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Cited by 165Evolution and Genetic DynamicsGenetic diversity and population structureForensic and Genetic Research

Parallel adaptation: one or many waves of advance of an advantageous allele?

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Ralph, Peter, Coop, Graham·2010·Genetics
DOI 10.1534/genetics.110.119594PMC PMC2954473
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Abstract

Models for detecting the effect of adaptation on population genomic diversity are often predicated on a single newly arisen mutation sweeping rapidly to fixation. However, a population can also adapt to a new environment by multiple mutations of similar phenotypic effect that arise in parallel, at the same locus or different loci. These mutations can each quickly reach intermediate frequency, preventing any single one from rapidly sweeping to fixation globally, leading to a “soft” sweep in the population. Here we study various models of parallel mutation in a continuous, geographically spread population adapting to a global selection pressure. The slow geographic spread of a selected allele due to limited dispersal can allow other selected alleles to arise and start to spread elsewhere in the species range. When these different selected alleles meet, their spread can slow dramatically and so initially form a geographic patchwork, a random tessellation, which could be mistaken for a signal of local adaptation. This spatial tessellation will dissipate over time due to mixing by migration, leaving a set of partial sweeps within the global population. We show that the spatial tessellation initially formed by mutational types is closely connected to Poisson process models of crystallization, which we extend. We find that the probability of parallel mutation and the spatial scale on which parallel mutation occurs are captured by a single compound parameter, a characteristic length, which reflects the expected distance a spreading allele travels before it encounters a different spreading allele. This characteristic length depends on the mutation rate, the dispersal parameter, the effective local density of individuals, and to a much lesser extent the strength of selection. While our knowledge of these parameters is poor, we argue that even in widely dispersing species, such parallel geographic sweeps may be surprisingly common. Thus, we predict that as more data become available, many more examples of intraspecies parallel adaptation will be uncovered.

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  • The fact that the sweeps at SLC24A5, SLC45A2, and TYRP1 occurred well after the divergence of Europeans and East Asians increased the chance of convergent adaptation by shortening the delay between local adaptive mutations relative to the time necessary for advantageous variants to spread across Eurasia.

    “Moreover, the fact that the sweeps at SLC24A5, SLC45A2, and TYRP1 occurred well after the divergence of Europeans and East Asians increased the chance of convergent adaptation by shortening the delay between local adaptive mutations relative to the time necessary for advantageous variants to spread across Eurasia (Ralph and Coop 2010).”

    From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Ralph and Coop 2010

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  • Recent theoretical work has shown that independent evolution may be an important determinant of geographic patterns of adaptation and could explain the observed scarcity of continental-wide sweeps in human populations, even when selective pressures are homogeneous.

    “Recent theoretical work (Ralph and Coop 2010) has shown that independent evolution may be an important determinant of geographic patterns of adaptation and could explain the observed scarcity of continental-wide sweeps in human populations (Coop et al. 2009;Pickrell et al. 2009), even when selective pressures are homogeneous.”

    From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Ralph and Coop 2010

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  1. [40]40. Kingman, J. F. C., 1993 Poisson Processes (Oxford Studies in Proba- bility, Vol. 3). Clarendon Press/Oxford University Press/Oxford Science Publications, New York.

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Authors
Ralph, P., & Coop, G.
Affiliations
University of California, Davis (US)
Corresponding author
Ralph, Peter
ORCID
Venue
Genetics
Publisher
Oxford University Press (OUP)
Published
2010-10-01
Volume
186
Issue
2
Pages
647-668
ISSN
  • 0016-6731 (ISSN-L)
  • 1943-2631
DOI
10.1534/genetics.110.119594
PMC
PMC2954473
OpenAlex
W2122577020
Cited by
165
References
125
Citations by year
2026: 4 · 2025: 8 · 2024: 6 · 2023: 7 · 2022: 8 · 2021: 10 · 2020: 10 · 2019: 18 · 2018: 9 · 2017: 8 · 2016: 7 · 2015: 15 · 2014: 8 · 2013: 20 · 2012: 14
FWCI
8.45
Type
journal article
Language
en
Open access
Licence
academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
Locations
  • Genetics (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • arXiv (Cornell University)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • 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
Keywords
parallel adaptation, soft sweeps, dispersal limitation, local adaptation, Poisson process model, crystallization, characteristic length, mutation rate, migration
MeSH terms
Adaptation, Physiological, Alleles, Animals, Computer Simulation, Humans, Models, Genetic, Mutation, Polymorphism, Genetic, Selection, Genetic, Genetic Variation, Models, Statistical, Poisson Distribution, Evolution, Molecular

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