Understanding the causes of gene expression variation is of major importance for many areas of biology. While cis-regulatory changes have long been suggested to be particularly important for adaptation, our understanding of what determines cis-regulatory variation remains limited in most species. Here, we have investigated the prevalence, selective importance, and genomic correlates of cis-regulatory variation in the outcrossing crucifer species Capsella grandiflora. We identify genes with cis-regulatory variation through analyses of allele-specific expression (ASE) in deep transcriptome sequencing data from flower buds and leaves, and use population genomic analyses of high-coverage whole genome resequencing data from both a range-wide sample and a natural population to quantify the impact of positive and purifying selection on these genes. Our results show that in C. grandiflora, cis-regulatory variation is pervasive, affecting an average of 35% of genes within individual plants. Genes harboring cis-regulatory variation are (1) under weaker purifying selection, (2) significantly more likely to harbor nearby transposable element (TE) insertions, and (3) undergo lower rates of adaptive substitutions in comparison to other genes. Using a linear model, we identified ASE as the strongest factor contributing to purifying selection when considered alongside several other commonly used contributing factors. In turn, the main genomic correlates of cis-regulatory variation are presence of nearby TE insertions and gene expression level; notably, the signal of relaxed positive and purifying selection on genes with ASE remains after controlling for expression level. Our results suggest that variation in the intensity of selection across the genome is a major determinant of the presence of intraspecific cis-regulatory variation in this outcrossing plant species.

Sexual reproduction is a trait shared by all complex life, but the complete account of its origin is missing. Virtually all theoretical work on the evolution of sex has been centered around the benefits of reciprocal recombination among nuclear genes, paying little attention to the evolutionary dynamics of the multi-copy mitochondrial genome. Here we develop a mathematical model to study the evolution of nuclear alleles inducing cell fusion in an ancestral population of clonal proto-eukaryotes. Segregational drift maintains high mitochondrial variance between clonally reproducing hosts, but the effect of segregation is opposed by cytoplasmic mixing which tends to reduce variation between cells in favor of higher heterogeneity within the cell. Despite the reduced long-term population fitness, alleles responsible for sexual cell fusion can spread to fixation. The evolution of sex requires negative epistatic interactions between mitochondrial mutations and is promoted by strong purifying selection, low mutant load and weak mitochondrial-nuclear associations. We argue that similar conditions were maintained during the late stages of eukaryogenesis, facilitating the evolution of sexual cell fusion and meiotic recombination without compromising the stability of the emerging complex cell.

Saccharomyces cerevisiae and its sibling species S. paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1,200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus as well as small number of S. kudriavzevii strains from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance.

Germline copy number variants (CNVs) are known to affect a large portion of the human genome and have been implicated in many diseases. Although whole-genome sequencing can help identify CNVs, existing analytical methods suffer from limited sensitivity and specificity. Here we show that this is in large part due to the non-uniformity of read coverage, even after intra-sample normalization, and that this is exacerbated in regions of low-mappability. To improve on this, we propose PopSV, an analytical method that uses multiple samples to control for technical variation and enables the robust detection of CNVs. We show that PopSV is able to detect up to 2.7 times more variants compared to previous methods, with an accuracy of about 90%. Applying PopSV to 640 normal and cancer whole-genome datasets, we demonstrate that CNVs affect on average 7.4 million DNA bases in each individual, a 23% increase versus previous estimates. Notably, we find that regions of low-mappability, which were often concealed in previous analyses, harbor approximately 10 times more CNVs than the rest of the genome and that this contrasts with somatic CNVs (sCNVs) that are nearly uniformly distributed. We also observe that CNVs are found more than expected near centromeres and telomeres, in segmental duplications, in specific types of satellite repeats and in some of the most recent families of transposable elements. Although CNVs are found to be depleted in protein-coding genes, we identify 7206 genes with at least one exonic CNV, 324 of which harbored CNVs that would have been missed if low-mappability regions had been excluded. Similarly, 2253 trait- and disease-associated loci are observed to overlap at least one CNV. Our results provide the most comprehensive map of CNVs across the human genome to date and demonstrate the broad functional impact of this type of genetic variation including in regions of low-mappability.

Genetic assimilation results from selection on phenotypic plasticity, but quantitative genetics models of linear reaction norms considering intercept and slope as traits do not fully incorporate the process of genetic assimilation. We argue that intercept-slope reaction norm models are insufficient representations of genetic effects on linear reaction norms, and that defining the intercept as a trait is unfortunate. Instead we suggest a model with three traits representing genetic effects that respectively (1) are independent of the environment, (2) alter the sensitivity of the phenotype to the environment, and (3) determine how the organism perceives the environment. The model predicts that, given sufficient additive genetic variation in environmental perception, the environmental value at which reaction norms tend to cross will respond rapidly to selection, and eventually become equal to the mean environment. Hence, in this model, genetic assimilation in a new environment becomes complete without changes in genetic correlations, genetic drift or imposing any fitness costs on maintaining plasticity. The asymptotic evolutionary outcome of this three-trait linear reaction norm generally entails a lower degree of phenotypic plasticity than the two-trait model, and maximum expected fitness does not occur at the mean trait values in the population.

Plants of the Cannabis genus are the only producers of phytocannabinoids, terpenoid compounds that strongly interact with evolutionarily ancient endocannabinoid receptors shared by most bilaterian taxa. For millennia, the plant has been cultivated for these compounds, but also for food, rope, paper, and clothing. Today, specialized varieties yielding high-quality textile fibers, nutritional seed oil or high cannabinoid content are cultivated across the globe. However, the genetic identities and histories of these diverse populations remain largely obscured. We analyzed the nuclear genomic diversity among 339 Cannabis varieties, and demonstrate the existence of at least three major groups of diversity. As well as being genetically distinct, each group produces unique cannabinoid and terpenoid content profiles. This combined analysis of population genomic and trait variation informs our understanding of the potential uses of different genetic variants for medicine and agriculture, providing valuable insights and tools for a rapidly emerging, valuable legal industry.

Genome sequencing studies of de novo mutations in humans have revealed surprising incongruities with our understanding of human germline mutation. In particular, the mutation rate observed in modern humans is substantially lower than that estimated from calibration against the fossil record, and the paternal age effect in mutations transmitted to offspring is much weaker than expected from our longstanding model of spermatogenesis. I consider possible explanations for these differences, including evolutionary changes in life history parameters such as generation time and the age of puberty, a possible contribution from undetected post-zygotic mutations early in embryo development, and variation in cellular mutation rates at different stages of the germline. I suggest a revised model of stem cell state transitions during spermatogenesis, in which ‘dark’ gonial stem cells play a more active role than hitherto envisaged, with a long cycle time undetected in experimental observations. More generally, I argue that the mutation rate and its evolution depend intimately on the structure of the germline in humans and other primates.