Clonal genetic variation in a Wolbachia-infected asexual wasp: horizontal transmission or historical sex?

Genetic stability of Aedes aegypti populations following invasion by wMel Wolbachia

Background

Wolbachia wMel is the most commonly used strain in rear and release strategies for Aedes aegypti mosquitoes that aim to inhibit the transmission of arboviruses such as dengue, Zika, Chikungunya and yellow fever. However, the long-term establishment of wMel in natural Ae. aegypti populations raises concerns that interactions between Wolbachia wMel and Ae. aegypti may lead to changes in the host genome, which could affect useful attributes of Wolbachia that allow it to invade and suppress disease transmission.

Results

We applied an evolve-and-resequence approach to study genome-wide genetic changes in Ae. aegypti from the Cairns region, Australia, where Wolbachia wMel was first introduced more than 10 years ago. Mosquito samples were collected at three different time points in Gordonvale, Australia, covering the phase before (2010) and after (2013 and 2018) Wolbachia releases. An additional three locations where Wolbachia replacement happened at different times across the last decade were also sampled in 2018. We found that the genomes of mosquito populations mostly remained stable after Wolbachia release, with population differences tending to reflect the geographic location of the populations rather than Wolbachia infection status. However, outlier analysis suggests that Wolbachia may have had an influence on some genes related to immune response, development, recognition and behavior.

Conclusions

Ae. aegypti populations remained geographically distinct after Wolbachia wMel releases in North Australia despite their Wolbachia infection status. At some specific genomic loci, we found signs of selection associated with Wolbachia, suggesting potential evolutionary impacts can happen in the future and further monitoring is warranted.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08200-1.

Assessment of the role of Wolbachia in mtDNA paraphyly and the evolution of unisexuality in Calligrapha (Coleoptera: Chrysomelidae)

Calligrapha is a New World leaf beetle genus that includes several unisexual species in northeastern North America. Each unisexual species had an independent hybrid origin involving different combinations of bisexual species. However, surprisingly, they all cluster in a single mtDNA clade and with some individuals of their parental species, which are in turn deeply polyphyletic for mtDNA. This pattern is suggestive of a selective sweep which, together with mtDNA taxonomic incongruence and occurrence of unisexuality in Calligrapha, led to hypothesize that Wolbachia might be responsible. I tested this hypothesis studying the correlation between diversity of Wolbachia and well-established mtDNA lineages in >500 specimens of two bisexual species of Calligrapha and their derived unisexual species. Wolbachia appears highly prevalent (83.4%), and fifteen new supergroup-A strains of the bacteria are characterized, belonging to three main classes: wCallA, occupying the whole species ranges, and wCallB and wCallC, narrowly parapatric, infecting beetles with highly divergent mtDNAs where they coexist. Most beetles (71.6%) carried double infections of wCallA with another sequence class. Bayesian inference of ancestral character states and association tests between bacterial diversity and the mtDNA genealogy show that each mtDNA lineage of Calligrapha has specific types of infection. Moreover, shifts can be explained by horizontal or vertical transfer from local populations to an expanding lineage and cytoplasmic incompatibility between wCallB and wCallC types, suggesting that the symbionts hitchhike with the host and are not responsible for selective mtDNA sweeps. Lack of evidence for sweeps and the fact that individuals in the unisexual clade are uninfected or infected by the widespread wCallA type indicate that Wolbachia does not induce unisexuality in Calligrapha, although they may manipulate host reproduction through cytoplasmic incompatibility.

A bioinformatics approach to identifying Wolbachia infections in arthropods

Wolbachia is the most widespread endosymbiont, infecting >20% of arthropod species, and capable of drastically manipulating the host's reproductive mechanisms. Conventionally, diagnosis has relied on PCR amplification; however, PCR is not always a reliable diagnostic technique due to primer specificity, strain diversity, degree of infection and/or tissue sampled. Here, we look for evidence of Wolbachia infection across a wide array of arthropod species using a bioinformatic approach to detect the Wolbachia genes ftsZ, wsp, and the groE operon in next-generation sequencing samples available through the NCBI Sequence Read Archive. For samples showing signs of infection, we attempted to assemble entire Wolbachia genomes, and in order to better understand the relationships between hosts and symbionts, phylogenies were constructed using the assembled gene sequences. Out of the 34 species with positively identified infections, eight species of arthropod had not previously been recorded to harbor Wolbachia infection. All putative infections cluster with known representative strains belonging to supergroup A or B, which are known to only infect arthropods. This study presents an efficient bioinformatic approach for post-sequencing diagnosis and analysis of Wolbachia infection in arthropods.

