Discovery of swimming larvae in Elmidae (Coleoptera: Byrrhoidea)

The aquatic larvae of the family Elmidae (Coleoptera) have been considered unable to swim because they lack swimming setae on their body and legs. We discovered that riffle beetle larvae (Leptelmis gracilis Sharp) are in fact able to swim. After opening the tuft‐like gills on the last abdominal segment they swim by repeatedly bending the abdomen into a U‐shape very quickly and in a wavy manner, while their head and thorax move anteriorly, resulting in a sigmoidal body shape. The flat bodies of L. gracilis larvae could be advantageous for swimming compared to the cylindrical or semicylindrical bodies of larvae in related genera.     

Physical gills in Elmidae (Coleoptera: Byrrhoidea): Structure and evolutionary pattern of plastron in Stenelmis and related genera

Many species within Elmidae (Coleoptera: Byrrhoidea) have plastrons composed of flattened setae. However, some genera display fine plastrons on the epicuticle, called plastron hairs. In Japanese elmids, members of the genera Stenelmis, Ordobrevia, Nomuraelmis and Leptelmis bear ventral plastron hairs. Based on a maximum likelihood tree including most Japanese genera within Elmidae, we found that these genera are monophyletic and that plastron hairs are a derived character in Elmidae. We also found that the genus Graphelmis bears jigsaw puzzle‐like plastron scales with plastron hair‐like projections, and is sister to the group with plastron hairs.     

Discrimination of two Japanese water pennies,Eubrianax granicollis Lewis and E. ramicornis Kiesenwetter (Coleoptera: Psephenidae), based on laboratory rearing and molecular taxonomy

Two psephenid beetles, Eubrianax granicollis Lewis and E. ramicornis Kiesenwetter, are common species on the main islands of Japan (i.e. Honshu, Shikoku and Kyushu), but diagnostic characters for larval identification are unknown. Two types of field‐collected Eubrianax larvae from Honshu and Kyushu were discriminated based on the distributions of granules on the dorsal surface. These larvae were assigned to E. granicollis and E. ramicornis by comparing them with larvae of the two species obtained via laboratory rearing. The two species were also identified unambiguously on the basis of their mitochondrial cytochrome oxidase subunit I (COI) gene sequences. Larval and pupal morphology are described based on laboratory‐reared specimens.     

基于线粒体细胞色素c氧化酶亚基I基因序列的帘蛤科贝类分子系统发育研究

对21种帘蛤科贝类线粒体细胞色素c氧化酶亚基Ⅰ(cytochrome c oxidase subunit I,COI)基因核苷酸序列进行了分析,以探讨这一序列在种质鉴定、分子系统发生研究中的应用价值。测序结果表明,所有物种扩增片段长度均为707 bp(含引物),序列A+T含量(62.4%—67.8%)明显高于G+C含量。物种间共有变异位点379个,其中简约信息位点334个;此区段共编码235个氨基酸,种间共有氨基酸变异位点100个。以COI基因片段序列为标记,用中国蛤蜊(Mactra chinensis)作外群,构建了35种帘蛤科贝类(其中14种贝类COI序列从GenBank下载)的系统发生树,结合拓扑结构分析和序列比对分析,结果表明:支持将短文蛤(Meretrix petechinalis)和丽文蛤(M.lusoria)订为文蛤(M.meretrix)的同物异名的观点,建议将丽文蛤和短文蛤订为文蛤的地理亚种;支持将薄片镜蛤(Dosinia corrugata)和D.angulosa订为2个独立种的观点;认为将波纹巴非蛤(Paphia undulata)和织锦巴非蛤(P.textile)订为2个独立种是合适的。COI基因序列含有丰富的遗传信息,适合作为帘蛤科贝类种群遗传结构和系统发生研究的分子标记。     

Molecular phylogeny of the genus Apatrobus (Coleoptera: Carabidae: Patrobinae) in western Japan

We performed a molecular phylogenetic analysis of the ground beetles Apatrobus (Carabidae), endemic to Japan, using the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear 28S rRNA (28S) genes. We focused on the species divergence in Kyushu, Shikoku and western Honshu and used 15 of 19 species and three populations with undetermined species in the DNA analysis. The gene trees showed that, of the Apatrobus species studied, A. hayachinensis Nakane from northern Honshu was not included in the monophyletic group of the other Apatrobus species and likely to be of a different genus. Divergence time estimation suggested that Apatrobus species excluding A. hayachinensis diverged 5.2 million years ago and the subsequent divergence of species occurred during the Pliocene and Pleistocene. In each of the main islands, Kyushu, Shikoku and Honshu, two or more distinct lineages occurred and all species had restricted distribution areas, suggesting that ancient dispersal and vicariance among the three main islands resulted in the nested biogeographical pattern of species distribution.     

