Complete mitochondrial genomes of three sea basses Lateolabrax (Perciformes,Lateolabracidae) species: Genome description and phylogenetic considerations

Genus Lateolabrax consists of three species, Japanese sea bass Lateolabrax japonicus, spotted sea bass Lateolabrax maculatus and blackfin sea bass Lateolabrax latus. The complete mitochondrial DNA (mtDNA) of the three sea basses were amplified and sequenced to characterize and discuss their phylogenetic relationships. The length of mitogenomes was 16,593 bp, 16,479 bp and 16,600 bp, respectively, and all of them consisted of 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region, which are typical for mtDNA of vertebrate. Most genes were encoded on the H-strand, except for the ND6 and eight tRNA genes encoding on the L-strand. A significant variation among the three species was detected in length of the control region. Phylogenetic relationship among the three species was constructed based on the datasets, including the 12 protein-coding genes (except ND6 gene), 22 tRNA and 2 rRNA sequences. The results supported the sister taxon between L. japonicus and L. maculatus. The genetic resources reported here are useful for further studies in taxonomy and phylogeny of the three sea basses and related species.     

The advantage of attending ants and gall aggregation for the gall wasp Andricus symbioticus (Hymenoptera: Cynipidae)

Summary Gall clusters of Andricus symbioticus secrete a sweet and sticky food attractive to ants. An ant exclusion experiment demonstrated the selective advantage of attending ants and gall aggregation for A. symbioticus. This gall wasp interacts with the gall-attending ants only through the host plant. Evolution of this symbiotic relationship seems to be associated with gall aggregation.Contribution from Laboratory of Entomology Kyoto Prefectural University, No. 249     

A phylogenetic analysis of higher-level gall wasp relationships (Hymenoptera: Cynipidae)

We present the most comprehensive analysis of higher-level relationships in gall wasps conducted thus far. The analysis was based on detailed study of the skeletal morphology of adults, resulting in 164 phylogenetically informative characters, complemented with a few biological characters. Thirty-seven cynipid species from thirty-one genera, including four genera of the apparently monophyletic Cynipini and almost all of the genera in the other tribes, were examined. The outgroup included exemplar species from three successively more distant cynipoid families: Figitidae (the sister group of the Cynipidae), Liopteridae and Ibaliidae. There was considerable homoplasy in the data, but many groupings in the shortest tree were nonetheless well supported, as indicated by bootstrap proportions and decay indices. Partitioning of the data suggested that the high level of homoplasy is characteristic of the Cynipidae and not the result of the amount of available phylogenetically conservative characters being exhausted. The analysis supported the monophyly of the Cynipini (oak gall wasps) which, together with the Rhoditini (the rose gall wasps), Eschatocerini and Pediaspidini formed a larger monophyletic group of gall inducers restricted to woody representatives of the eudicot subclass Rosidae. The inquilines (Synergini) were indicated to be monophyletic, whereas the Aylacini, primarily herb gall inducers, appeared as a paraphyletic assemblage of basal cynipid groups. The shortest tree suggests that the Cynipidae can be divided into three major lineages: one including the inquilines, the Aylacini genera associated with Rosaceae, and Liposthenes ; one consisting entirely of Aylacini genera, among them Aulacidea , Isocolus and Neaylax ; and one comprising the woody rosid gallers (the oak and rose gall wasps and allies), the Phanacis-Timaspis complex and the Aylacini genera associated with Papaveraceae.     

Population genetic structure and phylogeography of the oak gall wasp Andricus chodjaii (Hymenoptera: Cynipidae) in Turkey as inferred from mitochondrial and nuclear DNA sequences

Sequence data of mitochondrial cytochrome b gene and nuclear ITS2 region were used to assess genetic diversity, intraspecific phylogeography and population genetic structure of the oak gall wasp Andricus chodjaii from Turkey. We examined 293 individuals from 21 localities which generated 57 cyt b haplotypes and 8 ITS2 alleles. The average genetic diversity was 0.575 for cyt b and 0.202 ITS2, and the average nucleotide diversity 0.015 for cyt b gene and 0.001 for the ITS2 region. Phylogenetic analyses of cyt b haplotypes produced mostly similar topologies with geographically significant groupings. The ITS2 data provided less resolution without robust and apparent geographic structure. Population demographic analysis indicated that some eastern populations expanded, however, some others underwent either expansion or decline resulting in genetically structured populations. Molecular clock applied to the mtDNA data indicated that ingroup haplotypes diversified from the outgroup haplotypes around Early Pliocene. Further diversification events throughout Pleistocene resulted in major clade formations. It appears that geographic formations and glacial and interglacial cycles of Pleistocene were crucial for shaping the phylogeographic structure of A. chodjaii in Turkey.     

