Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii.

Studying how novel phenotypes originate and evolve is fundamental to the field of evolutionary biology as it allows us to understand how organismal diversity is generated and maintained. However, determining the basis of novel phenotypes is challenging as it involves orchestrated changes at multiple biological levels. Here, we aim to overcome this challenge by using a comparative species framework combining behavioral, gene expression, and genomic analyses to understand the evolutionary novel egg-laying substrate-choice behavior of the invasive pest species Drosophila suzukii. First, we used egg-laying behavioral assays to understand the evolution of ripe fruit oviposition preference in D. suzukii compared with closely related species D. subpulchrella and D. biarmipes as well as D. melanogaster. We show that D. subpulchrella and D. biarmipes lay eggs on both ripe and rotten fruits, suggesting that the transition to ripe fruit preference was gradual. Second, using two-choice oviposition assays, we studied how D. suzukii, D. subpulchrella, D. biarmipes, and D. melanogaster differentially process key sensory cues distinguishing ripe from rotten fruit during egg-laying. We found that D. suzukii's preference for ripe fruit is in part mediated through a species-specific preference for stiff substrates. Last, we sequenced and annotated a high-quality genome for D. subpulchrella. Using comparative genomic approaches, we identified candidate genes involved in D. suzukii's ability to seek out and target ripe fruits. Our results provide detail to the stepwise evolution of pest activity in D. suzukii, indicating important cues used by this species when finding a host, and the molecular mechanisms potentially underlying their adaptation to a new ecological niche.

Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists.

Mutualistic interactions with microbes have played a crucial role in the evolution and ecology of animal hosts. However, it is unclear what factors are most important in influencing particular host-microbe associations. While closely related animal species may have more similar microbiota than distantly related species due to phylogenetic contingencies, social partnerships with other organisms, such as those in which one animal farms another, may also influence an organism's symbiotic microbiome. We studied a mutualistic network of Brachymyrmex and Lasius ants farming several honeydew-producing Prociphilus aphids and Rhizoecus mealybugs to test whether the mutualistic microbiomes of these interacting insects are primarily correlated with their phylogeny or with their shared social partnerships. Our results confirm a phylogenetic signal in the microbiomes of aphid and mealybug trophobionts, with each species harbouring species-specific endosymbiont strains of Buchnera (aphids), Tremblaya and Sodalis (mealybugs), and Serratia (both mealybugs and aphids) despite being farmed by the same ants. This is likely explained by strict vertical transmission of trophobiont endosymbionts between generations. In contrast, our results show the ants' microbiome is possibly shaped by their social partnerships, with ants that farm the same trophobionts also sharing strains of sugar-processing Acetobacteraceae bacteria, known from other honeydew-feeding ants and which likely reside extracellularly in the ants' guts. These ant-microbe associations are arguably more "open" and subject to horizontal transmission or social transmission within ant colonies. These findings suggest that the role of social partnerships in shaping a host's symbiotic microbiome can be variable and is likely dependent on how the microbes are transmitted across generations.

Choosy Cannibals Preferentially Consume Siblings with Relatively Low Fitness Prospects.

When an individual can selfishly cannibalize a relative or altruistically set it free, the benefits of altruism will be positively associated with the relative's fitness prospects (the benefits it receives from altruism). We tested the prediction that altruism should be preferentially directed toward high-quality relatives using larvae of the New Mexican spadefoot toad (Spea multiplicata), a species in which tadpoles plastically express omnivore and carnivore ecomorphs. In a no-choice design, we presented carnivores with sibling or nonsibling omnivores varying in developmental stage, which is positively associated with survival in this toad's ephemeral larval environment. There was a significant interaction between relatedness and developmental stage on the probability of cannibalism: carnivores were overall more likely to cannibalize less developed omnivores, but this effect was exaggerated when the potential victim was a sibling. This evidence that altruists favor relatives with high fitness prospects highlights the numerous factors shaping altruism's payoffs.

The evolution and mutational robustness of chromatin accessibility in Drosophila.

The evolution of regulatory regions in the genome plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems has made it difficult to understand the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different tissues of Drosophila. We train hybrid convolution-attention neural networks to accurately predict ATAC-seq peaks using only local DNA sequences as input. We show that a model trained in one species has nearly identical performance when tested in another species, implying that the sequence determinants of accessibility are highly conserved. Indeed, model performance remains excellent even in distantly-related species. By using our model to examine species-specific gains in chromatin accessibility, we find that their orthologous inaccessible regions in other species have surprisingly similar model outputs, suggesting that these regions may be ancestrally poised for evolution. We then use in silico saturation mutagenesis to reveal evidence of selective constraint acting specifically on inaccessible chromatin regions. We further show that chromatin accessibility can be accurately predicted from short subsequences in each example. However, in silico knock-out of these sequences does not qualitatively impair classification, implying that chromatin accessibility is mutationally robust. Subsequently, we demonstrate that chromatin accessibility is predicted to be robust to large-scale random mutation even in the absence of selection. We also perform in silico evolution experiments under the regime of strong selection and weak mutation (SSWM) and show that chromatin accessibility can be extremely malleable despite its mutational robustness. However, selection acting in different directions in a tissue-specific manner can substantially slow adaptation. Finally, we identify motifs predictive of chromatin accessibility and recover motifs corresponding to known chromatin accessibility activators and repressors. These results demonstrate the conservation of the sequence determinants of accessibility and the general robustness of chromatin accessibility, as well as the power of deep neural networks as tools to answer fundamental questions in regulatory genomics and evolution.