Polymorphism observed in mitochondrial genes of red flour beetle,Tribolium castaneum (Coleoptera: Tenebrionidae) of different origin in laboratory cultures

Tribolium castaneum, a pest of stored grain, has a uniform morphology, preventing the visual identification of strains from different areas. Polymorphisms in the nucleotide sequences of the mitochondrial genes of this species were examined, and combined into seven haplotypes among the test insect specimens originating from Japan, Thailand, and Canada. These results suggested the potential for geographical differentiation.     

Mitochondrial DNA analysis of the introduced fall webworm, showing its shift in life cycle in Japan

The fall webworm, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), was introduced from North America into Japan in 1945. For the first three decades after its introduction, its life cycle was bivoltine. Thereafter, its life cycle shifted to trivoltine in south‐western areas of Japan. Two hypotheses have been proposed for the process that led to the shift in voltinism: one based on a single and the other on multiple independent colonizations. To test these hypotheses, mitochondrial (mt)DNA sequences were analyzed in the black‐headed type of 14 Japanese, one Korean and two North American populations of H. cunea. In addition, the same regions of mtDNA were compared with the red‐headed type of two North American populations. In the black‐headed type, mtDNA sequences were the same in all Japanese populations and in the Korean population, but sequences of the North American populations differed from each other and from those of the other populations. These results suggest that the process of the shift in voltinism occurred originally in Japan, and that the Japanese and the Korean population of H. cunea originated from a relatively small area in North America.     

Identification of mosquito bloodmeals using mitochondrial cytochrome oxidase subunit I and cytochrome b gene sequences

Abstract.  Primer pairs were designed and protocols developed to selectively amplify segments of vertebrate mitochondrial cytochrome oxidase subunit 1 (COI) and cytochrome b (Cyt b ) mtDNA from the bloodmeals of mosquitoes (Diptera: Culicidae). The protocols use two pairs of nested COI primers and one pair of Cyt b primers to amplify short segments of DNA. Resultant sequences are then compared with sequences in GenBank, using the BLAST function, for putative host identification. Vertebrate DNA was amplified from 88% of our sample of 162 wild-caught, blood-fed mosquitoes from Oregon, U.S.A. and GenBank BLAST searches putatively identified 98% of the amplified sequences, including one amphibian, seven mammalian and 14 avian species. Criteria and caveats for putative identification of bloodmeals are discussed.     

Study of COI sequences from endemic New Zealand aphids highlights high mitochondrial DNA diversity in Rhopalosiphina (Hemiptera: Aphididae)

Focussed searches were made across New Zealand between 2013 and 2016, for endemic aphids from the Schizaphis (Rhopalosiphina) genus, which is currently represented by two putative, undescribed species from the endemic host plants Aciphylla and Dracophyllum. Cytochrome c oxidase I (COI) gene sequences (48 in total) from the Schizaphis were analysed together with those from a broader collection of New Zealand endemic aphids that has been assembled since the year 2000. The bulk of the Schizaphis belonged to two clusters corresponding to the host plant genera. Two aphids from central North Island Dracophyllum represented a much diverged lineage without clear affiliations to other New Zealand Schizaphis. Inter-population variation in the New Zealand Schizaphis was high compared with that seen in international studies of Aphidinae and among populations of other endemic New Zealand Aphidina. Within Schizaphis from Dracophyllum, geography played an apparent role in genetic structuring, with populations from Taranaki (North Island) and especially Mt Lyford (South Island) being divergent from those on the South Island main divide. Two distinct lineages of Schizaphis, which co-occurred at some sites, were found on Aciphylla. Our sequence comparisons, including GMYC analyses, indicated up to five New Zealand Schizaphis lineages, and two newly discovered endemic Aphis species from the host plants Clematis and Hebe.     

Molecular systematics of the Chrysoperla carnea group (Neuroptera: Chrysopidae) in Europe

The green lacewing Chrysoperla carnea is a complex of cryptic species whose differentiation has been so far based upon morphology, ecophysiology, behaviour and preliminary mitochondrial DNA data using cytochrome oxidase subunit II (COII) and NADH dehydrogenase subunit II. In this work we extended the DNA data by screening nucleotide sequences of COII, cytochrome oxidase I, cytochrome b and the large ribosomal subunit of the mtDNA. These new data suggest that C. carnea s.s. is a well-supported, separate taxon, but that other taxa of the complex are not consistently differentiated by the current DNA data.     