湖南三地区麦氏安瘿蜂体内Wolbachia 的感染及其wsp基因序列分析

为检测麦氏安瘿蜂Andricus mairei Kieffer有无Wolbachia感染, 本研究对其岳阳、 长沙和邵阳3种群雌、 雄成虫体内Wolbachia的wsp基因进行了PCR检测, 进而对获得的基因片段进行了序列分析。结果显示, 麦氏安瘿蜂岳阳、 长沙及邵阳种群雌、 雄成虫均有Wolbachia感染, 除邵阳种群雌成虫的感染率为80%之外, 其他均为100%。3个种群Wolbachia的wsp基因序列长度皆为561 bp, 且序列完全一致。麦氏安瘿蜂Wolbachia的wsp基因序列与已知瘿蜂族(Cynipini) Neuroterus macropterus、 Biorhiza pallida及Andricus solitarius （strain 1）以及Synergini族Synergus crassicornis感染的Wolbachia的一致性达95%。除Synergini族Ceroptres cerri感染的Wolbachia属于B群（B group）之外, 瘿蜂感染的Wolbachia均属于A群（A group）。在NJ系统树中, 麦氏安瘿蜂与瘿蜂族Neuroterus macropterus、 Biorhiza pallida和Andricus solitarius （strain 1）及Synergini族Synergus crassicornis感染的Wolbachia聚合在同一分支。此外, 麦氏安瘿蜂岳阳、 长沙和邵阳种群均获得了雌、 雄成虫, 其雌性率分别为15.3%, 12.1%和19.8%, 表现出明显的雄性比偏高。结果提示与瘿蜂族的其他已报道的种类一样, Wolbachia与麦氏安瘿蜂的共生并不诱导其营产雌孤雌生殖。     

Discovery of an oak gall wasp (Hymenoptera: Cynipidae) inducing galls on deciduous oak trees in India

We report for the first time the occurrence of an oak gall wasp Andricus mukaigawae (Mukaigawa) (Hymenoptera: Cynipidae) on the deciduous oak Quercus griffithii Hook. F & Thomson ex Miq. in India. Andricus mukaigawae is the only cynipid species that has been observed to induce galls on deciduous oak species in India to date. In addition, this is the first record of a gall wasp species with a distribution extending all the way from the eastern Palearctic region to the Indian subcontinent, suggesting the existence of a close relationship between cynipid faunas on deciduous oak trees in the two regions.     

Complete mitochondrial genome of Odontobutis haifengensis (Perciformes,Odontobutiae): A unique rearrangement of tRNAs and additional non-coding regions identified in the genus Odontobutis

Herein, the complete mitochondrial genome of Odontobutis haifengensis was sequenced for the first time. The O. haifengensis mitogenome was 17,016 bp in length and included 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The genome organization, base composition, codon usage, and gene rearrangement was similar to other Odontobutis species. Furthermore, a tRNA gene rearrangement within the SLH cluster was found to be identical to other Odontobutis species. Moreover, the gene order and the positions of additional intergenic non-coding regions suggests that the observed unique gene rearrangement resulted from a tandem duplication and random loss of large-scale gene regions. Additionally, phylogenetic analysis showed that Odontobutis species form a monophyletic clade due to the conserved mitochondrial gene rearrangement. This study provides useful information that aids in a better understanding of mitogenomic diversity and evolutionary patterns of Odontobutidae species.     

Population dynamics of the chestnut gall wasp,Dryocosmus kuriphilus Yasumatsu (Hymenoptera: Cynipidae)

Summary During the course of a 10-year investigation on the population dynamics of Dryocosmus kuriphilus, a rapid decrease in the number of individuals was noticed in the adult stage. To detect the role of predation by spiders in causing this high adult mortality, spiders collected from the survey station were tested for their reaction to Drycosmus antiserum. About 2050% of the spiders collected during the emergence period of D. kuriphilus reacted positively, showing that the species of Thomisidae, Argiopidae, Agelenidae and Salticidae were the important predators. The predation ratio for the total adult wasp population was estimated at 8.1% in 1968, 20.2% in 1969 and much higher in 1970, increasing with decreasing population density of the wasps. However, the predation by spiders could not account for all of the adult mortality of D. kuriphilus.     

The rearranged mitochondrial genome of Podagrion sp. (Hymenoptera: Torymidae), a parasitoid wasp of mantis

The complete sequence of the mitochondrial genome of Podagrion sp. (Hymenoptera: Torymidae) is described. The mitogenome was 15,845 bp in size, and contained typical sets of mitochondrial genes. The base composition of the Podagrion sp. mitogenome was also biased toward A + T bases (81.8%). The mitochondrial genome of Podagrion sp. has a weak AT skew (0.07) and a strong GC skew (?0.26). Podagrion sp. exhibits a novel rearrangement compared with the ancestral order, including six protein-coding genes (nad3, cox3, atp6, atp8, cox2 and cox1), which have inverted to the minor strand from the major strand. The A + T-rich region of Podagrion sp., which is located between trnN and trnI, have five tandem repeats. The apomorphic rearrangements, including the conserved block “cox3-atp6-atp8-cox2-cox1-nad5-nad4-nad4l-nad6-cob” and the special locations of trnV and trnA, were mapped onto the phylogeny of Proctotrupomorpha.     

