DETECTING RANGE EXPANSIONS FROM GENETIC DATA
Open accessAbstract
We propose a method that uses genetic data to test for the occurrence of a recent range expansion and to infer the location of the origin of the expansion. We introduce a statistic ψ (the directionality index) that detects asymmetries in the 2D allele frequency spectrum of pairs of population. These asymmetries are caused by the series of founder events that happen during an expansion and they arise because low frequency alleles tend to be lost during founder events, thus creating clines in the frequencies of surviving low-frequency alleles. Using simulations, we show that ψ is more powerful for detecting range expansions than both FST and clines in heterozygosity. We also show how we can adapt our approach to more complicated scenarios such as expansions with multiple origins or barriers to migration and we illustrate the utility of ψ by applying it to a data set from modern humans.
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Requiring a minor allele frequency of 0.1 or lower in the merged Tonga, Samoa, and Fiji outgroup yielded 228,262 SNPs, whereas requiring minor alleles to be fixed in the Taiwan outgroup yielded 137,383 SNPs.
“(A 0.1 or lower minor allele frequency was required in the merged Tonga, Samoa, Fiji outgroup samples, yielding 228,262 SNPs, as opposed to the more stringent requirement of minor alleles being fixed in the Taiwan outgroup samples, following the procedure of Zhan et. al37, which yielded only 137,383 SNPs.)”
From Paths and timings of the peopling of Polynesia inferred from genomic networks (2021) · cites this paper as [37]
The Results > Application section describes an analysis of human populations using several hundred thousand loci, but gives neither of the claimed SNP counts. Searches for the Tonga–Samoa–Fiji and Taiwan outgroups, the two counts, and the stated allele-frequency criteria found no passage addressing those filters. (LLM, conf=0.76)
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Paths and timings of the peopling of Polynesia inferred from genomic networks
Ioannidis, A. G., Blanco-Portillo, J., Sandoval, K., Hagelberg, E., Barberena-Jonas, C., Hill, A. V. S., Rodríguez-Rodríguez, J. E., Fox, K., Robson, K., Haoa-Cardinali, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03902-8 · Cited by 124 · see citing works
The effective founder effect in a spatially expanding population
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- Authors
- Peter, B. M., & Slatkin, M.
- Affiliations
- University of California, Berkeley (US)
- Venue
- Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-08-27
- Volume
- 67
- Issue
- 11
- Pages
- 3274-3289
- ISSN
- 0014-3820 (ISSN-L)
- PMC
- PMC4282923
- OpenAlex
- W1952666299
- Cited by
- 173
- References
- 58
- Citations by year
- 2026: 10 · 2025: 11 · 2024: 14 · 2023: 21 · 2022: 22 · 2021: 17 · 2020: 11 · 2019: 15 · 2018: 21 · 2017: 11 · 2016: 7 · 2015: 7 · 2014: 5 · 2013: 1
- FWCI
- 4.42
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Evolution (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (R01-GM40282)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- range expansion, allele frequency spectrum, founder events, clinal variation, FST, heterozygosity, multiple origins, migration barriers, modern human populations, population genetics
- MeSH terms
- Gene Frequency, Genetics, Population, Geography, Humans, Models, Genetic, Population Dynamics, Genetic Variation
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