Mitochondrial COI Sequences Research Articles

A new species of Eoperipatus (Onychophora) from Vietnam reveals novel morphological characters for the South-East Asian Peripatidae

Although representatives of Peripatidae are widely distributed in South-East Asia, only three valid species of Eoperipatus and one species of Typhloperipatus have been described from this region. According to previous reports, the three species of Eoperipatus show little morphological variation and are difficult to distinguish from each other. In this study, we describe a new species of Eoperipatus from Vietnam, E. totorosp. nov., using morphological (light and scanning electron microscopy) and molecular data (mitochondrial COI and 12S rRNA sequences). A comparison with specimens of an undescribed species of Eoperipatus from Thailand revealed novel species-specific characters, including the characteristics of male crural complexes, distinct types of scales on the ventral body surface, the inner structure of the circular pits on the male genital pad, and the position and size of the anal gland pads in males. The results of our molecular analyses correspond with those of morphological studies. In contrast to previous assumptions, our findings suggest a high diversity of the South-East Asian Peripatidae, which requires further exploration.

Thrips tabaci population genetic structure and polyploidy in relation to competency as a vector of tomato spotted wilt virus.

Knowledge of population-level genetic differences can help explain variation among populations of insect vectors in their role in the epidemiology of specific viruses. Variation in competency to transmit Tomato spotted wilt virus (TSWV) that exists among populations of Thrips tabaci has been associated with the presence of cryptic species that exhibit different modes of reproduction and host ranges. However, recent findings suggest that vector competency of T. tabaci at any given location depends on the thrips and virus populations that are present. This study characterizes the population genetic structure of T. tabaci collected from four locations in North Carolina and examines the relationship between population genetic structure and variation in TSWV transmission by T. tabaci. Mitochondrial COI sequence analysis revealed the presence of two genetically distinct groups with one characterized by thelytokous, parthenogenetic reproduction and the other by arrhenotokous, sexual reproduction. Using a set of 11 microsatellite markers that we developed to investigate T. tabaci population genetic structure, we identified 17 clonal groups and found significant genetic structuring among the four NC populations that corresponded to the geographic locations where the populations were collected. Application of microsatellite markers also led to the discovery of polyploidy in this species. All four populations contained tetraploid individuals, and three contained both diploid and tetraploid individuals. Analysis of variation in transmission ofTSWV among isofemale lines initiated with individuals used in this study revealed that ‘clone assignment,’ ‘virus isolate’ and their interaction significantly influenced vector competency. These results highlight the importance of interactions between specific T. tabaci clonal types and specific TSWV isolates underlying transmission of TSWV by T. tabaci.

Phylogeography of <I>Anastrepha obliqua</I> Inferred With mtDNA Sequencing

Anastrepha obliqua (Macquart) (Diptera: Tephritidae), the West Indian fruit fly, is a frugivorous pest that occasionally finds its way to commercial growing areas outside its native distribution. It inhabits areas in Mexico, Central and South America, and the Caribbean with occasional infestations having occurred in the southern tier states (California, Florida, and Texas) of the United States. This fly is associated with many plant species and is a major pest of mango and plum. We examine the genetic diversity of the West Indian fruit fly based on mitochondrial COI and ND6 DNA sequences. Our analysis of 349 individuals from 54 geographic collections from Mexico, Central America, the Caribbean, and South America detected 61 haplotypes that are structured into three phylogenetic clades. The distribution of these clades among populations is associated with geography. Six populations are identified in this analysis: Mesoamerica, Central America, Caribbean, western Mexico, Andean South America, and eastern Brazil. In addition, substantial differences exist among these genetic types that warrants further taxonomic review.

Kiefferulus tainanus (Kieffer, 1912) is a distinct species, not a synonym of Kiefferulus barbatitarsis (Kieffer, 1911)

Morphological and molecular studies indicate that Kiefferulus tainanus (Kieffer 1912) is quite distinct from K. barbatitarsis (Kieffer 1911), and not a synonym of the latter species, as has previously been suggested. The suggestion of synonymy seems to have arisen in part from a comparison based on the figures of K. tainanus in Sasa (1979), which depict an unusually thickened male superior volsella. Other characters, and mitochondrial COI sequence, suggest the two species are not particularly closely related.

