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.     

High incidences and similar patterns of Wolbachia infection in fig wasp communities from three different continents

Abstract Wolbachia are endosymbiotic bacteria that infect numerous arthropod species. Previous studies in Panama and Australia revealed that the majority of fig wasp species harbor Wolbachia infections, but that similar patterns of incidence have evolved independently with different wasp species and Wolbachia strains on the two continents. We found Wolbachia infections in 25/47 species (53%) of fig wasp associated with 25 species of Chinese figs. Phylogenetic analyses of Wolbachia wsp sequences indicated that very similar strains are not obviously found in either closely related or ecologically linked fig wasps species. The extremely high prevalence of Wolbachia in fig wasps (over 50% of species infected) is not constrained by geographical origin and is a recurrent theme of fig wasp/Wolbachia interactions.     

Ancient onset of geographical divergence,interpopulation genetic exchange,and natural selection on the Mc1r coat‐colour gene in the house mouse (Mus musculus)

We examined genetic variation in house mice from India and Pakistan, a predominant part of the predicted homeland of this species and also the territory of the subspecies Mus musculus castaneus (CAS), using a nuclear marker for seven tandemly arranged genes (Fanca–Spire2–Tcf25–Mc1r–Def8–Afg3l1–Dbndd1) and compared them with those previously determined for mice from other parts of Eurasia. Construction of a network with the concatenate sequences yielded three distinct clusters representing the three major subspecies groups: CAS, Mus musculus domesticus (DOM) and Mus musculus musculus (MUS). STRUCTURE analysis provided evidence for further subdivision of CAS into two main haplogroups within the Indian subcontinent. Single‐gene networks revealed not only gene‐specific architecture for subgrouping in CAS, but also allelic exchange among subspecies. These results suggest the earlier onset of allopatric divergence in the predicted homeland (the Middle East and Indian subcontinent) and subsequent intermittent admixing via gene flow across the CAS haplogroups and among the three subspecies groups. A comparison of the levels of nucleotide diversity among the gene regions revealed a less divergent state in the chromosome region containing Mc1r and its adjacent genes, indicative of a selective sweep, suggesting the involvement of natural selection in the Mc1r allelic variation. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 778–794.     

Widespread mito‐nuclear discordance with evidence for introgressive hybridization and selective sweeps in Lycaeides

We investigated the extent and potential cause(s) of mitochondrial introgression within the polytypic North American Lycaeides species complex (Lepidoptera). By comparing population genetic structure based on mitochondrial DNA (COI and COII) and nuclear DNA (251 polymorphic amplified fragment length polymorphism markers), we detected substantial mito‐nuclear discordance, primarily involving a single mitochondrial haplotype (h01), which is likely due to mitochondrial introgression between differentiated Lycaeides populations and/or species. We detected reduced mitochondrial genetic diversity relative to nuclear genetic diversity in populations where mitochondrial haplotype h01 occurs, suggesting that the spread of this haplotype was facilitated by selection. We found no evidence that haplotype h01 is associated with increased fitness (in terms of survival to eclosion, fresh adult weight, and adult longevity) in a polymorphic Lycaeides melissa population. However, we did find a positive association between mitochondrial haplotype h01 and infection by the endoparasitic bacterium Wolbachia in one out of three lineages tested. Linkage disequilibrium between mitochondrial haplotype h01 and Wolbachia infection status may have resulted in indirect selection favouring the spread of haplotype h01 in at least one lineage of North American Lycaeides. These results illustrate the potential for introgressive hybridization to produce substantial mito‐nuclear discordance and demonstrate that an individual's mitochondrial and nuclear genome may have strikingly different evolutionary histories resulting from non‐neutral processes and intrinsic differences in the inheritance and biology of these genomes.     

Nuclear pseudogenes of mitochondrial DNA as a variable part of the human genome

INTRODUCTIONNuclearpseudogenesofmitochondrial(mt)DNAwereinitiallydiscoveredintheearly80's[1--6].However,mechanismsforthegenerationofmtDNApseudogenesarestillnotclearandmayvaryindifferentcases.BothRNA--[7--8]andDNAmediated[9--11]processeshavebeensugges...     

