The Genomics of Human Local Adaptation Rees, Jasmin S.; Castellano, Sergi; Andrés, Aida M.
Trends in genetics,
06/2020, Volume:
36, Issue:
6
Journal Article
Peer reviewed
Open access
Modern humans inhabit a variety of environments and are exposed to a plethora of selective pressures, leading to multiple genetic adaptations to local environmental conditions. These include ...adaptations to climate, UV exposure, disease, diet, altitude, or cultural practice and have generated important genetic and phenotypic differences amongst populations. In recent years, new methods to identify the genomic signatures of natural selection underlying these adaptations, combined with novel types of genetic data (e.g., ancient DNA), have provided unprecedented insights into the origin of adaptive alleles and the modes of adaptation. As a result, numerous instances of local adaptation have been identified in humans. Here, we review the most exciting recent developments and discuss, in our view, the future of this field.
Local adaptation has critically contributed to the (modest) genetic and phenotypic differentiation that exists among human groups, including in health-related traits that contribute to population health disparities.Local adaptation has happened on alleles of diverse origin (on new, pre-existing, and introgressed alleles) and through diverse mechanisms (monogenic and polygenic adaptation).Ancient DNA will play a key role in our understanding of local adaptation by improving inferences of past events. Further, it has revealed the importance of adaptive introgression, by which modern humans acquired adaptative alleles from archaic humans.Novel analysis methods will improve our power to identify targets of local adaptation, especially those with weak signatures. Combining genetic and environmental information promises to improve the identification of genomic targets and the corresponding selective force.
It is well known that sexual selection can target reproductive traits during successive pre‐ and post‐mating episodes of selection. A key focus of recent studies has been to understand and quantify ...how these episodes of sexual selection interact to determine overall variance in reproductive success. In this article, we review empirical developments in this field but also highlight the considerable variability in patterns of pre‐ and post‐mating sexual selection, attributable to variation in patterns of resource acquisition and allocation, ecological and social factors, genotype‐by‐environment interaction and possible methodological factors that might obscure such patterns. Our aim is to highlight how (co)variances in pre‐ and post‐mating sexually selected traits can be sensitive to changes in a range of ecological and environmental variables. We argue that failure to capture this variation when quantifying the opportunity for sexual selection may lead to erroneous conclusions about the strength, direction or form of sexual selection operating on pre‐ and post‐mating traits. Overall, we advocate for approaches that combine measures of pre‐ and post‐mating selection across contrasting environmental or ecological gradients to better understand the dynamics of sexual selection in polyandrous species. We also discuss some directions for future research in this area.
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Purifying selection reduces genetic diversity, both at sites under direct selection and at linked neutral sites. This process, known as background selection, is thought to play an important role in ...shaping genomic diversity in natural populations. Yet despite its importance, the effects of background selection are not fully understood. Previous theoretical analyses of this process have taken a backward-time approach based on the structured coalescent. While they provide some insight, these methods are either limited to very small samples or are computationally prohibitive. Here, we present a new forward-time analysis of the trajectories of both neutral and deleterious mutations at a nonrecombining locus. We find that strong purifying selection leads to remarkably rich dynamics: neutral mutations can exhibit sweep-like behavior, and deleterious mutations can reach substantial frequencies even when they are guaranteed to eventually go extinct. Our analysis of these dynamics allows us to calculate analytical expressions for the full site frequency spectrum. We find that whenever background selection is strong enough to lead to a reduction in genetic diversity, it also results in substantial distortions to the site frequency spectrum, which can mimic the effects of population expansions or positive selection. Because these distortions are most pronounced in the low and high frequency ends of the spectrum, they become particularly important in larger samples, but may have small effects in smaller samples. We also apply our forward-time framework to calculate other quantities, such as the ultimate fates of polymorphisms or the fitnesses of their ancestral backgrounds.
