Kelly A. Dyer

Evolutionarily Stable Infection by a Male-Killing Endosymbiont in Drosophila innubila: Molecular Evidence From the Host and Parasite Genomes

Maternally inherited microbes that spread via male-killing are common pathogens of insects, yet very little is known about the evolutionary duration of these associations. The few examples to date indicate very recent, and thus potentially transient, infections. A male-killing strain of Wolbachia has recently been discovered in natural populations of Drosophila innubila. The population-level effects of this infection are significant: ∼35% of females are infected, infected females produce very strongly female-biased sex ratios, and the resulting population-level sex ratio is significantly female biased. Using data on infection prevalence and Wolbachia transmission rates, infected cytoplasmic lineages are estimated to experience a ∼5% selective advantage relative to uninfected lineages. The evolutionary history of this infection was explored by surveying patterns of polymorphism in both the host and parasite genomes, comparing the Wolbachia wsp gene and the host mtDNA COI gene to five host nuclear genes. Molecular data suggest that this male-killing infection is evolutionarily old, a conclusion supported with a simple model of parasite and mtDNA transmission dynamics. Despite a large effective population size of the host species and strong selection to evolve resistance, the D. innubila-Wolbachia association is likely at a stable equilibrium that is maintained by imperfect maternal transmission of the bacteria rather than partial resistance in the host species.

Convergent evolution of strigolactone perception enabled host detection in parasitic plants

How plant parasites evolved to find hosts The seeds of parasitic plants need to be able to sense their hosts presence to germinate at the correct time and in the correct place. This is done through the detection of plant hormones, strigolactones. However, the origin of this sensory system is unknown. Conn et al. investigated the diversity of strigolactone receptors in multiple lineages of parasitic plants and their close relatives. They found a greater copy number and accelerated evolution in parasitic plants as compared with nonparasitic relatives. Functional analyses of parasitic plant strigolactone receptors in transgenic Arabidopsis suggested that convergent evolution has occurred to allow the parasitic plants to detect their hosts. Science, this issue p. 540 Obligate parasitic Orobanchaceae plants germinate after sensing strigolactones exuded from host roots. Obligate parasitic plants in the Orobanchaceae germinate after sensing plant hormones, strigolactones, exuded from host roots. In Arabidopsis thaliana, the α/β-hydrolase D14 acts as a strigolactone receptor that controls shoot branching, whereas its ancestral paralog, KAI2, mediates karrikin-specific germination responses. We observed that KAI2, but not D14, is present at higher copy numbers in parasitic species than in nonparasitic relatives. KAI2 paralogs in parasites are distributed into three phylogenetic clades. The fastest-evolving clade, KAI2d, contains the majority of KAI2 paralogs. Homology models predict that the ligand-binding pockets of KAI2d resemble D14. KAI2d transgenes confer strigolactone-specific germination responses to Arabidopsis thaliana. Thus, the KAI2 paralogs D14 and KAI2d underwent convergent evolution of strigolactone recognition, respectively enabling developmental responses to strigolactones in angiosperms and host detection in parasites.

Bayesian Estimation of Positively Selected Sites

In protein-coding DNA sequences, historical patterns of selection can be inferred from amino acid substitution patterns. High relative rates of nonsynonymous to synonymous changes (ω=dN/dS) are a clear indicator of positive, or directional, selection, and several recently developed methods attempt to distinguish these sites from those under neutral or purifying selection. One method uses an empirical Bayesian framework that accounts for varying selective pressures across sites while conditioning on the parameters of the model of DNA evolution and on the phylogenetic history. We describe a method that identifies sites under diversifying selection using a fully Bayesian framework. Similar to earlier work, the method presented here allows the rate of nonsynonymous to synonymous changes to vary among sites. The significant difference in using a fully Bayesian approach lies in our ability to account for uncertainty in parameters including the tree topology, branch lengths, and the codon model of DNA substitution. We demonstrate the utility of the fully Bayesian approach by applying our method to a data set of the vertebrate β-globin gene. Compared to a previous analysis of this data set, the hierarchical model found most of the same sites to be in the positive selection class, but with a few striking exceptions.

