Ongoing Coevolution of Wolbachia and a Widespread Invasive Ant, Anoplolepis gracilipes

Genome-wide detection of Wolbachia in natural Aedes aegypti populations using ddRAD-Seq

Background

Wolbachia, an endosymbiotic bacterium, is globally used to control arboviruses because of its ability to block arboviral replication and manipulate the reproduction of Wolbachia host, Aedes aegypti. Polymerase chain reaction (PCR)-based Wolbachia detection has been recently reported from natural Ae. aegypti populations. However, due to the technical limitations of PCR, such as primer incompatibility, PCR-based assays are not sufficiently reliable or accurate. In this study, we examined double digestion restriction site-associated DNA sequencing (ddRAD-Seq) efficiency and limitations in Wolbachia detection and quantification in field-collected Ae. aegypti natural populations in Metro Manila, the Philippines, compared with PCR-based assays.

Methods

A total of 217 individuals Ae. aegypti were collected from Metropolitan Manila, Philippines. We separated it into 14 populations consisting of 7 female and male populations. We constructed a library for pool ddRAD-Seq per population and also screened for Wolbachia by PCR assays using wsp and 16S rRNA. Wolbachia density per population were measured using RPS17 as the housekeeping gene.

Results

From 146,239,637 sequence reads obtained, 26,299 and 43,778 reads were mapped across the entire Wolbachia genome (with the wAlbA and wAlbB strains, respectively), suggesting that ddRAD-Seq complements PCR assays and supports more reliable Wolbachia detection from a genome-wide perspective. The number of reads mapped to the Wolbachia genome per population positively correlated with the number of Wolbachia-infected individuals per population based on PCR assays and the relative density of Wolbachia in the Ae. aegypti populations based on qPCR, suggesting ddRAD-Seq-based semi-quantification of Wolbachia by ddRAD-Seq. Male Ae. aegypti exhibited more reads mapped to the Wolbachia genome than females, suggesting higher Wolbachia prevalence rates in their case. We detected 150 single nucleotide polymorphism loci across the Wolbachia genome, allowing for more accurate the detection of four strains: wPip, wRi, TRS of Brugia malayi, and wMel.

Conclusions

Taken together, our results demonstrate the feasibility of ddRAD-Seq-based Wolbachia detection from field-collected Ae. aegypti mosquitoes.

Climate and Wolbachia Impacts on Anoplolepis gracilipes (Hymenoptera: Formicidae)

The yellow crazy ant (Anoplolepis gracilipes (Smith, 1857)) is a prominent invasive species exhibiting variable population dynamics. Through collecting long-term climate data and validating field surveys with MaxEnt SDM projections, our results indicated that winter temperature and precipitation accumulation strongly influence the population dynamics. An aggression analysis showed that A. gracilipes nests with higher aggression levels (over 2.5 scores) experienced a higher mean maximum temperature (31.84 ± 0.43 °C) and lower prevalence of wAgra (84.8 ± 4.70%) in A. gracilipes from June to October. The nest manipulation and aggression experiments confirmed that temperature increases aggression (1.3 to 2.8 scores) among A. gracilipes workers due to the reduced prevalence of wAgra. To the best of our knowledge, this is the first case of a notable reduction in the prevalence of Wolbachia (100 to 66%) within a colony of A. gracilipes while maintaining stable nests for further experiments.

The wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta microbiota are host specific and dominated by endosymbionts and environmental microorganisms

We characterized the microbial communities of the crop, midgut, hindgut, and ovaries of the wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta through 16S rRNA gene and ITS2 amplicon sequencing and a large-scale isolation campaign. The bacterial communities of these bees were dominated by endosymbionts of the genera Wolbachia and Spiroplasma. Bacterial and yeast genera representing the remaining predominant taxa were linked to an environmental origin. While only a single sampling site was examined for Andrena vaga, Anthophora plumipes, and Colletes cunicularius, and two sampling sites for Osmia cornuta, the microbiota appeared to be host specific: bacterial, but not fungal, communities generally differed between the analyzed bee species, gut compartments and ovaries. This may suggest a selective process determined by floral and host traits. Many of the gut symbionts identified in the present study are characterized by metabolic versatility. Whether they exert similar functionalities within the bee gut and thus functional redundancy remains to be elucidated.