Habitat selection is a fundamental animal behavior that shapes a wide range of ecological processes, including animal movement, nutrient transfer, trophic dynamics and population distribution. ...Although habitat selection has been a focus of ecological studies for decades, technological, conceptual and methodological advances over the last 20 yr have led to a surge in studies addressing this process. Despite the substantial literature focused on quantifying the habitat‐selection patterns of animals, there is a marked lack of guidance on best analytical practices. The conceptual foundations of the most commonly applied modeling frameworks can be confusing even to those well versed in their application. Furthermore, there has yet to be a synthesis of the advances made over the last 20 yr. Therefore, there is a need for both synthesis of the current state of knowledge on habitat selection, and guidance for those seeking to study this process. Here, we provide an approachable overview and synthesis of the literature on habitat‐selection analyses (HSAs) conducted using selection functions, which are by far the most applied modeling framework for understanding the habitat‐selection process. This review is purposefully non‐technical and focused on understanding without heavy mathematical and statistical notation, which can confuse many practitioners. We offer an overview and history of HSAs, describing the tortuous conceptual path to our current understanding. Through this overview, we also aim to address the areas of greatest confusion in the literature. We synthesize the literature outlining the most exciting conceptual advances in the field of habitat‐selection modeling, discussing the substantial ecological and evolutionary inference that can be made using contemporary techniques. We aim for this paper to provide clarity for those navigating the complex literature on HSAs while acting as a reference and best practices guide for practitioners.
Livestock populations are usually kept in groups. As a consequence, social interactions among individuals affect productivity, health, and welfare. Current selection methods (individual selection), ...however, ignore those interactions and yield suboptimal or in some cases even negative responses. In principle, selection between groups instead of individuals offers a solution, but has rarely been adopted in practice for two reasons. First, the relationship between group selection theory and common animal breeding concepts, such as the accuracy of selection, is unclear. Second, application of group selection requires keeping selection candidates in groups, which is often undesirable in practice. This work has two objectives. First, we derive expressions for the accuracy of individual and group selection, which provides a measurement of quality for those methods. Second, we investigate the opportunity to improve traits affected by interactions by using information on relatives kept in family groups, while keeping selection candidates individually. The accuracy of selection based on relatives is shown to be an analogy of the classical expression for traits not affected by interactions. Our results show that selection based on relatives offers good opportunities for effective genetic improvement of traits affected by interactions.
Naïve Bayes is one of the most popular data mining algorithms. Its efficiency comes from the assumption of attribute independence, although this might be violated in many real-world data sets. Many ...efforts have been done to mitigate the assumption, among which attribute selection is an important approach. However, conventional efforts to perform attribute selection in naïve Bayes suffer from heavy computational overhead. This paper proposes an efficient selective naïve Bayes algorithm, which adopts only some of the attributes to construct selective naïve Bayes models. These models are built in such a way that each one is a trivial extension of another. The most predictive selective naïve Bayes model can be selected by the measures of incremental leave-one-out cross validation. As a result, attributes can be selected by efficient model selection. Empirical results demonstrate that the selective naïve Bayes shows superior classification accuracy, yet at the same time maintains the simplicity and efficiency.
Heritable personality variation is subject to fluctuating selection in many animal taxa; a major unresolved question is why this is the case. A parsimonious explanation must involve a general ...ecological process: a likely candidate is the omnipresent spatiotemporal variation in conspecific density. We tested whether spatiotemporal variation in density within and among nest box plots of great tits (Parus major) predicted variation in selection acting on exploratory behaviour (n = 48 episodes of selection). We found viability selection favouring faster explorers under lower densities but slower explorers under higher densities. Temporal variation in local density represented the primary factor explaining personality‐related variation in viability selection. Importantly, birds did not anticipate changes in selection by means of adaptive density‐dependent plasticity. This study thereby provides an unprecedented example of the key importance of the interplay between fluctuating selection and lack of adaptive behavioural plasticity in maintaining animal personality variation in the wild.
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