Robust inference of genetic architecture in mapping studies.

The genetic architecture of a trait usually refers to the number and magnitude of loci that explain phenotypic variation. A description of genetic architecture can help us to understand how genetic variation is maintained, how traits have evolved and how phenotypes might respond to selection. However, linkage mapping and association studies can suffer from problems of bias, especially when conducted in natural populations where the opportunity to perform studies with very large sample sizes can be limited. In this issue of Molecular Ecology, Li and colleagues perform an association study of brain traits in ninespine sticklebacks Pungitius pungitius. They use a sophisticated approach that models all of the genotyped markers simultaneously; conventional approaches fit each marker individually. Although the single-marker and multi-marker approaches find similar regions of the genome that explain phenotypic variation, the overall conclusions about trait architecture are somewhat different, depending on the approach used. Single-marker methods identify regions that explain quite large proportions of genetic variation, whereas the multi-marker approach suggests the traits are far more polygenic. Simulations suggest the multi-marker approach is robust. This study highlights how molecular quantitative genetics in wild populations can be used to address hypothesis-driven questions, without making unrealistic assumptions about effect sizes of individual quantitative trait loci

Experimental evidence for ecological selection on genome variation in the wild

Understanding natural selection's effect on genetic variation is a major goal in biology, but the genome-scale consequences of contemporary selection are not well known. In a release and recapture field experiment we transplanted stick insects to native and novel host plants and directly measured allele frequency changes within a generation at 186 576 genetic loci. We observed substantial, genome-wide allele frequency changes during the experiment, most of which could be attributed to random mortality (genetic drift). However, we also documented that selection affected multiple genetic loci distributed across the genome, particularly in transplants to the novel host. Host-associated selection affecting the genome acted on both a known colour-pattern trait as well as other (unmeasured) phenotypes. We also found evidence that selection associated with elevation affected genome variation, although our experiment was not designed to test this. Our results illustrate how genomic data can identify previously underappreciated ecological sources and phenotypic targets of selection

Observational evidence that maladaptive gene flow reduces patch occupancy in a wild insect metapopulation

Theory predicts that dispersal throughout metapopulations has a variety of consequences for the abundance and distribution of species. Immigration is predicted to increase abundance and habitat patch occupancy, but gene flow can have both positive and negative demographic consequences. Here, we address the eco-evolutionary effects of dispersal in a wild metapopulation of the stick insect Timema cristinae, which exhibits variable degrees of local adaptation throughout a heterogeneous habitat patch network of two host-plant species. To disentangle the ecological and evolutionary contributions of dispersal to habitat patch occupancy and abundance, we contrasted the effects of connectivity to populations inhabiting conspecific host plants and those inhabiting the alternate host plant. Both types of connectivity should increase patch occupancy and abundance through increased immigration and sharing of beneficial alleles through gene flow. However, connectivity to populations inhabiting the alternate host-plant species may uniquely cause maladaptive gene flow that counters the positive demographic effects of immigration. Supporting these predictions, we find the relationship between patch occupancy and alternate-host connectivity to be significantly smaller in slope than the relationship between patch occupancy and conspecific-host connectivity. Our findings illustrate the ecological and evolutionary roles of dispersal in driving the distribution and abundance of species. This article is protected by copyright. All rights reserved

Geochemistry, faunal composition and trophic structure in reducing sediments on the southwest South Georgia margin

Despite a number of studies in areas of focused methane seepage, the extent of transitional sediments of more diffuse methane seepage, and their influence upon biological communities is poorly understood. We investigated an area of reducing sediments with elevated levels of methane on the South Georgia margin around 250 m depth and report data from a series of geochemical and biological analyses. Here, the geochemical signatures were consistent with weak methane seepage and the role of sub-surface methane consumption was clearly very important, preventing gas emissions into bottom waters. As a result, the contribution of methane-derived carbon to the microbial and metazoan food webs was very limited, although sulfur isotopic signatures indicated a wider range of dietary contributions than was apparent from carbon isotope ratios. Macrofaunal assemblages had high dominance and were indicative of reducing sediments, with many taxa common to other similar environments and no seep-endemic fauna, indicating transitional assemblages. Also similar to other cold seep areas, there were samples of authigenic carbonate, but rather than occurring as pavements or sedimentary concretions, these carbonates were restricted to patches on the shells of Axinulus antarcticus (Bivalvia, Thyasiridae), which is suggestive of microbe–metazoan interactions

Color phenotypes are under similar genetic control in two distantly related species of Timema stick insect

Ecology and genetics are both of general interest to evolutionary biologists as they can influence the phenotypic and genetic response to selection. The stick insects Timema podura and Timema cristinae exhibit a green/melanistic body color polymorphism that is subject to different ecologically based selective regimes in the two species. Here, we describe aspects of the genetics of this color polymorphism in T. podura, and compare this to previous results in T. cristinae. We first show that similar color phenotypes of the two species cluster in phenotypic space. We then use genome-wide association mapping to show that in both species, color is controlled by few loci, dominance relationships between color alleles are the same, and SNPs associated with color phenotypes colocalize to the same linkage group. Regions within this linkage group that harbor genetic variants associated with color exhibit elevated linkage disequilibrium relative to genome wide expectations, but more strongly so in T. cristinae. We use these results to discuss predictions regarding how the genetics of color could influence levels of phenotypic and genetic variation that segregate within and between populations of T. podura and T. cristinae, drawing parallels with other organisms

