Evolution of genes and genomes on the Drosophila phylogeny.

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Phylogenetic relationships of Sonoran Desert cactus beetles in the tribe Hololeptini (Coleoptera: Histeridae: Histerinae), with comments on the taxonomic status of Iliotona beyeri.

Nucleotide sequences from 16S rRNA and cytochrome c oxidase subunit I (COI) were used to examine phylogenetic relationships and evolution of beetles from the tribe Hololeptini (Coleoptera: Histeridae: Histerinae) that inhabit necrotic tissue of columnar cacti in the Sonoran Desert. Phylogenetic and morphological analyses revealed the presence of seven separate lineages, three representing species in the genus Iliotona, including I. beyeri stat. nov., and four species belonging to the genus Hololepta (sensu lato). The possible roles of historical vicariance and host plant associations on the evolution of the Hololeptini from the Sonoran Desert are discussed.

Genetic diversification and demographic history of the cactophilic pseudoscorpion Dinocheirus arizonensis from the Sonoran Desert.

Sequence data from a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene were used to examine phylogenetic relationships, estimate gene flow and infer demographic history of the cactophilic chernetid pseudoscorpion, Dinocheirus arizonensis (Banks), from the Sonoran Desert. Phylogenetic trees resolved two clades of D. arizonensis, one from mainland Sonora, Mexico and southern Arizona (clade I) and the other from the Baja California peninsula and southern Arizona (clade II). The two clades were separated by a mean genetic distance (d) of approximately 2.6%. Hierarchical analysis of molecular variance indicated highly significant population structuring in D. arizonensis (overall Phi(ST)=0.860; P<0.0001), with 80% of the genetic variation distributed among the two clades. Most pairwise comparisons of Phi(ST) among populations within each clade, however, were not significant. The results suggest that phoretic dispersal on vagile cactophilic insects such as the neriid cactus fly Odontoloxozus longicornis (Coquillett) provides sufficient gene flow to offset the accumulation of unique haplotypes within each clade of the non-vagile pseudoscorpion. Preliminary results on dispersal capability of O. longicornis were consistent with this conclusion. Tests designed to reconstruct demographic history from sequence data indicated that both clades of D. arizonensis, as well as O. longicornis, have experienced historical population expansions. Potential barriers to gene flow that may have led to genetic isolation and diversification in clades I and II of D. arizonensis are discussed.

Molecular evolution and population genetics of two Drosophila mettleri cytochrome P450 genes involved in host plant utilization.

Understanding the genetic basis of adaptation is one of the primary goals of evolutionary biology. The evolution of xenobiotic resistance in insects has proven to be an especially suitable arena for studying the genetics of adaptation, and resistant phenotypes are known to result from both coding and regulatory changes. In this study, we examine the evolutionary history and population genetics of two Drosophila mettleri cytochrome P450 genes that are putatively involved in the detoxification of alkaloids present in two of its cactus hosts: saguaro (Carnegiea gigantea) and senita (Lophocereus schottii). Previous studies demonstrated that Cyp28A1 was highly up-regulated following exposure to rotting senita tissue while Cyp4D10 was highly up-regulated following exposure to rotting saguaro tissue. Here, we show that a subset of sites in Cyp28A1 experienced adaptive evolution specifically in the D. mettleri lineage. Moreover, neutrality tests in several populations were also consistent with a history of selection on Cyp28A1. In contrast, we did not find evidence for positive selection on Cyp4D10, although this certainly does not preclude its involvement in host plant use. A surprising result that emerged from our population genetic analyses was the presence of significant genetic differentiation between flies collected from different host plant species (saguaro and senita) at Organ Pipe National Monument, Arizona, USA. This preliminary evidence suggests that D. mettleri may have evolved into distinctive host races that specialize on different hosts, a possibility that warrants further investigation.

Heritable endosymbionts of Drosophila.

Although heritable microorganisms are increasingly recognized as widespread in insects, no systematic screens for such symbionts have been conducted in Drosophila species (the primary insect genetic models for studies of evolution, development, and innate immunity). Previous efforts screened relatively few Drosophila lineages, mainly for Wolbachia. We conducted an extensive survey of potentially heritable endosymbionts from any bacterial lineage via PCR screens of mature ovaries in 181 recently collected fly strains representing 35 species from 11 species groups. Due to our fly sampling methods, however, we are likely to have missed fly strains infected with sex ratio-distorting endosymbionts. Only Wolbachia and Spiroplasma, both widespread in insects, were confirmed as symbionts. These findings indicate that in contrast to some other insect groups, other heritable symbionts are uncommon in Drosophila species, possibly reflecting a robust innate immune response that eliminates many bacteria. A more extensive survey targeted these two symbiont types through diagnostic PCR in 1225 strains representing 225 species from 32 species groups. Of these, 19 species were infected by Wolbachia while only 3 species had Spiroplasma. Several new strains of Wolbachia and Spiroplasma were discovered, including ones divergent from any reported to date. The phylogenetic distribution of Wolbachia and Spiroplasma in Drosophila is discussed.

Polyandry enhances offspring viability with survival costs to mothers only when mating exclusively with virgin males in Drosophila melanogaster.