Bacterial Pathogen Emergence Requires More than Direct Contact with a Novel Passerine Host

While direct contact may sometimes be sufficient to allow a pathogen to jump into a new host species, in other cases, fortuitously adaptive mutations that arise in the original donor host are also necessary. Viruses have been the focus of most host shift studies, so less is known about the importance of ecological versus evolutionary processes to successful bacterial host shifts. Here we tested whether direct contact with the novel host was sufficient to enable the mid-1990s jump of the bacterium Mycoplasma gallisepticum from domestic poultry to house finches (Haemorhous mexicanus). We experimentally inoculated house finches with two genetically distinct M. gallisepticum strains obtained either from poultry (Rlow) or from house finches (HF1995) during an epizootic outbreak. All 15 house finches inoculated with HF1995 became infected, whereas Rlow successfully infected 12 of 15 (80%) inoculated house finches. Comparisons among infected birds showed that, relative to HF1995, Rlow achieved substantially lower bacterial loads in the host respiratory mucosa and was cleared faster. Furthermore, Rlow-infected finches were less likely to develop clinical symptoms than HF1995-infected birds and, when they did, displayed milder conjunctivitis. The lower infection success of Rlow relative to HF1995 was not, however, due to a heightened host antibody response to Rlow. Taken together, our results indicate that contact between infected poultry and house finches was not, by itself, sufficient to explain the jump of M. gallisepticum to house finches. Instead, mutations arising in the original poultry host would have been necessary for successful pathogen emergence in the novel finch host.

Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp

Trait loss is a widespread phenomenon with pervasive consequences for a species’ evolutionary potential. The genetic changes underlying trait loss have only been clarified in a small number of cases. None of these studies can identify whether the loss of the trait under study was a result of neutral mutation accumulation or negative selection. This distinction is relatively clear-cut in the loss of sexual traits in asexual organisms. Male-specific sexual traits are not expressed and can only decay through neutral mutations, whereas female-specific traits are expressed and subject to negative selection. We present the genome of an asexual parasitoid wasp and compare it to that of a sexual lineage of the same species. We identify a short-list of 16 genes for which the asexual lineage carries deleterious SNP or indel variants, whereas the sexual lineage does not. Using tissue-specific expression data from other insects, we show that fifteen of these are expressed in male-specific reproductive tissues. Only one deleterious variant was found that is expressed in the female-specific spermathecae, a trait that is heavily degraded and thought to be under negative selection in L. clavipes. Although the phenotypic decay of male-specific sexual traits in asexuals is generally slow compared with the decay of female-specific sexual traits, we show that male-specific traits do indeed accumulate deleterious mutations as expected by theory. Our results provide an excellent starting point for detailed study of the genomics of neutral and selected trait decay.

The ghost sex-life of the paedogenetic beetle Micromalthus debilis

Genetic and sexual systems can be evolutionarily dynamic within and among clades. However, identifying the processes responsible for switches between, for instance, sexual and asexual reproduction, or cyclic and non-cyclic life histories remains challenging. When animals evolve parthenogenetic reproduction, information about the sexual mating system becomes lost. Here we report an extraordinary case where we have been able to resurrect sexual adults in a species of beetle that reproduces by parthenogenetic paedogenesis, without the production of adults. Via heat treatment, we were able to artificially induce adult beetles of Micromalthus debilis in order to describe its pre-paedogenetic mating system. Adults showed a highly female biased sex ratio, out-breeding behaviour, and sex-role reversal. Paedogenetic larvae of Micromalthus are infected with the endosymbiotic bacteria Rickettsia and Wolbachia. Clear signs of vestigialization in adults are concurrent with the loss of adults. Our data suggest an ancient female sex ratio bias that predates the loss of adults, perhaps associated with endosymbionts. We propose a model for the transition from a haplodiploid cyclical parthenogenetic life history to parthenogenetic paedogenesis. Paedogenetic development induces a new mechanism of sex ratio bias in midges, wasps and beetles.