The evolution of tissue migration in parasitic nematodes (Nematoda: Strongylida) inferred from a protein-coding mitochondrial gene

Polymerase chain reaction was used to amplify and sequence a 710-bp region of the mtDNA protein-encoding gene, cytochrome c oxidase subunit I, in nine nematodes belonging to the order Strongylida, one nematode from the order Rhabditida and two nematodes from the order Ascaridida. This study tested the hypothesis that in the Strongylida, tissue migration in orally infecting nematodes reflects a legacy of skin penetrating strategies of host infection that were retained after an oral route of infection became established (percutaneous transmission model). Phylogenetic analyses (NJ, MP, ML) consistently produced a single tree topology with two clades within the Strongylida, one containing nematodes that incorporated tissue migration as part of their life cycles, and the other containing nematodes with no tissue migration. Our analysis concluded that the ancestral Strongylida possessed skin penetrating and tissue migrating characters that were modified as members of the group progressed along one of two evolutionary pathways. In one pathway, skin penetration was lost but tissue migration was retained as the nematodes evolved an oral infection route. In the other, both skin penetration and tissue migration characters were lost as the nematodes evolved an oral infection route. These data support the hypothesis of percutaneous transmission as being ancestral in the Strongylida.     

Subterranean archipelago in the Australian arid zone: mitochondrial DNA phylogeography of amphipods from central Western Australia

In 1998, a unique subterranean ecosystem was discovered in numerous isolated calcrete (carbonate) aquifers in the arid Yilgarn region of Western Australia. Previous morphological and genetic analyses of a subterranean water beetle fauna suggest that calcrete aquifers are equivalent to closed island habitats that have been isolated for millions of years. We tested this hypothesis further by phylogeographic analyses of subterranean amphipods (Crangonyctoidea: Paramelitidae and Hyalidae) using mitochondrial DNA sequence data derived from the cytochrome oxidase I gene. Phylogenetic analyses and population genetic analyses (samova) provided strong evidence for the existence of at least 16 crangonyctoid and six hyalid divergent mitochondrial lineages, each restricted in their distribution to a single calcrete aquifer, in support of the 'subterranean island (archipelago) hypothesis' and extending its scope to include entirely water respiring invertebrates. Sequence divergence estimates between proximate calcrete populations suggest that calcretes have been isolated at least since the Pliocene, coinciding with a major aridity phase that led to the intermittent drying of surface water. The distribution of calcretes along palaeodrainage channels and on either side of drainage divides, have had less influence on the overall phylogeographic structure of populations, with evidence that ancestral crangonyctoid and hyalid species moved between catchments multiple times prior to their isolation within calcretes. At least two potential modes of evolution may account for the diversity of subterranean amphipod populations: dispersal/vicariance of stygobitic species or colonization of calcretes by surface species and independent evolution of stygobitic characteristics.     

Identifying the true oysters (Bivalvia: Ostreidae) with mitochondrial phylogeny and distance-based DNA barcoding

Oysters (family Ostreidae), with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. As a useful tool for molecular species identification, DNA barcoding might offer significant potential for oyster identification and taxonomy. This study used two mitochondrial fragments, cytochrome c oxidase I (COI) and the large ribosomal subunit (16S rDNA), to assess whether oyster species could be identified by phylogeny and distance-based DNA barcoding techniques. Relationships among species were estimated by the phylogenetic analyses of both genes, and then pairwise inter- and intraspecific genetic divergences were assessed. Species forming well-differentiated clades in the molecular phylogenies were identical for both genes even when the closely related species were included. Intraspecific variability of 16S rDNA overlapped with interspecific divergence. However, average intra- and interspecific genetic divergences for COI were 0-1.4% (maximum 2.2%) and 2.6-32.2% (minimum 2.2%), respectively, indicating the existence of a barcoding gap. These results confirm the efficacy of species identification in oysters via DNA barcodes and phylogenetic analysis.     

