Tom R. Booker

Genotype–environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted‐ Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating F ST . Performing GEA methods in analysis windows has the advantage that it takes advantage of the increased linkage disequilibrium expected surrounding sites subject to local adaptation. We analyse simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single‐SNP (single nucleotide polymorphism)‐based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes were sampled. Particularly troubling, we found that some GEA methods exhibit very high false positive rates. We applied the WZA to previously published data from lodgepole pine and identified candidate loci that were identified in the original study alongside numerous loci that were not found in the original study.

Quantifying the impact of human activity on the capacity of populations to persist is paramount to conservation biology, as numerous species and populations have already been driven to or beyond the brink of extinction. Those populations that persist are often a sobering example of the evolutionary power of human‐disturbance, such as the loss of tusks in African elephants resulting from ivory harvesting (Campbell‐Staton et al., 2021) and rapid life‐history evolution in northern Atlantic cod in response to fisheries (Olsen et al., 2004). These evolutionary responses reflect a delicate interplay between demographic and selective processes (e.g., evolutionary rescue: Bell & Gonzalez, 2009; Gomulkiewicz & Holt, 1995), both of which can modify genetic variation for fitness. While quantifying fitness remains a difficult challenge, generalizable insights into the evolutionary consequences of population collapse can be provided in systems with independent demographic shifts in response to human activity. Unfortunately, such was the case for sea otter populations across its range in the 18th and 19th centuries, where the fur‐trade had catastrophic, range‐wide effects on sea otter ( Enhydra lutris ) populations. In a From the Cover article in this issue of Molecular Ecology , Beichman et al. (2022) combine a population genomic spatiotemporal data set and theoretical simulations not only to quantify past demographic change in response to sea otter exploitation, but also to understand the consequences of population collapse on species persistence.

Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages, recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localized change in the effective population size, potentially leading to underestimation or overestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.