Activity variation in alcohol dehydrogenase paralogs is associated with adaptation to cactus host use in cactophilic Drosophila

Drosophila mojavensis and Drosophila arizonae are species of cactophilic flies that share a recent duplication of the alcohol dehydrogenase (Adh) locus. One paralog (Adh-2) is expressed in adult tissues and the other (Adh-1) in larvae and ovaries. Enzyme activity measurements of the ADH-2 amino acid polymorphism in D. mojavensis suggest that the Fast allozyme allele has a higher activity on 2-propanol than 1-propanol. The Fast allele was found at highest frequency in populations that utilize hosts with high proportions of 2-propanol, while the Slow allele is most frequent in populations that utilize hosts with high proportions of 1-propanol. This suggests that selection for ADH-2 allozyme alleles with higher activity on the most abundant alcohols is occurring in each D. mojavensis population. In the other paralog, ADH-1, significant differences between D. mojavensis and D. arizonae are associated with a previously shown pattern of adaptive protein evolution in D. mojavensis. Examination of protein sequences showed that a large number of amino acid fixations between the paralogs have occurred in catalytic residues. These changes are potentially responsible for the significant difference in substrate specificity between the paralogs. Both functional and sequence variation within and between paralogs suggests that Adh has played an important role in the adaptation of D. mojavensis and D. arizonae to their cactophilic life.     

Phenotypic plasticity in Drosophila cactophilic species: the effect of competition,density, and breeding sites

Changes in the environmental conditions experienced by naturally occurring populations are frequently accompanied by changes in adaptive traits allowing the organism to cope with environmental unpredictability. Phenotypic plasticity is a major aspect of adaptation and it has been involved in population dynamics of interacting species. In this study, phenotypic plasticity (i.e., environmental sensitivity) of morphological adaptive traits were analyzed in the cactophilic species Drosophila buzzatii and Drosophila koepferae (Diptera: Drosophilidae) considering the effect of crowding conditions (low and high density), type of competition (intraspecific and interspecific competition) and cacti hosts (Opuntia and Columnar cacti). All traits (wing length, wing width, thorax length, wing loading and wing aspect) showed significant variation for each environmental factor considered in both Drosophila species. The phenotypic plasticity pattern observed for each trait was different within and between these cactophilic Drosophila species depending on the environmental factor analyzed suggesting that body size‐related traits respond almost independently to environmental heterogeneity. The effects of ecological factors analyzed in this study are discussed in order to elucidate the causal factors investigated (type of competition, crowding conditions and alternative host) affecting the election of the breeding site and/or the range of distribution of these cactophilic species.     

Adaptation,ancestral variation and gene flow in a ‘Sky Island’ Drosophila species

Over time, populations of species can expand, contract, fragment and become isolated, creating subpopulations that must adapt to local conditions. Understanding how species maintain variation after divergence as well as adapt to these changes in the face of gene flow is of great interest, especially as the current climate crisis has caused range shifts and frequent migrations for many species. Here, we characterize how a mycophageous fly species, Drosophila innubila, came to inhabit and adapt to its current range which includes mountain forests in south‐western USA separated by large expanses of desert. Using population genomic data from more than 300 wild‐caught individuals, we examine four populations to determine their population history in these mountain forests, looking for signatures of local adaptation. In this first extensive study, establishing D. innubila as a key genomic "Sky Island" model, we find D. innubila spread northwards during the previous glaciation period (30–100 KYA) and have recently expanded even further (0.2–2 KYA). D. innubila shows little evidence of population structure, consistent with a recent establishment and genetic variation maintained since before geographic stratification. We also find some signatures of recent selective sweeps in chorion proteins and population differentiation in antifungal immune genes suggesting differences in the environments to which flies are adapting. However, we find little support for long‐term recurrent selection in these genes. In contrast, we find evidence of long‐term recurrent positive selection in immune pathways such as the Toll signalling system and the Toll‐regulated antimicrobial peptides.     

Microsatellite loci in the cactophilic species Drosophila antonietae (Diptera; Drosophilidae)

Morphometric and isoenzymatic data have showed little variation among Drosophila antonietae populations. This suggests historic gene flow, due to the distribution of these populations, which are associated with cacti along rivers, and natural selection on these markers. Microsatellite loci have high variability and are ideal for detecting gene flow and analysing population structure. Here we describe the isolation of seven polymorphic microsatellite loci in D. antonietae.     