The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements

Background

The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds.

Results

The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as “duplicate tRNA^Glu–CR” and “duplicate tRNA^Thr–tRNA^Pro and CR”, were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication - random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea.

Conclusions

The duplicate tRNAThr–CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr–CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-573) contains supplementary material, which is available to authorized users.     

A new species of Andricus oak gallwasp from China (Hymenoptera: Cynipidae: Cynipini)

As part of a study on the cynipids (Hymenoptera: Cynipidae: Cynipinae) in the Chinese fauna, we report in the present paper two species of Andricus Hartig from the tribe Cynipini, including one new species, namely, A. deqingis sp. n. from that country. In addition to new species, we also provide illustrated keys to east Palaearctic and Oriental species of this genus. The type specimens are deposited in the Hymenoptera Collection, Zhejiang A & F University, Lin’an, China.     

Molecular diversity and phylogeography of Andricus curtisii (Hymenoptera,Cynipidae) in Turkey

A 433-bp fragment of the mitochondrial cytochrome b gene and the entire nuclear ITS2 region were sequenced in an oak gall wasp species, Andricus curtisii, which represents 21 populations across its range in Turkey. Forty cytochrome b haplotypes and 63 ITS2 alleles were discovered among the 161 individuals studied. Remarkable genetic variation was detected in the species, with an average haplotype diversity (h) of 0.72 and 0.76 and an average nucleotide diversity (π) of 0.06 and 0.01 for the cyt b gene and the ITS region, respectively. Most populations were genetically distinct, possessing unique cytochrome b haplotypes. Maximum likelihood and Bayesian phylogenetic analyses and application of the haplotype network to both datasets revealed that the most basally located haplotypes/alleles were from the eastern part of Turkey. The detection of older sequences in the phylogenetic trees of the easterly located populations implied an eastern origin of the species. The application of a conventional insect mitochondrial DNA clock to the dataset suggested a splitting of ingroup haplotypes from the outgroup lineages predating the Pleistocene epoch and the formation of two major haplogroups that coincided with the oscillation of the early Pleistocene glaciations.     

Alien herbivores and native parasitoids: rapid developments and structure of the parasitoid and inquiline complex in an invading gall wasp Andricus quercuscalicis (Hymenoptera: Cynipidae)

Abstract.

• 1 Rapid and substantial changes have occurred in the parasitoid and inquiline community associated with the agamic galls of Andricus quercuscalicis since it invaded Britain in the late 1950s. The number of parasitoid and inquiline species has risen from one to thirteen over a 15-year period. Although the number of species has been relatively consistent over the last 8 years, the species composition has changed considerably and in a highly characteristic way during this period.
• 2 The parasitoid complex can be divided into two broadly distinct sets of parasitoid species; one set attacks only the gall former whereas the other set concentrates on the inquilines living in the wall of the gall.
• 3 The most dramatic change, however, is in the abundance of inquilines which were reported to be virtually absent in earlier studies on this community in Britain. Over a period of only 5 years, between 1988 and 1993, inquiline attack rose from less than 0.01 to an average of 0.26 inquilines per gall. The intensity of inquiline attack is geographically heterogenous, with high inquiline numbers restricted to south-east England. Because of the relatively high specificity of the parasitoids, high inquiline abundance is positively correlated with parasitoid species richness in knopper galls.
• 4 Parasitism rates, particularly on the gall former, were generally low (<10%). Over the last 5 years, however, seven parasitoid species have been consistently recorded and the mortality caused by these species has increased continuously. The species composition of the community associated with this alien gall wasp in Britain has quickly converged to the community known from its native range in continental Europe. Parasitoid species known to attack the galls of A.quercuscalisis on the continent have been recorded from it in Britain for the first time mainly in areas where inquilines have recently become abundant.
• 5 Since rates of parasitism of the gall former are still low, parasitoids are unlikely to play a major role in the population dynamics of this invading gall wasp at present, but the rapidly increasing inquiline and parasitoid attack could be a source of increased mortality for native cynipid species which are the alternative hosts of those parasitoid species.