基于部分线粒体细胞色素氧化酶亚基Ⅰ(mtCOI)DNA 序列的6种蝙蝠(翼手目:蝙蝠科)的分子系统进化关系

对贵州5种蝙蝠科蝙蝠的部分线粒体细胞色素氧化酶亚基ⅠDNA序列进行了测定,并结合从Genbank获得的爪哇伏翼的相应序列,以Pteropus dasymallus,P.scapulatus,Rousettus aegyptiacus为外群,运用贝叶斯法(Bayes-ian),最大似然法(Maximum Likelihood,ML)分析了这6种蝙蝠科蝙蝠的分子系统进化关系。结果表明:在贝叶斯,ML树中,这6种蝙蝠科的蝙蝠可分为3个分支:亚洲长翼蝠是第1个独立出来的分支;白腹管鼻蝠是继亚洲长翼蝠之后第2个分离出来的分支;第3个分支又分为两支,一支由大鼠耳蝠和小鼠耳蝠组成,另一支由南蝠和爪哇伏翼组成,支持将这4种蝙蝠同归于蝙蝠亚科的结论,从一定程度上否定了鼠耳蝠属和管鼻蝠亚科之间的姐妹类群关系,也不支持将鼠耳属提升为亚科。     

DNA barcodes identify marine fishes of São Paulo State,Brazil

Anthropogenic impacts are an increasing threat to the diversity of fishes, especially in areas around large urban centres, and many effective conservation actions depend on accurate species identification. Considering the utility of DNA barcoding as a global system for species identification and discovery, this study aims to assemble a DNA barcode reference sequence library for marine fishes from the coastal region of São Paulo State, Brazil. The standard 652 bp ‘barcode’ fragment of the cytochrome c oxidase subunit I (COI) gene was PCR amplified and bidirectionally sequenced from 678 individuals belonging to 135 species. A neighbour‐joining analysis revealed that this approach can unambiguously discriminate 97% of the species surveyed. Most species exhibited low intraspecific genetic distances (0.31%), about 43‐fold less than the distance among species within a genus. Four species showed higher intraspecific divergences ranging from 2.2% to 7.6%, suggesting overlooked diversity. Notably, just one species‐pair exhibited barcode divergences of <1%. This library is a first step to better know the molecular diversity of marine fish species from São Paulo, providing a basis for further studies of this fauna – extending the ability to identify these species from all life stages and even fragmentary remains, setting the stage for a better understanding of interactions among species, calibrating the estimations about species composition and richness in an ecosystem, and providing tools for authenticating bioproducts and monitoring illegal species exploitation.     

Population genetic diversity of Chinese sea bass (Lateolabrax maculatus) from southeast coastal regions of China based on mitochondrial COI gene sequences

Chinese sea bass (Lateolabrax maculatus), an important commercial and recreational fishery species in China, whose natural resources have decreased dramatically for decades due to overfishing and environmental changes. To provide guidelines for the source conservation and management, genetic diversity and population structure of L. maculatus were analyzed based on the mitochondrial cytochrome oxidase subunit I (COI) gene. Totally 192 individuals were sampled from five locations: Qingdao (QD), Chongming (CM), Dongtou (DT), Lieyu (LY) and Fangcheng (FC). After sequencing of a 586 bp fragment of COI gene, 20 haplotypes were defined. H4 (haplotype 4) and H8 were the dominant haplotypes and existed in all populations. Haplotype diversity (Hd) and nucleotide diversity (π) of each population ranged from 0.572 to 0.721 and from 0.00129 to 0.00271, respectively. The highest Hd and π were found in DT and LY populations, while the lowest value of Hd and π were in the QD population. Genetic distance ranged from 0.0031 to 0.0027 within populations and from 0.0018 to 0.0035 between populations. Analysis of molecular variance (AMOVA) revealed that significant genetic divergence was found in QD and FC populations. In addition, neutrality tests and mismatch distribution analysis indicated that this species experienced potential population expansion events.     

A new look at geographic and phylogenetic relationships within the species group surrounding Octopus vulgaris (Mollusca, Cephalopoda): indications of very wide distribution from mitochondrial DNA sequences

The distribution of Octopus vulgaris has not yet been completely clarified. For a long time, a cosmopolitan distribution with unknown distribution limits had been assumed. This assumption has recently been questioned and it has been postulated that the distribution is restricted to the Mediterranean and the northeastern Atlantic. However, as our previous studies show, the existence of O. vulgaris can be confirmed for the Mediterranean and the whole eastern Atlantic, and evidence is provided for its occurrence in the western Atlantic. The aim of the present work is to extend our previous data matrix and to clarify whether O. vulgaris exists in the northwestern Pacific. Therefore, the sequence variation in ostensible O. vulgaris from 13 localities in the Mediterranean (France), the Atlantic Ocean [Lanzarote, Senegal, South Africa (Atlantic, Indian Ocean), Tristan da Cunha, north, middle and south Brazil], the Caribbean Sea (Venezuela) and the Pacific Ocean (Taiwan, Japan and Costa Rica) was examined using the mitochondrial genes coding for the 16S rRNA and cytochrome oxidase subunit III (COIII). Sequence divergence was relatively low between populations of O. vulgaris from the Mediterranean, the eastern and western Atlantic (except north Brazil), Venezuela, Taiwan and Japan compared with other species of the genus Octopus . Trees constructed by using maximum likelihood, neighbour joining and maximum parsimony algorithms (PAUP) show the above-mentioned populations from the Mediterranean, the western and eastern Atlantic, Venezuela and the northwestern Pacific (Japan and Taiwan) as a monophyletic cluster. Thus, even if the Octopus vulgaris -like octopus from north Brazil should turn out a cryptic species, the data of this work not only support our hypothesis of the distribution of O. vulgaris in the Mediterranean, the eastern and western Atlantic but also show that O. vulgaris is present in the northwestern Pacific, namely in the waters of Taiwan and Japan.     