Identification of a genetic network for an ecologically relevant behavioural phenotype in Drosophila melanogaster

Pupation site choice of Drosophila third‐instar larvae is critical for the survival of individuals, as pupae are exposed to various biotic and abiotic dangers while immobilized during the 3–4 days of metamorphosis. This singular behavioural choice is sensitive to both environmental and genetic factors. Here, we developed a high‐throughput phenotyping approach to assay the variation in pupation height in Drosophila melanogaster, while controlling for possibly confounding factors. We find substantial variation of mean pupation height among sampled natural stocks and we show that the Drosophila Genetic Reference Panel (DGRP) reflects this variation. Using the DGRP stocks for genome‐wide association (GWA) mapping, 16 loci involved in determining pupation height could be resolved. The candidate genes in these loci are enriched for high expression in the larval central nervous system. A genetic network could be constructed from the candidate loci, which places scribble (scrib) at the centre, plus other genes known to be involved in nervous system development, such as Epidermal growth factor receptor (Egfr) and p53. Using gene disruption lines, we could functionally validate several of the initially identified loci, as well as additional loci predicted from network analysis. Our study shows that the combination of high‐throughput phenotyping with a genetic analysis of variation captured from the wild can be used to approach the genetic dissection of an environmentally relevant behavioural phenotype.     

UCP4C mediates uncoupled respiration in larvae of Drosophila melanogaster

Larvae of Drosophila melanogaster reared at 23°C and switched to 14°C for 1 h are 0.5°C warmer than the surrounding medium. In keeping with dissipation of energy, respiration of Drosophila melanogaster larvae cannot be decreased by the F‐ATPase inhibitor oligomycin or stimulated by protonophore. Silencing of Ucp4C conferred sensitivity of respiration to oligomycin and uncoupler, and prevented larva‐to‐adult progression at 15°C but not 23°C. Uncoupled respiration of larval mitochondria required palmitate, was dependent on Ucp4C and was inhibited by guanosine diphosphate. UCP4C is required for development through the prepupal stages at low temperatures and may be an uncoupling protein.     

Patterns of variation in wing morphology in the cactophilic Drosophila buzzatii and its sibling D. koepferae

Drosophila buzzatii and D. koepferae are two sibling species that breed on the necrotic tissues of several cactus species and show a certain degree of niche overlap. Also, they show differences in several life history traits, such as body size and developmental time, which probably evolved as a consequence of adaptation to different host plants. In this work we investigate the ecological and genetic factors affecting wing morphology variation both within and between species. Three wing traits were scored, distal and proximal wing length and width in isofemale lines reared in two of the most important host cacti: Opuntia sulphurea and Trichocereus terschekii. Our results revealed that differences between species and sexes in wing size and shape were significant, whereas the cactus factor was only significant for wing size. Intraspecific analyses showed that differences among isofemale lines were highly significant for both size and shape in both species, suggesting that an important fraction of variation in wing morphology has a genetic basis. Moreover, the line by cactus interaction, which can be interpreted as a genotype by environment interaction, also accounted for a significant proportion of variation. In summary, our study shows that wing size is phenotypically plastic and that populations of D. buzzatii and D. koepferae harbour substantial amounts of genetic variation for wing size and shape. Interspecific differences in wing size and shape are interpreted in terms of spatial predictability of the different host plants in nature.     

Oviposition preference and life history traits in cactophilic Drosophila koepferae and D. buzzatii in association with their natural hosts

