The evolution of group differences in changing environments
Open accessAbstract
The selection pressures that have shaped the evolution of complex traits in humans remain largely unknown, and in some contexts highly contentious, perhaps above all where they concern mean trait differences among groups. To date, the discussion has focused on whether such group differences have any genetic basis, and if so, whether they are without fitness consequences and arose via random genetic drift, or whether they were driven by selection for different trait optima in different environments. Here, we highlight a plausible alternative: that many complex traits evolve under stabilizing selection in the face of shifting environmental effects. Under this scenario, there will be rapid evolution at the loci that contribute to trait variation, even when the trait optimum remains the same. These considerations underscore the strong assumptions about environmental effects that are required in ascribing trait differences among groups to genetic differences.
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It is difficult to interpret QST and PST in the presence of environmental differences between groups.
“Moreover, we highlight the difficulty of interpreting QST and PST in the presence of environmental differences between groups, adding to recent arguments by Harpak and Przeworski (13).”
From Heritability within groups is uninformative about differences among groups: Cases from behavioral, evolutionary, and statistical genetics (2024) · cites this paper as Harpak and Przeworski [13]
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“, [29,30,39,74,75,82]): The mean polygenic effect could differ substantially even when the mean trait value does not differ at all (Fig 2, case A).”
BackgroundTread Lightly Interpreting Polygenic Tests of Selection
Novembre, J., & Barton, N. H. (2018) · Genetics · doi:10.1534/genetics.118.300786 · Cited by 97 · cited 3× · see citing works
“This interpretative ambiguity is heightened by the fact that traits are inevitably somewhat arbitrary constructs [6,40,48].”
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Modes of Rapid Polygenic Adaptation
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“, residual stratification in GWAS and the poor portability of PGS [21– 23,28,84,94,95]) and deeper conceptual issues, such as the problem of selection on correlated traits [6,30,53,62,92,96,97].”
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Reading tea leaves? Polygenic scores and differences in traits among groupsPreprint
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“Given these limitations, it is no surprise that PGS distributions differ among genetic ancestry groups, and indeed, current comparisons of PGS are very difficult to interpret [29].”
BackgroundAnalysis of Polygenic Score Usage and Performance in Diverse Human PopulationsPreprint
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BackgroundDisentangling selection on genetically correlated polygenic traits using whole-genome genealogies
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The omnigenic model and polygenic prediction of complex traits.
Mathieson, I. (2021) · American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.07.003 · Cited by 100 · see citing works
“On the other hand, as others have recently observed, changing environment and stabilizing selection can generate such a signal, even if there is no directional selection.(32) Taken together, these points suggest that it is not possible to reconstruct polygenic selection on complex traits based on genomic evidence alon…”
BackgroundPopulation differentiation of polygenic score predictions under stabilizing selection
Yair, S., & Coop, G. (2022) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0416 · Cited by 58 · see citing works
Applying an evolutionary mismatch framework to understand disease susceptibility
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Addressing the challenges of polygenic scores in human genetic research
Novembre, J., Stein, C. M., Asgari, S., Gonzaga-Jauregui, C. G., Landstrom, A. P., Lemke, A. A., Li, J. Z., Mighton, C. E., Taylor, M. R., & Tishkoff, S. A. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.10.012 · Cited by 49 · see citing works
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“Most traits associated with Bergmann ’ s rule and Allen ’ s rule are complex, meaning they are both polygenic and strongly in fl uenced by the environment (Falconer and Mackay 1996; Lynch and Walsh 1998; Yang et al. 2010; Harpak and Przeworski 2021).”
