An efficient algorithm for estimating population history from genetic data
Open accessPublished version of a preprint
Abstract
Abstract The Legofit statistical package uses genetic data to estimate parameters describing population history. Previous versions used computer simulations to estimate probabilities, an approach that limited both speed and accuracy. This article describes a new deterministic algorithm, which makes Legofit faster and more accurate. The speed of this algorithm declines as model complexity increases. With very complex models, the deterministic algorithm is slower than the stochastic one. In an application to simulated data sets, the estimates produced by the deterministic and stochastic algorithms were essentially identical. Reanalysis of a human data set replicated the findings of a previous study and provided increased support for the hypotheses that (a) early modern humans contributed genes to Neanderthals, and (b) a “superarchaic” population (which separated from all other humans early in the Pleistocene) was either large or deeply subdivided.
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There was interbreeding between Eurasian archaic populations and a distantly-related population, which diverged early in the Pleistocene.
“There was also interbreeding between Eurasian archaic populations and a distantlyrelated population, which diverged early in the Pleistocene 30,31 .”
From The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus <i>Homo</i> (2026) · cites this paper as [30]
Cites
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584 · see citing works
Neanderthal-Denisovan ancestors interbred with a distantly related hominin
Rogers, A. R., Harris, N. S., & Achenbach, A. A. (2020) · Science Advances · doi:10.1126/sciadv.aay5483 · Cited by 77 · see citing works
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The Genetic Legacy of Introgression from Two Deeply Divergent Lineages in the Genus <i>Homo</i>
Rogers, A. R., Islam, M. T., Brand, C. M., & Webster, T. H. (2026) · bioRxiv · doi:10.64898/2026.03.22.713509
Self-citation
- Authors
- Rogers, A. R.
- Affiliations
- University of Utah (US)
- Corresponding author
- Rogers, Alan R.
- ORCID
- Rogers, Alan R.
- Venue
- Peer Community Journal
- Publisher
- Peer Community In
- Published
- 2022-06-07
- Volume
- 2
- ISSN
- 2804-3871 (ISSN-L)
- OpenAlex
- W3123963638
- Cited by
- 7
- References
- 2
- Citations by year
- 2024: 2 · 2023: 1 · 2022: 2 · 2021: 2
- FWCI
- 0.75
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- cc-by
- Locations
- Peer Community Journal (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- OSF Preprints (OSF Preprints) (submittedVersion)
- Funders
- National Science Foundation (1945782, 1638840)
- University of Utah
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- deterministic algorithms, stochastic simulation, human population genetics, Neanderthal admixture, population subdivision, Pleistocene
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