ArticleMolecular biology and evolution2013
Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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60 citing papers in PubMed.
- Genetic Diversity and Runs of Homozygosity in Three Masu Salmon (Biomolecules · 2026Article
- Unknown Biases: Understanding How Anthropogenic Hybridization Impacts Genomic Diversity and Demographic Estimates.Animals : an open access journal from MDPI · 2026Article
- Targeted allele frequency tuning in breeding populations via alternative optimum contribution selection.Genetics · 2026Article
- Genetic parameters via predictivity in large populations under strong genomic selection.Genetics, selection, evolution : GSE · 2026Article
- Recent population history in Swedish cattle breeds.Genetics, selection, evolution : GSE · 2026Article
- PSMC-FAC: Automated Optimization of False-Negative Rate Corrections for Low-Coverage PSMC-Based Demographic Inference.Biology · 2026Article
- Farm animal evolution demonstrates hidden molecular basis of human traits.bioRxiv : the preprint server for biology · 2026Article
- A Similarity Matrix for Preserving Haplotype Diversity Amongst Parents in Genomic Selection.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2025Article
- Evaluation of genomic selection models using whole genome sequence data and functional annotation in Belgian Blue cattle.Genetics, selection, evolution : GSE · 2025Article
- Evaluation of crossbreeding strategies for improved adaptation and productivity in African smallholder cattle farms.Genetics, selection, evolution : GSE · 2025Article
- On the ability of the LR method to detect bias when there is pedigree misspecification and lack of connectedness.Genetics, selection, evolution : GSE · 2024Article
- The genomic natural history of the aurochs.Nature · 2024Article
- Accounting for the nuclear and mito genome in dairy cattle breeding-A simulation study.JDS communications · 2024Article
- Evaluation of heritability partitioning approaches in livestock populations.BMC genomics · 2024Article
- Swine global genomic resources: insights into wild and domesticated populations.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- Article
- Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer.Evolutionary applications · 2023Article
- Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.eLife · 2023Article
- A method for partitioning trends in genetic mean and variance to understand breeding practices.Genetics, selection, evolution : GSE · 2023Article
- Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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5 authors.
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Abstract
Whole-genome sequence is potentially the richest source of genetic data for inferring ancestral demography. However, full sequence also presents significant challenges to fully utilize such large data sets and to ensure that sequencing errors do not introduce bias into the inferred demography. Using whole-genome sequence data from two Holstein cattle, we demonstrate a new method to correct for bias caused by hidden errors and then infer stepwise changes in ancestral demography up to present. There was a strong upward bias in estimates of recent effective population size (Ne) if the correction method was not applied to the data, both for our method and the Li and Durbin (Inference of human population history from individual whole-genome sequences. Nature 475:493-496) pairwise sequentially Markovian coalescent method. To infer demography, we use an analytical predictor of multiloci linkage disequilibrium (LD) based on a simple coalescent model that allows for changes in Ne. The LD statistic summarizes the distribution of runs of homozygosity for any given demography. We infer a best fit demography as one that predicts a match with the observed distribution of runs of homozygosity in the corrected sequence data. We use multiloci LD because it potentially holds more information about ancestral demography than pairwise LD. The inferred demography indicates a strong reduction in the Ne around 170,000 years ago, possibly related to the divergence of African and European Bos taurus cattle. This is followed by a further reduction coinciding with the period of cattle domestication, with Ne of between 3,500 and 6,000. The most recent reduction of Ne to approximately 100 in the Holstein breed agrees well with estimates from pedigrees. Our approach can be applied to whole-genome sequence from any diploid species and can be scaled up to use sequence from multiple individuals.
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