Recent evidence demonstrates that novel protein-coding genes can arise de novo from nongenic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection. Here, we systematically characterize how these de novo emerging coding sequences impact fitness in budding yeast. Disruption of emerging sequences is generally inconsequential for fitness in the laboratory and in natural populations. Overexpression of emerging sequences, however, is enriched in adaptive fitness effects compared to overexpression of established genes. We find that adaptive emerging sequences tend to encode putative transmembrane domains, and that thymine-rich intergenic regions harbor a widespread potential to produce transmembrane domains. These findings, together with in-depth examination of the de novo emerging YBR196C-A locus, suggest a novel evolutionary model whereby adaptive transmembrane polypeptides emerge de novo from thymine-rich nongenic regions and subsequently accumulate changes molded by natural selection.

Ocean currents are expected to be the predominant environmental factor influencing the dispersal of planktonic larvae or spores; yet, their characterization as predictors of marine connectivity has been hindered by a lack of understanding of how best to use oceanographic data. We used a high-resolution oceanographic model output and Lagrangian particle simulations to derive oceanographic distances (hereafter called transport times) between sites studied for Macrocystis pyrifera genetic differentiation. We build upon the classical isolation-by-distance regression model by asking how much additional variability in genetic differentiation is explained when adding transport time as predictor. We explored the extent to which gene flow is dependent upon seasonal changes in ocean circulation. Because oceanographic transport between two sites is inherently asymmetric, we also compare the explanatory power of models using the minimum or the mean transport times. Finally, we compare the direction of connectivity as estimated by the oceanographic model and genetic assignment tests. We show that the minimum transport time had higher explanatory power than the mean transport time, revealing the importance of considering asymmetry in ocean currents when modelling gene flow. Genetic assignment tests were much less effective in determining asymmetry in gene flow. Summer-derived transport times, in particular for the month of June, which had the strongest current speed, greatest asymmetry and highest spore production, resulted in the best-fit model explaining twice the variability in genetic differentiation relative to models that use geographic distance or habitat continuity. The best overall model also included habitat continuity and explained 65% of the variation in genetic differentiation among sites.

Aim Past climate-driven range shifts shaped intraspecific diversities of species world-wide. Earlier studies, focused on glacial refugia, might have overlooked genetic erosion at lower latitudes associated with warmer periods. For marine species able to colonize deeper waters, depth shifts might be important for local persistence, preventing some latitudinal shifts, analogous to elevational refugia in terrestrial habitats. In this study, we asked whether past latitudinal or depth range shifts explain extant gene pools in Saccorhiza polyschides, a large habitat structuring brown alga distributed from coastal to offshore deep reefs.Location North-east Atlantic and western Mediterranean basin.Methods Genetic structure and diversity were inferred using seven microsatellite loci, for 27 sites throughout the entire distributional range. Ecological niche modelling (ENM) was performed with and without information about genetic structure (sub-taxon niche structure) to predict distributions for the Last Glacial Maximum (LGM), the warmer Mid-Holocene (MH) and the present.Results Both ENM approaches predicted a wider potential distribution in deeper waters than is presently known, a post-glacial expansion to northern shores and the extirpation of southern edges during the warmer MH. Genetic data corroborated range dynamics, revealing three major genetic groups with current boundaries in the Bay of Biscay and the Lisbon coastal region, pinpointing ancient refugial origins. Despite extensive southern range contraction, the southernmost warmer regions are still the richest in genetic diversity, indicating long-term persistence of large populations. ENMs suggested that this could only have been possible due to stable refugia in deeper reefs. Main conclusionsThe global distribution of gene pools of temperate marine forests is explained by past range shifts that structured both latitudinal glacial refugia and depth refugia during warmer periods. Deep rear edge populations play a fundamental role during periods of extreme climate, allowing persistence and retaining some of the largest genetic diversity pools of the species' distribution.

Aim Drivers of intraspecific biodiversity include past climate‐driven range shifts and contemporary ecological conditions mediating connectivity, but these are rarely integrated in a common comprehensive approach. This is particularly relevant for marine organisms, as ocean currents strongly influence population isolation or connectivity, keeping or diluting the signatures left by past climates. Here we ask whether the coupling between past range shifts and contemporary connectivity explain the extant gene pools of Laminaria ochroleuca, a large brown alga structuring important marine forests from shallow to deep infralittoral grounds. Location Northeastern Atlantic Ocean. Taxon Laminaria ochroleuca. Methods We estimated population genetic diversity and structure of L. ochroleuca across its entire distribution range using 15 polymorphic microsatellite markers. This was compared with the outcomes of a palaeoclimatic model predicting latitudinal and depth range shifts from the Last Glacial Maximum (LGM) to the present. Genetic differentiation was further compared with potential connectivity inferred with a biophysical model developed with high‐resolution data from HYCOM (Hybrid Coordinate Ocean Model). Results The biogeographical distribution of genetic variability showed overall agreement with the predictions from independently inferred past range shifts. Multiple regions of persistence were identified in deep and upwelling settings at the lowest latitudes of the current species distribution, where higher and unique genetic diversity was retained. The biophysical model revealed that despite the possibility of long‐distance migration, contemporary oceanographic barriers strongly restrict connectivity of isolated genetic lineages. Main conclusions Integrating different processes at biogeographical scales explained the extant gene pools of marine forests of L. ochroleuca. Low‐latitude genetic relics harbour a disproportional evolutionary significance, persisting as ancient populations in isolated deep and upwelling climate refugia. Their inferred rates of dispersal may be insufficient to accommodate anticipated climate warming.

Abstract. Isolation by distance (IBD) models are widely used to predict levels of genetic connectivity as a function of Euclidean distance, and although recent studies have used GISlandscape ecological approaches to improve the predictability of spatial genetic structure, few if any have addressed the effect of habitat continuity on gene flow. Landscape effects on genetic connectivity are even less understood in marine populations, where habitat mapping is particularly challenging. In this study, we model spatial genetic structure of a habitatstructuring species, the giant kelp Macrocystis pyrifera, using highly variable microsatellite markers. GIS mapping was used to characterize habitat continuity and distance between sampling sites along the mainland coast of the Santa Barbara Channel, and their roles as predictors of genetic differentiation were evaluated. Mean dispersal distance (r) and effective population size (N e ) were estimated by comparing our IBD slope with those from simulations incorporating habitat continuity and spore dispersal characteristics of the study area. We found an allelic richness of 7-50 alleles/locus, which to our knowledge is the highest reported for macroalgae. The best regression model relating genetic distance to habitat variables included both geographic distance and habitat continuity, which were respectively, positively and negatively related to genetic distance. Our results provide strong support for a dependence of gene flow on both distance and habitat continuity and elucidate the combination of N e and r that explained genetic differentiation.