Complex patterns of sex-biased demography in canines

Phung, Tanya N.; Wayne, Robert K.; Wilson, Melissa A.; Lohmueller, Kirk E.

doi:10.1101/362731

Cited by 4 publications

(4 citation statements)

References 46 publications

(6 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Data (filtered VCF and BED files representing putatively neutral regions) available from the Dryad Digital Repository: https://doi.org/10.5061/dryad. jd820r4 [51].…”

Section: (B) Population Genetic Analysesmentioning

confidence: 99%

Complex patterns of sex-biased demography in canines

et al. 2019

Self Cite

View full text Add to dashboard Cite

The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices, such as male-biased migration and multiple paternity, have been observed in wolves, recent breeding practices could have led to female-biased mating patterns in breed dogs. For example, breed dogs are thought to have experienced a popular sire effect, where a small number of males father many offspring with a large number of females. Here we use genetic variation data to test how widespread sex-biased mating practices in canines are during different evolutionary time points. Using whole-genome sequence data from 33 dogs and wolves, we show that patterns of diversity on the X chromosome and autosomes are consistent with a higher number of reproducing males than females over ancient evolutionary history in both dogs and wolves, suggesting that mating practices did not change during early dog domestication. By contrast, since breed formation, we found evidence for a larger number of reproducing females than males in breed dogs, consistent with the popular sire effect. Our results confirm that canine demography has been complex, with opposing sex-biased processes occurring throughout their history. The signatures observed in genetic data are consistent with documented sex-biased mating practices in both the wild and domesticated populations, suggesting that these mating practices are pervasive.

show abstract

“…Data (filtered VCF and BED files representing putatively neutral regions) available from the Dryad Digital Repository: https://doi.org/10.5061/dryad. jd820r4 [51].…”

Section: (B) Population Genetic Analysesmentioning

confidence: 99%

Complex patterns of sex-biased demography in canines

et al. 2019

Self Cite

View full text Add to dashboard Cite

show abstract

“…Because whole-genome sequence data would have an increased density of SNPs, we repeated our analyses using two sets of sequence data. The first dataset represents samples from four different breeds of dog: Pug (N=15) with approximately 47X coverage (47), Labrador Retriever (N=10) with approximately 30X coverage (48), Tibetan Mastiff (N=9) with approximately 15X coverage (49), Border Collie (N=7) with approximately 24X coverage (48). The second dataset was previously published (see 16), and contains 220 samples from human populations.…”

Section: Resultsmentioning

confidence: 99%

The impact of identity-by-descent on fitness and disease in natural and domesticated Canid populations

Mooney

Yohannes

Lohmueller

2020

Preprint

Self Cite

View full text Add to dashboard Cite

Domestic dogs have experienced population bottlenecks, recent inbreeding, and strong artificial selection. These processes have simplified the genetic architecture of complex traits, allowed deleterious variation to persist, and increased both identity-by-descent (IBD) segments and runs of homozygosity (ROH). As such, dogs provide an excellent model for examining how these evolutionary processes influence disease. We assembled a dataset containing 4,414 breed dogs, 327 village dogs, and 380 wolves genotyped at 117,288 markers and phenotype data for clinical and morphological phenotypes. Breed dogs have an enrichment of IBD and ROH, relative to both village dogs and wolves and we use these patterns to show that breed dogs have experienced differing severities of bottlenecks in their recent past. We then found that ROH burden is associated with phenotypes in breed dogs, such as lymphoma. We next test the prediction that breeds with greater ROH have more disease alleles reported in Online Mendelian Inheritance in Animals (OMIA). Surprisingly, the number of causal variants identified correlates with the popularity of that breed rather than the ROH or IBD burden, suggesting an ascertainment bias in OMIA. Lastly, we use the distribution of ROH across the genome to identify genes with depletions of ROH as potential hotspots for inbreeding depression and find multiple exons where ROH are never observed. Our results suggest that inbreeding has played a large role in shaping genetic and phenotypic variation in dogs, and that there remains an excess of understudied breeds that can reveal new disease-causing variation.Significance StatementDogs and humans have coexisted together for thousands of years, but it was not until the Victorian Era that humans practiced selective breeding to produce the modern standards we see today. Strong artificial selection during the breed formation period has simplified the genetic architecture of complex traits and caused an enrichment of identity-by-descent (IBD) segments in the dog genome. This study demonstrates the value of IBD segments and utilizes them to infer the recent demography of canids, predict case-control status for complex traits, locate regions of the genome potentially linked to inbreeding depression, and to identify understudied breeds where there is potential to discover new disease-associated variants.

show abstract

“…The ratio of X chromosome to autosome diversity has long been of interest in exploring aspects of population history, particularly those that are sex-biased (15, 19, 21, 51, 69). Analyzing these ratios in the same way across 26 human populations gives us an unprecedented look at how this measure changes across a variety of demographic histories and different regions of the X chromosome.…”

Section: Discussionmentioning

confidence: 99%

Genomic and demographic processes differentially influence genetic variation across the X chromosome

Cotter

Webster

Wilson

2021

Preprint

Self Cite

View full text Add to dashboard Cite

Mutation, recombination, selection, and demography affect genetic variation across the genome. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. The X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these processes, notably the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. Here we investigate diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. We find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1 and highest on the non-recombining X chromosome, with the XTR falling in between, suggesting that the XTR (usually included in the non-recombining X) may need to be considered separately in future studies. We also observed strong population-specific effects on genetic diversity; not only does genetic variation differ on the X and autosomes among populations, but the effects of linked selection on the X relative to autosomes have been shaped by population-specific history. The substantial variation in patterns of variation across these regions provides insight into the unique evolutionary history contained within the X chromosome.Significance StatementDemography and selection affect the X chromosome differently from non-sex chromosomes. However, the X chromosome can be subdivided into multiple distinct regions that facilitate even more fine-scaled assessment of these processes. Here we study regions of the human X chromosome in 26 populations to find evidence that recombination may be mutagenic in humans and that the X-transposed region may undergo recombination. Further we observe that the effects of selection and demography act differently on the X chromosome relative to the autosomes across human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.

show abstract

Complex patterns of sex-biased demography in canines

Cited by 4 publications

References 46 publications

Complex patterns of sex-biased demography in canines

Complex patterns of sex-biased demography in canines

The impact of identity-by-descent on fitness and disease in natural and domesticated Canid populations

Genomic and demographic processes differentially influence genetic variation across the X chromosome

Contact Info

Product

Resources

About