The hitchhiker's guide to Europe: the infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi

Wolbachia is a maternally inherited and ubiquitous endosymbiont of insects. It can hijack host reproduction by manipulations such as cytoplasmic incompatibility (CI) to enhance vertical transmission. Horizontal transmission of Wolbachia can also result in the colonization of new mitochondrial lineages. In this study, we present a 15‐year‐long survey of Wolbachia in the cherry fruit fly Rhagoletis cerasi across Europe and the spatiotemporal distribution of two prevalent strains, wCer1 and wCer2, and associated mitochondrial haplotypes in Germany. Across most of Europe, populations consisted of either 100% singly (wCer1) infected individuals with haplotype HT1, or 100% doubly (wCer1&2) infected individuals with haplotype HT2, differentiated only by a single nucleotide polymorphism. In central Germany, singly infected populations were surrounded by transitional populations, consisting of both singly and doubly infected individuals, sandwiched between populations fixed for wCer1&2. Populations with fixed infection status showed perfect association of infection and mitochondria, suggesting a recent CI‐driven selective sweep of wCer2 linked with HT2. Spatial analysis revealed a range expansion for wCer2 and a large transition zone in which wCer2 splashes appeared to coalesce into doubly infected populations. Unexpectedly, the transition zone contained a large proportion (22%) of wCer1&2 individuals with HT1, suggesting frequent intraspecific horizontal transmission. However, this horizontal transmission did not break the strict association between infection types and haplotypes in populations outside the transition zone, suggesting that this horizontally acquired Wolbachia infection may be transient. Our study provides new insights into the rarely studied Wolbachia invasion dynamics in field populations.

No Accumulation of Transposable Elements in Asexual Arthropods

Transposable elements (TEs) and other repetitive DNA can accumulate in the absence of recombination, a process contributing to the degeneration of Y-chromosomes and other nonrecombining genome portions. A similar accumulation of repetitive DNA is expected for asexually reproducing species, given their entire genome is effectively nonrecombining. We tested this expectation by comparing the whole-genome TE loads of five asexual arthropod lineages and their sexual relatives, including asexual and sexual lineages of crustaceans (Daphnia water fleas), insects (Leptopilina wasps), and mites (Oribatida). Surprisingly, there was no evidence for increased TE load in genomes of asexual as compared to sexual lineages, neither for all classes of repetitive elements combined nor for specific TE families. Our study therefore suggests that nonrecombining genomes do not accumulate TEs like nonrecombining genomic regions of sexual lineages. Even if a slight but undetected increase of TEs were caused by asexual reproduction, it appears to be negligible compared to variance between species caused by processes unrelated to reproductive mode. It remains to be determined if molecular mechanisms underlying genome regulation in asexuals hamper TE activity. Alternatively, the differences in TE dynamics between nonrecombining genomes in asexual lineages versus nonrecombining genome portions in sexual species might stem from selection for benign TEs in asexual lineages because of the lack of genetic conflict between TEs and their hosts and/or because asexual lineages may only arise from sexual ancestors with particularly low TE loads.

Characteristics, phenotype, and transmission of Wolbachia in the sweet potato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), and its parasitoid Eretmocerus sp. nr. emiratus (Hymenoptera: Aphelinidae)

Wolbachia is a common intracellular bacterial endosymbiont of insects, causing a variety of effects including reproductive manipulations such as cytoplasmic incompatibility (CI). In this study, we characterized Wolbachia in the whitefly Bemisia tabaci and in the whitefly parasitoid Eretmocerus sp. nr. emiratus. We also tested for horizontal transmission of Wolbachia between and within trophic levels, and we determined the phenotype of Wolbachia in E. sp. nr. emiratus. Using multilocus sequence typing and phylogenetic analyses, we found that B. tabaci and E. sp. nr. emiratus each harbor a different and unique strain of Wolbachia. Both strains belong to the phylogenetic supergroup B. No evidence for horizontal transmission of Wolbachia between and within trophic levels was found in our study system. Finally, crossing results were consistent with a CI phenotype; when Wolbachia-infected E. sp. nr. emiratus males mate with uninfected females, wasp progeny survival dropped significantly, and the number of females was halved. This is the first description of CI caused by Wolbachia in the economically important genus Eretmocerus. Our study underscores the expectation that horizontal transmission events occur rarely in the dynamics of secondary symbionts such as Wolbachia, and highlights the importance of understanding the effects of symbionts on the biology of natural enemies.