Predicting skeletal stature using ancient DNA
Cox, S. L., Moots, H. M., Stock, J. T., Shbat, A., Bitarello, B. D., Nicklisch, N., Alt, K. W., Haak, W., Rosenstock, E., Ruff, C. B., et al. (2021) · American Journal of Biological Anthropology · doi:10.1002/ajpa.24426 · Cited by 30 · see citing works
Human genetic admixture through the lens of population genomics
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“This observed lack of transferability is likely explained by a combination of both technical and evolutionary reasons, including genotyping array ascertainment bias [152], allele frequency variation among cohorts due to unique population histories and selective pressures [153,154], differences in linkage disequilibriu…”
BackgroundVeller, C., & Coop, G. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002511 · Cited by 78 · see citing works
1,000 ancient genomes uncover 10,000 years of natural selection in EuropePreprint
Le, M. K., Smith, O. S., Akbari, A., Harpak, A., Reich, D., & Narasimhan, V. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.24.505188 · Cited by 75 · see citing works
Self-citationLottery, luck, or legacy. A review of “The Genetic Lottery: Why DNA matters for social equality”
Coop, G., & Przeworski, M. (2022) · Evolution; international journal of organic evolution · doi:10.1111/evo.14449 · Cited by 28 · see citing works
“Since ancestry groups differ in linkage disequilibrium patterns and allele frequencies, these factors alone lead PGS to be increasingly poor predictors of phenotypic differences in more distantly related ancestries, and they are compounded by differences in environmental effects and gene-by-environment interactions (M…”
BackgroundSelf-citationPolygenic adaptation leads to a higher reproductive fitness of native Tibetans at high altitude
He, Y., Guo, Y., Zheng, W., Yue, T., Zhang, H., Wang, B., Feng, Z., Ouzhuluobu, Cui, C., Liu, K., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.08.021 · Cited by 31 · see citing works
Substance use and common contributors to morbidity: A genetics perspective
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Veller, C., & Coop, G. (2023) · doi:10.1101/2023.02.26.530052 · Cited by 79
“Importantly, this form of selection can occur 518 even if the mean phenotype of the two populations does not change (Harpak and Przeworski 2021; Yair 519 and Coop 2022).”
BackgroundBird, K. A. (2021) · American Journal of Physical Anthropology · doi:10.1002/ajpa.24216 · Cited by 19 · see citing works
“The difficulty in distinguishing between divergent positive selection and the stabilizing selection of adjusting to a new environment while leaving the trait optimally unchanged presents another reason for caution in interpretation (Harpak & Przeworski, 2020).”
BackgroundMaintenance of Complex Trait Variation: Classic Theory and Modern Data
Koch, E. M., & Sunyaev, S. R. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.763363 · Cited by 18 · see citing works
“Such optimums and maladaptive phenotypes are defined within a given environmental context (Harpak and Przeworski, 2021).”
BackgroundThe background and legacy of Lewontin's apportionment of human genetic diversity
Novembre, J. (2022) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0406 · Cited by 20 · see citing works
Schraiber, J. G., & Edge, M. D. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2319496121 · Cited by 17 · see citing works
Socio-cultural practices may have affected sex differences in stature in Early Neolithic Europe
Cox, S. L., Nicklisch, N., Francken, M., Wahl, J., Meller, H., Haak, W., Alt, K. W., Rosenstock, E., & Mathieson, I. (2023) · Nature Human Behaviour · doi:10.1038/s41562-023-01756-w · Cited by 15 · see citing works
“However, attempting to analyse changing patterns of variation based solely on genetic data is difficult—genotypes do not necessarily equate to phenotypes due to the effect of the environment 1 .”
Smith, S. P., Shahamatdar, S., Cheng, W., Zhang, S., Paik, J., Graff, M., Haiman, C. A., Matise, T. C., North, K. E., Peters, U., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.03.005 · Cited by 17 · see citing works
Jennings, M. V., Martínez‐Magaña, J. J., Courchesne‐Krak, N. S., Cupertino, R. B., Vilar‐Ribó, L., Bianchi, S. B., Hatoum, A. S., Atkinson, E. G., Giusti‐Rodríguez, P., Montalvo‐Ortiz, J. L., et al. (2024) · EBioMedicine · doi:10.1016/j.ebiom.2024.105086 · Cited by 15 · see citing works
Drown, M. K., DeLiberto, A. N., Ehrlich, M. A., Crawford, D., & Oleksiak, M. (2021) · Royal Society Open Science · doi:10.1098/rsos.210440 · Cited by 13
Evolution of phenotypic variance in response to a novel hot environment
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Konner, M. J., & Eaton, S. B. (2023) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21987 · Cited by 14 · see citing works
“selection; consequently, such components of mammalian biology are relatively buffered against alteration.(147,148) On the other hand, it has”
BackgroundUnveiling recent and ongoing adaptive selection in human populations
Gao, Z. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002469 · Cited by 24 · see citing works
“Environmental changes can alter not only the optimal trait level (Fig 1; dashed purple arrow) but also the mean environmental contribution to the phenotype (Fig 1; solid purple arrow), which induces “genetic compensation” in the opposite direction [84,94].”