Chromosome-wide linkage disequilibrium as a consequence of meiotic drive

Adaptation by natural selection proceeds most efficiently when alleles compete solely on the basis of their effects on the survival and reproduction of their carriers. A major condition for this is equal Mendelian segregation, but meiotic drive can short-circuit this process. The evolution of drive often involves multiple, interacting genetic components, together with enhancers and suppressors of drive. Chromosomal inversions that suppress crossing over are also frequently associated with drive systems. This study investigates the effects of these processes on patterns of molecular evolution in the fly Drosophila recens, which is polymorphic for a driving X chromosome (XD). Whereas standard wild-type chromosomes exhibit high levels of polymorphism at multiple loci, all of the XD chromosomes effectively carry a single multilocus haplotype that spans at least 130 cM. The XD is associated with a complex set of inversions that completely suppresses recombination between the standard wild-type chromosome and XD in heterozygous females, which maintain nonrandom associations among loci that presumably interact epistatically for the expression of drive. The long-term costs of foregoing recombination may be substantial; in combination with its low equilibrium frequency, this makes the XD chromosome susceptible to the accumulation of deleterious mutations. Consistent with this, XD chromosomes are apparently fixed for a recessive mutation that causes female sterility. Thus, the XD in D. recens appears to be in chromosome-wide linkage disequilibrium and in the early stages of mutational degradation.

The Ecology and Evolutionary Dynamics of Meiotic Drive

Meiotic drivers are genetic variants that selfishly manipulate the production of gametes to increase their own rate of transmission, often to the detriment of the rest of the genome and the individual that carries them. This genomic conflict potentially occurs whenever a diploid organism produces a haploid stage, and can have profound evolutionary impacts on gametogenesis, fertility, individual behaviour, mating system, population survival, and reproductive isolation. Multiple research teams are developing artificial drive systems for pest control, utilising the transmission advantage of drive to alter or exterminate target species. Here, we review current knowledge of how natural drive systems function, how drivers spread through natural populations, and the factors that limit their invasion.

REPRODUCTIVE CHARACTER DISPLACEMENT OF EPICUTICULAR COMPOUNDS AND THEIR CONTRIBUTION TO MATE CHOICE IN DROSOPHILA SUBQUINARIA AND DROSOPHILA RECENS

Interactions between species can alter selection on sexual displays used in mate choice within species. Here we study the epicuticular pheromones of two Drosophila species that overlap partially in geographic range and are incompletely reproductively isolated. Drosophila subquinaria shows a pattern of reproductive character displacement against Drosophila recens, and partial behavioral isolation between conspecific sympatric versus allopatric populations, whereas D. recens shows no such variation in mate choice. First, using manipulative perfuming experiments, we show that females use pheromones as signals for mate discrimination both between species and among populations of D. subquinaria. Second, we show that patterns of variation in epicuticular compounds, both across populations and between species, are consistent with those previously shown for mating probabilities: pheromone compositions differ between populations of D. subquinaria that are allopatric versus sympatric with D. recens, but are similar across populations of D. recens regardless of overlap with D. subquinaria. We also identify differences in pheromone composition among allopatric regions of D. subquinaria. In sum, our results suggest that epicuticular compounds are key signals used by females during mate recognition, and that these traits have diverged among D. subquinaria populations in response to reinforcing selection generated by the presence of D. recens.

Epicuticular Compounds of Drosophila subquinaria and D. recens : Identification, Quantification, and Their Role in Female Mate Choice

The epicuticle of various Drosophila species consists of long-chain cuticular hydrocarbons (CHCs) and their derivatives that play a role in waterproofing and a dynamic means of chemical communication. Here, via gas chromatography and mass spectrometry, we identified and quantified the epicuticular composition of D. recens and D. subquinaria, two closely related species that show a pattern of reproductive character displacement in nature. Twenty-four compounds were identified with the most abundant, 11-cis-Vaccenyl acetate, present only in males of each species. Also exclusive to males were five tri-acylglycerides. The 18 remaining compounds were CHCs, all shared between the sexes and species. These CHCs were composed of odd carbon numbers (C29, C31, C33, and C35), with an increase in structural isomers in the C33 and C35 groups. Saturated hydrocarbons comprise only methyl-branched alkanes and were found only in the C29 and C31 groups. Alkenes were the least prevalent, with alkadienes dominating the chromatographic landscape in the longer chain lengths. Sexual dimorphism was extensive with 6/8 of the logcontrast CHCs differing significantly in relative concentration between males and females in D. recens and D. subquinaria, respectively. Males of the two species also differed significantly in relative concentration of six CHCs, while females differed in none. Female-choice mating trials revealed directional sexual selection on male CHCs in a population of each species, consistent with female mate preferences for these traits. The sexual selection vectors differed significantly in multivariate trait space, suggesting that different pheromone blends determine male attractiveness in each species.

