Biology subjects

Peter L. Ralph

Publications and source records attributed to Peter L. Ralph.

5 recordsLinked to original sources

bioRxiv2016

Adaptation in isolated populations: when does it happen and when can we tell?

Isolated populations with novel phenotypes present an exciting opportunity to uncover the genetic basis of ecologically significant adaptation, and genomic scans for positive selection in such populations have often, but not always, led to candidate genes directly related to an adaptive phenotype. However, in many cases these populations were established by a severe bottleneck, which can make identifying targets of selection problematic. Here we simulate severe bottlenecks and subsequent selection on standing variation, mimicking adaptation after establishment of a new small population, such as an island or an artificial selection experiment. Using simulations of single loci under positive selection and population genetics theory, we examine how population size and age of the population isolate affects the ability of outlier scans for selection to identify adaptive alleles using both single site measures and haplotype structure. We find and explain an optimal combination of selection strength, starting frequency, and age of the adaptive allele, which we refer to as a Goldilocks zone, where adaptation is likely to occur, and yet the adaptive variants are most likely to derive from a single ancestor (a \"hard\" selective sweep); in this zone, four commonly used statistics detect selection with high power. Real-world examples of both island colonization and experimental evolution studies are discussed. Our study provides concrete considerations to be made before embarking on whole genome sequencing of differentiated populations.

Evolutionary Biology↗

bioRxiv2015

The Spatial Mixing of Genomes in Secondary Contact Zones

Recent genomic studies have highlighted the important role of admixture in shaping genome-wide patterns of diversity. Past admixture leaves a population genomic signature of linkage disequilibrium (LD), reflecting the mixing of parental chromosomes by segregation and recombination. The extent of this LD can be used to infer the timing of admixture. However, the results of inference can depend strongly on the assumed demographic model. Here, we introduce a theoretical framework for modeling patterns of LD in a geographic contact zone where two differentiated populations are diffusing back together. We derive expressions for the expected LD and admixture tract lengths across geographic space as a function of the age of the contact zone and the dispersal distance of individuals. We develop an approach to infer age of contact zones using population genomic data from multiple spatially sampled populations by fitting our model to the decay of LD with recombination distance. We use our approach to explore the fit of a geographic contact zone model to three human population genomic datasets from populations along the Indonesian archipelago, populations in Central Asia and populations in India.

Evolutionary Biology↗

bioRxiv2015

A Spatial Framework for Understanding Population Structure and Admixture.

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build \"geogenetic maps,\" which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.\n\nAuthor SummaryIn this paper, we introduce a statistical method for inferring, for a set of sequenced samples, a map in which the distances between population locations reflect genetic, rather than geographic, proximity. Two populations that are sampled at distant locations but that are genetically similar (perhaps one was recently founded by a colonization event from the other) may have inferred locations that are nearby, while two populations that are sampled close together, but that are genetically dissimilar (e.g., are separated by a barrier), may have inferred locations that are farther apart. The result is a \"geogenetic\" map in which the distances between populations are effective distances, indicative of the way that populations perceive the distances between themselves: the \"organisms-eye view\" of the world. Added to this, \"admixture\" can be thought of as the outcome of unusually long-distance gene flow; it results in relatedness between populations that is anomalously high given the distance that separates them. We depict the effect of admixture using arrows, from a source of admixture to its target, on the inferred map. The inferred geogenetic map is an intuitive and information-rich visual summary of patterns of population structure.

Evolutionary Biology↗

bioRxiv2014

The role of standing variation in geographic convergent adaptation

The extent to which populations experiencing shared selective pressures adapt through a shared genetic response is relevant to many questions in evolutionary biology. In a number of well studied traits and species, it appears that convergent evolution within species is common. In this paper, we explore how standing, genetic variation contributes to convergent genetic responses in a geographically spread population, extending our previous work on the topic. Geographically limited dispersal slows the spread of each selected allele, hence allowing other alleles - newly arisen mutants or present as standing variation - to spread before any one comes to dominate the population. When such alleles meet, their progress is substantially slowed - if the alleles are selectively equivalent, they mix slowly, dividing the species range into a random tessellation, which can be well understood by analogy to a Poisson process model of crystallization. In this framework, we derive the geographic scale over which a typical allele is expected to dominate, the time it takes the species to adapt as a whole, and the proportion of adaptive alleles that arise from standing variation. Finally, we explore how negative pleiotropic effects of alleles before an environment change can bias the subset of alleles that contribute to the species adaptive response. We apply the results to the many geographically localized G6PD deficiency alleles thought to confer resistance to malaria, where the large mutational target size makes it a likely candidate for adaptation from standing variation, despite the selective cost of G6PD deficiency alleles in the absence of malaria. We find the numbers and geographic spread of these alleles matches our predictions reasonably well, consistent with the view that they arose from a combination of standing variation and new mutations since the advent of malaria. Our results suggest that much of adaptation may be geographically local even when selection pressures are homogeneous. Therefore, we argue that caution must be exercised when arguing that strongly geographically restricted alleles are necessarily the outcome of local adaptation. We close by discussing the implications of these results for ideas of species coherence and the nature of divergence between species.

Evolutionary Biology↗

bioRxiv2014

Convergent Evolution During Local Adaptation to Patchy Landscapes

Species often encounter, and adapt to, many patches of locally similar environmental conditions across their range. Such adaptation can occur through convergent evolution as different alleles arise and spread in different patches, or through the spread of alleles by migration acting to synchronize adaptation across the species. The tension between the two reflects the degree of constraint imposed on evolution by the underlying genetic architecture versus how effectively selection acts to inhibit the geographic spread of locally adapted alleles. This paper studies a model of the balance between these two routes to adaptation in continuous environments with patchy selection pressures. We address the following questions: How long does it take for a novel, locally adapted allele to appear in a patch of habitat where it is favored through mutation? Or, through migration from another, already adapted patch? Which is more likely to occur, as a function of distance between the patches? How can we tell which has occurred, i.e. what population genetic signal is left by the spread of migrant alleles and how long does this signal persist for? To answer these questions we decompose the migration-selection equilibrium surrounding an already adapted patch into families of migrant alleles, in particular treating those rare families that reach new patches as spatial branching processes. This provides a way to understand the role of geographic separation between patches in promoting convergent adaptation and the genomic signals it leaves behind. We illustrate these ideas using the convergent evolution of cryptic coloration in the rock pocket mouse, Chaetodipus intermedius, as an empirical example.\n\nAuthor SummaryOften, a large species range will include patches where the species differs because it has adapted to locally differing conditions. For instance, rock pocket mice are often found with a coat color that matches the rocks they live in, and the difference in coloration is known to be controlled genetically. Sometimes, similar genetic changes have occurred independently in different patches, suggesting that there were few accessible ways to evolve the locally adaptive form. However, the genetic basis could also be shared if rare migrants may carry the locally beneficial genotypes between nearby patches, despite being at a disadvantage between the patches. We use a mathematical model of random migration to determine how quickly adaptation is expected to occur through new mutation or migration from other patches, and study in more detail what we would expect successful migrations between patches to look like. The results are useful for determining whether similar adaptations in different locations are likely to have the same genetic basis or not, and more generally in understanding how species adapt to patchy, heterogeneous landscapes.

Evolutionary Biology↗