Polymorphism in the internal transcribed spacer (ITS) region of the ribosomal DNA among different Fusarium species

Fusarium species causing wilt diseases in different plants were characterised by comparing nonpathogenic and different pathogenic species using rDNA RFLP analysis. The ITS (internal transcribed spacer) region of 12 isolates belonging to the section Elegans, Laseola, Mortiella, Discolor, Gibbosum, Lateritium and Sporotrichiella were amplified by universal ITS primers (ITS-1 and ITS-4) using polymerase chain reaction (PCR). Amplified products, which ranged from 522 to 565 bp were obtained from all 12 Fusarium isolates. The amplified products were digested with seven restriction enzymes, and restriction fragment length polymorphism (RFLP) patterns were analysed. A dendrogram derived from PCR-RFLP analysis of the rDNA region divided the Fusarium isolates into three major groups. Assessment of molecular variability based on rDNA RFLP clearly indicated that Fusarium species are heterogeneous and most of the forma speciales have close evolutionary relationships.     

Genetic variation and phylogeny of Scandinavian species of Grania (Annelida: Clitellata: Enchytraeidae), with the discovery of a cryptic species

Individuals of five nominal species of Grania (Annelida: Clitellata: Enchytraeidae) were collected from locations in Sweden, Norway and France, for studies on the intraspecific variation at the Cytochrome Oxidase I (COI) locus of mitochondrial DNA and internal transcribed spacer (ITS) region of nuclear DNA. It was found that the previously described morphospecies in general contain low variation compared to the between‐species variation in both loci. In one instance, however, an individual morphologically indistinguishable from G. ovitheca was found to be deviant and instead cluster with G. postclitellochaeta both by COI and ITS. We describe this individual as a new species: G. occulta sp.n. Furthermore, phylogenetic analyses were conducted, showing a close relationship between G. variochaeta, G. occulta, G. ovitheca and G. postclitellochaeta, as well as between G. pusilla and G. maricola. Using the results from the phylogenetic analyses, we discuss the evolution of morphological characters in Scandinavian species of Grania.     

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.     

Phylogeographic patterns of two tiger beetle species at both sides of the strait of Gibraltar (Coleoptera: Cicindelini)

The Strait of Gibraltar is one of the major barriers to gene flow between land masses of Europe and Africa at the western end of the Mediterranean. Since the opening of the Strait at the end of the Miocene 5.33 million years ago (Mya) it has exerted a strong influence on the dispersal and colonization of whole biotas, particularly with regard to the retreat of organisms during glaciation peaks and the northward colonization events during the warm periods of Pleistocene. The aim of this study is to elucidate the influence of the Strait of Gibraltar in the gene flow among populations of two tiger beetle species collected in Morocco, Cicindela campestris (L. 1758) and Lophyra flexuosa (Fabricius 1787), with regard to both new and published data from populations of southern Iberia. The phylogeographic analysis showed that Moroccan haplotypes of L. flexuosa belonged to a single coastal mitochondrial clade and that populations at both sides of` the Strait of Gibraltar were genetically well connected. The haplotype network of C. campestris showed that Moroccan populations made up a robust cluster clearly differentiated from those of Iberian and other European populations. These differences are thought to reflect the distinct evolutionary history (dispersal capacity, ecological strategies) of both species, as L. flexuosa shows an almost continuous distribution on the coasts located at both sides of the West Mediterranean, whereas C. campestris shows a patchy distribution and prefers montane habitats in the Western Palaearctic.     

Review of the sawfly genus Empria (Hymenoptera, Tenthredinidae) in Japan

The following eleven Empria species are reported from Japan: Empria candidata (Fallén, 1808), Empria japonica Heidemaa & Prous, 2011, Empria liturata (Gmelin, 1790), Empria loktini Ermolenko, 1971, Empria plana (Jakowlew, 1891), Empria quadrimaculata Takeuchi, 1952, Empria rubicola Ermolenko, 1971, Empria tridens (Konow, 1896), Empria tridentis Lee & Ryu, 1996, Empria honshuana Prous & Heidemaa, sp. n., and Empria takeuchii Prous & Heidemaa, sp. n. The lectotypes of Poecilosoma pallipes Matsumura, 1912, Empria itelmena Malaise, 1931, Tenthredo candidata Fallén, 1808, and Tenthredo (Poecilostoma) hybrida Erichson, 1851 are designated. Empria itelmena Malaise, 1931, syn. n. is synonymized with Empria plana (Jakowlew, 1891). Poecilosoma pallipes Matsumura, 1912, previously assigned to Empria, is transferred to Monsoma, creating Monsoma pallipes (Matsumura, 1912), comb. n. Results of phylogenetic analyses using mitochondrial (COI) and nuclear (ITS1 and ITS2) sequences are also provided.     

