Genetic variability in the three genomes of Nasonia: nuclear, mitochondrial and Wolbachia

Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species

BACKGROUND

Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages.

RESULTS

The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages.

CONCLUSIONS

The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.

Disentangling a Holobiont - Recent Advances and Perspectives in Nasonia Wasps

The parasitoid wasp genus Nasonia (Hymenoptera: Chalcidoidea) is a well-established model organism for insect development, evolutionary genetics, speciation, and symbiosis. The host-microbiota assemblage which constitutes the Nasonia holobiont (a host together with all of its associated microbes) consists of viruses, two heritable bacterial symbionts and a bacterial community dominated in abundance by a few taxa in the gut. In the wild, all four Nasonia species are systematically infected with the obligate intracellular bacterium Wolbachia and can additionally be co-infected with Arsenophonus nasoniae. These two reproductive parasites have different transmission modes and host manipulations (cytoplasmic incompatibility vs. male-killing, respectively). Pioneering studies on Wolbachia in Nasonia demonstrated that closely related Nasonia species harbor multiple and mutually incompatible Wolbachia strains, resulting in strong symbiont-mediated reproductive barriers that evolved early in the speciation process. Moreover, research on host-symbiont interactions and speciation has recently broadened from its historical focus on heritable symbionts to the entire microbial community. In this context, each Nasonia species hosts a distinguishable community of gut bacteria that experiences a temporal succession during host development and members of this bacterial community cause strong hybrid lethality during larval development. In this review, we present the Nasonia species complex as a model system to experimentally investigate questions regarding: (i) the impact of different microbes, including (but not limited to) heritable endosymbionts, on the extended phenotype of the holobiont, (ii) the establishment and regulation of a species-specific microbiota, (iii) the role of the microbiota in speciation, and (iv) the resilience and adaptability of the microbiota in wild populations subjected to different environmental pressures. We discuss the potential for easy microbiota manipulations in Nasonia as a promising experimental approach to address these fundamental aspects.

The expanding genetic toolbox of the wasp Nasonia vitripennis and its relatives

The parasitoid wasp Nasonia represents a genus of four species that is emerging as a powerful genetic model system that has made and will continue to make important contributions to our understanding of evolutionary biology, development, ecology, and behavior. Particularly powerful are the haplodiploid genetics of the system, which allow some of the advantages of microbial genetics to be applied to a complex multicellular eukaryote. In addition, fertile, viable hybrids can be made among the four species in the genus. This makes Nasonia exceptionally well suited for evolutionary genetics approaches, especially when combined with its haploid genetics and tractability in the laboratory. These features are complemented by an expanding array of genomic, transcriptomic, and functional resources, the application of which has already made Nasonia an important model system in such emerging fields as evolutionary developmental biology and microbiomics. This article describes the genetic and genomic advantages of Nasonia wasps and the resources available for their genetic analysis.

A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities?

Evolution in allopatric populations can lead to incompatibilities that result in reduced hybrid fitness and ultimately reproductive isolation upon secondary contact. The Dobzhansky-Muller (DM) model nicely accounts for the evolution of such incompatibilities. Although DM incompatibilities were originally conceived as resulting of interactions between nuclear genes, recent studies have documented cases where incompatibilities have arisen between nuclear and mitochondrial genomes (mtDNA). Although mtDNA comprises only a tiny component (typically <<0.01%) of an organism's genetic material, several features of mtDNA may lead to a disproportionate contribution to the evolution of hybrid incompatibilities: (i) essentially all functions of mtDNA require interaction with nuclear gene products. All mtDNA-encoded proteins are components of the oxidative phosphorylation (OXPHOS) system and all mtDNA-encoded RNAs are part of the mitochondrial protein synthetic machinery; both processes require interaction with nuclear-encoded proteins for function. (ii) Transcription and replication of mtDNA also involve mitonuclear interactions as nuclear-encoded proteins must bind to regulatory motifs in the mtDNA to initiate these processes. (iii) Although features of mtDNA vary amongst taxa, metazoan mtDNA is typically characterized by high nucleotide substitution rates, lack of recombination and reduced effective population sizes that collectively lead to increased chance fixation of mildly deleterious mutations. Combined, these features create an evolutionary dynamic where rapid mtDNA evolution favours compensatory nuclear gene evolution, ultimately leading to co-adaptation of mitochondrial and nuclear genomes. When previously isolated lineages hybridize in nature or in the lab, intergenomic co-adaptation is disrupted and hybrid breakdown is observed; the role of intergenomic co-adaptation in hybrid breakdown and speciation will generally be most pronounced when rates of mtDNA evolution are high or when restricted gene flow results in significant population differentiation.

