A new study highlights the need to consider local structure in detecting positive selection. Genes from the genome

Bacteria becoming antibiotic-resistant, insects becoming insect-resistant, and organisms adapting to hostile environments are all examples of adaptive evolution through natural selection. Each adaptive event leaves its mark in an organism’s DNA. Beneficial alleles become fixed and can be detected in the majority of the population. By understanding this process, population geneticists and evolutionary biologists know how species have changed over time and what events, such as diseases and environmental changes, have threatened their survival.

During adaptation, an advantageous allele increases its frequency in a population due to positive selection. As a result, closely linked alleles on a chromosome can “hiccup” together to a high frequency, thereby reducing genetic variation in the genomic vicinity of the beneficial allele. This process is called selective sweep. New research published in Genetics implements a new simulation model to understand how population structure affects signatures of selective sweeps in population genomic data.

A number of methods are already available to detect electoral sweeps. Most of these methods are based on the classic selective sweep model, which assumes that the population is homogeneously mixed and that individuals mate randomly (so-called “panexia”). However, in the real world many populations live within large geographic ranges, where individuals are usually compatible with individuals that live nearby and randomly disperse only locally throughout the range, thus violating the classic sweep model’s assumption that populations are homogeneously mixed.

To better understand how such geographic population structure affects sweep signatures and dynamics, Chotai et al. Individual-based simulations of selected sweeps in populations whose individuals reside within a two-dimensional geographic range with local dispersal and admixture. Their results revealed the following important differences in the dynamics of selective sweeps compared to the classical sweep model: a) limited dispersal of alleles can reduce the spread of an adaptive allele and thus reduce the probability of its fixation compared to expectations of equal size, b) differences in downstream differential conflicts can alter divergence in a selection system. An enrichment of intermediate-frequency single-nucleotide polymorphisms compared to the panmictic scenario, and d) a less dispersed haplotype frequency spectrum, may alter the observed haplotype structure around the swept locus, with characteristic changes.

Additionally, the researchers investigated whether the degree of spatial structure required for these effects to emerge might be relevant to real-world populations. By comparing the dispersal rates and selection coefficients of known vectors in nature, such as lactose tolerance in humans, coloration in monarch butterflies, and insecticide resistance. anopheles mosquito, the researchers concluded that these effects may indeed be observable in real-world selection events.

Overall, this study suggests that current methods for studying selective sweeps should consider the influence of spatial structure on their detection, especially when the populations involved occupy large geographic ranges with limited dispersal.