Cannibalism and predation as paths for horizontal passage of Wolbachia between terrestrial isopods

The alpha-proteobacteria Wolbachia are the most widespread endosymbionts in arthropods and nematodes. Mainly maternally inherited, these so-called sex parasites have selected several strategies that increase their vertical dispersion in host populations. However, the lack of congruence between the Wolbachia and their host phylogenies suggests frequent horizontal transfers. One way that could be used for horizontal Wolbachia transfers between individuals is predation. The aim of this study was to test whether horizontal passage of Wolbachia is possible when an uninfected terrestrial isopod eats an infected one. After having eaten Armadillidium vulgare harbouring Wolbachia, the predator-recipients (the two woodlice A. vulgare and Porcellio dilatatus dilatatus) that were initially Wolbachia-free were tested positive for the presence of Wolbachia both by quantitative PCR and Fluorescence in situ Hybridization (FISH). Even if the titers were low compared to vertically infected individuals, this constitutes the first demonstration of Wolbachia occurrence in various organs of an initially uninfected host after eating an infected one.

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

Wolbachia are maternally inherited symbiotic bacteria, commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. The evolutionary history of endosymbionts like Wolbachia can be revealed by integrating information on infection status in natural populations with patterns of sequence variation in Wolbachia and host mitochondrial genomes. Here we use whole-genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe, and Africa to predict Wolbachia infection status, estimate relative cytoplasmic genome copy number, and reconstruct Wolbachia and mitochondrial genome sequences. Overall, 63% of Drosophila strains were predicted to be infected with Wolbachia by our in silico analysis pipeline, which shows 99% concordance with infection status determined by diagnostic PCR. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and imperfect transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent global replacement of ancestral Wolbachia and mtDNA lineages, but our data suggest that the derived wMel lineage arose several thousand years ago, not in the 20th century as previously proposed. Our data also provide evidence that this global replacement event is incomplete and is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats. This study provides a complete genomic analysis of the evolutionary mode and temporal dynamics of the D. melanogaster–Wolbachia symbiosis, as well as important resources for further analyses of the impact of Wolbachia on host biology.

Host–microbe interactions play important roles in the physiology, development, and ecology of many organisms. Studying how hosts and their microbial symbionts evolve together over time is crucial for understanding the impact that microbes have on host biology. With the advent of high-throughput sequencing technologies, it is now possible to obtain complete genomic information for hosts and their associated microbes. Here we use whole-genome sequences from ∼300 strains of the fruitfly Drosophila melanogaster to reveal the evolutionary history of this model species and its intracellular bacterial symbiont Wolbachia. The major findings of this study are that Wolbachia in D. melanogaster is inherited strictly through the egg with no evidence of horizontal transfer from other species, that the genealogies of Wolbachia and mitochondrial genomes are virtually the same, and that both Wolbachia and mitochondrial genomes show evidence for a recent incomplete global replacement event, which has left remnant lineages in North America, Europe, and Africa. We also use the fact that Wolbachia and mitochondrial genomes have the same genealogy to estimate the rate of molecular evolution for Wolbachia, which allows us to put dates on key events in the history of this important host–microbe model system.

Transposable element proliferation as a possible side effect of endosymbiont manipulations

The mode of reproduction has been predicted to affect the proliferation of transposable elements (TEs). A population that switches from sexual to asexual reproduction could either accumulate TEs because purifying selection becomes less efficient, or a decrease in TE load because the opportunity for horizontal transmission is reduced. A third possibility is that the mechanism that induces asexual reproduction affects TE dynamics as a side effect. We propose two such mechanisms that might explain recently described patterns of TE abundance in sexual and asexual lineages of the parasitoid wasp Leptopilina clavipes. Asexual reproduction in this species is induced by endosymbiotic Wolbachia bacteria. In order to achieve parthenogenesis in its host, Wolbachia might remove methylation or interfere with Argonaute proteins. Both methylation and Argonaute proteins are known to control TE activity in other species. By interfering with either, Wolbachia might therefore secondarily hamper the control of specific TEs.