Phylogeography of Nasonia vitripennis (Hymenoptera) indicates a mitochondrial-Wolbachia sweep in North America

Here we report evidence of a mitochondrial-Wolbachia sweep in North American populations of the parasitoid wasp Nasonia vitripennis, a cosmopolitan species and emerging model organism for evolutionary and genetic studies. Analysis of the genetic variation of 89 N. vitripennis specimens from Europe and North America was performed using four types of genetic markers: a portion of the mitochondrial cytochrome oxidase I gene, nine polymorphic nuclear microsatellites, sequences from 11 single-copy nuclear markers and six Wolbachia genes. The results show that the European populations have a sevenfold higher mitochondrial sequence variation than North American populations, but similar levels of microsatellite and nuclear gene sequence variation. Variation in the North American mitochondria is extremely low (pi=0.31%), despite a highly elevated mutation rate (approximately 35-40 times higher than the nuclear genes) in the mitochondria of Nasonia. The data are indicative of a mitochondrial sweep in the North American population, possibly due to Wolbachia infections that are maternally co-inherited with the mitochondria. Owing to similar levels of nuclear variation, the data could not resolve whether N. vitripennis originated in the New or the Old World.

Distribution of Wolbachia infection in Chorthippus parallelus populations within and beyond a Pyrenean hybrid zone

Two subspecies of the meadow grasshopper Chorthippus parallelus meet in a secondary hybrid zone in the Pyrenees. We have recently detected Wolbachia infection in this extensively studied species. C. p. parallelus (Cpp) and C. p. erythropus (Cpe) harbour bacteria from the B and F supergroups, but they differ noticeably in the incidence and type of infection present in their populations. We can distinguish different regional infection patterns that are associated with the distribution of pure and hybrid C. parallelus individuals. The northern pattern of low-level infection characterizes Cpp populations, whereas the southern pattern of high-level infection affects Cpe locations. These patterns converge in the hybrid zone and generate a third infection pattern featuring an extremely high degree of co-infection with the two Wolbachia types in hybrids. The distribution of Wolbachia among the studied populations encourages us to consider the possibility that this bacterium has a significant influence on the origin, maintenance and dynamics of this hybrid zone, given the reproductive alterations that are often associated with Wolbachia.

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

Background

Flesh flies in the genus Sarcophaga are important models for investigating endocrinology, diapause, cold hardiness, reproduction, and immunity. Despite the prominence of Sarcophaga flesh flies as models for insect physiology and biochemistry, and in forensic studies, little genomic or transcriptomic data are available for members of this genus. We used massively parallel pyrosequencing on the Roche 454-FLX platform to produce a substantial EST dataset for the flesh fly Sarcophaga crassipalpis. To maximize sequence diversity, we pooled RNA extracted from whole bodies of all life stages and normalized the cDNA pool after reverse transcription.

Results

We obtained 207,110 ESTs with an average read length of 241 bp. These reads assembled into 20,995 contigs and 31,056 singletons. Using BLAST searches of the NR and NT databases we were able to identify 11,757 unique gene elements (E<0.0001) representing approximately 9,000 independent transcripts. Comparison of the distribution of S. crassipalpis unigenes among GO Biological Process functional groups with that of the Drosophila melanogaster transcriptome suggests that our ESTs are broadly representative of the flesh fly transcriptome. Insertion and deletion errors in 454 sequencing present a serious hurdle to comparative transcriptome analysis. Aided by a new approach to correcting for these errors, we performed a comparative analysis of genetic divergence across GO categories among S. crassipalpis, D. melanogaster, and Anopheles gambiae. The results suggest that non-synonymous substitutions occur at similar rates across categories, although genes related to response to stimuli may evolve slightly faster. In addition, we identified over 500 potential microsatellite loci and more than 12,000 SNPs among our ESTs.

Conclusion

Our data provides the first large-scale EST-project for flesh flies, a much-needed resource for exploring this model species. In addition, we identified a large number of potential microsatellite and SNP markers that could be used in population and systematic studies of S. crassipalpis and other flesh flies.