The evolution and mutational robustness of chromatin accessibility in Drosophila.

BACKGROUND: The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates the understanding of the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different species and tissues of Drosophila. RESULTS: We train hybrid convolution-attention neural networks to accurately predict ATAC-seq peaks using only local DNA sequences as input. We show that our models generalize well across substantially evolutionarily diverged species of insects, implying that the sequence determinants of accessibility are highly conserved. Using our model to examine species-specific gains in accessibility, we find evidence suggesting that these regions may be ancestrally poised for evolution. Using in silico mutagenesis, we show that accessibility can be accurately predicted from short subsequences in each example. However, in silico knock-out of these sequences does not qualitatively impair classification, implying that accessibility is mutationally robust. Subsequently, we show that accessibility is predicted to be robust to large-scale random mutation even in the absence of selection. Conversely, simulations under strong selection demonstrate that accessibility can be extremely malleable despite its robustness. Finally, we identify motifs predictive of accessibility, recovering both novel and previously known motifs. CONCLUSIONS: These results demonstrate the conservation of the sequence determinants of accessibility and the general robustness of chromatin accessibility, as well as the power of deep neural networks to explore fundamental questions in regulatory genomics and evolution.

A comparison of the nutritional physiology and gut microbiome of urban and rural house sparrows (Passer domesticus).

Urbanization influences food quality and availability for many wild species, but our knowledge of the consequences urbanization has on the nutritional physiology of these animals is currently limited. To fill this gap, we captured House Sparrows (Passer domesticus) from rural and urban environments and hypothesized that increased access to human refuse in urban areas may significantly alter the gut microbiome and nutritional physiology of Sparrows. While there were no significant differences in circulating triglycerides or free glycerol concentrations between populations, urban birds had significantly greater blood glucose concentrations, which suggests greater circulating glucagon concentrations, accessibility to carbohydrates, and/or higher rates of gluconeogenesis in an urban setting. Rural birds had significantly more plasma uric acid, suggesting that they may metabolize more proteins or experience lower inflammation than urban birds. Rural birds also had significantly higher liver free glycerol concentrations, indicating that they metabolize more fat than urban birds. There were no significant differences in the relative abundance of gut microbial taxa at the phyla level between the two populations, but linear discriminant analysis effect size (LEfSe) showed that urban House Sparrows were more enriched with class- and order-level microbes from the phylum Proteobacteria, which are implicated in several mammalian intestinal and extra-intestinal diseases. These findings demonstrate that urbanization significantly alters the nutritional physiology and the composition of the gut microbiome of House Sparrows.

Pathophysiological responses to a schistosome infection in a wild population of mourning doves (Zenaida macroura).

The blood trematode Gigantobilharzia huronensis typically infects passerine birds and has not been reported in other orders of wild birds. However, in the summer of 2011 in Tempe, Arizona, USA, mourning doves (Zenaida macroura; order: Columbiformes) were collected with infections of G. huronensis. This is the first report of a natural schistosome infection found in wild populations of doves. We sought to determine if G. huronensis infections alter the general body condition and physiology of doves, a seemingly unlikely host for this parasite. Specifically, we hypothesized that birds infected with schistosomes would exhibit reduced weight as well as increased markers of stress and immune system activation. Adult male mourning doves (n=14) were captured using walk-in style funnel traps. After weighing the birds, blood and mesenteric tissue samples were collected. We measured biomarkers of stress including circulating heat shock proteins (HSPs) 60 and 70, as well as oxidized lipoproteins in schistosome-infected and non-infected birds. Indices of immune system reactivity were assessed using agglutination and lysis assays in addition to determining the leukocyte to erythrocyte ratios and prevalence of hemoparasite infections from blood smears. Schistosome-infected mourning doves had significantly increased oxidative stress and evidence of HSP70 mobilization. There was no evidence for weight loss in schistosome-infected birds nor evidence of significant immune system activation associated with schistosome infection. This may be a reflection of the small sample size available for the study. These findings suggest that schistosome infections have pathological effects in doves, but the lack of mature worms suggests that infected birds in this sampling may not have been suitable hosts for parasite maturation.