A latitudinal gradient of reference genomes DOI Creative Commons
Ethan Linck, Carlos Daniel Cadena

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 13, 2024

Abstract Global inequality rooted in legacies of colonialism and uneven development can lead to systematic biases scientific knowledge. In ecology evolutionary biology, findings, funding research effort are disproportionately concentrated at high latitudes while biological diversity is low latitudes. This discrepancy may have a particular influence fields like phylogeography, molecular conservation genetics, where the rise genomics has increased cost technical expertise required apply state-of-the-art methods. Here we ask whether fundamental biogeographic pattern—the latitudinal gradient species richness tetrapods—is reflected available reference genomes, an important data resource for various applications tools biodiversity conservation. We also sequencing approaches differ between South North, reviewing last five years genetics four leading journals. find that extant genomes scarce relative latitudes, reduced-representation whole-genome applied taxa North. conclude with recommendations close this gap improve international collaborations genomics.

Language: Английский

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
On the road to losing connectivity: Faecal samples provide genome‐wide insights into anthropogenic impacts on two large herbivore species in central India DOI Creative Commons
Abhinav Tyagi, Nidhi Yadav, Awadhesh Pandit

et al.

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

Citations

4
Swatting Flies: Biting Insects as Non‐Invasive Samplers for Mammalian Population Genomics DOI Creative Commons
Anubhab Khan,

Ryan Carter,

Chengetai D. Mpamhanga

et al.

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

Citations

0
Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high-throughput sequencing DOI Creative Commons
Anubhab Khan, Yulianto Yulianto, Sabhrina Gita Aninta

et al.

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

Citations

0
Trace DNA from kill sites identifies individual predators DOI
Himanshu Chhattani, Abishek Harihar,

Rounak Dean

et al.

Biological Conservation, Journal Year: 2025, Volume and Issue: 307, P. 111117 - 111117

Published: April 28, 2025

Language: Английский

Citations

0
A Latitudinal Gradient of Reference Genomes DOI Creative Commons
Ethan Linck, Carlos Daniel Cadena

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 14, 2024

ABSTRACT Global inequality rooted in legacies of colonialism and uneven development can lead to systematic biases scientific knowledge. In ecology evolutionary biology, findings, funding research effort are disproportionately concentrated at high latitudes, while biological diversity is low latitudes. This discrepancy may have a particular influence fields like phylogeography, molecular conservation genetics, where the rise genomics has increased cost technical expertise required apply state‐of‐the‐art methods. Here, we ask whether fundamental biogeographic pattern—the latitudinal gradient species richness tetrapods—is reflected available reference genomes, an important data resource for various applications tools biodiversity conservation. We also sequencing approaches differ between South North, reviewing last 5 years genetics four leading journals. find that extant genomes scarce relative latitudes reduced representation whole‐genome applied taxa North. conclude with recommendations close this gap improve international collaborations genomics.

Language: Английский

Citations

3
Genome‐wide single nucleotide polymorphism (SNP) markers from fecal samples reveal anthropogenic impacts on connectivity: case of a small carnivore in the central Indian landscape DOI
Abhinav Tyagi, Anubhab Khan, Prachi Thatte

et al.

Animal Conservation, Journal Year: 2022, Volume and Issue: 25(5), P. 648 - 659

Published: March 15, 2022

Abstract Maintaining gene flow among fragmented habitat patches is critical for the long‐term persistence of wild species. Landscape genetics tools are often used to understand impact landscape features on populations. The ability detect relationship between and depends power genetic used, which increases with number genotyped loci. Next‐generation sequencing (NGS) based methods allow genotyping a high loci but challenging implement non‐invasive samples, commonly in conservation research. Here we assess heterogeneity jungle cat ( Felis chaus ) movement using genome‐wide single nucleotide polymorphism (SNP) markers obtained from fecal methylation‐based DNA (MBD) enrichment method. We successfully 20 individuals at 2246 SNP compared our results previous study that microsatellite 93 individuals. Our demonstrate efficiency robustness MBD approach samples generating data endangered cryptic species concern. analyses revealed roads human‐dominated land‐use negatively central India. explicitly quantified uncertainty concluded several thousand SNPs fewer provide more than tens microsatellites individuals, quantifying effects flow. insight into impacts anthropogenic modification an often‐ignored small carnivore Insights connectivity such can help policymakers wildlife managers move beyond contingent charismatic devise holistic landscape‐level management plans multiple carnivores.

Language: Английский

Citations

10
The year of the tiger and the year of tiger genomes! DOI Creative Commons
Anubhab Khan

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(2), P. 327 - 329

Published: Oct. 29, 2022

Tigers are endangered apex predators. They typify species because they elusive, rare, and face numerous threats across their range. also symbolize conservation. However, it is very difficult to study tigers of stated nature. Also, tiger conservation a geopolitically sensitive topic, making use the studies propose evidence-based management that allows recovery, especially in context genetics. Zhang et al. (Mol. Ecol. Resour., 2022) have created valuable rare resources aid community conserving tigers. First, present chromosome level genome assemblies South China an Amur tiger. Second, whole sequences 16 captive Additionally, by using model demographic history these populations, estimate inbreeding potential captivity. This approach particularly important genetic now only remaining option for tigers, extinct wild. In other words, individuals our hope some day restoring wild populations

Language: Английский

Citations

10
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

Citations

8
Recapitulating whole genome based population genetic structure for Indian wild tigers through an ancestry informative marker panel DOI Open Access
Anubhab Khan,

Swathy M. Krishna,

Uma Ramakrishnan

et al.

Heredity, Journal Year: 2021, Volume and Issue: 128(2), P. 88 - 96

Published: Dec. 2, 2021

Language: Английский

Citations

8