Abstract:Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small–isolated and two large–connected populations in India. As expected, the small–isolated p… Show more
“…Figure 3An overview of the nuclear DNA studies in Bengal tigers to date reveals population structure as inferred based on population structure analysis of these populations at optimal K . We include three previously published studies (table 1, rows 2, 4, and 5) [12,38,39] and the two nuclear marker analyses in this paper. We show this in the context of assumed differences in power to detect structure based on the sampling scheme (number of markers and number of individuals) and number of areas sampled as the number of protected areas.…”
Section: Resultsmentioning
confidence: 99%
“…For nuclear DNA the number of loci corresponds to actual number of variants used, whereas for mitochondrial DNA number of loci is the total number of base pairs sequenced.DNA typetype of variantsnumber of locinumber of individualsnumber populations sampleddata sourceanalysisnuclearSNP198 930378Khan et al . [38]this studyArmstrong et al . [36]Liu et al .…”
Section: Methodsmentioning
confidence: 96%
“…These additional analyses allow us to further compare nuclear versus mitochondrial markers and SNP versus microsatellite markers, while also assessing the impact on the number of markers and number of populations sampled. Whole-genome data (including both nuclear and mitochondrial sequence data) were available from three published studies; two that assess population structure across all tiger subspecies [ 36 , 39 ] and one on assessing inbreeding among tiger populations within India [ 38 ]. We used SNP panel data from [ 10 ], which used an extensive dataset of primarily non-invasive samples to screen for the taqpep locus mutation for pseudo-melanism within Bengal tigers as part of a panel of 123 SNP loci.…”
Section: Methodsmentioning
confidence: 99%
“…However, demographic history of Bengal tigers, modelled by Armstrong et al [36], revealed earliest divergence of the NE population 3000-5000 years prior to divergence among all other populations. This divergence is potentially why we see greatest population differentiation between the NE and other populations in the An overview of the nuclear DNA studies in Bengal tigers to date reveals population structure as inferred based on population structure analysis of these populations at optimal K. We include three previously published studies (table 1, rows 2, 4, and 5) [12,38,39] and the two nuclear marker analyses in this paper. We show this in the context of assumed differences in power to detect structure based on the sampling scheme (number of markers and number of individuals) and number of areas sampled as the number of protected areas.…”
Section: (B) Nuclear Markersmentioning
confidence: 99%
“…They also highlight strategies for mitigation, including identifying source populations for assisted translocation based on sharing of homozygous tracts. Khan et al [38] quantified inbreeding and mutation load among the three (NW, south, central) tiger populations within India using whole genomes and showed that the individuals in the NW population, which separates first in most structure analyses, have higher inbreeding on average compared to other tigers in India. They also predict potential loss of function and deleterious alleles in the tiger genomes.…”
Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60–70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics.
This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
“…Figure 3An overview of the nuclear DNA studies in Bengal tigers to date reveals population structure as inferred based on population structure analysis of these populations at optimal K . We include three previously published studies (table 1, rows 2, 4, and 5) [12,38,39] and the two nuclear marker analyses in this paper. We show this in the context of assumed differences in power to detect structure based on the sampling scheme (number of markers and number of individuals) and number of areas sampled as the number of protected areas.…”
Section: Resultsmentioning
confidence: 99%
“…For nuclear DNA the number of loci corresponds to actual number of variants used, whereas for mitochondrial DNA number of loci is the total number of base pairs sequenced.DNA typetype of variantsnumber of locinumber of individualsnumber populations sampleddata sourceanalysisnuclearSNP198 930378Khan et al . [38]this studyArmstrong et al . [36]Liu et al .…”
Section: Methodsmentioning
confidence: 96%
“…These additional analyses allow us to further compare nuclear versus mitochondrial markers and SNP versus microsatellite markers, while also assessing the impact on the number of markers and number of populations sampled. Whole-genome data (including both nuclear and mitochondrial sequence data) were available from three published studies; two that assess population structure across all tiger subspecies [ 36 , 39 ] and one on assessing inbreeding among tiger populations within India [ 38 ]. We used SNP panel data from [ 10 ], which used an extensive dataset of primarily non-invasive samples to screen for the taqpep locus mutation for pseudo-melanism within Bengal tigers as part of a panel of 123 SNP loci.…”