The Leptynia hispanica species complex (Insecta Phasmida): polyploidy, parthenogenesis, hybridization and more

The Leptynia hispanica stick insect species complex includes bisexuals, triploid and tetraploid parthenogenetic populations, suggesting that polyploidy has played a central role in the evolution of this complex. An analysis of karyotype, mitochondrial DNA (cox2) and nuclear DNA (ef1-alpha) markers was carried out to clarify phylogenetic relationships and microevolutionary/phylogeographical patterns of the L. hispanica complex. Our analyses suggested a subdivision of bisexual populations into four groups, tentatively proposed as incipient species. Moreover, triploids and tetraploids showed two independent origins, the latter being more ancient than the former. From ef1-alpha analysis, triploids showed hybrid constitution, while the hybrid constitution of tetraploids is likely, but more data are needed. We suggest that L. hispanica is a case of 'geographical parthenogenesis' with parthenogenetic strains colonizing large peripheral ranges, and bisexuals confined to glacial refuge areas. Moreover, the age, wide distribution and competitive advantage of polyploids over diploids, demonstrate their significance in the evolution of the L. hispanica species complex.     

A new species of Camaenidae (Gastropoda,Pulmonata) from Nusa Penida and Lombok Islands,Indonesia: novelty in a well-known fauna

A new species of camaenid land snail, Vulnus wallacei Páll-Gergely, Otani & Hosoda n. sp. is described from Nusa Penida and Lombok Islands, Indonesia. The new species is putatively classified into the genus Vulnus, which is only known so far from the Northern Maluku Islands. The genital anatomy, especially the presence of a well-developed penial sheath in V. wallacei, suggests a close relationship with Australian camaenids. However, the molecular phylogeny based on partial cytochrome c oxidase I, and 16S and 28S ribosomal RNA genes shows that the new species falls outside the cluster of all Australian Camaenidae.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:D28554D0-3578-4E95-8849-09EAFB7D30F7     

Non-seasonal clade-specificity and subclade microvariation in symbiotic dinoflagellates (Symbiodinium spp.) in Zoanthus sansibaricus (Anthozoa: Hexacorallia) at Kagoshima Bay, Japan

While much work has investigated the genetic diversity of symbiotic dinoflagellate genus Symbiodinium Freudenthal in cnidarians, investigations into such diversity over temporal scales (seasonal and/or annual) remain scarce. Here, we have sequenced the internal transcribed spacer of ribosomal DNA (ITS‐rDNA) of Symbiodinium from samples of designated Zoanthus sansibaricus Carlgren (Anthozoa: Hexacorallia) colonies collected for 12 months (August 2004–July 2005) at a high latitude non‐reefal coral community at Sakurajima, Kagoshima Bay, Japan (31°35′N, 130°35′E). Our results show that despite large ocean temperature changes (15.0–29.0°C) throughout the one‐year experimental period, Z. sansibaricus colonies contained only clade C Symbiodinium from many different subclade C1/C3‐related novel types not previously reported. While no temporal changes in clade‐level associations were seen, there were consistent and extremely large amounts (145 unique sequences out of 153 total obtained sequences) of genotypic microvariation observed in our obtained sequences. Despite Z. sansibaricus acquiring Symbiodinium horizontally and the presence of various other Symbiodinium clades (A, G) and subclades (e.g. C15 and derived subclades) in the immediate environment, Z. sansibaricus at Sakurajima specifically associates with subclade C1/C3‐related Symbiodinium. While subclades C1/C3 have been found in a variety of different environments and are believed to be ancestral, ‘generalist’ types of Symbiodinium, C1/C3‐related clades such as seen here may be more adapted to specialized niches. We theorize that specific and year‐round association with many different types of subclade C1/C3‐related Symbiodinium helps Z. sansibaricus to survive in the fluctuating Sakurajima environment.     