Recent multiple introductions of the gall‐forming aphid Pemphigus bursarius into Japanese islands

AbstractRecently, the number of collection records of Pemphigus galls from Populus nigra has been increasing in Japan. To identify the galls on P. nigra, mitochondrial COI sequences were analyzed from galling aphid samples collected on P. nigra in Tokyo and Hokkaido. From the BLAST search and neighbor‐joining (NJ) analysis, the aphid samples were identified as Pemphigus bursarius, which has not been recorded from Japan. Two samples from Tokyo and Hokkaido showed a genetic difference of 0.30%. This result suggests that different strains of P. bursarius might have been introduced into the Japanese islands at least twice.

Amphinemura palmeni is a valid Holarctic stonefly species (Plecoptera: Nemouridae)

The taxonomic status of Amphinemura palmeni, a rare stonefly from northern Fennoscandia, was re-evaluated in amorphological study combined with analyses of mitochondrial COI and nuclear 28S sequences. Taxon sampling includedA. standfussi, with which A. palmeni has been confused, the Nearctic A. linda and seven other Amphinemura species.Amphinemura palmeni is confirmed as a valid species, and A. norvegica and A. linda identified as junior synonyms. Thespecies is illustrated with line drawings, photographs and SEM micrographs. Its COI haplotype diversity is compared with the intraspecific diversity in other stonefly species.

Revision of the freshwater genus Atyaephyra (Crustacea,Decapoda, Atyidae) based on morphological and molecular data.

Atyaephyra de Brito Capello, 1867 was described from the Mediterranean region almost 200 years ago. Since then, the genus has been recorded from various freshwater habitats in Europe, North Africa and the Middle East. Despite its long history, the taxonomic status of Atyaephyra species remains confusing and uncertain. Consequently numerous specimens from the known range of Atyaephyra were analysed using morphological characters and mitochondrial COI sequences in an attempt to clarify the taxonomy of this genus. The present study recognises seven Atyaephyra species, more than twice as many as previously recorded (three), four of which are considered as new. The new species are described, additional information to the original descriptions are provided for the remaining three taxa, while neotypes of Atyaephyra desmarestii Millet, 1831 and Atyaephyra stankoi Karaman, 1972 are designated to stabilize their taxonomy. Non-overlapping distinguishing morphological characters are used to discriminate the examined material into five species, e.g., Atyaephyra desmarestii, Atyaephyra stankoi, Atyaephyra orientalis Bouvier, 1913, Atyaephyra thyamisensis sp. n., Atyaephyra strymonensis sp. n. In addition, the genetic analysis supports the existence of multiple phylogenetic clades in the broader Mediterranean area and distinguishes two new cryptic species, namely Atyaephyra tuerkayi sp. n. and Atyaephyra acheronensis sp. n. The geographic distribution of these species is confirmed and their phylogenetic relationships are described.

Distributional records of Tor mahseerTor tor(Hamilton, 1822) from Southern India

Summary During exploratory surveys in the tributaries (Penganga and Satnala) of Godavari and (Bheema) Krishna basins, specimens of mahseer were collected. The morpho-meristic characteristics of these specimens conformed to the taxonomic keys for Tor tor. The mitochondrial COI sequences of these specimens clustered with the T. tor specimens from the River Narmada and were distinct from the other mahseer such as T. khudree and T. mussullah, which are known to exist in the rivers of the region. This confirmed the distribution of T. tor in the rivers of peninsular India and indicated an extended distribution of the known range. The major predominating habitat characteristics of collection areas were cobbles mixed with gravel, and a riparian cover of shrubs and trees. The occurrence of fingerling size specimens in the river suggests that the species has adapted and is likely to have established self-recruiting populations in these rivers.

Biogeographical patterns of variation in Western European populations of the great green bush-cricket (Tettigonia viridissima; Orthoptera Tettigoniidae)

The great green bush-cricket, Tettigonia viridissima, is at the northern limits of its geographic distribution in the UK and has suffered a significant reduction in population abundance and range over the last 50 years, now being largely confined to the southern UK. This study uses five characters to investigate differences between UK and mainland Western European populations, questioning the possibility that UK populations might represent a distinct species or sub-species and thus deserve special conservation status. Males of T. viridissima from UK, France and Spain were compared using morphometry, flight, male calling song and analysis of mitochondrial DNA sequences. Results suggest morphological differences between UK population samples and continental Europe with the UK samples showing shorter wing length relative to body length than populations in continental Europe. Morphological differences between French and Spanish populations followed a size cline related to latitude with more southerly populations showing larger features. Analysis of male flight distances and calling song showed significant differences with increased flight distance and minimum stridulation following a southerly latitude which correlates with wing length results. No differences consistent with geographical distributions were found in mitochondrial DNA COI sequence alignments. Morphological differences could be due to developmental differences linked to differing temperature clines or a non-adaptive difference caused by the colonisation history of the species. The consequences of morphometric variation on flight function and stridulation in bush-crickets are discussed.

