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The effect of consanguinity on coalescence times on the X chromosome

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  • Cotter, Daniel J.
  • Severson, Alissa L.
  • Rosenberg, Noah A.

Abstract

Consanguineous unions increase the frequency at which identical genomic segments are inherited along separate paths of descent, decreasing coalescence times for pairs of alleles drawn from an individual who is the offspring of a consanguineous pair. For an autosomal locus, it has recently been shown that the mean time to the most recent common ancestor (TMRCA) for two alleles in the same individual and the mean TMRCA for two alleles in two separate individuals both decrease with increasing consanguinity in a population. Here, we extend this analysis to the X chromosome, considering X-chromosomal coalescence times under a coalescent model with diploid, male–female mating pairs. We examine four possible first-cousin mating schemes that are equivalent in their effects on autosomes, but that have differing effects on the X chromosome: patrilateral-parallel, patrilateral-cross, matrilateral-parallel, and matrilateral-cross. In each mating model, we calculate mean TMRCA for X-chromosomal alleles sampled either within or between individuals. We describe a consanguinity effect on X-chromosomal TMRCA that differs from the autosomal pattern under matrilateral but not under patrilateral first-cousin mating. For matrilateral first cousins, the effect of consanguinity in reducing TMRCA is stronger on the X chromosome than on the autosomes, with an increased effect of parallel-cousin mating compared to cross-cousin mating. The theoretical computations support the utility of the model in understanding patterns of genomic sharing on the X chromosome.

Suggested Citation

  • Cotter, Daniel J. & Severson, Alissa L. & Rosenberg, Noah A., 2021. "The effect of consanguinity on coalescence times on the X chromosome," Theoretical Population Biology, Elsevier, vol. 140(C), pages 32-43.
    • Handle: RePEc:eee:thpobi:v:140:y:2021:i:c:p:32-43
    DOI: 10.1016/j.tpb.2021.03.004
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    References listed on IDEAS

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    1. Severson, Alissa L. & Carmi, Shai & Rosenberg, Noah A., 2021. "Variance and limiting distribution of coalescence times in a diploid model of a consanguineous population," Theoretical Population Biology, Elsevier, vol. 139(C), pages 50-65.
    2. Ramachandran, Sohini & Rosenberg, Noah A. & Feldman, Marcus W. & Wakeley, John, 2008. "Population differentiation and migration: Coalescence times in a two-sex island model for autosomal and X-linked loci," Theoretical Population Biology, Elsevier, vol. 74(4), pages 291-301.
    3. Carmi, Shai & Wilton, Peter R. & Wakeley, John & Pe’er, Itsik, 2014. "A renewal theory approach to IBD sharing," Theoretical Population Biology, Elsevier, vol. 97(C), pages 35-48.
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    1. Cotter, Daniel J. & Severson, Alissa L. & Carmi, Shai & Rosenberg, Noah A., 2022. "Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating," Theoretical Population Biology, Elsevier, vol. 147(C), pages 1-15.

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