BackgroundPopulations, Traits, and Their Spatial Structure in Humans
Sohail, M., Izarraras-Gomez, A., & Vecchyo, D. O. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab272 · Cited by 10 · see citing works
“These can also change the genetic variation for a trait under stabilizing selection (Harpak and Przeworski 2021).”
BackgroundInfluentialTesting for differences in polygenic scores in the presence of confounding
Blanc, J., & Berg, J. J. (2023) · bioRxiv · doi:10.1101/2023.03.12.532301 · Cited by 8
“Finally, the interpretation of associations between polygeic scores and 545 axes of ancestry variation remains challenging in general, as differences in polygenic scores do not 546 necessarily translate into differences in phenotype [12], and associations between polygenic scores 547 and patterns of ancestry variation…”
Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy
Ebel, E. R., Uricchio, L. H., Petrov, D. A., & Egan, E. S. (2022) · Trends in Parasitology · doi:10.1016/j.pt.2021.12.007 · Cited by 11 · see citing works
“While environmental variation can complicate inference of population-specific selection [49], Africans and Europeans might be expected to have distinct MCV optima, given differences in malaria prevalence and the protective value of lowMCV.”
BackgroundEffects of ancestry, agriculture, and lactase persistence on the stature of prehistoric Europeans
Cox, S. L., Kaymak-Loveless, K., Shin, C., Alihodžić, T., Alt, K. W., Atanassova, N., Binder, D., Čaušević-Bully, M., Chohadzhiev, A., Chokhadzhiev, S., et al. (2025) · bioRxiv · doi:10.1101/2025.07.11.664181 · Cited by 6
“Though we assume a change in polygenic score reflects a change in phenotype, it can equally signal a shift in environment with no change in the resulting phenotype [16].”
Polygenic selection to a changing optimum under self–fertilisation
Hartfield, M., & Glémin, S. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011312 · Cited by 5 · see citing works
Schraiber, J. G., & Edge, M. D. (2023) · doi:10.1101/2023.11.06.565864 · Cited by 16 · see citing works
“Moreover, we highlight the difficulty of interpreting Q ST and P ST in the presence of environmental differences between groups, adding to recent arguments by Harpak and Przeworski (2021).”
On the potential for GWAS with phenotypic population means and allele-frequency data (popGWAS)
Pfenninger, M. (2025) · bioRxiv · doi:10.1101/2024.06.12.598621 · Cited by 5
“I assumed therefore that environmental influence on the phenotypic trait variance among populations has been statistically removed as much as possible (Harpak & Przeworski, 2021).”
Gene–environment interactions and the case of body mass index and obesity: How much do they matter?
Huangfu, Y., Palloni, A., Beltrán‐Sánchez, H., & McEniry, M. (2023) · PNAS Nexus · doi:10.1093/pnasnexus/pgad213 · Cited by 5 · see citing works
Predicting the direction of phenotypic difference
Gokhman, D., Harris, K. D., Carmi, S., & Greenbaum, G. (2025) · Nature Communications · doi:10.1038/s41467-025-62355-z · Cited by 8 · see citing works
“However, in phenotypes that evolve under stabilizing selection in the face of shifting environments, genetic and environmental effects canhave different or opposing trends 33,34 .”
Predicting the direction of phenotypic difference
Gokhman, D., Harris, K. D., Carmi, S., & Greenbaum, G. (2024) · bioRxiv · doi:10.1101/2024.02.22.581566 · Cited by 4
“However, in phenotypes that evolve under stabilizing selection in the face of shifting environments, genetic and environmental effects can have opposing trends (25).”
BackgroundRepresentation in genetic studies affects inference about genetic architecturePreprint
Cole, J. M., Rybacki, S., Smith, S. P., Smith, O. S., & Harpak, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.12.699135 · Cited by 1 · see citing works
Self-citationAñorve-Garibay, V., Huerta‐Sánchez, E., Sohail, M., & Vecchyo, D. O.-D. (2025) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2025.05.009 · Cited by 5 · see citing works
Testing for differences in polygenic scores in the presence of confounding
Blanc, J., & Berg, J. J. (2025) · Genetics · doi:10.1093/genetics/iyaf071 · Cited by 14 · see citing works
“Effect size heterogeneity can cause many difficulties with the interpretation of positive associations between polygenic scores and axes of population structure (as several papers have noted, see Novembre and Barton 2018; Rosenberg et al. 2019; Harpak and Przeworski 2021).”
