polygenic adaptation - senecio7の日記

Stephan W & John S 2020 Polygenic adaptation in a population of finite size. Entropy 22:907.

in recent years, due to the advance of genome-wide association studies (GWAS), polygenic selection was studied using quantitative genetics models that are formulated in terms of allele frequency changes in a large number of loci across the whole genome
selection acts on a phenotypic trait
a genotype-phenotype map is assumed to bridge the gap to population genetics
polygenic adaptation driven by a large number of weakly selected loci is not nearly as well studied as the case of strong positive selection leading to selective sweeps
reviews by Pritchard et al. (2010) [17] and Pritchard and Di Rienzo (2010) [18] drew the attention of population geneticists to this type of selection
these papers predicted that allele frequencies change by small amounts when a large number of genetic loci of minor effect sizes control a phenotypic trait
it is not obvious whether polygenic adaptation may be so fast, as suggested by an increasing number of cases reported in the recent literature
De Vladar and Barton (2014) [29] and Jain and Stephan (2015) [30] used a deterministic model to analyze the dynamics of adaptation after a sudden environmental shift of the fitness optimum of a phenotypic trait in the absense of genetic drift
the equilibrium allele frequencies of the deterministic model do not agree with the frequencies typically observed in GWAS
Simons et al. (2018) [35] proposed a model of selection that simultaneously acts on multiple traits (pleiotropy)
Stetter et al. (2018) [36] and Thornton (2019) [37] used extensive forward simulations to analyze a model (though with relatively few selected loci) that also includes neutral loci linked to selected ones
the model of Höllinger et al. (2019) [33] is different from ours in that the loci controlling a trait are not explicitly given, but instead a genome-wide mutation rate is used as a proxy
we first review the work of John and Stephan (2020) [34] in which we described a stochastic treatment of the equilibrium phase before the shift of the fitness optimum

Equation (19) predicts that after an environmental change the allele frequencies shift coherently into the same direction
this is an important property of polygenic selection
it may help detecting this type of selection, although the frequency shifts at individual loci are in general small
including genetic drift, however, leads to a more complex picture of polygenic adaptation
we find a good agreement between Equation (13) and the simulation for the deviation Δc₁ of the population mean from the optimum within the short-term phase
for the allele frequencies, however, we get a reasonable agreement of the deterministic prediction of Equations (19) and simulations only when the effect sizes are sufficiently large and allele frequencies at the time of the environmental shift are intermediate
the reason is that genetic drift slows down the increase of the allele frequencies and hence reduces the expected differences between the allele frequencies at the end of the short-term phase and those at t = 0
as a consequence, while trait-increasing alleles with intermediately high equilibrium frequencies contribute positively to changes of the trait mean (i.e., are aligned with the direction of the optimum shift), alleles with low or high frequencies may not stay aligned with the optimum shift

alleles with very low or high frequencies are subject to stronger drift and thus may not stay aligned with the direction of the optimum shift

do selective sweeps occur in polygenic adaptation?
selective sweeps may arise in restricted parameter ranges, but only when most alleles have large effects
strong selective fixations have been observed in simulations in the initial rapid phase
fixations driven by relatively weak selection may occur in the prolonged equilibration period, but these would not lead to sweeps
in highly polygenic models large-effect alleles almost never sweep to fixation, while alleles of moderate effects may go to fixation
in general, in quantitative genetics models, selective sweeps are rare
this does not contradict Thornton’s (2019) [37] observation of sweeps in cases in which the trait is not highly polygenic
this was also found by Jain and Stephan (2017a) [31] when the number of loci controlling a trait was not large