Drosophila koepferae and D. buzzatii are two closely related cactophilic species inhabiting the arid lands of southern South America. Previous studies have shown that D. buzzatii breeds primarily on the necrotic cladodes of several Opuntia cacti and D. koepferae on the rotting stems of columnar cacti of the genera Trichocereus and Cereus. In this paper, we analyze the patterns of host plant utilization in a locality where both Drosophila species are sympatric. Field studies showed an absence of differential attraction of adult flies to the rots of two major host cacti: O. sulphurea and T. terschekii. However, the proportion of D. buzzatii flies emerged from the rotting cladodes of O. sulphurea was significantly higher than in T. terschekii. In laboratory experiments, egg to adult viability in single species cultures varied when both Drosophila species were reared in media prepared with O. sulphurea or T. terschekii. In addition, between-species comparisons of flies emerged from single species cultures showed that D. buzzatii adults were smaller and developed faster than D. koepferae. Furthermore, analysis of flies emerged in mixed species cultures showed differences in oviposition preference and oviposition behavior. We discuss the observed between-species differences and suggest that these traits are the result of adaptation to specific patterns of spatial and temporal predictability of their respective preferred host plants: columnar are less dense and less ephemeral resources, whereas the opuntias are more abundant, and fast rotting cacti. This revised version was published online in July 2006 with corrections to the Cover Date.     

Mito‐nuclear discordance with evidence of shared ancestral polymorphism and selection in cactophilic species of Drosophila

The Drosophila serido haplogroup is a monophyletic group composed of the following four cryptic and cactophilic species that are endemic to eastern Brazil: D. borborema, D. gouveai, D. seriema and D. serido. Here, we investigate the mito‐nuclear discordance in these species found among the cytochrome c oxidase subunit I (COI) mitochondrial gene, the autosomal alpha‐Esterase‐5 (α‐Est5) and the X‐linked period gene (per). Our analysis indicates that shared polymorphisms in these three molecular markers may be explained by the maintenance of ancestral polymorphisms rather than introgressive hybridization. The primary structures of COI, per and α‐Est5 genes evolve primarily under purifying selection, but we detected some sites that evolved under positive selection in α‐Est5. Considering the high variability of cacti species in eastern Brazil and the role attributed to Drosophila esterases in digestion metabolism and/or the detoxification of several compounds found in cactus tissues, we conjecture about the role of natural selection triggered by host shifts as an important factor in the intraspecific diversification of the D. serido haplogroup.     

Early events in speciation: Cryptic species of Drosophila aldrichi

Understanding the earliest events in speciation remains a major challenge in evolutionary biology. Thus identifying species whose populations are beginning to diverge can provide useful systems to study the process of speciation. Drosophila aldrichi, a cactophilic fruit fly species with a broad distribution in North America, has long been assumed to be a single species owing to its morphological uniformity. While previous reports either of genetic divergence or reproductive isolation among different D. aldrichi strains have hinted at the existence of cryptic species, the evolutionary relationships of this species across its range have not been thoroughly investigated. Here we show that D. aldrichi actually is paraphyletic with respect to its closest relative, Drosophila wheeleri, and that divergent D. aldrichi lineages show complete hybrid male sterility when crossed. Our data support the interpretation that there are at least two species of D. aldrichi, making these flies particularly attractive for studies of speciation in an ecological and geographical context.     

Niche evolution and thermal adaptation in the temperate species Drosophila americana

The study of ecological niche evolution is fundamental for understanding how the environment influences species' geographical distributions and their adaptation to divergent environments. Here, we present a study of the ecological niche, demographic history and thermal performance (locomotor activity, developmental time and fertility/viability) of the temperate species Drosophila americana and its two chromosomal forms. Temperature is the environmental factor that contributes most to the species' and chromosomal forms' ecological niches, although precipitation is also important in the model of the southern populations. The past distribution model of the species predicts a drastic reduction in the suitable area for the distribution of the species during the last glacial maximum (LGM), suggesting a strong bottleneck. However, DNA analyses did not detect a bottleneck signature during the LGM. These contrasting results could indicate that D. americana niche preference evolves with environmental change, and thus, there is no evidence to support niche conservatism in this species. Thermal performance experiments show no difference in the locomotor activity across a temperature range of 15 to 38 °C between flies from the north and the south of its distribution. However, we found significant differences in developmental time and fertility/viability between the two chromosomal forms at the model's optimal temperatures for the two forms. However, results do not indicate that they perform better for the traits studied here in their respective optimal niche temperatures. This suggests that behaviour plays an important role in thermoregulation, supporting the capacity of this species to adapt to different climatic conditions across its latitudinal distribution.     