EVOLUTIONARY DYNAMICS OF A SPATIALLY STRUCTURED HOST-PARASITE ASSOCIATION: DROSOPHILA INNUBILA AND MALE-KILLING WOLBACHIA

Abstract The mode and tempo of host‐parasite evolution depend on population structure and history and the strength of selection that the species exert on each other. Here we genetically and epidemiologically characterize populations of the mycophagous fly Drosophila innubila and its male‐killing Wolbachia endosymbiont, with the aim of integrating the local through global nature of this association. Drosophila innubila inhabit the forested “sky island”regions of the of the southwestern United States and northern Mexico, where its distribution is highly fragmented. We examine geographically isolated sky island populations of D. innubila, surveying the frequency and expression of Wolbachia infection as well as the distribution of genetic variation within and among populations of the host and parasite. In all populations, Wolbachia infection is associated with virtually complete male‐killing, thus providing no evidence for the evolution of population‐specific interaction phenotypes or local resistance. Although Wolbachia infection occurs in each of the main populations, there is variation among populations in the prevalence of infection and the resulting population‐level sex ratio of D. innubila. Among these populations, the nuclear genes of D. innubila show moderate, though significant, differentiation. In contrast, the host mitochondrial DNA (mtDNA), which shares transmission with Wolbachia, exhibits substantially greater geographic differentiation, even after accounting for differences in transmission between nuclear and mitochondrial genes. We suggest that this pattern is caused by local Wolbachia‐but not D. innubila‐fluctuations in prevalence that increase the severity of drift experienced only by the mtDNA. Overall, our data suggest that the association between D. innubila and male‐killing Wolbachia is ecologically dynamic within local populations, but evolutionarily coherent across the species as a whole.

Wolbachia-mediated persistence of mtDNA from a potentially extinct species.

Drosophila quinaria is polymorphic for infection with Wolbachia, a maternally transmitted endosymbiont. Wolbachia‐infected individuals carry mtDNA that is only distantly related to the mtDNA of uninfected individuals, and the clade encompassing all mtDNA haplotypes within D. quinaria also includes the mtDNA of several other species of Drosophila. Nuclear gene variation reveals no difference between the Wolbachia‐infected and uninfected individuals of D. quinaria, indicating that they all belong to the same interbreeding biological species. We suggest that the Wolbachia and the mtDNA with which it is associated were derived via interspecific hybridization and introgression. The sequences in the Wolbachia and the associated mtDNA are ≥6% divergent from those of any known Drosophila species. Thus, in spite of nearly complete species sampling, the sequences from which these mitochondria were derived remain unknown, raising the possibility that the donor species is extinct. The association between Wolbachia infection and mtDNA type within D. quinaria suggests that Wolbachia may be required for the continued persistence of the mtDNA from an otherwise extinct Drosophila species. We hypothesize that pathogen‐protective effects conferred by Wolbachia operate in a negative frequency‐dependent manner, thus bringing about a stable polymorphism for Wolbachia infection.

EXPRESSION AND MODULATION OF EMBRYONIC MALE-KILLING IN DROSOPHILA INNUBILA: OPPORTUNITIES FOR MULTILEVEL SELECTION

Abstract Organisms and the symbionts they harbor may experience opposing forces of selection. In particular, the contrasting inheritance patterns of maternally transmitted symbionts and their hosts nuclear genes can engender conflict among organizational levels over the optimal host offspring sex ratio. This study uses a male‐killing Wolbachia endosymbiont and its host Drosophila innubila to experimentally address the potential for multilevel selection in a host‐symbiont system. We show that bacterial density can vary among infected females, and that females with a higher density have a more female‐biased offspring sex ratio. Furthermore, bacterial density is an epigenetic and heritable trait: females with a low bacterial load have daughters with a lower‐than‐average bacterial density, whose offspring then experience less severe male‐killing. For infected sons, the probability of embryonic mortality increases with the bacterial density in their mothers. The frequency distribution of Wolbachia density among individual D. innubila females, and therefore the dynamics of infection within populations of these flies, results both from processes affecting the growth and regulation of bacterial populations within cytoplasmic lineages and from selection among cytoplasmic lineages that vary in bacterial density. Estimates of effective population size of Wolbachia within cytoplasmic lineages and of D. innubila at the host population level suggest that selection among cytoplasmic lineages is likely to overwhelm the results of selection within lineages.