Population Genomics of Pooled Samples: Unveiling Symbiont Infrapopulation Diversity and Host-Symbiont Coevolution

Microscopic symbionts represent crucial links in biological communities. However, they present technical challenges in high-throughput sequencing (HTS) studies due to their small size and minimal high-quality DNA yields, hindering our understanding of host-symbiont coevolution at microevolutionary and macroevolutionary scales. One approach to overcome those barriers is to pool multiple individuals from the same infrapopulation (i.e., individual host) and sequence them together (Pool-Seq), but individual-level information is then compromised. To simultaneously address both issues (i.e., minimal DNA yields and loss of individual-level information), we implemented a strategic Pool-Seq approach to assess variation in sequencing performance and categorize genetic diversity (single nucleotide polymorphisms (SNPs)) at both the individual-level and infrapopulation-level for microscopic feather mites. To do so, we collected feathers harboring mites (Proctophyllodidae: Amerodectes protonotaria) from four individual Prothonotary Warblers (Parulidae: Protonotaria citrea). From each of the four hosts (i.e., four mite infrapopulations), we conducted whole-genome sequencing on three extraction pools consisting of different numbers of mites (1 mite, 5 mites, and 20 mites). We found that samples containing pools of multiple mites had more sequencing reads map to the feather mite reference genome than did the samples containing only a single mite. Mite infrapopulations were primarily genetically structured by their associated individual hosts (not pool size) and the majority of SNPs were shared by all pools within an infrapopulation. Together, these results suggest that the patterns observed are driven by evolutionary processes occurring at the infrapopulation level and are not technical signals due to pool size. In total, despite the challenges presented by microscopic symbionts in HTS studies, this work highlights the value of both individual-level and infrapopulation-level sequencing toward our understanding of host-symbiont coevolution at multiple evolutionary scales.

Population genetic structure of the globally introduced big-headed ant in Taiwan

Global commerce and transportation facilitate the spread of invasive species. The African big-headed ant, Pheidole megacephala (Fabricius), has achieved worldwide distribution through globalization. Since the late 19th century, Taiwan has served as a major seaport because of its strategic location. The population genetic structure of P. megacephala in Taiwan is likely to be shaped by international trade and migration between neighboring islands. In this study, we investigated the population genetics of P. megacephala colonies sampled from four geographical regions in Taiwan and elucidated the population genetic structures of P. megacephala sampled from Taiwan, Okinawa, and Hawaii. We observed a low genetic diversity of P. megacephala across regions in Taiwan. Moreover, we noted low regional genetic differentiation and did not observe isolation by distance, implying that long-distance jump dispersal might have played a crucial role in the spread of P. megacephala. We sequenced the partial cytochrome oxidase I gene and observed three mitochondrial haplotypes (TW1-TW3). TW1 and TW3 most likely originated from populations within the species' known invasive range, suggesting that secondary introduction is the predominant mode of introduction for this invasive ant. TW2 represents a novel haplotype that was previously unreported in other regions. P. megacephala populations from Taiwan, Okinawa, and Hawaii exhibited remarkable genetic similarity, which may reflect their relative geographic proximity and the historical connectedness of the Asia-Pacific region.

First Polycipivirus and Unmapped RNA Virus Diversity in the Yellow Crazy Ant, Anoplolepis gracilipes