New information on the invasive to Europe aphid species Brachycaudus divaricatae Shaposhnikov, 1956 (Hemiptera: Aphididae)

Brachycaudus divaricatae (Hemiptera: Aphididae), a recent invader to Europe, has already reached Czech Republic. Partial sequences of mitochondrial COI and nuclear EF-1α genes have been analysed across the sixteen Czech samples of B. divaricatae, together with morphometric analysis of the same samples based on eighteen morphological characters of the apterous viviparous females. For comparative studies, thirteen samples from the Eastern Baltic region of Europe (Latvia, Lithuania and Poland) were used. All sampled populations appeared similar in their genetic and morphological characters studied. One haplotype of mitochondrial COI gene was predominant; it was characteristic for all samples from Czech Republic and 8 out of 13 samples from Eastern Baltic region. Two other haplotypes were found in the Eastern Baltic region only. Four different haplotypes of EF-1α gene were detected. Most of the samples (except one sample from the Eastern Baltic region and two samples from Czech Republic) had the same haplotype. Out of remaining three haplotypes, one was unique for the Eastern Baltic region, whilst two were found in Czech Republic only. For the present, Moravia is the southernmost region in Europe, where B. divaricatae has been already reported. Presumably, this invasive aphid species has entered the Czech Republic from the north via the Moravian Gate, a natural pass formed by the depression between the Western Carpathians and Eastern Sudetes.

Integrative Taxonomy and Molecular Phylogeny of Genus Aplysina (Demospongiae: Verongida) from Mexican Pacific

Integrative taxonomy provides a major approximation to species delimitation based on integration of different perspectives (e.g. morphology, biochemistry and DNA sequences). The aim of this study was to assess the relationships and boundaries among Eastern Pacific Aplysina species using morphological, biochemical and molecular data. For this, a collection of sponges of the genus Aplysina from the Mexican Pacific was studied on the basis of their morphological, chemical (chitin composition), and molecular markers (mitochondrial COI and nuclear ribosomal rDNA: ITS1-5.8-ITS2). Three morphological species were identified, two of which are new to science. A. clathrata sp. nov. is a yellow to yellow-reddish or -brownish sponge, characterized by external clathrate-like morphology; A. revillagigedi sp. nov. is a lemon yellow to green, cushion-shaped sometimes lobate sponge, characterized by conspicuous oscules, which are slightly elevated and usually linearly distributed on rims; and A. gerardogreeni a known species distributed along the Mexican Pacific coast. Chitin was identified as the main structural component within skeletons of the three species using FTIR, confirming that it is shared among Verongida sponges. Morphological differences were confirmed by DNA sequences from nuclear ITS1-5.8-ITS2. Mitochondrial COI sequences showed extremely low but diagnostic variability for Aplysina revillagigedi sp. nov., thus our results corroborate that COI has limited power for DNA-barcoding of sponges and should be complemented with other markers (e.g. rDNA). Phylogenetic analyses of Aplysina sequences from the Eastern Pacific and Caribbean, resolved two allopatric and reciprocally monophyletic groups for each region. Eastern Pacific species were grouped in general accordance with the taxonomic hypothesis based on morphological characters. An identification key of Eastern Pacific Aplysina species is presented. Our results constitute one of the first approximations to integrative taxonomy, phylogeny and evolutionary biogeography of Eastern Pacific marine sponges; an approach that will significantly contribute to our better understanding of their diversity and evolutionary history.

Co-phylogeography and morphological evolution of sika deer lice (Damalinia sika) with their hosts (Cervus nippon)

Lice are obligate parasites of mammals and birds and have become an important model for studies of host-parasite co-evolution and co-phylogenetics. Population genetic and phylogeographic studies represent an important bridge between microevolution and co-phylogenetic patterns. We examine co-phylogeographic patterns in sika deer and their parasitic lice. Co-phylogeographic patterns in deer and lice were evaluated using homologous regions of mitochondrial COI sequences. The phylogeographic breaks recovered for deer populations matched those of previous studies. Comparisons of the phylogeographic tree topology for deer lice with that of their hosts revealed a significant level of congruence. However, comparisons of genetic distances between deer and lice suggested that one of the estimated co-divergence events is more likely a recent host switch. Taking into account genetic divergence, there is not strong evidence for complete phylogeographic co-divergence between deer and their parasitic lice. However, mitochondrial phylogenies only track genetic structure of female lineages, and the incongruence between deer and louse phylogeography may be explained by louse migration mediated by male deer. Morphological analysis of head shape variation based on an elliptic Fourier descriptor showed that overall morphological variation contained phylogenetic signal, suggesting that in general morphology of these lice evolves congruent to population history.

