The relative impact of evolving pleiotropy and mutational correlation on trait divergence

Both pleiotropic connectivity and mutational correlations can restrict the decoupling of traits under divergent selection, but it is unknown which is more important in trait evolution. To address this question, we create a model that permits within-population variation in both pleiotropic connectivity and mutational correlation, and compare their relative importance to trait evolution. Specifically, we developed an individual-based stochastic model where mutations can affect whether a locus affects a trait and the extent of mutational correlations in a population. We find that traits can decouple whether there is evolution in pleiotropic connectivity or mutational correlation, but when both can evolve, then evolution in pleiotropic connectivity is more likely to allow for decoupling to occur. The most common genotype found in this case is characterized by having one locus that maintains connectivity to all traits and another that loses connectivity to the traits under stabilizing selection (subfunctionalization). This genotype is favored because it allows the subfunctionalized locus to accumulate greater effect size alleles, contributing to increasingly divergent trait values in the traits under divergent selection without changing the trait values of the other traits (genetic modularization). These results provide evidence that partial subfunctionalization of pleiotropic loci may be a common mechanism of trait decoupling under regimes of corridor selection.Peer reviewe

Domestication syndrome via indirect selection in simulated cereal grains

Domestication syndrome in cereal grains is commonly thought to be the product of domestication through a combination of direct artificial selection and indirect natural selection by humans. We propose an agent-based model of grain domestication. We simulate cereal grains with four genes that impact their reproductive cycle undergoing harvesting and selective planting by simulated humans. When direct artificial selection is applied to one gene domestication syndrome emerges in the other genes as a result of indirect natural selection. In the absence of direct artificial selection no domestication syndrome emerged, consistent with periods of predomestication cultivation in human history. Domesticated variants are strongest when humans select for traits inconsistent with the wild type traits, and weakest when humans select for traits consistent with the wild type

Inbred lab mice are not isogenic:Genetic variation within inbred strains used to infer the mutation rate per nucleotide site

For over a century, inbred mice have been used in many areas of genetics research to gain insight into the genetic variation underlying traits of interest. The generalizability of any genetic research study in inbred mice is dependent upon all individual mice being genetically identical, which in turn is dependent on the breeding designs of companies that supply inbred mice to researchers. Here, we compare whole-genome sequences from individuals of four commonly used inbred strains that were procured from either the colony nucleus or from a production colony (which can be as many as ten generations removed from the nucleus) of a large commercial breeder, in order to investigate the extent and nature of genetic variation within and between individuals. We found that individuals within strains are not isogenic, and there are differences in the levels of genetic variation that are explained by differences in the genetic distance from the colony nucleus. In addition, we employ a novel approach to mutation rate estimation based on the observed genetic variation and the expected site frequency spectrum at equilibrium, given a fully inbred breeding design. We find that it provides a reasonable per nucleotide mutation rate estimate when mice come from the colony nucleus (~7.9 × 10−9 in C3H/HeN), but substantially inflated estimates when mice come from production colonies

RAD-QTL mapping reveals both genome-level parallelism and different genetic architecture underlying the evolution of body shape in Lake Whitefish (Coregonus clupeaformis) species pairs

Parallel changes in body shape may evolve in response to similar environmental conditions, but whether such parallel phenotypic changes share a common genetic basis is still debated. The goal of this study was to assess whether parallel phenotypic changes could be explained by genetic parallelism, multiple genetic routes, or both. We first provide evidence for parallelism in fish shape by using geometric morphometrics among 300 fish representing five species pairs of Lake Whitefish. Using a genetic map comprising 3438 restriction site-associated DNA sequencing single-nucleotide polymorphisms, we then identified quantitative trait loci underlying body shape traits in a backcross family reared in the laboratory. A total of 138 body shape quantitative trait loci were identified in this cross, thus revealing a highly polygenic architecture of body shape in Lake Whitefish. Third, we tested for evidence of genetic parallelism among independent wild populations using both a single-locus method (outlier analysis) and a polygenic approach (analysis of covariation among markers). The single-locus approach provided limited evidence for genetic parallelism. However, the polygenic analysis revealed genetic parallelism for three of the five lakes, which differed from the two other lakes. These results provide evidence for both genetic parallelism and multiple genetic routes underlying parallel phenotypic evolution in fish shape among populations occupying similar ecological niches.Keywords : Adaptive radiation, Parallel evolution, Fish body shape, Geometric morphometrics, Genotyping-by-sequencing

Pleiotropy or linkage? Their relative contributions to the genetic correlation of quantitative traits and detection by multitrait GWA studies

Genetic correlations between traits may cause correlated responses to selection. Previous models described the conditions under which genetic correlations are expected to be maintained. Selection, mutation, and migration are all proposed to affect genetic correlations, regardless of whether the underlying genetic architecture consists of pleiotropic or tightly linked loci affecting the traits. Here, we investigate the conditions under which pleiotropy and linkage have different effects on the genetic correlations between traits by explicitly modeling multiple genetic architectures to look at the effects of selection strength, degree of correlational selection, mutation rate, mutational variance, recombination rate, and migration rate. We show that at mutation-selection(-migration) balance, mutation rates differentially affect the equilibrium levels of genetic correlation when architectures are composed of pairs of physically linked loci compared to architectures of pleiotropic loci. Even when there is perfect linkage (no recombination within pairs of linked loci), a lower genetic correlation is maintained than with pleiotropy, with a lower mutation rate leading to a larger decrease. These results imply that the detection of causal loci in multitrait association studies will be affected by the type of underlying architectures, whereby pleiotropic variants are more likely to be underlying multiple detected associations. We also confirm that tighter linkage between nonpleiotropic causal loci maintains higher genetic correlations at the traits and leads to a greater proportion of false positives in association analyses.Peer reviewe

Detecting Signatures of Selection in a Population of Lake Whitefish (Coregonus clupeaformis) Subject to Overharvesting in Lesser Slave Lake, Alberta

Size-selective harvest has been common practice in over-exploited commercial fish populations. Yet, few studies have shown that selective harvest also implicates non-random selection with regards to genetic composition, or have considered genetic population structure, even though this is necessary to implicate harvest in the evolution of over-exploited fish stocks. I investigated both genetic population structure and selection in a historically over-exploited lake whitefish (Coregonus clupeaformis) population associated with fisheries-induced evolution in Lesser Slave Lake, Alberta, Canada. Archived samples DNA of lake whitefish caught between 1986 and 1999 were genotyped at 20 microsatellite or 51 SNP loci associated with growth the species. Multi-mesh test-netting represents random harvests of genetic variability, whereas individuals harvested using commercial mesh nets represented non-random samples with respect to genetic composition in one SNP associated with metabolism. Selective removal of genetic variation can have unintended evolutionary consequences, which may lead to the collapse of fish stocks