The yellow crazy ant, Anoplolepis gracilipes is a widespread invasive ant that poses significant threats to local biodiversity. Yet, compared to other global invasive ant species such as the red imported fire ant (Solenopsis invicta) or the Argentine ant (Linepithema humile), little is known about the diversity of RNA viruses in the yellow crazy ant. In the current study, we generated a transcriptomic database for A. gracilipes using a high throughput sequencing approach to identify new RNA viruses and characterize their genomes. Four virus species assigned to Dicistroviridae, two to Iflaviridae, one to Polycipiviridae, and two unclassified Riboviria viruses were identified. Detailed genomic characterization was carried out on the polycipivirus and revealed that this virus comprises 11,644 nucleotides with six open reading frames. Phylogenetic analysis and pairwise amino acid identity comparison classified this virus into the genus Sopolycivirus under Polycipiviridae, which is tentatively named "Anoplolepis gracilipes virus 3 (AgrV-3)". Evolutionary analysis showed that AgrV-3 possesses a high level of genetic diversity and elevated mutation rate, combined with the common presence of multiple viral strains within single worker individuals, suggesting AgrV-3 likely evolves following the quasispecies model. A subsequent field survey placed the viral pathogen "hotspot" of A. gracilipes in the Southeast Asian region, a pattern consistent with the region being recognized as part of the ant's native range. Lastly, infection of multiple virus species seems prevalent across field colonies and may have been linked to the ant's social organization.

Wolbachia Infection in Native Populations of the Invasive Tawny Crazy Ant Nylanderia fulva

Antagonistic interactions can affect population growth and dispersal of an invasive species. Wolbachia are intracellular endosymbiont bacteria that infect arthropod and nematode hosts and are able to manipulate reproduction, which in some cases leads to cocladogenesis. Moreover, the presence of the strictly maternally transferred Wolbachia in a population can indirectly induce selective sweeps on the hosts' mitochondria. Ants have a Wolbachia infection rate of about 34%, which makes phylogenetic studies using mitochondrial markers vulnerable of being confounded by the effect of the endosymbiont. Nylanderia fulva is an invasive ant native to South America, considered a pest in the United States. Its distribution and biology are poorly known in its native range, and the taxonomic identity of this and its closely related species, Nylanderia pubens, has only recently been understood with the aid of molecular phylogenies. Aiming at estimating robust phylogenetic relationships of N. fulva in its native range, we investigated the presence and pattern of Wolbachia infection in populations of N. fulva from Argentina, part of its native range, to account for its possible effect on the host population structure. Using the ftsZ gene, 30 nests of N. fulva and four from sympatric Nylanderia species were screened for the presence of Wolbachia. We sequenced the MLST genes, the highly variable gene wsp, as well as glyQ, a novel target gene for which new primers were designed. Phylogeny of the ants was estimated using mtDNA (COI). We found supergroup A Wolbachia strains infecting 73% of N. fulva nests and two nests of Nylanderia sp. 1. Wolbachia phylogenetic tree inferred with MLST genes is partially congruent with the host phylogeny topology, with the exception of a lineage of strains shared by ants from different N. fulva clades. Furthermore, by comparing with Wolbachia sequences infecting other ants, we found that the strains infecting different N. fulva clades are not monophyletic. Our findings suggest there are three recent independent horizontally transmitted Wolbachia infections in N. fulva, and we found no evidence of influence of Wolbachia in the host mtDNA based phylogeny.

Wolbachia 16S rRNA haplotypes detected in wild Anopheles stephensi in eastern Ethiopia

BACKGROUND

About two out of three Ethiopians are at risk of malaria, a disease caused by the parasites Plasmodium falciparum and Plasmodium vivax. Anopheles stephensi, an invasive vector typically found in South Asia and the Middle East, was recently found to be distributed across eastern and central Ethiopia and is capable of transmitting both P. falciparum and P. vivax. The detection of this vector in the Horn of Africa (HOA) coupled with widespread insecticide resistance requires that new methods of vector control be investigated in order to control the spread of malaria. Wolbachia, a naturally occurring endosymbiotic bacterium of mosquitoes, has been identified as a potential vector control tool that can be explored for the control of malaria transmission. Wolbachia could be used to control the mosquito population through suppression or potentially decrease malaria transmission through population replacement. However, the presence of Wolbachia in wild An. stephensi in eastern Ethiopia is unknown. This study aimed to identify the presence and diversity of Wolbachia in An. stephensi across eastern Ethiopia.

METHODS

DNA was extracted from An. stephensi collected from eastern Ethiopia in 2018 and screened for Wolbachia using a 16S targeted PCR assay, as well as multilocus strain typing (MLST) PCR assays. Haplotype and phylogenetic analysis of the sequenced 16S amplicons were conducted to compare with Wolbachia from countries across Africa and Asia.

