Emily L. Behrman

Populations adapting to heterogeneous environments often harbor many alleles that covary with environmental gradients, yet how so many adaptive variants can be maintained and show signatures of local adaptation remains unclear. Epistatic non-additive interactions among alleles may concentrate fitness effects at specific allelic combinations to shape complex traits and facilitate adaptation. We evaluate compositional epistasis among three intronic SNPs in the couch potato ( cpo ) gene, each independently clinal along the North American latitudinal gradient, using recombinant outbred populations fixed for distinct three-locus combinations. Flies carrying all three temperate alleles ( cpo ^TTA ) or all three tropical alleles ( cpo ^CGT ) show non-additive increases in traits associated with fitness in their respective environments: dormancy, starvation resistance, and lipid storage in temperate flies and fecundity in tropical flies. Intermediate genotype combinations generally show weaker and negative deviations from additive predictions. Temperate genotypes show reduced cpo expression and independently create predicted transcription factor binding sites, suggesting a regulatory basis for the observed phenotypic effects. Consistent with selection shaping haplotype frequencies against a backdrop of ongoing recombination, the temperate and tropical genotypes are enriched above random expectation across the latitudinal cline, with directionally consistent but non-significant seasonal patterns. Our findings demonstrate that non-additive interactions among non-coding variants within a single gene can produce large, pleiotropic fitness effects and shape genotype distributions in natural populations, providing a mechanism by which a small number of regulatory variants can underlie complex climatic adaptation.

Maternally transmitted Wolbachia occupy roughly half of terrestrial arthropod species, but the factors maintaining their variable population frequencies are poorly understood. In Drosophila melanogaster , the w Mel Wolbachia variant occurs at intermediate and variable frequencies globally. We document rapid w Mel frequency shifts up to 0.33 between consecutive weeks in experimental and natural orchards in the eastern United States, with frequencies peaking at intermediate temperatures and declining at thermal extremes. Seven years of seasonal sampling at a Pennsylvania orchard showed w Mel frequencies consistently higher in summer than fall, consistent with temperature-dependent maternal transmission. Bayesian models applied to 248 locations across five continents and 42 years of sampling corroborated the previously described w Mel frequency cline in eastern Australia but found no latitudinal pattern on any other continent. Precipitation seasonality and driest-quarter precipitation were the strongest global predictors, absorbing the among-continent w Mel frequency variation that latitude left unexplained. Wet-season temperature predicted w Mel frequency in Australia, where the wettest quarter coincides with summer and peak host reproduction. Analysis of 339 individually sequenced w Mel genomes identified 38 w Mel SNPs associated with latitude, but these associations did not persist after accounting for cytoplasmic lineage structure, and 35 of the 38 were private to a remnant southwestern European lineage. Our results establish that local climatic conditions shape w Mel frequencies globally, plausibly through effects on maternal transmission fidelity that depend on the seasonal alignment of warm temperatures with host reproduction. w Mel genomic variation, in contrast, reflects the incomplete replacement of ancestral w MelCS by w Mel, rather than local adaptation.

We have identified a Drosophila species which exhibits spontaneous and robust intermale sexual behavior. D. santomea males distinguish conspecific sexes but court both vigorously and seldom attack. Elevated intermale courtship stems from at least three evolutionarily derived pheromonal changes. In males, the sexually monomorphic cuticular pheromone 7-tricosene promotes rather than inhibits courtship and the courtship-inhibiting olfactory pheromone cVA is reduced 84-92% compared to close relatives. The third switch is in D. santomea females, where cVA suppresses rather than promotes sexual receptivity. Female cVA aversion and male cVA reduction may have co-evolved to maintain efficient intraspecific mating but prevent hybridization with the sympatric sibling species D . yakuba . High intermale courtship and low cVA also co-occur and appear selectively derived in a distant monomorphic species D. persimilis , implying pheromonal and social behavioral convergence. Changes in pheromone valence and levels may therefore explain the recent evolutionary emergence of intermale sexual behavior in Drosophila .

Adaptation is often modeled as an immediate response to the environment currently experienced, yet we demonstrate that past conditions can continue to shape future genomic change, independent of the present environment. Using seven years of longitudinal genomic, environmental, and phenotypic data from a wild Drosophila melanogaster population, spanning more than 75 generations, we identify two genomically independent temporal modes of adaptation: a concurrent mode, tracking the current environment, and a lagged mode, carrying the imprint of a prior period forward. Despite acting on largely distinct genetic variants, both modes converge on shared neural and developmental pathways, most strongly in genes with broad phenotypic effects, suggesting that the circuitry linking environmental sensing to behavior is a recurring target of multi-temporal selection. These results show that adaptation can proceed simultaneously across distinct timescales, a pattern that may be widespread wherever selection recurs in structured, predictable ways.