Reinforcement’s incidental effects on reproductive isolation between conspecifics

Reinforcement—the process whereby maladaptive hybridization leads to the strengthening of prezygotic isolation between species—has a long history in the study of speciation. Because reinforcement affects traits involved in mate choice and fertility, it can have indirect effects on reproductive isolation between populations within species. Here we review examples of these “cascading effects of reinforcement” (CER) and discuss different mechanisms through which they can arise. We discuss three factors that are predicted to influence the potential occurrence of CER: rates of gene flow among populations, the strength of selection acting on the traits involved in reinforcement, and the genetic basis of those traits. We suggest that CER is likely if (1) the rate of gene flow between conspecific populations is low; (2) divergent selection acts on phenotypes involved in reinforcement between sympatric and allopatric populations; and (3) the genetic response to reinforcement differs among conspecific populations subject to parallel reinforcing selection. Future work continuing to address gene flow, selection, and the genetic basis of the traits involved in the reinforcement will help develop a better understanding of reinforcement as a process driving the production of species diversity, both directly and incidentally

Correlated evolution of male and female reproductive traits drive a cascading effect of reinforcement in Drosophila yakuba

Selection against maladaptive hybridization can drive the evolution of reproductive isolation in a process called reinforcement. While the importance of reinforcement in evolution has been historically debated, many examples now exist. Despite these examples, we typically lack a detailed understanding of the mechanisms limiting the spread of reinforced phenotypes throughout a species' range. Here we address this issue in the fruit fly Drosophila yakuba, a species that hybridizes with its sister species D. santomea and is undergoing reinforcement in a well-defined hybrid zone on the island of São Tomé. Within this region, female D. yakuba show increased postmating-prezygotic (gametic) isolation towards D. santomea when compared with females from allopatric populations. We use a combination of natural collections, fertility assays, and experimental evolution to understand why reinforced gametic isolation in D. yakuba is confined to this hybrid zone. We show that, among other traits, D. yakuba males from sympatric populations sire fewer progeny than allopatric males when mated to allopatric D. yakuba females. Our results provide a novel example of reinforcement acting on a postmating-prezygotic trait in males, resulting in a cascade of reproductive isolation among conspecific populations

Genomic signatures of admixture and selection are shared among populations of <i>Zaprionus indianus</i> across the western hemisphere

Introduced species have become an increasingly common component of biological communities around the world. A central goal in invasion biology is therefore to identify the demographic and evolutionary factors that underlie successful introductions. Here we use whole genome sequences, collected from populations in the native and introduced range of the African fig fly, Zaprionus indianus, to quantify genetic relationships among them, identify potential sources of the introductions, and test for selection at different spatial scales. We find that geographically widespread populations in the western hemisphere are genetically more similar to each other than to lineages sampled across Africa, and that these populations share a mixture of alleles derived from differentiated African lineages. Using patterns of allele‐sharing and demographic modelling we show that Z. indinaus have undergone a single expansion across the western hemisphere with admixture between African lineages predating this expansion. We also find support for selection that is shared across populations in the western hemisphere, and in some cases, with a subset of African populations. This suggests either that parallel selection has acted across a large part of Z. indianus's introduced range; or, more parsimoniously, that Z. indianus has experienced selection early on during (or prior‐to) its expansion into the western hemisphere. We suggest that the range expansion of Z. indianus has been facilitated by admixture and selection, and that management of this invasion could focus on minimizing future admixture by controlling the movement of individuals within this region rather than between the western and eastern hemisphere

Correlated evolution of male and female reproductive traits drive a cascading effect of reinforcement in Drosophila yakuba

Selection against maladaptive hybridization can drive the evolution of reproductive isolation in a process called reinforcement. While the importance of reinforcement in evolution has been historically debated, many examples now exist. Despite these examples, we typically lack a detailed understanding of the mechanisms limiting the spread of reinforced phenotypes throughout a species' range. Here we address this issue in the fruit fly Drosophila yakuba, a species that hybridizes with its sister species D. santomea and is undergoing reinforcement in a well-defined hybrid zone on the island of São Tomé. Within this region, female D. yakuba show increased postmating-prezygotic (gametic) isolation towards D. santomea when compared with females from allopatric populations. We use a combination of natural collections, fertility assays, and experimental evolution to understand why reinforced gametic isolation in D. yakuba is confined to this hybrid zone. We show that, among other traits, D. yakuba males from sympatric populations sire fewer progeny than allopatric males when mated to allopatric D. yakuba females. Our results provide a novel example of reinforcement acting on a postmating-prezygotic trait in males, resulting in a cascade of reproductive isolation among conspecific populations