DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics.

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics

Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation

The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. We look for evidence of accelerated divergence between D. montana and D. virilis, a previously sequenced relative, and do not find strong evidence for divergent selection on coding sequence variation. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. We also re-sequenced three populations of D. montana from its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales

Northern Drosophila montana flies show variation both within and between cline populations in the critical day length evoking reproductive diapause

Reproductive diapause, and its correct timing, plays an important role in the life cycle of many insect species living in a seasonally varying environment at high latitudes. In the present paper we have documented variation in the critical day length (CDL) for adult reproductive diapause and the steepness of photoperiodic response curves (PPRCs) in seven clinal populations of Drosophila montana in Finland between the latitudes 61 and 67(o)N, paying special attention to variation in these traits within and between cline populations. The isofemale lines representing these populations showed a sharp transition from 0 to 100 percent in females' diapause incidence in the shortening day lengths, indicated by steep PPRCs. The mean CDL showed a clear latitudinal cline decreasing by 1.6 hours from North to South regardless of the age of the lines, variation within the populations (i.e. among lines) in this trait being up to three hours. The steepness of the PPRCs correlated with the age of the line and this trait showed no clear latitudinal cline. Further studies on a large number of lines from one D. montana population confirmed that while maintaining the flies in diapause preventing conditions in the laboratory has no effect on CDL, older lines had steeper PPRCs. High variation in CDL within and between D. montana cline populations is likely to be heritable and provide a good potential for the evolution of photoperiodic responses. Information on genetic variation in life-history traits, such as diapause, is of utmost importance for predicting the ability of insects to survive in seasonally changing environmental conditions and to respond to long term changes in the length of the growing period e.g. by postponing the timing of diapause towards shorter day length and later calendar date

Involvement of circadian oscillation(s) in the photoperiodic time measurement and the induction of reproductive diapause in a northern Drosophila species

An ability to predict forthcoming changes in environmental conditions and get prepared for them in advance is crucial for the survival and reproduction of organisms living in a seasonally changing environment. We have studied the possible involvement of circadian oscillator(s) in the photoperiodic timer controlling seasonal responses by tracing Drosophila montana females' diapause induction in constant darkness and in a classical Nanda-Hamner experiment. Nearly all females developed ovaries in continuous darkness, which shows the direct development to be their default developmental pathway in the absence of photoperiods. In Nanda-Hamner experiment the females' diapause incidence was close to zero in light:dark cycle 12:4 (photoperiod 16 h) and increased to nearly 100% in 12:8 and 12:12 (photoperiods 20 and 24 h). In longer photoperiods (28-72 h) the females' diapause percentages decreased gradually along with an increase in the length of the dark period, showing no peaks of high diapause incidence in the multiples of 24 h. These findings suggest that the photoperiodic timer of D. montana is based on heavily damping circadian oscillator(s) or that it lacks strong oscillators. Damping of the photoperiodic timer under prolonged nights and constant darkness fits well with our earlier finding that these flies lose their locomotor activity rhythm in constant darkness, and suggests that the mechanisms underlying females' photoperiodic diapause response and their free-running locomotor activity rhythm may be partly based on same oscillators

Multiple paths to cold tolerance : the role of environmental cues, morphological traits and the circadian clock gene vrille

Background Tracing the association between insect cold tolerance and latitudinally and locally varying environmental conditions, as well as key morphological traits and molecular mechanisms, is essential for understanding the processes involved in adaptation. We explored these issues in two closely-related species, Drosophila montana and Drosophila flavomontana, originating from diverse climatic locations across several latitudes on the coastal and mountainous regions of North America. We also investigated the association between sequence variation in one of the key circadian clock genes, vrille, and cold tolerance in both species. Finally, we studied the impact of vrille on fly cold tolerance and cold acclimation ability by silencing it with RNA interference in D. montana. Results We performed a principal component analysis (PCA) on variables representing bioclimatic conditions on the study sites and used latitude as a proxy of photoperiod. PC1 separated the mountainous continental sites from the coastal ones based on temperature variability and precipitation, while PC2 arranged the sites based on summer and annual mean temperatures. Cold tolerance tests showed D. montana to be more cold-tolerant than D. flavomontana and chill coma resistance (CTmin) of this species showed an association with PC2. Chill coma recovery time (CCRT) of both species improved towards northern latitudes, and in D. flavomontana this trait was also associated with PC1. D. flavomontana flies were darkest in the coast and in the northern mountainous populations, but coloration showed no linkage with cold tolerance. Body size decreased towards cold environments in both species, but only within D. montana populations largest flies showed fastest recovery from cold. Finally, both the sequence analysis and RNAi study on vrille suggested this gene to play an essential role in D. montana cold resistance and acclimation, but not in recovery time. Conclusions Our study demonstrates the complexity of insect cold tolerance and emphasizes the need to trace its association with multiple environmental variables and morphological traits to identify potential agents of natural selection. It also shows that a circadian clock gene vrille is essential both for short- and long-term cold acclimation, potentially elucidating the connection between circadian clock system and cold tolerance.peerReviewe

Divergence and introgression among the virilis group of Drosophila

Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains 12 species that are geographically widespread and show varying levels of prezygotic and postzygotic isolation. Here, we use de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and desiccation tolerance, and may be related to the evolution of sexual isolation and adaptation. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and more recent gene flow between closely related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome as has been found in other systems. Our results show how ancient and recent introgressions confuse phylogenetic reconstruction, but may play an important role during early radiation of a group.peerReviewe

Functional Genomics Offers New Tests of Speciation Hypotheses

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Diapause affects cuticular hydrocarbon composition and mating behavior of both sexes in Drosophila montana

Environmental cues, mainly photoperiod and temperature, are known to control female adult reproductive diapause in several insect species. Diapause enhances female survival during adverse conditions and postpones progeny production to the favorable season. Male diapause (a reversible inability to inseminate receptive females) has been studied much less than female diapause. However, if the males maximized their chances to fertilize females while minimizing their energy expenditure, they would be expected to be in diapause at the same time as females. We investigated Drosophila montana male mating behavior under short‐day conditions that induce diapause in females and found the males to be reproductively inactive. We also found that males reared under long‐day conditions (reproducing individuals) court reproducing postdiapause females, but not diapausing ones. The diapausing flies of both sexes had more long‐chain and less short‐chain hydrocarbons on their cuticle than the reproducing ones, which presumably increase their survival under stressful conditions, but at the same time decrease their attractiveness. Our study shows that the mating behavior of females and males is well coordinated during and after overwintering and it also gives support to the dual role of insect cuticular hydrocarbons in adaptation and mate choice.peerReviewe