Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating

Cotter, Daniel J.; Severson, Alissa L.; Carmi, Shai; Rosenberg, Noah A.

doi:10.1016/j.tpb.2022.07.002

Cited by 2 publications

(6 citation statements)

References 27 publications

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“…This study has investigated the effect of consanguinity on X-chromosomal ROH and IBD-sharing. Under a coalescent model with consanguinity, we had previously obtained autosomal ( Severson et al 2019 , 2021 ) and X-chromosomal ( Cotter et al 2021 , 2022 ) distributions of coalescence times. Here, we have combined results on coalescence times with calculations based on properties of recombination to predict features of ROH and IBD-sharing under the model.…”

Section: Discussionmentioning

confidence: 99%

“…We showed that in relation to values seen in a nonconsanguineous population, X-chromosomal within-individual coalescence times are reduced by consanguinity to a greater extent than are X-chromosomal between-individual coalescence times ( Cotter et al 2021 , Table 1 ). Here, extending the results on genomic sharing from Palamara et al (2012) , we use the limiting coalescence-time distributions from Cotter et al (2022) to derive theoretical predictions for features of ROH and IBD-sharing on the X-chromosome and the autosomes.…”

Section: Theorymentioning

confidence: 95%

“…We have previously studied the effects of first-cousin consanguinity on coalescence times ( Cotter et al 2021 , 2022 ). Under a coalescent model, extending work of Campbell (2015) and Severson et al .…”

Section: Theorymentioning

confidence: 99%

“…One set of population-genetic signatures that has the potential to be informative about sex-specific phenomena concerns features of genomic sharing: patterns in runs of homozygosity (ROH) and identity-by-descent (IBD) sharing on autosomes and the X chromosome ( Buffalo et al 2016 ; Cai et al 2023 ). Recently, we have studied the distribution of the time to the most recent common ancestor (

) for pairs of autosomal lineages and pairs of X-chromosomal lineages in diploid coalescent models under different types of consanguinity, considering coalescence of lineages within an individual and lineages in separate individuals ( Severson et al 2019 , 2021 ; Cotter et al 2021 , 2022 ). This analysis finds that consanguinity decreases

both for lineage pairs in the same individual and for lineage pairs in individuals in different mating pairs.…”

Section: Introductionmentioning

confidence: 99%

“…Further, because genomic sharing at a locus increases with decreasing

, consanguinity increases genomic sharing both within (ROH) and between individuals (IBD) ( Severson et al 2019 ). Considering autosomal and X-chromosomal systems separately, relationships between consanguinity levels and

values produce predictions about relative values of autosomal and X-chromosomal ROH and IBD—with consanguinity that proceeds via matrilateral first-cousin mating reducing X-chromosomal coalescence times to a greater extent than patrilateral first-cousin mating ( Cotter et al 2021 , 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing

Cotter,

Severson,

Kang

et al. 2023

G3: Genes, Genomes, Genetics

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Runs of homozygosity (ROH) and identity-by-descent (IBD) sharing can be studied in diploid coalescent models by noting that ROH and IBD-sharing at a genomic site are predicted to be inversely related to coalescence times—which in turn can be mathematically obtained in terms of parameters describing consanguinity rates. Comparing autosomal and X-chromosomal coalescent models, we consider ROH and IBD-sharing in relation to consanguinity that proceeds via multiple forms of first-cousin mating. We predict that across populations with different levels of consanguinity, (1) in a manner that is qualitatively parallel to the increase of autosomal IBD-sharing with autosomal ROH, X-chromosomal IBD-sharing increases with X-chromosomal ROH, owing to the dependence of both quantities on consanguinity levels; (2) even in the absence of consanguinity, X-chromosomal ROH and IBD-sharing levels exceed corresponding values for the autosomes, owing to the smaller population size and lower coalescence time for the X chromosome than for autosomes; (3) with matrilateral consanguinity, the relative increase in ROH and IBD-sharing on the X chromosome compared to the autosomes is greater than in the absence of consanguinity. Examining genome-wide SNPs in human populations for which consanguinity levels have been estimated, we find that autosomal and X-chromosomal ROH and IBD-sharing levels generally accord with the predictions. We find that each 1% increase in autosomal ROH is associated with an increase of 2.1% in X-chromosomal ROH, and each 1% increase in autosomal IBD-sharing is associated with an increase of 1.6% in X-chromosomal IBD-sharing. For each calculation, particularly for ROH, the estimate is reasonably close to the increase of 2% predicted by the population-size difference between autosomes and X chromosomes. The results support the utility of coalescent models for understanding patterns of genomic sharing and their dependence on sex-biased processes.

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Section: Discussionmentioning

confidence: 99%

Section: Theorymentioning

confidence: 95%

Section: Theorymentioning

confidence: 99%

both for lineage pairs in the same individual and for lineage pairs in individuals in different mating pairs.…”

Section: Introductionmentioning

confidence: 99%

“…Further, because genomic sharing at a locus increases with decreasing

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing

Cotter,

Severson,

Kang

et al. 2023

G3: Genes, Genomes, Genetics

Self Cite

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On the number of genealogical ancestors tracing to the source groups of an admixed population

et al. 2023

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Members of genetically admixed populations possess ancestry from multiple source groups, and studies of human genetic admixture frequently estimate ancestry components corresponding to fractions of individual genomes that trace to specific ancestral populations. However, the same numerical ancestry fraction can represent a wide array of admixture scenarios within an individual’s genealogy. Using a mechanistic model of admixture, we consider admixture genealogically: how many ancestors from the source populations does the admixture represent? We consider African-Americans, for whom continent-level estimates produce a 75–85% value for African ancestry on average and 15–25% for European ancestry. Genetic studies together with key features of African-American demographic history suggest ranges for parameters of a simple three-epoch model. Considering parameter sets compatible with estimates of current ancestry levels, we infer that if all genealogical lines of a random African-American born during 1960–1965 are traced back until they reach members of source populations, the mean over parameter sets of the expected number of genealogical lines terminating with African individuals is 314 (interquartile range 240–376), and the mean of the expected number terminating in Europeans is 51 (interquartile range 32–69). Across discrete generations, the peak number of African genealogical ancestors occurs in birth cohorts from the early 1700s, and the probability exceeds 50% that at least one European ancestor was born more recently than 1835. Our genealogical perspective can contribute to further understanding the admixture processes that underlie admixed populations. For African-Americans, the results provide insight both on how many of the ancestors of a typical African-American might have been forcibly displaced in the Transatlantic Slave Trade and on how many separate European admixture events might exist in a typical African-American genealogy.

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Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating

Cited by 2 publications

References 27 publications

Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing

Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing

On the number of genealogical ancestors tracing to the source groups of an admixed population

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