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The Origins of Lactase Persistence in Europe
Open accessAbstract
Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (-13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the--13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and unlinked genetic markers in Europe and western Asia's geographic space. Using data on--13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the--13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe.
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![Figure 1 Approximate marginal posterior density estimates of demographic and evolutionary parameters. ABC was performed using regression adjustment and weighting, following acceptance at the 0.5% tolerance level [32]. The upper and lower 2.5% of each distribution are shaded. For some parameters the estimated 95% credible intervals lie outside the upper prior bound. This is a consequence of the regression adjustment stage of ABC when using rectangular priors [32]. Points in which the parameter value is close to the boundary, but with summary statistics that are distant from those observed, can have their parameter values projected outside the boundary. Parameters estimated are (A) Interdemic bidirectional geneflow, (B) Intrademic bidirectional geneflow, (C) the rate of cultural diffusion of subsistence practices, (D) the selective advantage of a LP allele among dairying farmers, (E) the proportion of individuals in a deme available for sporadic long-distance migration, and the average mobility – in number of demes moved – of (F) hunter-gatherers, (G) non-dairying farmers, and (H) dairying farmers.](/paper-figures/695f885bed8643029a839c56d8ea5cad/the-origins-of-lactase-persistence-in-europe-figure-1.jpg)
![Figure 4 Estimates of the date of origin for LP/dairying coevolution and the contribution of people living in the deme of origin for LP/dairying co-evolution, and its eight surrounding demes, to the modern European gene pool. Although not parameters of the model sensu stricto, estimates were calculated as with all model parameters by using ABC with regression adjustment and weighting, following acceptance at the 0.5% tolerance level [32]. The date of origin for LP/dairying coevolution (A) is given in thousands of years before present, and the contribution of people living in the deme of origin for LP/dairying co-evolution, and its 8 surrounding demes, to the modern European gene pool (B) is given as a percentage. The upper and lower 2.5% of each distribution are shaded.](/paper-figures/adf6eb55754443ee90554f89c146c509/the-origins-of-lactase-persistence-in-europe-figure-4.jpg)
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“although the selective sweep has been modelled as originating between Central Europe and the Balkans ~4–6,000 years BC (ref. 34).”
From Genome flux and stasis in a five millennium transect of European prehistory (2014) · cites this paper as [34]
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Citations
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“This frequently cited mechanism [9,41,42,44,63–65] was not included in our model and thus would seem to have negative explanatory power.”
BackgroundSimoons, F. J. (2001) · Ecology of Food and Nutrition · doi:10.1080/03670244.2001.9991661 · Cited by 12
Zur Frühentwicklung der Haustiere
Röhrs, M., & Herre, W. (1961) · Journal of Animal Breeding and Genetics · doi:10.1111/j.1439-0388.1961.tb01300.x · Cited by 11
Effects of culture: geographical and historical approaches.
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- JD Vigne, 2007, Was milk a “secondary product” in the Old World Neolithisation process? Its role in the domestication of cattle, sheep and goats., Anthropozoologica, 42, 9
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Population genomics of Bronze Age Eurasia
Allentoft, M. E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. B., Schroeder, H., Ahlström, T., Vinner, L., et al. (2015) · Nature · doi:10.1038/nature14507 · Cited by 1,550
Approximate Bayesian Computation (ABC) in practice
Csilléry, K., Blum, M. G. B., Gaggiotti, O. E., & François, O. (2010) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2010.04.001 · Cited by 1,302
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Self-citationApproximate Bayesian Computation in Evolution and Ecology
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“ABC has also been used to model parameters relating to selection on lactase persistence in a spatially explicit modelling framework (Itan et al., 2009; Gerbault et al., 2009).”
MethodSelf-citation
Metadata
- Authors
- Itan, Y., Powell, A., Beaumont, M. A., Burger, J., & Thomas, M. G.
- Affiliations
- University College London (GB)
- University of Reading (GB)
- Corresponding author
- Thomas, Mark G.
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-08-28
- Volume
- 5
- Issue
- 8
- Pages
- e1000491
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC2722739
- OpenAlex
- W2151227169
- Cited by
- 569
- References
- 79
- Citations by year
- 2026: 16 · 2025: 52 · 2024: 18 · 2023: 17 · 2022: 20 · 2021: 31 · 2020: 39 · 2019: 43 · 2018: 26 · 2017: 44 · 2016: 29 · 2015: 46 · 2014: 46 · 2013: 39 · 2012: 41
- FWCI
- 19.89
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Explore Bristol Research (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion, cc-by)
- Funders
- Arts and Humanities Research Council
- Topics
- Health Sciences › Medicine › Gastroenterology › Digestive system and related health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- lactase persistence, lactase gene, dairy production, gene-culture coevolution, positive selection, Neolithic, demic diffusion, approximate Bayesian computation, vitamin D, European ancestry, ancient DNA, subsistence strategies, West Asia
- MeSH terms
- Alleles, Bayes Theorem, Computer Simulation, Diet, Europe, Gene Frequency, Genetic Markers, Geography, Haplotypes, Humans, Lactose, Polymorphism, Genetic, Vitamin D, Evolution, Molecular, Computational Biology, Lactase
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