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Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes.

Publication ,  Journal Article
Ai, H; Zhang, M; Yang, B; Goldberg, A; Li, W; Ma, J; Brandt, D; Zhang, Z; Nielsen, R; Huang, L
Published in: Molecular biology and evolution
October 2021

Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We resequenced 80 Eurasian pigs from nine different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex-biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y chromosomes.

Duke Scholars

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Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

October 2021

Volume

38

Issue

11

Start / End Page

5051 / 5065

Related Subject Headings

  • Y Chromosome
  • Swine
  • Sus scrofa
  • Polymorphism, Single Nucleotide
  • Male
  • Humans
  • Haplotypes
  • Evolutionary Biology
  • Breeding
  • Biological Evolution
 

Citation

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Ai, H., Zhang, M., Yang, B., Goldberg, A., Li, W., Ma, J., … Huang, L. (2021). Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes. Molecular Biology and Evolution, 38(11), 5051–5065. https://doi.org/10.1093/molbev/msab230
Ai, Huashui, Mingpeng Zhang, Bin Yang, Amy Goldberg, Wanbo Li, Junwu Ma, Debora Brandt, Zhiyan Zhang, Rasmus Nielsen, and Lusheng Huang. “Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes.Molecular Biology and Evolution 38, no. 11 (October 2021): 5051–65. https://doi.org/10.1093/molbev/msab230.
Ai H, Zhang M, Yang B, Goldberg A, Li W, Ma J, et al. Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes. Molecular biology and evolution. 2021 Oct;38(11):5051–65.
Ai, Huashui, et al. “Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes.Molecular Biology and Evolution, vol. 38, no. 11, Oct. 2021, pp. 5051–65. Epmc, doi:10.1093/molbev/msab230.
Ai H, Zhang M, Yang B, Goldberg A, Li W, Ma J, Brandt D, Zhang Z, Nielsen R, Huang L. Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes. Molecular biology and evolution. 2021 Oct;38(11):5051–5065.
Journal cover image

Published In

Molecular biology and evolution

DOI

EISSN

1537-1719

ISSN

0737-4038

Publication Date

October 2021

Volume

38

Issue

11

Start / End Page

5051 / 5065

Related Subject Headings

  • Y Chromosome
  • Swine
  • Sus scrofa
  • Polymorphism, Single Nucleotide
  • Male
  • Humans
  • Haplotypes
  • Evolutionary Biology
  • Breeding
  • Biological Evolution