High virulence of Wolbachia after host switching: when autophagy hurts

Wolbachia are widespread endosymbionts found in a large variety of arthropods. While these bacteria are generally transmitted vertically and exhibit weak virulence in their native hosts, a growing number of studies suggests that horizontal transfers of Wolbachia to new host species also occur frequently in nature. In transfer situations, virulence variations can be predicted since hosts and symbionts are not adapted to each other. Here, we describe a situation where a Wolbachia strain (wVulC) becomes a pathogen when transfected from its native terrestrial isopod host species (Armadillidium vulgare) to another species (Porcellio d. dilatatus). Such transfer of wVulC kills all recipient animals within 75 days. Before death, animals suffer symptoms such as growth slowdown and nervous system disorders. Neither those symptoms nor mortalities were observed after injection of wVulC into its native host A. vulgare. Analyses of wVulC's densities in main organs including Central Nervous System (CNS) of both naturally infected A. vulgare and transfected P. d. dilatatus and A. vulgare individuals revealed a similar pattern of host colonization suggesting an overall similar resistance of both host species towards this bacterium. However, for only P. d. dilatatus, we observed drastic accumulations of autophagic vesicles and vacuoles in the nerve cells and adipocytes of the CNS from individuals infected by wVulC. The symptoms and mortalities could therefore be explained by this huge autophagic response against wVulC in P. d. dilatatus cells that is not triggered in A. vulgare. Our results show that Wolbachia (wVulC) can lead to a pathogenic interaction when transferred horizontally into species that are phylogenetically close to their native hosts. This change in virulence likely results from the autophagic response of the host, strongly altering its tolerance to the symbiont and turning it into a deadly pathogen.

Characterizing the causes of a virulence increase when a parasite jumps from one host species to another is fundamental to the understanding of disease emergence. In this context, we studied the bacterium Wolbachia wVulC, a natural symbiont of one terrestrial isopod species that becomes a pathogen when transfected into individuals of another species. Before death, recipient animals suffer various symptoms including nervous system disorders caused by the multiplication of wVulC. Interestingly, the quantification of wVulC loads showed similar titers in the individuals from both the recipient and native species. The difference between the two host species lies in the way they respond to the invasion of wVulC and not in their resistance per se: While the recipient host species exhibits an acute autophagic response leading to central nervous system cells disorganization, this phenomenon was not observed in the native host species, which seems to better tolerate the bacterium. Together, our results show that tolerance can be a better evolutionary strategy to counteract parasite damage than to activate a putative resistance pathway which, as a double-edged sword, can arm the host itself and increase the virulence of a parasite.

Occasional males in parthenogenetic populations of Asobara japonica (Hymenoptera: Braconidae): low Wolbachia titer or incomplete coadaptation?

Wolbachia are endosymbiotic bacteria known to manipulate the reproduction of their hosts. Some populations of the parasitoid wasp Asobara japonica are infected with Wolbachia and reproduce parthenogenetically, while other populations are not infected and reproduce sexually. Wolbachia-infected A. japonica females regularly produce small numbers of male offspring. Because all females in the field are infected and infected females are not capable of sexual reproduction, male production seems to be maladaptive. We investigated why these females nevertheless produce males. We tested three hypotheses: high rearing temperatures could result in higher offspring sex ratios (more males), low Wolbachia titer of the mother could lead to higher offspring sex ratios and/or the Wolbachia infection is of relatively recent origin and not enough time has passed to allow complete coadaptation between Wolbachia and host. In all, 33% of the Wolbachia-infected females produced males and 56% of these males were also infected with Wolbachia. Neither offspring sex ratio nor male infection frequency was significantly affected by rearing temperature or Wolbachia concentration of the mother. The mitochondrial DNA sequence of one of the uninfected populations was identical to that of two of the infected populations. Therefore, the initial Wolbachia infection of A. japonica must have occurred recently. Mitochondrial sequence variation among the infected populations suggests that the spread of Wolbachia through the host populations involved horizontal transmission. We conclude that the occasional male production by Wolbachia-infected females is most likely a maladaptive side effect of incomplete coevolution between symbiont and host in this relatively young infection.