating contrasting histories recent possibly intense inbreeding bottleneck events. Demographic analyses reveal similar ancient all individuals during Pleistocene except Asiatic which shows more rapid decline size. show substantial influence reference genome choice inference demographic history heterozygosity. Conclusions demonstrate that when comparing heterozygosity estimates those inferred different references should not be compared to each other. In addition, or amount taken reflective species, these can differ substantially among individuals. This high-quality will greatly aid continuing research conservation efforts rapidly moving towards becoming danger extinction.

Language: Английский

Citations

50
Chromosome‐scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger DOI Creative Commons
Le Zhang, Tianming Lan, Chuyu Lin

et al.

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(2), P. 330 - 347

Published: June 20, 2022

Abstract The South China tiger ( Panthera tigris amoyensis , SCT) is the most critically endangered subspecies of due to functional extinction in wild. Inbreeding depression observed among captive population descended from six wild ancestors, resulting high juvenile mortality and low reproduction. We assembled characterized first SCT genome an improved Amur P. t. altaica AT) named AmyTig1.0 PanTig2.0. two genomes are continuous comprehensive any yet reported at chromosomal level. By using resequencing data 15 13 AT individuals, we investigated genomic signature inbreeding SCT. results indicated that effective size experienced three phases decline, ~5.0–1.0 thousand years ago, 100 since breeding 1963. found 43 long runs homozygosity fragments were shared by all individuals covered a total length 20.63% genome. also detected large proportion identical‐by‐descent segments across population, especially on ChrB4. Deleterious nonsynonymous single nucleotide polymorphic sites loss‐of‐function mutations with extensive potential influences, despite these loads having been purged depression. Our research provides invaluable resource for formulation genetic management policies such as developing genome‐based rescue strategy.

Language: Английский

Citations

24
Ancient DNA reveals genetic admixture in China during tiger evolution DOI
Xin Sun,

Yue-Chen Liu,

Mikhail P. Tiunov

et al.

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(11), P. 1914 - 1929

Published: Aug. 31, 2023

Language: Английский

Citations

13
Network-based hierarchical population structure analysis for large genomic data sets DOI Creative Commons
Gili Greenbaum, Amir Rubin, Alan R. Templeton

et al.

Genome Research, Journal Year: 2019, Volume and Issue: 29(12), P. 2020 - 2033

Published: Nov. 6, 2019

Analysis of population structure in natural populations using genetic data is a common practice ecological and evolutionary studies. With large genomic sets now appearing more frequently across the taxonomic spectrum, it becoming increasingly possible to reveal many hierarchical levels structure, including fine-scale clusters. To analyze these sets, methods need be appropriately suited challenges extracting multilevel from whole-genome data. Here, we present network-based approach for constructing representations The use community-detection algorithms network theory generates perspective on representation that method produces. computationally efficient, requires relatively few assumptions regarding biological processes underlie We show by analyzing model plant species

Language: Английский

Citations

42
Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild? DOI Creative Commons
Anubhab Khan,

Kaushalkumar Patel,

Subhadeep Bhattacharjee

et al.

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

Citations

36
Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation DOI Creative Commons
Qing Wang, Tianming Lan, Haimeng Li

et al.

Communications Biology, Journal Year: 2022, Volume and Issue: 5(1)

Published: Aug. 25, 2022

Poaching and trafficking have a substantial negative impact on the population growth range expansion of Chinese pangolin (Manis pentadactyla). However, recently reported activities pangolins in several sites Guangdong province China indicate promising sign for recovery this threatened species. Here, we re-sequence genomes 15 individuals perform comprehensive genomics analyses with previously published 22 individuals. These are found to be divided into three distinct populations. Multiple lines evidence existence newly discovered (CPA) comprises entirely from province. The other two populations (CPB CPC) been documented. genetic differentiation CPA CPC is extremely large (F

Language: Английский

Citations

21
Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead DOI Creative Commons
Michael J. Stanhope, Kristina Ceres, Qi Sun

et al.

iScience, Journal Year: 2022, Volume and Issue: 26(1), P. 105815 - 105815

Published: Dec. 17, 2022

Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity historical demographic comparisons other shark species. The exhibited low variation, 8.7% 2.77 Gbp in runs homozygosity (ROH) > 1 Mbp 74.4% ROH >100 kbp. 4.98 had considerably greater <1% Mbp. Both these sharks experienced precipitous declines effective population size (Ne) over last 250 thousand years. While a large Ne that may have enabled retention higher genomic data suggest possibly more concerning picture hammerhead, need evaluation additional individuals.

Language: Английский

Citations

20
High frequency of an otherwise rare phenotype in a small and isolated tiger population DOI Creative Commons
Vinay Sagar, Christopher B. Kaelin, Meghana Natesh

et al.

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

Citations

26