Section: Methodsmentioning
confidence: 99%
“…However, demographic history of Bengal tigers, modelled by Armstrong et al [36], revealed earliest divergence of the NE population 3000-5000 years prior to divergence among all other populations. This divergence is potentially why we see greatest population differentiation between the NE and other populations in the An overview of the nuclear DNA studies in Bengal tigers to date reveals population structure as inferred based on population structure analysis of these populations at optimal K. We include three previously published studies (table 1, rows 2, 4, and 5) [12,38,39] and the two nuclear marker analyses in this paper. We show this in the context of assumed differences in power to detect structure based on the sampling scheme (number of markers and number of individuals) and number of areas sampled as the number of protected areas.…”
Section: (B) Nuclear Markersmentioning
confidence: 99%
“…They also highlight strategies for mitigation, including identifying source populations for assisted translocation based on sharing of homozygous tracts. Khan et al [38] quantified inbreeding and mutation load among the three (NW, south, central) tiger populations within India using whole genomes and showed that the individuals in the NW population, which separates first in most structure analyses, have higher inbreeding on average compared to other tigers in India. They also predict potential loss of function and deleterious alleles in the tiger genomes.…”
Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60–70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics.
This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
Koalas are an iconic, endangered, Australian marsupial. Disease, habitat destruction, and catastrophic mega‐fires have reduced koalas to remnant patches of their former range. With increased likelihood of extreme weather events and ongoing habitat clearing across Australia, koala populations are vulnerable to further declines and isolation. Small, isolated populations are considered at risk when there is increased inbreeding, erosion of genomic diversity, and loss of adaptive potential, all of which reduce their ability to respond to prevailing threats. Here, we characterized the current genomic landscape of koalas using data from The Koala Genome Survey, a joint initiative between the Australian Federal and New South Wales Governments that aimed to provide a future‐proofed baseline genomic dataset across the koala's range in eastern Australia. We identified several regions of the continent where koalas have low genomic diversity and high inbreeding, as measured by runs of homozygosity. These populations included coastal sites along southeast Queensland and northern and mid‐coast New South Wales, as well as southern New South Wales and Victoria. Analysis of genomic vulnerability to future climates revealed that northern koala populations were more at risk due to the extreme expected changes in this region, but that the adaptation required was minimal compared with other species. Our genomic analyses indicate that continued development, particularly linear infrastructure along coastal sites, and resultant habitat destruction are causing isolation and subsequent genomic erosion across many koala populations. Habitat protection and the formation of corridors must be employed for all koala populations to maintain current levels of diversity. For highly isolated koala populations, active management may be the only way to improve genomic diversity in the short term. If koalas are to be conserved for future generations, reversing their genomic isolation must be a priority in conservation planning.
Dingoes arrived in Australia during the mid‐Holocene and are the top‐order terrestrial predator on the continent. Although dingoes subsequently spread across the continent, the initial founding population(s) could have been small. We investigated this hypothesis by sequencing the whole genomes of three dingoes and also obtaining the genome data from nine additional dingoes and 56 canines, including wolves, village dogs and breed dogs, and examined the signatures of bottlenecks and founder effects. We found that the nucleotide diversity of dingoes was low, 36% less than highly inbred breed dogs and 3.3 times lower than wolves. The number of runs of homozygosity (RoH) segments in dingoes was 1.6–4.7 times higher than in other canines. While examining deleterious mutational load, we observed that dingoes carried elevated ratios of nonsynonymous‐to‐synonymous diversities, significantly higher numbers of homozygous deleterious Single Nucleotide Variants (SNVs), and increased numbers of loss of function SNVs, compared to breed dogs, village dogs, and wolves. Our findings can be explained by bottlenecks and founder effects during the establishment of dingoes in mainland Australia. These findings highlight the need for conservation‐based management of dingoes and the need for wildlife managers to be cognisant of these findings when considering the use of lethal control measures across the landscape.
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