RESULTS

Twenty out of the 184 mosquitoes screened were positive for Wolbachia, with multiple haplotypes detected. In addition, phylogenetic analysis revealed two superclades, representing Wolbachia supergroups A and B (bootstrap values of 81 and 72, respectively) with no significant grouping of geographic location or species. A subclade with a bootstrap value of 89 separates the Ethiopian haplotype 2 from other sequences in that superclade.

CONCLUSIONS

These findings provide the first evidence of natural Wolbachia populations in wild An. stephensi in the HOA. They also identify the need for further research to confirm the endosymbiotic relationship between Wolbachia and An. stephensi and to investigate its utility for malaria control in the HOA.

Biology, Ecology, and Management of the Invasive Longlegged Ant, Anoplolepis gracilipes

The longlegged ant (Anoplolepis gracilipes) is one of the most damaging invasive tramp ants globally. It is generally found between latitudes 27°N and 27°S in Asia, although it has been introduced to other continents. Its native range remains debatable, but it is believed to be in Southeast Asia. Anoplolepis gracilipes invasion has many serious ecological consequences, especially for native invertebrate, vertebrate, and plant communities, altering ecosystem dynamics and functions. We examine and synthesize the literature about this species' origin and distribution, impacts on biodiversity and ecosystems, biology and ecology, chemical control, and potential biocontrol agents. We highlight emerging research needs on the origin and invasion history of this species, its reproductive mode, its relationship with myrmecophiles, and its host-microbial interactions, and we discuss future research directions.

Cytoplasmic incompatibility between Old and New World populations of a tramp ant

Reproductive manipulation by endosymbiotic Wolbachia can cause unequal inheritance, allowing the manipulator to spread and potentially impacting evolutionary dynamics in infected hosts. Tramp and invasive species are excellent models to study the dynamics of host-Wolbachia associations because introduced populations often diverge in their microbiomes after colonizing new habitats, resulting in infection polymorphisms between native and introduced populations. Ants are the most abundant group of insects on earth, and numerous ant species are classified as highly invasive. However, little is known about the role of Wolbachia in these ecologically dominant insects. Here, we provide the first description of reproductive manipulation by Wolbachia in an ant. We show that Old and New World populations of the cosmotropic tramp ant Cardiocondyla obscurior harbor distinct Wolbachia strains, and that only the Old World strain manipulates host reproduction by causing cytoplasmic incompatibility (CI) in hybrid crosses. By uncovering a symbiont-induced mechanism of reproductive isolation in a social insect, our study provides a novel perspective on the biology of tramp ants and introduces a new system for studying the evolutionary consequences of CI.

Comparative genome sequencing reveals insights into the dynamics of Wolbachia in native and invasive cherry fruit flies

Wolbachia is a maternally inherited obligate endosymbiont that can induce a wide spectrum of effects in its host, ranging from mutualism to reproductive parasitism. At the genomic level, recombination within and between strains, transposable elements, and horizontal transfer of strains between host species make Wolbachia an evolutionarily dynamic bacterial system. The invasive cherry fruit fly Rhagoletis cingulata arrived in Europe from North America ~40 years ago, where it now co‐occurs with the native cherry pest R. cerasi. This shared distribution has been proposed to have led to the horizontal transfer of different Wolbachia strains between the two species. To better understand transmission dynamics, we performed a comparative genome study of the strain wCin2 in its native United States and invasive European populations of R. cingulata with wCer2 in European R. cerasi. Previous multilocus sequence genotyping (MLST) of six genes implied that the source of wCer2 in R. cerasi was wCin2 from R. cingulata. However, we report genomic evidence discounting the recent horizontal transfer hypothesis for the origin of wCer2. Despite near identical sequences for the MLST markers, substantial sequence differences for other loci were found between wCer2 and wCin2, as well as structural rearrangements, and differences in prophage, repetitive element, gene content, and cytoplasmic incompatibility inducing genes. Our study highlights the need for whole‐genome sequencing rather than relying on MLST markers for resolving Wolbachia strains and assessing their evolutionary dynamics.