Systematics and taxonomy of theruficornisgroup of genusMerodonMeigen (Diptera: Syrphidae)

We revise theruficornisgroup of species ofMerodonMeigen (Diptera, Syrphidae) providing an illustrated key, a discussion of taxonomic characters and a morphological diagnosis. A total of 18 species from theruficornisgroup are treated including distributional data. Descriptions are provided for seven new species:M. gallicusVujić & Radenkovićsp.n.,M. hoplitisHurkmanssp.n.,M. lamellatusVujić & Radenkovićsp.n.,M. nigripodusVujić & Hayatsp.n.,M. ovaloidesVujić & Radenkovićsp.n.,M. ponticusVujić & Radenkovićsp.n., andM. turcicusVujić & Hayatsp.n.The taxonM. auripesSack, is redefined and a neotype designated. Lectotypes are designated forM. graecusLoew;M. planicepsLoew andM. crymensisParamonov. The monophyly and systematic position of this species group was assessed based on parsimony and maximum likelihood analyses of mitochondrial COI and nuclear 28S rDNA sequences. A very high level of endemism was observed in theruficornisspecies group. Among 18 taxa, 12 are limited‐range endemics, present in few mountain areas or in a small part of the total range of the group. These endemics clearly show the importance of geographic isolation in the process of speciation.

Recent history of the European Nassarius nitidus (Gastropoda): phylogeographic evidence of glacial refugia and colonization pathways

Because marine species respond differentially to factors governing survival and gene flow, closely related taxa may display dissimilar phylogeographic histories. New data for the patchily distributed gastropod Nassarius nitidus throughout its Atlantic–Mediterranean range (collected during 2008 and 2009) were used to investigate its phylogeography and recent demography. Results based on mitochondrial COI sequences of 422 N. nitidus individuals from 15 localities revealed contrasting phylogeographic and demographic patterns among N. nitidus populations from each basin. Data suggest the existence of two glacial refugia, one in the Atlantic, around the Iberian Peninsula, and the other in the Paleo-Mediterranean Sea (Adriatic). Bayesian skyline reconstructions suggest that the Adriatic population of N. nitidus remained largely unaffected by the Last Glacial Maximum (LGM), whereas the Iberian Atlantic region experienced dramatic exponential growth after its conclusion. Contemporary North Sea populations of N. nitidus are the endpoint of a leading-edge recolonization process from a southern position. Additionally, a reanalysis of pre-existing material for the continuously distributed close congener N. reticulatus was used to compare both species in the late histories. In contrast to N. nitidus, N. reticulatus prospered during the LGM and experienced an earlier Atlantic expansion during the previous interglacial period. Despite similar life history and dispersal potential, the results here presented suggest that subtle differences in microhabitat requirements between the two species have had important consequences for their particular distribution in response to glacial events.

Fig trees at the northern limit of their range: the distributions of cryptic pollinators indicate multiple glacial refugia

Climatic oscillations during the last few million years had well-documented effects on the distributions and genomes of temperate plants and animals, but much less is known of their impacts on tropical and subtropical species. In contrast to Europe and North America, ice-sheets did not cover most of China during glacial periods, and the effects of glacial cycles were less dramatic. Fig trees are a predominantly tropical group pollinated by host-specific fig wasps. We employed partial mitochondrial COI (918 bp) and nuclear ITS2 (462 bp) gene sequences to investigate the genetic structure and demographic histories of the wasps that pollinate the subtropical Ficus pumila var. pumila in Southeastern China. Deep genetic divergence in both mitochondrial (7.2-11.6%) and nuclear genes (1.6-2.9%) indicates that three pollinator species are present and that they diverged about 4.72 and 6.00 Myr bp. This predates the Quaternary ice ages, but corresponds with the formation of the Taiwan Strait and uplifting of the Wuyi-Xianxia Mountains. The three pollinators have largely allopatric distribution patterns in China and display different postglacial demographic histories. Wiebesia spp. 1 and 2 occupy, respectively, the northern and southern regions of the mainland host range. Their populations both underwent significant postglacial spatial expansions, but at different times and at different rates. Wiebesia sp. 3 is largely restricted to northern islands and shows less evidence of recent population expansion. Their mainly allopatric distributions and different demographic histories are consistent with host plant postglacial expansion from three distinct refugia and suggest one mechanism whereby fig trees gain multiple pollinators.