Secondary contact and local adaptation contribute to genome‐wide patterns of clinal variation in Drosophila melanogaster

Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome‐wide among populations of Drosophila melanogaster sampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this hybridization event likely contributed to genome‐wide patterns of parallel clinal variation between continents. The pervasive effects of admixture mean that differentiation at only several hundred loci can be attributed to the operation of spatially varying selection using an F_ST outlier approach. Our results provide novel insight into the well‐studied system of clinal differentiation in D. melanogaster and provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as temperate endemics.     

Monophyly of Wolbachia pipientis genomes within Drosophila melanogaster: geographic structuring,titre variation and host effects across five populations

Wolbachia pipientis is one of the most widely studied endosymbionts today, yet we know little about its short‐term adaptation and evolution. Here, using a set of 91 inbred Drosophila melanogaster lines from five populations, we explore patterns of diversity and recent evolution in the Wolbachia strain wMel. Within the D. melanogaster lines, we identify six major mitochondrial clades and four wMel clades. Concordant with past studies, the Wolbachia haplotypes contain an overall low level of nucleotide diversity, yet they still display geographic structuring. Using Bayesian analysis informed with demographic estimates of colonization times, we estimate that all extant D. melanogaster mitochondrial haplotypes coalesce to a Wolbachia‐infected ancestor approximately 2200 years ago. Finally, we measure wMel titre within the infected flies and find that titre varies across populations, an effect attributable to host genetic factors. This demonstration of local phenotypic divergence suggests that intraspecific host genetic variation plays a key role in shaping this model symbiotic system.     

Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments

Studying the mechanisms that enable coral populations to inhabit spatially varying thermal environments can help evaluate how they will respond in time to the effects of global climate change and elucidate the evolutionary forces that enable or constrain adaptation. Inshore reefs in the Florida Keys experience higher temperatures than offshore reefs for prolonged periods during the summer. We conducted a common garden experiment with heat stress as our selective agent to test for local thermal adaptation in corals from inshore and offshore reefs. We show that inshore corals are more tolerant of a 6‐week temperature stress than offshore corals. Compared with inshore corals, offshore corals in the 31 °C treatment showed significantly elevated bleaching levels concomitant with a tendency towards reduced growth. In addition, dinoflagellate symbionts (Symbiodinium sp.) of offshore corals exhibited reduced photosynthetic efficiency. We did not detect differences in the frequencies of major (>5%) haplotypes comprising Symbiodinium communities hosted by inshore and offshore corals, nor did we observe frequency shifts (‘shuffling’) in response to thermal stress. Instead, coral host populations showed significant genetic divergence between inshore and offshore reefs, suggesting that in Porites astreoides, the coral host might play a prominent role in holobiont thermotolerance. Our results demonstrate that coral populations inhabiting reefs <10‐km apart can exhibit substantial differences in their physiological response to thermal stress, which could impact their population dynamics under climate change.     

Experimental evolution reveals habitat‐specific fitness dynamics among Wolbachia clades in Drosophila melanogaster

The diversity and infection dynamics of the endosymbiont Wolbachia can be influenced by many factors, such as transmission rate, cytoplasmic incompatibility, environment, selection and genetic drift. The interplay of these factors in natural populations can result in heterogeneous infection patterns with substantial differences between populations and strains. The causes of these heterogeneities are not yet understood, partly due to the complexity of natural environments. We present experimental evolution as a new approach to study Wolbachia infection dynamics in replicate populations exposed to a controlled environment. A natural Drosophila melanogaster population infected with strains of Wolbachia belonging to different clades evolved in two laboratory environments (hot and cold) for 1.5 years. In both treatments, the rate of Wolbachia infection increased until fixation. In the hot environment, the relative frequency of different Wolbachia clades remained stable over 37 generations. In the cold environment, however, we observed marked changes in the composition of the Wolbachia population: within 15 generations, one Wolbachia clade increased more than 50% in frequency, whereas the other two clades decreased in frequency, resulting in the loss of one clade. The frequency change was highly reproducible not only among replicates, but also when flies that evolved for 42 generations in the hot environment were transferred to the cold environment. These results document how environmental factors can affect the composition of Wolbachia in D. melanogaster. The high reproducibility of the pattern suggests that experimental evolution studies can efficiently determine the functional basis of habitat‐specific fitness among Wolbachia strains.