Geographical diversification of the genus Cicer (Leguminosae: Papilionoideae) inferred from molecular phylogenetic analyses of chloroplast and nuclear DNA sequences

Cicer L. (Leguminosae: Papilionoideae) consists of 42 species of herbaceous or semi-shrubby annuals and perennials distributed throughout the temperate zones of the Northern Hemisphere. The origin and geographical relationships of the genus are poorly understood. We studied the geographical diversification and phylogenetic relationships of Cicer using DNA sequence data sampled from two plastid regions, trnK / matK and trnS - trnG , and two nuclear regions, the internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions of nuclear ribosomal DNA, from 30 species. The results from the phylogenetic analyses of combined nuclear and chloroplast sequence data revealed four well-supported geographical groups: a Middle Eastern group, a West-Central Asian group, an Aegean–Mediterranean group, and an African group. Age estimates for Cicer based on methods that do not assume a molecular clock (for example, penalized likelihood) demonstrate that the genus has a Mediterranean origin with considerable diversification in the Miocene/Pliocene epochs. Geological events, such as mountain orogenesis and environmental changes, are major factors for the dispersal of Cicer species. The early divergence of African species and their geographically distinct region in the genus suggest a broader distribution pattern of the genus in the past than at present.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154 , 175–186.     

Phylogeny of Ptychostomum （Bryaceae,Musci） inferred from sequences of nuclear ribosomal DNA internal transcribed spacer （ITS） and chloroplast rps4

The phylogeny of Ptychostomum was first spacer （ITS） region of the nuclear ribosomal （nr） DNA DNA rps4 sequences. Maximum parsimony, maximum undertaken based on analysis of the internal transcribed and by combining data from nrDNA ITS and chloroplast likelihood, and Bayesian analyses all support the conclusion that the reinstated genus Ptychostomum is not monophyletic. Ptychostomum funkii （Schwagr.） J. R. Spence （≡ Bryum funkii Schwaigr.） is placed within a clade containing the type species of Bryum, B. argenteum Hedw. The remaining members of Ptychostomum investigated in the present study constitute another well-supported clade. The results are congruent with previous molecular analyses. On the basis of phylogenetic evidence, we agree with transferring B. amblyodon Mull. Hal. （≡ B. inclinatum （Brid.） Turton≡ Bryum archangelicum Bruch ＆ Schimp.）, Bryum lonchocaulon Mull. Hal., Bryum pallescens Schleich. ex Schwaigr., and Bryum pallens Sw. to Ptychostomum.     

Genomic variation in the mitochondrially encoded cytochrome b (MT-CYB) and 16S rRNA (MT-RNR2) genes: characterization of eight endangered Pecoran species

In an effort to develop species-specific identification markers, we examined genetic variants and molecular signatures within genes encoding mitochondrial cytochrome b and 16S rRNA in eight endangered Pecoran species endemic to the Indian peninsula. Our results revealed that the cytochrome b gene exhibited higher sequence diversity than the 16S rRNA gene, both between and within species. However, the 16S rRNA gene harboured a larger number of species-specific mutation sites compared with the cytochrome b gene, suggesting that it could be useful for species identification. Indeed, we successfully used 'forensically informative nucleotide sequencing' (FINS) analysis of the 16S rRNA gene to identify two previously unknown biological specimens.     

DNA barcoding analysis of Coleoidea (Mollusca: Cephalopoda) from Chinese waters

Coleoids are part of the Cephalopoda class, which occupy an important position in most oceans both at an ecological level and at a commercial level. Nevertheless, some coleoid species are difficult to distinguish with traditional morphological identification in cases when specimens are heavily damaged during collection or when closely related taxa are existent. As a useful tool for rapid species assignment, DNA barcoding may offer significant potential for coleoid identification. Here, we used two mitochondrial fragments, cytochrome c oxidase I and the large ribosomal subunit (16S rRNA), to assess whether 34 coleoids accounting for about one-third of the Chinese coleoid fauna could be identified by DNA barcoding technique. The pairwise intra- and interspecific distances were assessed, and relationships among species were estimated by NJ and bayesian analyses. High levels of genetic differentiation within Loliolus beka led to an overlap between intra- and interspecific distances. All remaining species forming well-differentiated clades in the NJ and bayesian trees were identical for both fragments. Loliolus beka possessed two mitochondrial lineages with high levels of intraspecific distances, suggesting the occurrence of cryptic species. This study confirms the efficacy of DNA barcoding for identifying species as well as discovering cryptic diversity of Chinese coleoids. It also lays a foundation for other ecological and biological studies of Coleoidea.     

