The DOI matches its Crossref record; 83 of the 83 references it cites were found in a registry or an index.
On the limits of fitting complex models of population history to f-statistics
Open accessAbstract
Our understanding of population history in deep time has been assisted by fitting admixture graphs (AGs) to data: models that specify the ordering of population splits and mixtures, which along with the amount of genetic drift and the proportions of mixture, is the only information needed to predict the patterns of allele frequency correlation among populations. The space of possible AGs relating populations is vast, and thus most published studies have identified fitting AGs through a manual process driven by prior hypotheses, leaving the majority of alternative models unexplored. Here, we develop a method for systematically searching the space of all AGs that can incorporate non-genetic information in the form of topology constraints. We implement this findGraphs tool within a software package, ADMIXTOOLS 2 , which is a reimplementation of the ADMIXTOOLS software with new features and large performance gains. We apply this methodology to identify alternative models to AGs that played key roles in eight publications and find that in nearly all cases many alternative models fit nominally or significantly better than the published one. Our results suggest that strong claims about population history from AGs should only be made when all well-fitting and temporally plausible models share common topological features. Our re-evaluation of published data also provides insight into the population histories of humans, dogs, and horses, identifying features that are stable across the models we explored, as well as scenarios of populations relationships that differ in important ways from models that have been highlighted in the literature.
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Cites
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“Unsurprisingly, most of these claims failed to replicate in follow- up studies in independent sets of samples (Ioannidis, 2005; Border et al., 2019; Collins et al., 2012; Duncan et al., 2019).”
ResultA draft sequence of the Neandertal genome
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Self-citationInference of population splits and mixtures from genome-wide allele frequency data
Pickrell, J. K., & Pritchard, J. K. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002967 · Cited by 2,731
The complete genome sequence of a Neanderthal from the Altai Mountains
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Self-citationMassive migration from the steppe was a source for Indo-European languages in Europe
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Kim, K., Kim, D., Hanotte, O., Lee, C., Kim, H., & Jeong, C. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad257 · Cited by 24
Population genomics of the muskox' resilience in the near absence of genetic variation
Pečnerová, P., Lord, E., Garcia‐Erill, G., Hanghøj, K., Rasmussen, M. S., Meisner, J., Liu, X., van der Valk, T., Santander, C. G., Quinn, L., et al. (2024) · Molecular Ecology · doi:10.1111/mec.17205 · Cited by 19
BioMaster: Multi-agent System for Automated Bioinformatics Analysis Workflow
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Past human expansions shaped the spatial pattern of Neanderthal ancestry
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Metadata
- Authors
- Maier, R., Flegontov, P., Flegontova, O., Işıldak, U., Changmai, P., & Reich, D.
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2023-06-29
- Volume
- 12
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W4365483636
- Cited by
- 270
- References
- 83
- FWCI
- 38.23
- Type
- journal article
- Language
- en
- Open access
- gold
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