Biology subjects

Whitlock, M.

Publications and source records attributed to Whitlock, M..

4 recordsLinked to original sources

bioRxiv2025

Evolutionary rescue in a consumer-resource system: Adaptation and persistence depend on the affected ecological traits

With evolutionary rescue, a population that is declining due to an environmental change adapts to its environment, avoiding extinction. Previous theoretical work has explored the effects of negative density-dependence on rescue, showing that it may aid or hinder persistence. However, these models typically assume that it is only population intrinsic growth rates, r, or carrying capacity, K, that are negatively affected, and do not model density-dependence explicitly. Here, we analyze evolutionary rescue in a consumer-resource species following an abrupt environmental change, characterizing how rescue is dependent on the ecological effects of the environmental change on the consumer, which differently affect r and K through subsequent interactions with an explicit non-substitutable resource species. We derive approximate analytical predictions for the fixation probabilities of beneficial alleles, mutational supply, and times to extinction, which work well when selection is weak and individual turnover rates are low. We demonstrate that consumer rescue is dependent on the ecological effect of the environmental change, the resident life-history of the population, and the genetic architectures of evolving traits (monogenic versus polygenic). Our model suggests that measurements of intrinsic growth rates alone will be insufficient to predict rescue probabilities. This work extends our understanding of the interplay between ecology and evolution in influencing population persistence.

evolutionary biology↗

bioRxiv2021

The WZA: A window-based method for characterizing genotype-environment association

Genotype environment association (GEA) studies have the potential to elucidate 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 FST. We analyze simulations modelling local adaptation to heterogeneous environments either using a GEA method that controls for population structure or an uncorrected approach. In the majority of cases we tested, the WZA either outperformed single-SNP based approaches or performed similarly. The WZA outperformed individual SNP approaches when the measured environment is not perfectly correlated with the true selection pressure or when a small number of individuals or demes was sampled. We apply the WZA to previously published data from lodgepole pine and identified candidate loci that were not found in the original study.

evolutionary biology↗

bioRxiv2021

The genetics of assisted gene flow: immediate costs and long-term benefits

Plant and animal populations are facing several novel risks such as human-mediated habitat fragmentation and climate change that threaten their long-term productivity and persistence. With the genetic health of many populations deteriorating due to climate change outpacing physiological adaptation, human interventions in the form of assisted gene flow (AGF) may provide genetic variation to adapt populations to predicted climate change scenarios and result in more robust and productive populations. We ran genetic simulations to mimic a variety of AGF scenarios and measured their outcomes on population-level fitness to answer the question: in which circumstances is it worthwhile to perform AGF? Based on the parameters we explored, AGF may be harmful in certain situations over the short term (e.g., the first [~]10-20 generations), due to outbreeding depression and introducing deleterious genetic variation. Moreover, under many parameter sets, the benefits of AGF were relatively weak or took many generations to accrue. In general, when the adaptive trait is controlled by many loci of small effect, the benefits of assisted gene flow take much longer to realize-potentially too long for most climate-related management decisions. We also show that when translocation effort is divided across several generations and outbreeding depression is strong, the recipient population experiences a smaller decrease in fitness as compared to moving all individuals in a single effort. Importantly, in most cases, we show that the genomic integrity of the recipient population remains relatively intact following AGF; the amount of genetic material from the donor population typically ends up constituting no more of the recipient populations genome than the fraction introduced. Our results will be useful for conservation practitioners and silviculturists, for instance, aiming to intervene and adaptively manage so that populations maintain a robust genetic health and maintain productivity into the future given anthropogenic climate change.

evolutionary biology↗

bioRxiv2020

Variation in recombination rate affects detection of FST outliers under neutrality

Genome scans can potentially identify genetic loci involved in evolutionary processes such as local adaptation and gene flow. Here, we show that recombination rate variation across a neutrally evolving genome gives rise to mixed sampling distributions of mean FST[Formula], a common population genetic summary statistic. In particular, we show that in regions of low recombination the distribution of [Formula] estimates have more variance and a longer tail than in more highly recombining regions. Determining outliers from the genome-wide distribution without taking local recombination rate into consideration may therefore increase the frequency of false positives in low recombination regions and be overly conservative in more highly recombining ones. We perform genome-scans on simulated and empirical Drosophila melanogaster datasets and, in both cases, find patterns consistent with this neutral model. Similar patterns are observed for other summary statistics used to capture variation in the coalescent process. Linked selection, particularly background selection, is often invoked to explain heterogeneity in [Formula] across the genome, but here we point out that even under neutrality, statistical artefacts can arise due to variation in recombination rate. Our results highlight a flaw in the design of genome scan studies and suggest that without estimates of local recombination rate, interpreting the genomic landscape of any summary statistic that captures variation in the coalescent process will be very difficult.

evolutionary biology↗