ArticleMolecular biology and evolution2013
Efficient moment-based inference of admixture parameters and sources of gene flow.
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 65 papers.
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Who cites it
65 citing papers in PubMed, 156 citations in OpenAlex.
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- Jointly representing long-range genetic similarity and spatially heterogeneous isolation-by-distance.PLoS genetics · 2025Article
- Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA.Genetics · 2024Article
- Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies.Molecular biology and evolution · 2024Article
- Morphometrics and Phylogenomics of Coca (Erythroxylum spp.) Illuminate Its Reticulate Evolution, With Implications for Taxonomy.Molecular biology and evolution · 2024Article
- Large-scale lexical and genetic alignment supports a hybrid model of Han Chinese demic and cultural diffusions.Nature human behaviour · 2024Article
- The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data.Genetics, selection, evolution : GSE · 2024Article
- Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies.bioRxiv : the preprint server for biology · 2023Article
- Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes.PLoS genetics · 2023Article
- Methods for Assessing Population Relationships and History Using Genomic Data.Annual review of genomics and human genetics · 2023Review
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- Historical Routes for Diversification of Domesticated Chickpea Inferred from Landrace Genomics.Molecular biology and evolution · 2023Article
- When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression inInsects · 2023Article
- The expansion of agriculture has shaped the recent evolutionary history of a specialized squash pollinator.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Bayesian inference of admixture graphs on Native American and Arctic populations.PLoS genetics · 2023Article
- Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing.Scientific reports · 2022Article
- Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex.Ecology and evolution · 2022Article
- The genetic architecture of phenotypic diversity in the Betta fish (Science advances · 2022Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for complicated models involving many populations. Here, we present MixMapper, an efficient, interactive method for constructing phylogenetic trees including admixture events using single nucleotide polymorphism (SNP) genotype data. MixMapper implements a novel two-phase approach to admixture inference using moment statistics, first building an unadmixed scaffold tree and then adding admixed populations by solving systems of equations that express allele frequency divergences in terms of mixture parameters. Importantly, all features of the model, including topology, sources of gene flow, branch lengths, and mixture proportions, are optimized automatically from the data and include estimates of statistical uncertainty. MixMapper also uses a new method to express branch lengths in easily interpretable drift units. We apply MixMapper to recently published data for Human Genome Diversity Cell Line Panel individuals genotyped on a SNP array designed especially for use in population genetics studies, obtaining confident results for 30 populations, 20 of them admixed. Notably, we confirm a signal of ancient admixture in European populations-including previously undetected admixture in Sardinians and Basques-involving a proportion of 20-40% ancient northern Eurasian ancestry.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.