     

No host‐associated differentiation in the gall wasp Diplolepis rosae (Hymenoptera: Cynipidae) on three dog rose species

Differences in quality and quantity of secondary compounds, as well as in leaf traits of host plants, may influence the host choice of herbivores. Different host preferences could lead to host‐associated differentiation, the first step of sympatric speciation. In the present study, we investigated whether the rose gall wasp Diplolepis rosae L. (Hymenoptera: Cynipidae) shows genetic differentiation related to its host plants (Rosa canina L., Rosa corymbifera Borkh., and Rosa rubiginosa L.). These three host species radiated recently and subsequently expanded their range. Therefore, we expected a diversification within the closely‐associated phytophagous insects. The process of genetic differentiation should be intensified in D. rosae by its close relationship to the host plant, as well as by its parthenogenetic reproduction (infection rate by Wolbachia sp. of almost 100%). However, using 106 polymorphic amplified fragment length polymorphism markers, we found no genetic differentiation among the wasps from different host plants. The population structuring between geographical localities was also low, suggesting considerable gene flow between sites. In part, the low genetic differentiation between sites is explained by the wide distribution of host species and hybrids between host plants. Hybrids with intermediate traits may facilitate the gene flow between wasp populations exploiting different host species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 369–377.     

Gene rearrangements in gekkonid mitochondrial genomes with shuffling,loss, and reassignment of tRNA genes

Background

Vertebrate mitochondrial genomes (mitogenomes) are 16–18 kbp double-stranded circular DNAs that encode a set of 37 genes. The arrangement of these genes and the major noncoding region is relatively conserved through evolution although gene rearrangements have been described for diverse lineages. The tandem duplication-random loss model has been invoked to explain the mechanisms of most mitochondrial gene rearrangements. Previously reported mitogenomic sequences for geckos rarely included gene rearrangements, which we explore in the present study.

Results

We determined seven new mitogenomic sequences from Gekkonidae using a high-throughput sequencing method. The Tropiocolotes tripolitanus mitogenome involves a tandem duplication of the gene block: tRNA^Arg, NADH dehydrogenase subunit 4L, and NADH dehydrogenase subunit 4. One of the duplicate copies for each protein-coding gene may be pseudogenized. A duplicate copy of the tRNA^Arg gene appears to have been converted to a tRNA^Gln gene by a C to T base substitution at the second anticodon position, although this gene may not be fully functional in protein synthesis. The Stenodactylus petrii mitogenome includes several tandem duplications of tRNA^Leu genes, as well as a translocation of the tRNA^Ala gene and a putative origin of light-strand replication within a tRNA gene cluster. Finally, the Uroplatus fimbriatus and U. ebenaui mitogenomes feature the apparent loss of the tRNA^Glu gene from its original position. Uroplatus fimbriatus appears to retain a translocated tRNA^Glu gene adjacent to the 5’ end of the major noncoding region.

Conclusions

The present study describes several new mitochondrial gene rearrangements from Gekkonidae. The loss and reassignment of tRNA genes is not very common in vertebrate mitogenomes and our findings raise new questions as to how missing tRNAs are supplied and if the reassigned tRNA gene is fully functional. These new examples of mitochondrial gene rearrangements in geckos should broaden our understanding of the evolution of mitochondrial gene arrangements.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-930) contains supplementary material, which is available to authorized users.     

The complete mitochondrial genome of Eterusia aedea (Lepidoptera,Zygaenidae) and comparison with other zygaenid moths

Zygaenidae comprises >1036 species, including many folivorous pests in agriculture. In the present study, the complete mitochondrial genome (mitogenome) of a major pest of tea trees, Eterusia aedea was determined. The 15,196-bp circular genome contained the common set of 37 mitochondrial genes (including 13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and exhibited the similar genomic features to reported Zygaenidae mitogenome. Comparative analyses of Zygaenidae mitogenomes showed a typical evolutionary trend of lepidopteran mitogenomes. In addition, we also investigated the gene order of lepidopteran mitogenomes and proposed that the novel gene order trnA-trnR-trnN-trnE-trnS-trnF from Zygaenidae and Gelechiidae and most other gene rearrangements of this tRNA cluster evolved independently. Finally, the mitogenomic phylogeny of Lepidoptera was reconstructed based on multiple mitochondrial datasets. And all the phylogenetic results revealed the sister relationships of Cossoidea and Zygaenoidea with both BI and ML methods, which is the first stable mitogenomic evidence for this clade.     

Cytological investigations of parthenogenesis in gall wasps (Cynipidae,Hymenoptera)

The chromosome number was determined in eleven heterogonous species of gall-wasps on caks and in four species which reproduce by constant parthenogenesis on wild roses. One of the latter group proved to be a natural triploid. Maturation was studied in representative forms from synapsis through diakinesis and the abortive first division to the second division in the laid egg. Chromosome regulation in the developing egg, the production of parthenogones of different sex and the role of the sperm are discussed briefly.