The global impact of Wolbachia on mitochondrial diversity and evolution

The spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce indirect selective sweeps on host mitochondria, to which they are linked within the cytoplasm. The resulting reduction in effective population size might lead to smaller mitochondrial diversity and reduced efficiency of natural selection. While documented in several host species, it is currently unclear if such a scenario is common enough to globally impact the diversity and evolution of mitochondria in Wolbachia‐infected lineages. Here, we address this question using a mapping of Wolbachia acquisition/extinction events on a large mitochondrial DNA tree, including over 1000 species. Our analyses indicate that on a large phylogenetic scale, other sources of variation, such as mutation rates, tend to hide the effects of Wolbachia. However, paired comparisons between closely related infected and uninfected taxa reveal that Wolbachia is associated with a twofold reduction in silent mitochondrial polymorphism, and a 13% increase in nonsynonymous substitution rates. These findings validate the conjecture that the widespread distribution of Wolbachia infections throughout arthropods impacts the effective population size of mitochondria. These effects might in part explain the disconnection between genetic diversity and demographic population size in mitochondria, and also fuel red‐queen‐like cytonuclear co‐evolution through the fixation of deleterious mitochondrial alleles.     

Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA

With the completion of the first gymnosperm mitochondrial genome (mtDNA) from Cycas taitungensis and the availability of more mtDNA taxa in the past 5 years, we have conducted a systematic analysis of DNA transfer from chloroplast genomes (cpDNAs) to mtDNAs (mtpts) in 11 plants, including 2 algae, 1 liverwort, 1 moss, 1 gymnosperm, 3 monocots, and 3 eudicots. By using shared gene order and boundaries between different mtpts as the criterion, the timing of cpDNA transfer during plant evolution was estimated from the phylogenetic tree reconstructed independently from concatenated protein-coding genes of 11 available mtDNAs. Several interesting findings emerged. First, frequent DNA transfer from cpDNA to mtDNA occurred at least as far back as the common ancestor of extant gymnosperms and angiosperms, about 300 MYA. The oldest mtpt is trnV(uac)-trnM(cau)-atpE-atpB-rbcL. Three other mtpts--psaA-psaB, rps19-trnH(gug)-rpl2-rpl23, and psbE-psbF--were dated to the common ancestor of extant angiosperms, at least 150 MYA. However, all protein-coding genes of mtpts have degenerated since their first transfer. Therefore, mtpts contribute nothing to the functioning of mtDNA but junk sequences. We discovered that the cpDNA transfers have occurred randomly at any positions of the cpDNAs. We provide strong evidence that the cp-derived tRNA-trnM(cau) is the only mtpt (1 out of 3 cp-derived tRNA shared by seed plants) truly transferred from cpDNA to mtDNA since the time of the common ancestor of extant gymnosperms and angiosperms. Our observations support the proposition of Richly and Leister (2004) that "primary insertions of organellar DNAs are large and then diverge and fragment over evolutionary time."     

Hybridization and divergence in multi‐species oak (Quercus) communities

Oaks (Quercus: Fagaceae) commonly interbreed yet retain their morphological, genetic and ecological distinctiveness. Post‐zygotic isolation mechanisms, such as ecologically dependent selection on adaptive loci, may therefore limit introgression. To test this hypothesis, we quantified hybridization and genetic divergence across the contact zone of four red oaks (Quercus section Lobatae) in the Great Lakes region of North America using a suite of 259 amplified fragment length polymorphisms and 27 genic and genomic microsatellite markers. First, we identified hybrids using genetic structure analysis and confirmed the reliability of our assignments via simulations. Then, we identified candidate loci for species maintenance with three complementary tests for selection and obtained partial gene sequences linked to an outlier locus and three other loci. We detected evidence of recent hybridization among all species and considerable gene flow between Q. ellipsoidalis and Q. velutina. Overall, c. 20% of Q. velutina had recent ancestry from Q. ellipsoidalis, whereas nearly 30% of Q. ellipsoidalis had a Q. velutina ancestor. Most loci were negligibly to weakly differentiated among species, but two gene‐linked microsatellites deviated significantly from neutral expectations in multiple, complementary outlier tests. Both outlier loci were located in the same 15‐cM bin on an existing Q. robur linkage map, a region under divergent selection in other oak species. Adaptive loci in this highly differentiated genomic region may contribute to ecological divergence among species and limit introgression.     

Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers

Molecular variation is often used to infer the demographic history of species, but sometimes the complexity of species history can make such inference difficult. The willow warbler, Phylloscopus trochilus, shows substantially less geographical variation than the chiffchaff, Phylloscopus collybita, both in morphology and in mitochondrial DNA (mtDNA) divergence. We therefore predicted that the willow warbler should harbour less nuclear DNA diversity than the chiffchaff. We analysed sequence data obtained from multiple samples of willow warblers and chiffchaffs for the mtDNA cytochrome b gene and four nuclear genes. We confirmed that the mtDNA diversity among willow warblers is low (pi = 0.0021). Sequence data from three nuclear genes (CHD-Z, AFLP-WW1 and MC1R) not linked to the mitochondria demonstrated unexpectedly high nucleotide diversity (pi values of 0.0172, 0.0141 and 0.0038) in the willow warbler, on average higher than the nucleotide diversity for the chiffchaff (pi values of 0.0025, 0.0017 and 0.0139). In willow warblers, Tajima's D analyses showed that the mtDNA diversity, but not the nuclear DNA diversity, has been reduced relative to the neutral expectation of molecular evolution, suggesting the action of a selective sweep affecting the maternally inherited genes. The large nuclear diversity seen within willow warblers is not compatible with processes of neutral evolution occurring in a population with a constant population size, unless the long-term effective population size has been very large (N(e) > 10(6)). We suggest that the contrasting patterns of genetic diversity in the willow warbler may reflect a more complex evolutionary history, possibly including historical demographic fluctuations or historical male-biased introgression of nuclear genes from a differentiated population of Phylloscopus warblers.     

Detection of two different mitochondrial genomes in a gall wasp species,Andricus mairei (Hymenoptera: Cynipoidea: Cynipidae)

Mitochondrial genomes (mitogenomes) have been used widely in comparative and evolutionary genomics, molecular evolution, phylogenetics, and population genetics, but very limited information is available for the family Cynipidae. In this report, we described the mitogenome of Andricus mairei. The mitogenome of A. mairei was 16,514 bp in length and contained a typical set of 37 genes. Two control regions (CRs) were detected, one being a partial reverse repeat of the other. In a comparison with the putative ancestral mitogenome, gene rearrangements were found in transfer RNA (tRNA) genes, protein-coding genes and ribosomal RNA (rRNA) genes. Consistent with other Cynipidae species, the gene rearrangement of A. mairei had four obvious characteristics: trnE and trnF had inverted and swapped positions; rrnL and rrnS genes had moved into the cob–nad1 junction; a novel tRNA gene cluster trnL1–trnI–trnL2–trnW–trnM–trnQ had been formed between nad1 and nad2; and trnV had inverted and moved to the nad2–cox1 gene junction. Furthermore, A. mairei had two types of mitochondrial circular DNA molecules. Type II differed from type I in an inverted rearrangement of a large fragment of 3349 nucleotides, including two CRs and two rRNA genes.     

Wolbachia infection complexity among insects in the tropical rice-field community

Wolbachia are a group of intracellular bacteria that cause reproductive alterations in their arthropod hosts. Widely discordant host and Wolbachia phylogenies indicate that horizontal transmission of these bacteria among species sometimes occurs. A likely means of horizontal transfer is through the feeding relations of organisms within communities. Feeding interactions among insects within the rice-field insect community have been well documented in the past. Here, we present the results of a polymerase chain reaction-based survey and phylogenetic analysis of Wolbachia strains in the rice-field insect community of Thailand. Our field survey indicated that 49 of 209 (23.4%) rice-field insect species were infected with Wolbachia. Of the 49 infected species, 27 were members of two feeding complexes: (i) a group of 13 hoppers preyed on by 2 mirid species and parasitized by a fly species, and (ii) 2 lepidopteran pests parasitized by 9 wasp species. Wolbachia strains found in three hoppers, Recilia dorsalis, Nephotettix malayanus and Nisia nervosa, the two mirid predators, Cyrtorhinus lividipennis and Tytthus chinensis, and the fly parasitoid, Tomosvaryella subvirescens, were all in the same Wolbachia clade. In the second complex, the two lepidopteran pests, Cnaphalocrocis medinalis and Scirpophaga incertulas, were both infected with Wolbachia from the same clade, as was the parasitoid Tropobracon schoenobii. However, none of the other infected parasitoid species in this feeding complex was infected by Wolbachia from this clade. Mean (+/- SD) genetic distance of Wolbachia wsp sequences among interacting species pairs of the hopper feeding complex (0.118 +/- 0.091 nucleotide sequence differences), but not for the other two complexes, was significantly smaller than that between noninteracting species pairs (0.162 +/- 0.079 nucleotide sequence differences). Our results suggest that some feeding complexes, such as the hopper complex described here, could be an important means by which Wolbachia spreads among species within arthropod communities.     