First description of the male of Gonatopus javanus (R.C.L. Perkins) determined by mitochondrial COI sequence (Hymenoptera: Dryinidae)

AbstractGonatopus javanus (R.C.L. Perkins) was newly recorded from Japan and India. The males collected together with females of G. javanus from Japan were identified as previously unknown opposite sex of the species because they share identical sequences of mitochondrial COI. The sequence was different from that of G. clavipes (Thunberg) by 11%. The male of G. javanus was described as new to science. Doratulina producta (Matsumura) is implied as host in Japan. The utility of molecular marker to identify the dryinid taxa showing sexual dimorphism is discussed.

Study of mitochondrial COI and nuclear ITS2 sequences of Mongolian specimens of the Polyommatus eros-group (Lepidoptera: Lycaenidae)

Study of mitochondrial COI and nuclear ITS2 sequences of Mongolian specimens of the Polyommatus eros-group (Lepidoptera: Lycaenidae)

Population Subdivision of the Brackish-Water Crab Deiratonotus cristatus on the Japanese Coast

We investigated the genetic structure of populations of the brackish-water crab Deiratonotus cristatus (de Man, 1895) (family Camptandriidae) on the Japanese coast, together with morphological and the ecological variations. Genetic characteristics of the local populations based on mitochondrial DNA COI sequence data have revealed genetic differentiation between many populations, with the haplotype networks forming three geographical clades: a clade occurring on the Pacific coast, one occurring predominantly in northern Hokkaido, Kyushu and the Seto Inland Sea, and a third occurring in the Ryukyu Islands. Male pleopod morphology, carapace length relative to carapace width, and carapace width of adult crabs varied inconsistently among the geographic groups corresponding to the three clades. Life history traits were similar throughout, although differences in the breeding season were apparent between populations on the Pacific coast, and in the Seto Inland Sea and the Ryukyu Islands.

Genetic Isolation between the Western and Eastern Pacific Populations of Pronghorn Spiny Lobster Panulirus penicillatus

The pronghorn spiny lobster, Panulirus penicillatus, is a circumtropical species which has the widest global distribution among all the species of spiny lobster, ranging throughout the entire Indo-Pacific region. Partial nucleotide sequences of mitochondrial DNA COI (1,142–1,207 bp) and 16S rDNA (535–546 bp) regions were determined for adult and phyllosoma larval samples collected from the Eastern Pacific (EP)(Galápagos Islands and its adjacent water), Central Pacific (CP)(Hawaii and Tuamotu) and the Western Pacific (WP)(Japan, Indonesia, Fiji, New Caledonia and Australia). Phylogenetic analyses revealed two distinct large clades corresponding to the geographic origin of samples (EP and CP+WP). No haplotype was shared between the two regional samples, and average nucleotide sequence divergence (Kimura's two parameter distance) between EP and CP+WP samples was 3.8±0.5% for COI and 1.0±0.4% for 16S rDNA, both of which were much larger than those within samples. The present results indicate that the Pacific population of the pronghorn spiny lobster is subdivided into two distinct populations (Eastern Pacific and Central to Western Pacific), with no gene flow between them. Although the pronghorn spiny lobster have long-lived teleplanic larvae, the vast expanse of Pacific Ocean with no islands and no shallow substrate which is known as the East Pacific Barrier appears to have isolated these two populations for a long time (c.a. 1MY).

Morphological and Molecular Comparison of Hemigrapsus crenulatus (Milne Edwards, 1837) (Brachyura: Varunidae) from New Zealand and Chile: Was Miss Rathbun Right?

Abstract The estuarine crab Hemigrapsus crenulatus (H. Milne Edwards, 1837) is a native of New Zealand, but it is also known from the coast of Chile some 8900 km eastwards across the Pacific. Mary Rathbun (1898) was the first person to call crabs from the Chilean coast, H. crenulatus, saying that they were conspecific with crabs described by Milne Edwards (1837). However, Bennett (1964) took the advice of H. Balss that the Chilean species should be known as Hemigrapsus granarius (Nicolet, 1849). No type specimens are available for either of these species. We have used mitochondrial 16S rRNA and COI sequences derived from fresh specimens to find out who was correct. There are few if any consistent morphological differences between populations from either side of the South Pacific and very few molecular differences (only 3 fixed nucleotide differences out of 1190 bp total sequenced – 0.25%). None of these differences exceed variation within either population, so we must declare Miss Rathbun the winner! The ...