Error rates in QST –FST comparisons depend on genetic architecture and estimation procedures
Liu, J. J., & Edge, M. D. (2024) · bioRxiv · doi:10.1101/2024.10.28.620737 · Cited by 3
“To rule out environmental explanations for trait differentiation, it is important that Q ST be estimated from individuals raised in a common garden rather than sampled directly from natural populations (Brommer, 2011; Edelaar et al., 2011; Harpak and Przeworski, 2021; Schraiber and Edge, 2024).”
BackgroundLin, L., Andersen, M. K., Stæger, F. F., Li, Z., Hanghøj, K., Linneberg, A. R., Grarup, N., Jørgensen, M. E., Hansen, T. F., Moltke, I., et al. (2024) · Genome Medicine · doi:10.1186/s13073-024-01326-3 · Cited by 5 · see citing works
“With the availability of large-scale genome-wide association studies, polygenic scores (PGS) can be used as a way to estimate mean genotypic values [2], but the Fig.”
BackgroundMethodInfluentialDoes standard adjustment for genomic population structure capture direct genetic effects?Preprint
Sotoudeh, R., Trejo, S., Harpak, A., & Conley, D. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.03.592431 · Cited by 3 · see citing works
“…in environmental effects, in fact, may induce genetic selection to restore optimal fitness; this would, in turn, lead to changes in allele frequency along the same dimensions as the ‘confounding’ environmental difference—i.e., the PC space (Harpak and Przeworski 2021; Mills and Mathieson 2022).”
BackgroundSelf-citationPolygenic prediction of human complex traits using ancient DNA
Mathieson, I. (2025) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2025.102396 · Cited by 2 · see citing works
Human genetics: An extreme fitness landscape.
Mathieson, I. (2023) · Current Biology · doi:10.1016/j.cub.2023.09.023 · Cited by 2
Quantifying direct genetic signal captured by principal component adjustment
Sotoudeh, R., Trejo, S., Harpak, A., & Conley, D. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2525790123 · Cited by 1 · see citing works
Self-citationGenomic insights into natural selection in recent human history
Skoglund, P., & Mathieson, I. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-01010-9
Human genetics: A Holocene revolution?
Mathieson, I. (2026) · Current Biology · doi:10.1016/j.cub.2026.05.015
Tread lightly interpreting group differences in genetic riskPreprint
Kleman, N., Lin, M., Gignoux, C., & Zaidi, A. A. (2026) · arXiv.org · doi:10.48550/arxiv.2605.23164
“Skin pigmentation remains a conspicuous example, yet how many other traits affected by similar processes but less easily detected[26]?”
2023 ASHG Scientific Achievement Award
Przeworski, M. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.12.014
Self-citationSocio-cultural practices may have affected sexual dimorphism in stature in Early Neolithic EuropePreprint
Cox, S. L., Nicklisch, N., Francken, M., Wahl, J., Meller, H., Haak, W., Alt, K. W., Rosenstock, E., & Mathieson, I. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.21.529406 · Cited by 1 · see citing works
- Authors
- Harpak, A., & Przeworski, M.
- Affiliations
- Columbia University (US)
- Corresponding author
- Harpak, Arbel
- Przeworski, Molly
- Venue
- PLOS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2021-01-25
- Volume
- 19
- Issue
- 1
- Pages
- e3001072
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC7861633
- OpenAlex
- W3092640579
- Cited by
- 50
- References
- 116
- Citations by year
- 2026: 5 · 2025: 7 · 2024: 9 · 2023: 9 · 2022: 11 · 2021: 8 · 2020: 1
- FWCI
- 5.37
- Type
- journal article
- Language
- en
- Update notices
- new_version (2021-02-04)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- arXiv (Cornell University) (cc-by)
- Funders
- Simons Foundation (633313)
- National Institutes of Health
- National Human Genome Research Institute (R01HG011432)
- National Institute of General Medical Sciences (R01GM121372)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Social Sciences › Psychology › Experimental and Cognitive Psychology › Evolutionary Psychology and Human Behavior
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Animal Behavior and Reproduction
- Keywords
- group differences, complex traits, stabilizing selection, environmental change, genetic drift, human evolution, selection pressure, rapid evolution
- MeSH terms
- Animals, Environment, Biological Evolution, Humans, Models, Genetic, Phenotype, Selection, Genetic, Genetic Variation, Multifactorial Inheritance, Quantitative Trait Loci, Genetic Drift, Genetic Speciation, Genetic Association Studies, Climate Change, Gene-Environment Interaction
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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