The occurrence of mountain hare mitochondrial DNA in wild brown hares

If interspecific hybrids are fertile and backcross to either parental species, transmission of mitochondrial DNA over the species barrier can occur. To investigate if such transmission has occurred between the brown hare Lepus europeus Pall and the mountain hare L. timidus L. in Scandinavia, an analysis of genetic variation in mitochondrial DNA from 36 hares, collected from 15 localities, was performed. Sequence divergence of mtDNA between species was estimated at 8 ± 1% (SD). Intraspecific mtDNA sequence divergence varied between 0.09 and 0.38% in brown hares and 0.10 and 1.44% in mountain hares. In six out of 18 brown hares examined, two different haplotypes of mountain hare origin were detected, demonstrating a transmission of mtDNA haplotypes from mountain hares to brown hares. The results indicate that interspecific hybridization between the two species occurs in wild populations.     

The complete mitochondrial genomes of two vent squat lobsters,Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications

Hydrothermal vents are considered as one of the most extremely harsh environments on the Earth. In this study, the complete mitogenomes of hydrothermal vent squat lobsters, Munidopsis lauensis and M. verrilli, were determined through Illumina sequencing and compared with other available mitogenomes of anomurans. The mitogenomes of M. lauensis (17,483 bp) and M. verrilli (17,636 bp) are the largest among all Anomura mitogenomes, while the A+T contents of M. lauensis (62.40%) and M. verrilli (63.99%) are the lowest. The mitogenomes of M. lauensis and M. verrilli display novel gene arrangements, which might be the result of three tandem duplication–random loss (tdrl) events from the ancestral pancrustacean pattern. The mitochondrial gene orders of M. lauensis and M. verrilli shared the most similarities with S. crosnieri. The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri. Positive selection analysis revealed that eighteen residues in seven genes (atp8, Cytb, nad3, nad4, nad4l, nad5, and nad6) of the hydrothermal vent anomurans were positively selected sites.     

Genetic structure of sibling butterfly species affected by Wolbachia infection sweep: evolutionary and biogeographical implications

It was recently recognized that in Japan, the common yellow butterfly, Eurema hecabe, consists of two sibling species, which have been unnamed yet and tentatively called yellow (Y) type and brown (B) type. We investigated the diversity of nuclear and mitochondrial genes in Japanese populations of Y type and B type of E. hecabe. The phylogeny based on nuclear genes agreed with the distinction between Y type and B type, which had been also supported by a wide array of biological data. However, the phylogeny based on mitochondrial genes did not reflect the distinction. PCR survey of Wolbachia revealed that B-type populations were all infected while Y-type populations contained both infected and uninfected individuals. A single genotype of Wolbachia, which was inferred to be a CI-inducing strain from their wsp gene sequence, was prevalent in these populations. Notably, the mitochondrial phylogeny was in perfect agreement with the pattern of Wolbachia infection, suggesting that the Wolbachia infection had affected the mitochondrial genetic structure of the host insects. Probably, the Wolbachia strain and the associated mitochondrial genomes have been occasionally introduced from B-type populations to Y-type populations through migration and subsequent interspecific hybridization, and CI-driven population sweep has been spreading the Wolbachia strain and the particular mitochondrial haplotypes, which originated from B-type populations, into Y-type populations. On the basis of these results together with the geological and biogeographical knowledge of the Japanese Archipelago, we proposed an evolutionary hypothesis on the invasion and spread of Wolbachia infection in B-type and Y-type of E. hecabe.     

