Genomic divergence and adaptive convergence in Drosophila simulans from Evolution Canyon, Israel

Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei

Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains a captivating topic in evolutionary biology. However, the pattern of genetic divergence underlying this process across the genome may vary between species and mating systems. Here, we present evidence that Brachypodium stacei, an annual and highly selfing grass model species, has undergone sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses together with lab experiments mimicking the two opposite environmental conditions suggest that diploid B. stacei populations have diverged sympatrically in two slopes characterized by distinct biomes at Evolution Canyon I (ECI), Mount Carmel, Israel. Despite ongoing gene flow, primarily facilitated by seed dispersal, the level of gene flow has progressively decreased over time. This local adaptation involves the scattered divergence of many unlinked loci across the total genome that include both coding genes and noncoding regions. Additionally, we have identified significant differential expressions of genes related to the ABA signaling pathway and contrasting metabolome composition between the arid- vs. forest-adapted B. stacei populations in ECI. These results suggest that multiple small loci involved in environmental responses act additively to account for ecological adaptations by this selfing species in contrasting environments.

Lack of alignment across yeast-dependent life-history traits may limit Drosophila melanogaster dietary specialization

Heterogeneity in food resources is a major driver of local adaptation and speciation. Dietary specialization typically involves multiple life‐history traits and may thus be limited by the extent to which these traits adapt in concert. Here, we use Drosophila melanogaster, representing an intermediate state in the generalist‐specialist continuum, to explore the scope for dietary specialization. D. melanogaster has a close association with yeast, an essential but heterogeneous food resource. We quantify how different D. melanogaster strains from around the globe respond to different yeast species, across multiple yeast‐dependent life‐history traits including feeding, mating, egg‐laying, egg development and survival. We find that D. melanogaster strains respond to different yeast species in different ways, indicating distinct fly strain–yeast interactions. However, we detect no evidence for trade‐offs: fly performance tends to be positively rather than negatively correlated across yeast species. We also find that the responses to different yeast species are not aligned across traits: different life‐history traits are maximized on different yeast species. Finally, we confirm that D. melanogaster is a resource generalist: it can grow, reproduce and survive on all the yeast species we tested. Together, these findings provide a possible explanation for the limited extent of dietary specialization in D. melanogaster.

Conserved ecophysiology despite disparate microclimatic conditions in a gecko

Microscale differences in the habitats organisms occupy can influence selection regimes and promote intraspecific variation of traits. Temperature-dependent traits can be locally adapted to climatic conditions or be highly conserved and insensitive to directional selection under all but the most extreme regimes, and thus be similar across populations. The opposing slopes of Nahal Oren canyon in the Carmel Mountains, Israel, are strikingly different: the south-facing slope receives intensive solar radiation, is hot and supports mostly annual vegetation, whereas the north-facing slope is ~10°C cooler, more humid, and supports Mediterranean woodland. We examined whether these differences manifest in the thermal physiology of a common gecko species Ptyodactylus guttatus in controlled laboratory conditions. We predicted that geckos from the hotter south-facing slope would prefer higher temperatures, have faster gut passage times, lower metabolic and evaporative water loss rates, and start diel activity earlier compared with north-facing slope conspecifics. Contrary to these predictions, there were no differences between any of the ecophysiological traits in geckos from the opposing slopes. Nevertheless, our data showed that individuals from the north-facing slope were generally more active in earlier hours of the afternoon compared with south-facing individuals. We suggest that P. guttatus individuals disperse between the slopes and either gene-flow or behavioral plasticity deter local adaptation, resulting in similar physiological traits. Perhaps a stronger contrast in climatic conditions and a stronger barrier are needed to result in interpopulation divergence in temperature-dependent traits.

Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements

Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, presumably due to reduced effective population sizes resulting from a reproductive division of labor, or whether an initial accumulation of repetitive elements leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution. Using phylogenetically informed analyses, we find that eusocial species have larger genomes with more transposable elements (TEs) and microsatellite repeats than noneusocial species. Interestingly, different TE subclasses contribute to the accumulation in different species. Phylogenetic path analysis testing alternative causal relationships between sociality and genome architecture is most consistent with the hypothesis that TEs modulate the relationship between sociality and genome architecture. Although eusociality appears to influence TE accumulation, ancestral state reconstruction suggests moderate TE abundances in ancestral species could have fueled the initial transitions to eusociality. Ultimately, we highlight a complex and dynamic relationship between genome and social evolution, demonstrating that sociality can influence the evolution of the genome, likely through changes in demography related to patterns of reproductive skew.

Tirant Stealthily Invaded Natural Drosophila melanogaster Populations during the Last Century

It was long thought that solely three different transposable elements (TEs)-the I-element, the P-element, and hobo-invaded natural Drosophila melanogaster populations within the last century. By sequencing the "living fossils" of Drosophila research, that is, D. melanogaster strains sampled from natural populations at different time points, we show that a fourth TE, Tirant, invaded D. melanogaster populations during the past century. Tirant likely spread in D. melanogaster populations around 1938, followed by the I-element, hobo, and, lastly, the P-element. In addition to the recent insertions of the canonical Tirant, D. melanogaster strains harbor degraded Tirant sequences in the heterochromatin which are likely due to an ancient invasion, likely predating the split of D. melanogaster and D. simulans. These degraded insertions produce distinct piRNAs that were unable to prevent the novel Tirant invasion. In contrast to the I-element, P-element, and hobo, we did not find that Tirant induces any hybrid dysgenesis symptoms. This absence of apparent phenotypic effects may explain the late discovery of the Tirant invasion. Recent Tirant insertions were found in all investigated natural populations. Populations from Tasmania carry distinct Tirant sequences, likely due to a founder effect. By investigating the TE composition of natural populations and strains sampled at different time points, insertion site polymorphisms, piRNAs, and phenotypic effects, we provide a comprehensive study of a natural TE invasion.

The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe

Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here, we report fourteen DNA viruses detected in a metagenomic analysis of 6668 pool-sequenced Drosophila, sampled from forty-seven European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a double-stranded RNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to twelve segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2 per cent or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D.melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.