A Genealogical Look at Shared Ancestry on the X Chromosome

Buffalo, Vince; Mount, Stephen M.; Coop, Graham

doi:10.1534/genetics.116.190041

Cited by 11 publications

(8 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…g ., all individuals of a given sex) can stabilize on much shorter timescales than the expected genetic contributions of individuals. Our work supports our growing theoretical understanding of differences in expected genetic contributions (81) and reproductive values on sex chromosomes (82, 83). Further understanding and quantifying the relationship between reproductive value on autosomes versus Z chromosomes is an important question for future work.…”

Section: Discussionsupporting

confidence: 82%

Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed jay population

Driscoll

Beaudry

Cosgrove

et al. 2021

Preprint

View full text Add to dashboard Cite

Sex-biased demography, including sex-biased survival or migration, can impact allele frequency changes across the genome. In particular, we can expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well as differences in effective population size, transmission modes, and the strength and mode of selection. Here, we demonstrate the role that sex differences in life history played in shaping short-term evolutionary dynamics across the genome. We used a 25-year pedigree and genomic dataset from a long-studied population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of sex-biased demography and inheritance in shaping genome-wide allele frequency trajectories. We used gene dropping simulations to estimate individual genetic contributions to future generations and to model drift and immigration on the known pedigree. We quantified differential expected genetic contributions of males and females over time, showing the impact of sex-biased dispersal in a monogamous system. Due to female-biased dispersal, more autosomal variation is introduced by female immigrants. However, due to male-biased transmission, more Z variation is introduced by male immigrants. Finally, we partitioned the proportion of variance in allele frequency change through time due to male and female contributions. Overall, most allele frequency change is due to variance in survival and births. Males and females have similar contributions to autosomal allele frequency change, but males have higher contributions to allele frequency change on the Z chromosome. Our work shows the importance of understanding sex-specific demographic processes in accounting for genome-wide allele frequency change in wild populations.

show abstract

Section: Discussionsupporting

confidence: 82%

Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed jay population

Driscoll

Beaudry

Cosgrove

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Genetic males have only one copy of it, while females have two, which causes sex-specific inheritance and recombination patterns (for example, males must have inherited their X chromosomes from their mothers). Therefore, IBD sharing on the X chromosome can provide information about sex-specific relatedness and demography 50 . Our work here focused on the autosomes that make up most of the human genome; however, one can in principle apply ancIBD to imputed female X chromosomes.…”

Section: Discussionmentioning

confidence: 99%

Accurate detection of identity-by-descent segments in human ancient DNA

Ringbauer,

Huang,

Akbari

et al. 2023

Nat Genet

View full text Add to dashboard Cite

Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.

show abstract

“…A number of studies have explored the peculiar consequences of the distinction between genealogical and genetic ancestors ( Wiuf and Hein 1997 ; Baird et al 2003 ; Matsen and Evans 2008 ; Gravel and Steel 2015 ; Buffalo et al 2016 ; Kelleher et al 2016 ). For example, one simulation study ( Rohde et al 2004 ), based on earlier mathematical work ( Chang 1999 ), argued that the most recent genealogical ancestor shared by all living humans might have lived as few as 5,000 years ago, even though the most recent genetic ancestor lived much earlier.…”

Section: Introductionmentioning

confidence: 99%

Counting the genetic ancestors from source populations in members of an admixed population

Agranat-Tamir,

Mooney,

Rosenberg

2024

Genetics

View full text Add to dashboard Cite

In a genetically admixed population, admixed individuals possess genealogical and genetic ancestry from multiple source groups. Under a mechanistic model of admixture, we study the number of distinct ancestors from the source populations that the admixture represents. Combining a mechanistic admixture model with a recombination model that describes the probability that a genealogical ancestor is a genetic ancestor, for a member of a genetically admixed population, we count genetic ancestors from the source populations—those genealogical ancestors from the source populations who contribute to the genome of the modern admixed individual. We compare patterns in the numbers of genealogical and genetic ancestors across the generations. To illustrate the enumeration of genetic ancestors from source populations in an admixed group, we apply the model to the African-American population, extending recent results on the numbers of African and European genealogical ancestors that contribute to the pedigree of an African-American chosen at random, so that we also evaluate the numbers of African and European genetic ancestors who contribute to random African-American genomes. The model suggests that the autosomal genome of a random African-American born in the interval 1960-1965 contains genetic contributions from a mean of 162 African (standard deviation 47, interquartile range 127 to 192) and 32 European ancestors (standard deviation 14, interquartile range 21 to 43). The enumeration of genetic ancestors can potentially be performed in other diploid species in which admixture and recombination models can be specified.

show abstract

A Genealogical Look at Shared Ancestry on the X Chromosome

Cited by 11 publications

References 49 publications

Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed jay population

Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed jay population

Accurate detection of identity-by-descent segments in human ancient DNA

Counting the genetic ancestors from source populations in members of an admixed population

Contact Info

Product

Resources

About