Evolutionary and taxonomic relationships among Far-Eastern salmonid fishes inferred from mitochondrial DNA divergence

Mitochondrial DNA (mtDNA) restriction analysis was used to examine the evolutionary and taxonomic relationships among 11 taxa of the subfamily Salmoninae. The genera Brachymystax and Hucho were closely related, diverging by sequence divergence estimates of 3.1%. Because the mtDNA sequence divergence between blunt- and sharp-snouted forms of Brachymystax (2.24%) was similar to divergence level of Brachymystax and Hucho , then taking into account the distinct morphological, ecological and allozyme differences between them, it is possible to recognize these forms as two separate species. The subgenus Parahucho formed a very distinct group differing by 6.35–7.08% (sequence divergence estimate) from both Brachymystax and Hucho and must be considered as a valid genus. The UPGMA and neighbour-joined phenograms showed that the five genera studied are divided into two main groupings: (1) Hucho, Brachymystax and Salvelinus ; and (2) Oncorhynchus and Parahucho species. The mtDNA sequence divergence estimates between these groupings were about 8.1%. However, the subsequent bootstrap analysis of mtDNA RFLP data did not support the monophyly of the latter grouping. The concordance of morphological and mtDNA phylogenetic patterns is discussed.     

Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing

This study establishes a phylogenetic framework for the natural geographic isolates of the widely studied nematode species Caenorhabditis elegans. Virtually complete mitochondrial genomes are sequenced from 27 C. elegans natural isolates to characterize mitochondrial divergence patterns and to investigate the evolutionary history of the C. elegans hermaphrodite lineages. Phylogenetic analysis of mitochondrial sequences reveals the presence of two major C. elegans hermaphrodite clades (designated clade I and clade II). Fifty-six nuclear loci, widely distributed across the five autosomes and the X chromosome, are also analyzed in a subset of the C. elegans isolates to evaluate nuclear divergence patterns and the extent of mating between different strains. A comparison of the phylogenetic tree derived from mitochondrial data with the phylogenetic tree derived from nuclear data reveals only one inconsistency in the distribution of isolates into clades I and II, suggesting that mating between divergent C. elegans strains is an infrequent event in the wild.     

传粉和非传粉榕小蜂线粒体基因组进化差异

[目的]目前关于榕小蜂类群的线粒体基因组报道很少,本研究旨在探讨传粉和非传粉榕小蜂两个群体的线粒体基因组的进化差异.[方法]以15种榕小蜂的线粒体基因组(其中11种的线粒体基因组为新测定)数据为基础,采用比较线粒体基因组学方法,分析榕小蜂的线粒体基因组序列和进化特征.[结果]本研究新测定的11个榕小蜂物种的近全长线粒体...     

Patterns of polymorphism and gene flow of gender-associated mitochondrial DNA lineages in European mussel populations

Mussels of the genus Mytilus have two types of mitochondrial DNA (mtDNA). The M type is transmitted paternally and the F type is transmitted maternally. RFLP analysis is used to assess phylogenetic relationships and nucleotide diversity and divergence for both mtDNA genomes in European populations of M. edulis and Atlantic and Mediterranean forms of M. galloprovincialis. Ten restriction endonucleases were used to assay variation in regions of the ND2 and COIII genes for a total of 77 individuals. F and M genomes show a concordant phylogenetic split into two major divergent clades, one specific to Mediterranean M. galloprovincialis and the other containing haplotypes from the three taxa. For both genomes, the geographical distribution of mtDNA variation suggests: (i) extensive levels of mtDNA introgression; (ii) asymmetric mtDNA gene flow from Atlantic to Mediterranean populations; and (iii) recurrent historical hybridization events. Significantly higher mtDNA diversity and divergence are observed for the M than F genome in all three Mytilus taxa, although the evolutionary forces responsible for these differences cannot be resolved. The extensive mtDNA gene flow between European Mytilus taxa conflicts with the restricted mtDNA introgression observed in American mussels , implying geographical variation in the nature of nuclear/mtDNA interactions regulating biparental inheritance.