A prominent hypothesis for polyandry says that male-male competitive drivers induce males to coerce already-mated females to copulate, suggesting that females are more likely to be harassed in the presence of multiple males. This early sociobiological idea of male competitive drive seemed to explain why sperm-storing females mate multiply. Here, we describe an experiment eliminating all opportunities for male-male behavioral competition, while varying females' opportunities to mate or not with the same male many times, or with many other males only one time each. We limited each female subject's exposure to no more than one male per day over her entire lifespan starting at the age at which copulations usually commence. We tested a priori predictions about relative lifespan and daily components of RS of female Drosophila melanogaster in experimental social situations producing lifelong virgins, once-mated females, lifelong monogamous, and lifelong polyandrous females, using a matched-treatments design. Results included that (1) a single copulation enhanced female survival compared to survival of lifelong virgins, (2) multiple copulations enhanced the number of offspring for both monogamous and polyandrous females, (3) compared to females in lifelong monogamy, polyandrous females paired daily with a novel, age-matched experienced male produced offspring of enhanced viability, and (4) female survival was unchallenged when monogamous and polyandrous females could re-mate with age- and experienced-matched males. (5) Polyandrous females daily paired with novel virgin males had significantly reduced lifespans compared to polyandrous females with novel, age-matched, and experienced males. (6) Polyandrous mating enhanced offspring viability and thereby weakened support for the random mating hypothesis for female multiple mating. Analyzes of nonequivalence of variances revealed opportunities for within-sex selection among females. Results support the idea that females able to avoid constraints on their behavior from simultaneous exposure to multiple males can affect both RS and survival of females and offspring.

Flies across the water: genetic differentiation and reproductive isolation in allopatric desert Drosophila.

Between sister species of Drosophila, both pre- and postzygotic reproductive isolation commonly appear by the time a Nei's genetic distance of 0.5 is observed. The degree of genetic differentiation present when allopatric populations of the same Drosophila species exhibit incipient reproductive isolation has not been systematically investigated. Here we compare the relationship between genetic differentiation and pre- and postzygotic isolation among allopatric populations of three cactophilic desert Drosophila: D. mettleri, D. nigrospiracula, and D. mojavensis. The range of all three is interrupted by the Gulf of California, while two species, D. mettleri and D. mojavensis, have additional allopatric populations residing on distant Santa Catalina Island, off the coast of southern California. Significant population structure exists within all three species, but only for allopatric populations of D. mojavensis is significant isolation at the prezygotic level observed. The genetic distances for the relevant populations of D. mojavensis were in the range of 0.12, similar to that for D. mettleri whose greatest D = 0.11 was unassociated with any form of isolation. These observations suggest further investigations of Drosophila populations with genetic distances in this range be undertaken to identify any potential patterns in the relationship between degree of genetic differentiation and the appearance of pre- and/or postzygotic isolation.

Host plant adaptation in Drosophila mettleri populations.

The process of local adaptation creates diversity among allopatric populations, and may eventually lead to speciation. Plant-feeding insect populations that specialize on different host species provide an excellent opportunity to evaluate the causes of ecological specialization and the subsequent consequences for diversity. In this study, we used geographically separated Drosophila mettleri populations that specialize on different host cacti to examine oviposition preference for and larval performance on an array of natural and non-natural hosts (eight total). We found evidence of local adaptation in performance on saguaro cactus (Carnegiea gigantea) for populations that are typically associated with this host, and to chemically divergent prickly pear species (Opuntia spp.) in a genetically isolated population on Santa Catalina Island. Moreover, each population exhibited reduced performance on the alternative host. This finding is consistent with trade-offs associated with adaptation to these chemically divergent hosts, although we also discuss alternative explanations for this pattern. For oviposition preference, Santa Catalina Island flies were more likely to oviposit on some prickly pear species, but all populations readily laid eggs on saguaro. Experiments with non-natural hosts suggest that factors such as ecological opportunity may play a more important role than host plant chemistry in explaining the lack of natural associations with some hosts.

The wild side of life: Drosophila reproduction in nature.

Drosophila species vary in the rates at which females remate and the number of sperm they receive in the laboratory. In species such as D. melanogaster and D. pseudoobscura, in which females receive thousands of sperm and remate infrequently compared with species such as D. hydei and D. nigrospiracula, where females receive only a few hundred sperm and remate many times in a day, wild caught females should produce far more progeny. We tested this prediction by collecting, directly from nature, females of six species whose remating rates and number of sperm received vary from high to low and assessing the proportion of females with sperm and the number of progeny females produce. Over 95% of D. pseudoobscura and D. melanogaster females were inseminated while far fewer of the other species contained any sperm. In addition, D, pseudoobscura females produced progeny for over two weeks, D. melanogaster for over a week, while D. hydei and D. nigrospiracula females ran out of sperm after 1-2 d. These observations suggest extreme sperm limitation in these latter species.

Sexual isolation and mating propensity among allopatric Drosophila mettleri populations.

Drosophila mettleri is found in deserts of North America breeding in soil soaked by the juices of necrotic cacti. Saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) are the usual host cacti in Mexico and Arizona, while prickly pear (Opuntia spp.) is used by an isolated population on Santa Catalina Island off the southern California Coast. Populations of D. mettleri show significant local genetic differentiation, especially when geographical isolation is coupled with host shifts. We tested for evidence of sexual isolation among allopatric populations of D. mettleri using a variety of choice and no-choice tests. Populations exhibited significant differences in mating propensity, which translated into significant deviations from random mating. While in some cases these deviations were consistent with sexual isolation, in others, negative assortative mating was observed. No relationship between degree of genetic differentiation and the appearance of sexual isolation was detected.