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Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Khan, Anubhab ; Patel, Kaushalkumar ; Shukla, Harsh ; Viswanathan, Ashwin ; van der Valk, Tom ; Borthakur, Udayan ; Nigam, Parag ; Zachariah, Arun ; Jhala, Yadavendradev V ; Kardos, Marty ; Ramakrishnan, Uma

Proceedings of the National Academy of Sciences - PNAS, 2021-12, Vol.118 (49) [Periódico revisado por pares]

United States: National Academy of Sciences

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  • Título:
    Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers
  • Autor: Khan, Anubhab ; Patel, Kaushalkumar ; Shukla, Harsh ; Viswanathan, Ashwin ; van der Valk, Tom ; Borthakur, Udayan ; Nigam, Parag ; Zachariah, Arun ; Jhala, Yadavendradev V ; Kardos, Marty ; Ramakrishnan, Uma
  • Assuntos: Alleles ; Animal Distribution ; Animal populations ; Animals ; Biological Sciences ; Conservation of Natural Resources ; Gene frequency ; Gene sequencing ; Genetic diversity ; Genetic Variation ; Genome ; Genomes ; Genomics ; Habitat fragmentation ; Homozygosity ; Homozygotes ; Inbreeding ; Inbreeding depression ; India ; Load ; Missense mutation ; Mutation ; Panthera tigris ; Population ; Population genetics ; Population growth ; Population viability ; Populations ; Purging ; Tigers - genetics
  • É parte de: Proceedings of the National Academy of Sciences - PNAS, 2021-12, Vol.118 (49)
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
    Author contributions: A.K. and U.R. designed research; A.K., K.P., H.S., T.v.d.V., M.K., and U.R. performed research; U.B., P.N., A.Z., and Y.V.J. contributed samples; A.K., A.V., M.K., and U.R. analyzed data; and A.K., A.V., Y.V.J., M.K., and U.R. wrote the paper.
    Edited by Leif Andersson, Uppsala Universitet, Uppsala, Sweden, and approved October 25, 2021 (received for review November 4, 2020)
  • Descrição: 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 population had substantially higher average genomic inbreeding ( = 0.57) than the large-connected ( = 0.35 and = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.
  • Editor: United States: National Academy of Sciences
  • Idioma: Inglês
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