Conservation priorities for endangered Indian tigers through a genomic lens

Natesh, Meghana; Atla, Goutham; Nigam, Parag; Jhala, Yadvendradev V.; Zachariah, Arun; Borthakur, Udayan; Ramakrishnan, Uma

doi:10.1038/s41598-017-09748-3

Cited by 36 publications

(57 citation statements)

References 65 publications

(72 reference statements)

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“…2009). Natesh et al . (in press) considered the genetic diversity and structure across the Indian subcontinent of tigers, a species that now occupies 7% of its historical range.…”

Section: Examplesmentioning

confidence: 99%

“…Using 10,184 SNPs, Natesh et al . (in press) identified a north-western subpopulation (dark blue cluster i in Figure 6A), a north/northeastern subpopulation (green cluster II), a central subpopulation (orange cluster III), and a southern subpopulation (purple cluster IV).…”

Section: Examplesmentioning

confidence: 99%

“…The exact relationship between subpopulations, however was unclear. From the pairwise F ST values reported in Table 2 of Natesh et al . (in press), levels of divergence between subpopulation I and all other subpopulations were high, suggesting isolation with limited gene flow.…”

Section: Examplesmentioning

confidence: 99%

“…(in press), levels of divergence between subpopulation I and all other subpopulations were high, suggesting isolation with limited gene flow. fastSTRUCTURE analyses performed by Natesh et al . (in press) suggested connectivity between subpopulations II and III (Figure 6A).…”

Section: Examplesmentioning

confidence: 99%

“…(A) Map of the distribution of tigers with sampling locations, and fastSTRUCTURE plot. The figure is adapted from Natesh et al . (in press).…”

Section: Examplesmentioning

confidence: 99%

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Coalescent theory of migration network motifs

Alcala

Goldberg

Ramakrishnan

et al. 2017

Preprint

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Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, F ST , and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a large mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with small density have the largest F ST . In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into several disconnected components. We illustrate our results using two example datasets-sky island birds of genus Brachypteryx and Indian tigers-identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity and for designing strategies to alter population migration networks to maximize genetic variation in the context of conservation of endangered species.KEYWORDS coalescent theory; genetic differentiation; network; population structure Correctly predicting the effect of connectivity patterns on the 8 expected amount of nucleotide diversity and genetic differentia-9 tion is important in a range of settings. In population genetics,

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“…2009). Natesh et al . (in press) considered the genetic diversity and structure across the Indian subcontinent of tigers, a species that now occupies 7% of its historical range.…”

Section: Examplesmentioning

confidence: 99%

Section: Examplesmentioning

confidence: 99%

Section: Examplesmentioning

confidence: 99%

Section: Examplesmentioning

confidence: 99%

“…(A) Map of the distribution of tigers with sampling locations, and fastSTRUCTURE plot. The figure is adapted from Natesh et al . (in press).…”

Section: Examplesmentioning

confidence: 99%

See 3 more Smart Citations

Coalescent theory of migration network motifs

Alcala

Goldberg

Ramakrishnan

et al. 2017

Preprint

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Can Bengal Tiger (Panthera tigris tigris) endure the future climate and land use change scenario in the East Himalayan Region? Perspective from a multiple model framework

Deka,

Ali,

Ahamad

et al. 2023

Ecology and Evolution

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Large mammals are susceptible to land use and climate change, unless they are safeguarded within large, protected areas. It is crucial to comprehend the effects of these changes on mammals to develop a conservation plan. We identified ecological hotspots that can sustain an ecosystem for the endangered Bengal tiger (Panthera tigris tigris), an umbrella species. We developed three distinct ensemble species distribution models (SDMs) for the Bengal tiger in the Indian East Himalayan Region (IEHR). The first model served as the baseline and considered habitat type, climate, land cover, and anthropogenic threats. The second model focused on climate, land use, and anthropogenic threats, the third model focused on climate variables. We projected the second and third models onto two future climate scenarios: RCP 4.5 and RCP 8.5. We evaluated the threats possess to protected areas within eco‐sensitive zone based on the potential tiger habitat. Finally, we compared the potential habitat with the IUCN tiger range. Our study revealed that the Brahmaputra valley will serve as the primary habitat for tigers in the future. However, considering the projected severe climate scenarios, it is anticipated that tigers will undergo a range shift towards the north and east, especially in high‐altitude regions. Very high conservation priority areas, which make up 3.4% of the total area, are predominantly located in the riverine corridor of Assam. High conservation priority areas, which make up 5.5% of total area are located in Assam and Arunachal Pradesh. It is important to note that conservation priority areas outside of protected areas pose a greater threat to tigers. We recommend reassessing the IUCN Red List's assigned range map for tigers in the IEHR, as it is over‐predicted. Our study has led us to conclude both land use and climate change possess threats to the future habitat of tigers. The outcomes of our study will provide crucial information on identifying habitat hotspots and facilitate appropriate conservation planning efforts.

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

Khan

Patel

Bhattacharjee

et al. 2020

Ecology and Evolution

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

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Conservation priorities for endangered Indian tigers through a genomic lens

Cited by 36 publications

References 65 publications

Coalescent theory of migration network motifs

Coalescent theory of migration network motifs

Can Bengal Tiger (Panthera tigris tigris) endure the future climate and land use change scenario in the East Himalayan Region? Perspective from a multiple model framework

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

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