Genomic evidence for the Chinese mountain cat as a wildcat conspecific (
            <i>Felis silvestris bieti</i>
            ) and its introgression to domestic cats

He, Yu; Xing, Yue-Ting; Meng, Hao; He, Bing; Li, Wenjing; Qi, Xin-Zhang; Zhao, Jian-You; Zhuang, Yan; Xu, Xiao; Yamaguchi, Nobuyuki; Driscoll, Carlos A.; O’Brien, Stephen J.; Luo, Shu‐Jin

doi:10.1126/sciadv.abg0221

Cited by 24 publications

(19 citation statements)

References 60 publications

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“…The persistence of these ancient and diverged lineages in the Indian subcontinent may be due in part to the region’s unique topography and paleoenvironmental history. Similar patterns of locally divergent lineages have been observed in Trans-Himalayan red pandas ( Hu et al 2020 ) and Chinese mountain cats ( Yu et al 2021 ). Together, these findings point to the importance of the Indian subcontinent and Trans-Himalayan region as refugia during the Pleistocene ( Sharma et al 2004 ; Costa 2017 ) that enabled the persistence of divergent lineages.…”

Section: Discussionsupporting

confidence: 71%

Genome Sequencing of a Gray Wolf from Peninsular India Provides New Insights into the Evolution and Hybridization of Gray Wolves

Wang

Thakur

Jhala

et al. 2022

Genome Biology and Evolution

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The gray wolf (Canis lupus) is among the few large carnivores that survived the Late Pleistocene megafaunal extinctions. Thanks to their complex history of admixture and extensive geographic range, the number of gray wolf subspecies and their phylogenetic relationships remain poorly understood. Here, we perform whole-genome sequencing of a gray wolf collected from peninsular India that was phenotypically distinct from gray wolves outside India. Genomic analyses reveal that the Indian gray wolf is an evolutionarily distinct lineage that diverged from other extant gray wolf lineages ∼110 thousand years ago. Demographic analyses suggest that the Indian wolf population declined continuously decline since separating from other gray wolves and, today, has exceptionally low genetic diversity. We also find evidence for pervasive and mosaic gene flow between the Indian wolf and African canids including African wolf, Ethiopian wolf, and African wild dog despite their current geographical separation. Our results support the hypothesis that the Indian subcontinent was a Pleistocene refugium and center of diversification and further highlight the complex history of gene flow that characterized the evolution of gray wolves.

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Section: Discussionsupporting

confidence: 71%

Genome Sequencing of a Gray Wolf from Peninsular India Provides New Insights into the Evolution and Hybridization of Gray Wolves

Wang

Thakur

Jhala

et al. 2022

Genome Biology and Evolution

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“…Previous studies have showed genetic introgression of wild relatives in domestic animals such as sheep, goat, pig, dog, cattle, yak, cattle, rabbit, horse, and chicken ( Ai et al 2015 ; Medugorac et al 2017 ; Jones et al 2018 ; Wu et al 2018 ; Lawal et al 2020 ; Wang et al 2020 ; Zheng et al 2020 ; Cao et al 2021 ; Yu et al 2021 ; ). The proportion of wild introgression varies from 0.05% to 27.3% depending on the populations of domestic animals and the relevant wild relatives ( supplementary table S48, Supplementary Material online).…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Cao

Liu

et al. 2021

Molecular Biology and Evolution

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Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole-genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms (SNPs), ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7068586C) in the 3’-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed pre-historical migrations from the Near Eastern domestication center to South-and-Southeast Asia, and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation and selection of sheep.

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“…Recent studies of Chinese random-bred cats and the local wildcat species/subspecies ( F.s. bieti ) suggest the noted introgression of this wildcat with random-bred cats in China does not explain the distinctive genetics of Far Eastern and Western European random-bred cats; further, the agricultural center near the middle Yangtze and Yellow Rivers is likely not a second domestication site for cats (Yu et al 2021 ). While these previous studies all support the domesticated F.s.…”

Section: Introductionmentioning

confidence: 99%

Genetics of randomly bred cats support the cradle of cat domestication being in the Near East

et al. 2022

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Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats’ predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor’s (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.

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Genomic evidence for the Chinese mountain cat as a wildcat conspecific ( Felis silvestris bieti ) and its introgression to domestic cats

Cited by 24 publications

References 60 publications

Genome Sequencing of a Gray Wolf from Peninsular India Provides New Insights into the Evolution and Hybridization of Gray Wolves

Genome Sequencing of a Gray Wolf from Peninsular India Provides New Insights into the Evolution and Hybridization of Gray Wolves

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Genetics of randomly bred cats support the cradle of cat domestication being in the Near East

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