ArticleMolecular ecology resources2020
Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer.
Article in Molecular ecology resources, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Genetics and genomics of hybridization.Nature reviews. Genetics · 2026Review
- diempy: fast and reference-free genome polarization and chromosome painting.G3 (Bethesda, Md.) · 2026Article
- On the Causes of Correlated Genomic Ancestry Across Contrasting Hybridization Histories in a Monkeyflower Species Pair.Molecular ecology · 2026Article
- Increased rates of hybridization in swordtails are associated with water pollution.Current biology : CB · 2026Article
- Increased rates of hybridization in swordtails are associated with water pollution.bioRxiv : the preprint server for biology · 2026Article
- On the causes of correlated genomic ancestry across contrasting hybridization histories in a monkeyflower species pair.bioRxiv : the preprint server for biology · 2026Article
- Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2026Article
- Predicting Migratory Survival in a Songbird Hybrid Zone Using Machine Learning.Research square · 2025Article
- Insertion of an invading retrovirus regulates a novel color trait in swordtail fish.bioRxiv : the preprint server for biology · 2025Article
- Admixture Mapping Reveals Evidence for Multiple Mitonuclear Incompatibilities in Swordtail Fish Hybrids.Molecular ecology · 2025Article
- The genetics of extrinsic postzygotic selection in a migratory divide between subspecies of the Swainson's thrush.Nature communications · 2025Article
- Pervasive gene flow despite strong and varied reproductive barriers in swordtails.Nature ecology & evolution · 2025Article
- Opportunities and challenges of local ancestry in genetic association analyses.American journal of human genetics · 2025Review
- Repeatable Selection on Large Ancestry Blocks in an Avian Hybrid Zone.Molecular biology and evolution · 2025Article
- Fluctuating reproductive isolation and stable ancestry structure in a fine-scaled mosaic of hybridizing Mimulus monkeyflowers.PLoS genetics · 2025Article
- Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism.Current biology : CB · 2024Article
- Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization.PLoS biology · 2024Article
- Pervasive gene flow despite strong and varied reproductive barriers in swordtails.bioRxiv : the preprint server for biology · 2024Article
- Experimental evolution of hybrid populations to identify Dobzhansky-Muller incompatibility loci.Ecology and evolution · 2024Article
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3 authors.
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Abstract
It has become clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference methods. Due to the diverse effects of admixture, this interest is shared across disparate fields, from human genetics to research in ecology and evolutionary biology. However, local ancestry inference methods are sensitive to a range of biological and technical parameters which can impact accuracy. Here we present paired simulation and ancestry inference pipelines, mixnmatch and ancestryinfer, to help researchers plan and execute local ancestry inference studies. mixnmatch can simulate arbitrarily complex demographic histories in the parental and hybrid populations, selection on hybrids, and technical variables such as coverage and contamination. ancestryinfer takes as input sequencing reads from simulated or real individuals, and implements an efficient local ancestry inference pipeline. We perform a series of simulations with mixnmatch to pinpoint factors that influence accuracy in local ancestry inference and highlight useful features of the two pipelines. mixnmatch is a powerful tool for simulations of hybridization while ancestryinfer facilitates local ancestry inference on real or simulated data.
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