Life and death of an influential passenger: Wolbachia and the evolution of CI-modifiers by their hosts

Background

Wolbachia are intracellular bacteria widely distributed among arthropods and nematodes. In many insect species these bacteria induce a cytoplasmic incompatibility (CI) between sperm of infected males and eggs of uninfected females. From an evolutionary point of view, CI is puzzling: In order to induce this modification-rescue system, Wolbachia affect sperm of infected males even though Wolbachia are only transmitted maternally. Phylogenetic studies of Wolbachia and hosts show that the bacteria rarely cospeciate with their hosts, indicating that infections are lost in host species. However, the mechanisms leading to Wolbachia loss are not well understood.

Results

Using a population genetic model, we investigate the spread of host mutants that enhance or repress Wolbachia action by affecting either bacterial transmission or the level of CI. We show that host mutants that decrease CI-levels in males (e.g. by reducing Wolbachia-density during spermatogenesis) spread, even at cost to mutant males. Increase of these mutants can lead to loss of Wolbachia infections, either as a direct consequence of their increase or in a step-wise manner, and we derive analytically a threshold penetrance above which a mutation's spread leads to extinction of Wolbachia. Selection on host modifiers is sexually antagonistic in that, conversely, host mutants that enhance Wolbachia in females are favoured whereas suppressors are not.

Conclusions

Our results indicate that Wolbachia is likely to be lost from host populations on long evolutionary time scales due to reduction of CI levels in males. This can occur either by evolution of single host modifiers with large effects or through accumulation of several modifier alleles with small effects on Wolbachia action, even at cost to mutant males and even if infected hosts do not incur fecundity costs. This possibility is consistent with recent findings and may help to explain the apparent short evolutionary persistence times of Wolbachia in many host systems.

Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp nasonia (hymenoptera: pteromalidae)

We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally <10 times faster). A McDonald and Kreitman test shows that the between-species frequency of fixed replacement sites relative to silent sites is significantly higher compared with within-species polymorphisms in 2 mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a "Compensation-Draft Feedback"; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus accelerating the process of amino acid substitutions.

Modes of acquisition of Wolbachia: horizontal transfer, hybrid introgression, and codivergence in the Nasonia species complex

Wolbachia are maternally inherited bacteria that infect a large number of insects and are responsible for different reproductive alterations of their hosts. One of the key features of Wolbachia biology is its ability to move within and between host species, which contributes to the impressive diversity and range of infected hosts. Using multiple Wolbachia genes, including five developed for Multi-Locus Sequence Typing (MLST), the diversity and modes of movement of Wolbachia within the wasp genus Nasonia were investigated. Eleven different Wolbachia were found in the four species of Nasonia, including five newly identified infections. Five infections were acquired by horizontal transmission from other insect taxa, three have been acquired by hybridization between two Nasonia species, which resulted in a mitochondrial-Wolbachia sweep from one species to the other, and at least three have codiverged during speciation of their hosts. The results show that a variety of transfer mechanisms of Wolbachia are possible even within a single host genus. Codivergence of Wolbachia and their hosts is uncommon and provides a rare opportunity to investigate long-term Wolbachia evolution within a host lineage. Using synonymous divergence among codiverging infections and host nuclear genes, we estimate Wolbachia mutation rates to be approximately one-third that of the nuclear genome.

Molecular phylogenetics and reproductive incompatibility in a complex of cryptic species of aphid parasitoids

We infer the phylogeny of a complex of cryptic species and populations of parasitic wasps and examine how reproductive incompatibility maps onto the molecular phylogeny. We used four nuclear (28S-D2, ITS1, ITS2, ArgK) and two mitochondrial (COI, COII) gene regions to analyze relationships among populations in the Aphelinus varipes species complex (Hymenoptera: Aphelinidae) from throughout Eurasia (France, Georgia, Israel, China, Korea and Japan) and from three aphid hosts (Aphis glycines, Diuraphis noxia and Rhopalosiphum padi; Hemiptera: Aphididae). A combined analysis of 21 genotypes of Aphelinus resulted in six most-parsimonious trees, and successive approximations character-weighting selected two of these as best supported by the data. All six gene regions were necessary to fully resolve the relationships among taxa. Four clades within the A. varipes complex were distinguished: (1) Aphelinus kurdjumovi, (2) Aphelinus hordei, (3) Aphelinus atriplicis, Aphelinus varipes, and Aphelinus albipodus, and (4) Aphelinus certus (populations from China, Korea, and Japan). Based on rates of nucleotide substitutions, these clades diverged between 78 and 526 thousand years ago during a period of repeated glaciations in Eurasia. In laboratory crosses, A. kurdjumovi, A. hordei, and A. varipes were reproductively incompatible with one another and all other populations. A. atriplicis was incompatible with these three species, but not with A. certus. The populations of A. certus from China, Japan, and Korea were reproductively compatible with one another but not with the other populations. Thus, with one exception, entities that were phylogenetically distinct were also reproductively incompatible with one another. Our evidence on molecular differentiation and reproductive incompatibility supports recognition of at least five cryptic species in the A. varipes complex. We discuss likely reasons for the high rate of speciation in this complex.