To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched in large chromosomal inversions, and we find a broad concordance between seasonal and spatial allele frequency change. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. Our results suggest that fluctuating selection is an important evolutionary force affecting patterns of genetic variation in Drosophila.

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution and population structure of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 population samples from over 100 locations in >20 countries on four continents based on a combination of 121 unpublished and 150 previously published genomic datasets. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched in large chromosomal inversions and we find a broad concordance between seasonal and spatial allele frequency change. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. Our results suggest that fluctuating selection is an important evolutionary force affecting patterns of genetic variation in Drosophila .

Learning is a general mechanism of adaptive behavioural plasticity whose benefits and costs depend on the environment. Thus, seasonal oscillations in temperate environments between winter and summer might produce cyclical selection pressures that would drive rapid evolution of learning performance in multivoltine populations. To test this hypothesis, we investigated the evolutionary dynamics of learning ability over this rapid seasonal timescale in a natural population of Drosophila melanogaster . Associative learning was tested in common garden-raised flies collected from nature in the spring and fall over three consecutive years. The spring flies consistently learned better than fall flies, revealing seasonal evolution of improved learning performance in nature. Fecundity showed the opposite seasonal pattern, suggesting a trade-off between learning and reproduction. This trade-off also held within population: more fecund individual females learned less well. This trade-off is mediated at least in part by natural polymorphism in the RNA binding protein couch potato ( cpo ), with a genotype favoured during summer showing poorer learning performance and higher fecundity than a genotype favoured over winter. Thus, seasonal environments can drive rapid cyclical evolution of learning performance, but the evolutionary dynamics may be driven by trade-offs generated by pleiotropic effects of causative alleles selected for other reasons.

Understanding the rate of evolutionary change and the genetic architecture that facilitates rapid adaptation is a current challenge in evolutionary biology. Comparative studies show that genes with immune function are among the most rapidly evolving genes across a range of taxa. Here, we use immune defence in natural populations ofDrosophila melanogasterto understand the rate of evolution in natural populations and the genetics underlying rapid change. We probed the immune system using the natural pathogensEnterococcus faecalisandProvidencia rettgerito measure post-infection survival and bacterial load of wildD. melanogasterpopulations collected across seasonal time along a latitudinal transect along eastern North America (Massachusetts, Pennsylvania and Virginia). There are pronounced and repeatable changes in the immune response over the approximately 10 generations between spring and autumn collections, with a significant but less distinct difference observed among geographical locations. Genes with known immune function are not enriched among alleles that cycle with seasonal time, but the immune function of a subset of seasonally cycling alleles in immune genes was tested using reconstructed outbred populations. We find that flies containing seasonal alleles inThioester-containing protein 3(Tep3) have different functional responses to infection and that epistatic interactions among seasonalTep3andDrosomycin-like 6(Dro6) alleles underlie the immune phenotypes observed in natural populations. This rapid, cyclic response to seasonal environmental pressure broadens our understanding of the complex ecological and genetic interactions determining the evolution of immune defence in natural populations.

Understanding the rate of evolutionary change and the genetic architecture that facilitates rapid adaptation is a current challenge in evolutionary biology. Comparative studies show that genes with immune function are among the most rapidly evolving genes in a range of taxa. Here, we use immune defense in natural populations of D. melanogaster to understand the rate of evolution in natural populations and the genetics underlying the rapid change. We probed the immune system using the natural pathogens Enterococcus faecalis and Providencia rettgeri to measure post-infection survival and bacterial load of wild D. melanogaster populations collected across seasonal time along a latitudinal transect on the eastern North America (Massachusetts, Pennsylvania, and Virginia). There are pronounced and repeatable changes in the immune response over approximately 10 generations between the spring and fall populations with a significant but less distinct difference among geographic locations. Genes with known immune function are not enriched among alleles that cycle with seasonal time, but the immune function of a subset of seasonally cycling alleles in immune genes was tested using reconstructed outbred populations. We find that flies containing seasonal alleles in Thioester-containing protein 3 (Tep3) have different functional responses to infection and that epistatic interactions among seasonal Tep3 and Drosomycin-like 6 (Dro6) alleles produce the immune phenotypes observed in natural populations. This rapid, cyclic response to seasonal environmental pressure broadens our understanding of the complex ecological and genetic interactions determining the evolution of immune defense in natural populations.