Molecular phylogeny of parasitic Platyhelminthes based on sequences of partial 28S rDNA D1 and mitochondrial cytochrome c oxidase subunit I

The phylogenic relationships existing among 14 parasitic Platyhelminthes in the Republic of Korea were investigated via the use of the partial 28S ribosomal DNA (rDNA) D1 region and the partial mitochondrial cytochrome c oxidase subunit 1 (mCOI) DNA sequences. The nucleotide sequences were analyzed by length, G + C %, nucleotide differences and gaps in order to determine the analyzed phylogenic relationships. The phylogenic patterns of the 28S rDNA D1 and mCOI regions were closely related within the same class and order as analyzed by the PAUP 4.0 program, with the exception of a few species. These findings indicate that the 28S rDNA gene sequence is more highly conserved than are the mCOI gene sequences. The 28S rDNA gene may prove useful in studies of the systematics and population genetic structures of parasitic Platyhelminthes.     

Identification of forensically important blow fly species (Diptera: Calliphoridae) in China by mitochondrial cytochrome oxidase I gene differentiation

Abstract Unambiguous and rapid sarcosaphagous insect species identification is an essential requirement for forensic investigations. Although some insect species are difficult to classify morphologically, they can be effectively identified using molecular methods based on similarity with abundant authenticated reference DNA sequences in local databases. However, local databases are still relatively incomplete in China because of the large land area with distinct regional conditions. In this study, 75 forensically important blow flies were collected from 23 locations in 16 Chinese provinces, and a 278‐bp segment of the cytochrome oxidase subunit I gene of all specimens was successfully sequenced. Phylogenetic analysis of the sequenced segments showed that all Calliphorid specimens were properly assigned into nine species with relatively strong supporting values, thus indicating that the 278‐bp cytochrome oxidase subunit one region is suitable for identification of Calliphorid species. The clear difference between intraspecific threshold and interspecific divergence confirmed the potential of this region for Calliphorid species identification, especially for distinguishing between morphologically similar species. Intraspecific geographic variations were observed in Lucilia sericata (Meigen, 1826) and Lucilia caesar (Linnaeus, 1758).     

Phylogeny and divergence time of island tiger beetles of the genus Cylindera (Coleoptera: Cicindelidae) in East Asia

To examine the diverse colonization histories in eight tiger beetle species of the genus Cylindera (Coleoptera: Cicindelidae) on the East Asian islands, we conducted phylogenetic analyses and divergence time estimation using mitochondrial cytochome oxidase subunit I (COI) and nuclear 28S rDNA sequences. The island fauna consisted of four subgenera: Apterodela, Cicindina, Ifasina, and Cylindera. Apterodela is a flightless group with large bodies, whereas the others are fliers with small bodies. In Apterodela, the divergence among endemic species in Taiwan, Japan, and the mainland was ancient (2.1–4.7 Mya), as expected from their flightlessness. Their dispersal might have occurred across the extended landmass in East Asia during the Pliocene. In the subgenus Cicindina, Cylindera elisae has spread throughout East Asia, from which an endemic species, Cylindera bonina, was derived on the oceanic Bonin Islands during the early Pleistocene (0.9 Mya). This indicates the significance of Cylindera bonina, which is currently confined to a single island, for conservation. In the subgenus Ifasina, Cylindera kaleea is widely distributed in East Asia, and its sister species Cylindera humerula, endemic to Okinawa Island, diverged 1.0 Mya, whereas Cylindera psilica on Taiwan and the Yaeyama Islands diverged approximately 0.8 Mya. In the subgenus Cylindera, the colonization of Cylindera gracilis in Japan from the mainland occurred during the last glacial period. With the exception of C. bonina, which likely colonized new territories by flight or drifting, other dispersal events might have used land connections that occurred repeatedly during the Pliocene and Pleistocene. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 715–727.