Bidirectional incompatibility among divergent Wolbachia and incompatibility level differences among closely related Wolbachia in Nasonia

Most insect groups harbor obligate bacterial symbionts from the alpha-proteobacterial genus Wolbachia. These bacteria alter insect reproduction in ways that enhance their cytoplasmic transmission. One of the most common alterations is cytoplasmic incompatibility (CI) - a post-fertilization modification of the paternal genome that renders embryos inviable or unable to complete diploid development in crosses between infected males and uninfected females or infected females harboring a different strain. The parasitic wasp species complex Nasonia (N. vitripennis, N. longicornis and N. giraulti) harbor at least six different Wolbachia that cause CI. Each species have double infections with a representative from both the A and B Wolbachia subgroups. CI relationships of the A and B Wolbachia of N. longicornis with those of N. giraulti and N. vitripennis are investigated here. We demonstrate that all pairwise crosses between the divergent A strains are bidirectionally incompatible. We were unable to characterize incompatibility between the B Wolbachia, but we establish that the B strain of N. longicornis induces no or very weak CI in comparison to the closely related B strain in N. giraulti that expresses complete CI. Taken together with previous studies, we show that independent acquisition of divergent A Wolbachia has resulted in three mutually incompatible strains, whereas codivergence of B Wolbachia in N. longicornis and N. giraulti is associated with differences in CI level. Understanding the diversity and evolution of new incompatibility strains will contribute to a fuller understanding of Wolbachia invasion dynamics and Wolbachia-assisted speciation in certain groups of insects.

Supergroup F Wolbachia bacteria parasitise lice (Insecta: Phthiraptera)

We studied six species of lice from three of the four suborders of lice. These lice were infected with Wolbachia bacteria from supergroups A and F. This is the first report of an infection of supergroup F Wolbachia in lice. To date, Wolbachia from supergroup F have been found in filarial nematodes, Mansonella spp., and, rarely, in insects. We inferred the phylogeny of the Wolbachia from lice and representatives of all Wolbachia supergroups, with nucleotide sequences from the small subunit ribosomal RNA gene (SSU rRNA). There was no evidence of congruence between the taxon of louse and the Wolbachia bacteria that infect lice. There is no evidence that Wolbachia and their louse hosts co-evolved at least at the level of Wolbachia supergroups. We propose a novel mechanism for the horizontal transfer of Wolbachia between different species of lice from birds: transfer of Wolbachia during phoresis by hippoboscid flies.

Paternal chromosome segregation during the first mitotic division determines Wolbachia-induced cytoplasmic incompatibility phenotype

The most common Wolbachia-induced phenotype in insects is cytoplasmic incompatibility (CI), which occurs when sperm from infected males fertilize eggs from uninfected females. CI produces distinct phenotypes in three closely related haplo-diploid species of the genus Nasonia: mortality in N. longicornis and N. giraulti, and conversion to male development in N. vitripennis. We demonstrate that the majority of CI-induced mortality occurs during embryogenesis and that the pattern of paternal chromosome segregation during the first mitosis is a good predictor of CI phenotype. In N. giraulti and N. longicornis, the paternal chromosomes mis-segregate, producing abnormal nuclei connected by chromatin bridges. Consequently, these embryos arrest development with very few and abnormal nuclei. In contrast, the paternal genome in N. vitripennis is either not segregated or mis-segregates to one of the two daughter nuclei. Consequently, these embryos continue development utilizing the maternally derived haploid nuclei, resulting in male offspring. The latter class is the first documented example of asymmetric mitotic segregation of abnormal chromosomes. We conclude that in haplo-diploids, CI-induced embryonic lethality occurs only when abnormal paternal genome segregation affects both products of the first mitotic division. This is the first study to associate differences in types of CI with specific cytological defects.