Diglyphus isaea (Hymenoptera: Eulophidae): a probable complex of cryptic species that forms an important biological control agent of agromyzid leaf miners

Diglyphus isaea ( Walker 1838 ) (Hymenoptera: Eulophidae) is a primary parasitoid of agromyzid leaf miners (Diptera: Agromyzidae) and has been commercialized as a biological control agent. Diglyphus isaea occurs throughout much of the world and different populations are morphologically identical. Using nuclear ribosomal internal transcribed spacer 1 (ITS1) sequences, we examined variation among Chinese populations of D. isaea . Phylogenetic analyses combined with an analysis of sympatry indicated that D. isaea consists of at least four species in mainland China. The results imply that ITS1 is an efficient marker for identifying congeneric species of parasitic waSPS, and that cryptic species could be common in temperate and subtropical regions.     

中国（虫,*）目昆虫二新纪录属与二新种记述(（虫,*）目:（虫,*）科,异（虫,*）科)

本文报道中国■目昆虫■科Ｐｈａｓｍａｔｉｄａｅ与异■科Ｈｅｔｅｒｏｎｅｍｉｉｄａｅ各１新纪录属：叶尾■属ＡＣｒｏ－ｐｈｙｌｌａ　Ｇｒａｙ和副厚■属Ｐａｒａｐａｃｈｙｍｏｒｐｈａ　Ｂｒｕｎｎｅｒ;及其各１新种：四川叶尾■Ａｃｒｏｐｈｙｌｌａ　ｓｉｃｈｕａｎｅｎｓｉｓ,ｓｐ．ｎｏｖ．和四刺副厚■Ｐａｒａｐａｃｈｙｍｏｒｐｈａ ｔｅｔｒａｃａｎｔｈａ,ｓｐ．ｎｏｖ．模式标本保存于西北农业大学昆虫标本馆。     

Population structure and species boundary delimitation of cryptic Dioryctria moths: an integrative approach

Accurate delimitation of species boundaries is especially important in cryptic taxa where one or more character sources are uninformative or are in conflict. Rather than relying on a single marker to delimit species, integrative taxonomy uses multiple lines of evidence such as molecular, morphological, behavioural and geographic characters to test species limits. We examine the effectiveness of this approach by testing the delimitation of two cryptic Nearctic species of Dioryctria (Lepidoptera: Pyralidae) using three independent molecular markers [cytochrome c oxidase I (COI), second internal transcribed spacer unit (ITS2), and elongation factor 1alpha (EF1alpha)], forewing variation and larval host plant association. Although mitochondrial DNA (mtDNA) haplotypes do not form reciprocally monophyletic clades, restricted gene flow between COI haplotype groups, and concordance with ITS2 genotypes, forewing variation and host plant associations support delimitation of two Nearctic species: eastern Dioryctria reniculelloides and western Dioryctria pseudotsugella. Conversely, EF1alpha genotype variation was incongruent with the two previous markers. A case of discordance between COI and ITS2 was detected, suggesting either introgression due to hybridization or retained ancestral polymorphism due to incomplete coalescence. This study is consistent with other similar literature where molecular loci in closely related species progress from shared to fixed haplotypes/alleles, and from polyphyletic to reciprocally monophyletic relationships, although loci may vary in these characteristics despite maintenance of genomic integrity between distinct species. In particular, mtDNA in other studies generally showed a lower rate of fixation of differences than did X-linked or autosomal loci, reinforcing the need to use an integrative approach for delimiting species.     

Gracilaria vermiculophylla: A western Pacific species of Gracilariaceae (Rhodophyta) first recorded from the eastern Pacific

We report Gracilaria vermiculophylla (Ohmi) Papenfuss from the Pacific coast of North America based on a morphoanatomical revision and comparison of sequences of the nuclear gene coding for the small subunit of ribosomal RNA and the internal transcribed spacers of populations from Baja California, Mexico and Hiroshima, Japan. It is the first convincing report of this species out of its center of distribution in western north Pacific, where it has been considered as a synonym of former ‘G. verrucosa’ records. G. vermiculophylla also occurs in central California as indicated by internal transcribed spacer sequences of a previously unknown Gracilaria Greville material. In the northeastern Pacific G. vermiculophylla is characterized by a robust somewhat vermiform, well‐branched cylindrical thallus, with gradual cell size transition from cortex to medulla, deep spermatangial conceptacles, regular chains of carposporangia and carposporangial initials, downwardly oriented tubular nutritive cells, but rarely with upwardly oriented tubular nutritive cells. In some features of its cystocarp anatomy G. vermiculophylla is related to Gracilariopsis E. Y. Dawson or Hydropuntia Montagne and it is a relevant species for discussions about Gracilariaceae genera.     

Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera)

Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.     

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.     

Towards a monophyletic genus Albinaria (Gastropoda, Pulmonata): the first molecular study into the phylogenetic position of eastern Albinaria species

Recent molecular phylogenetic studies of the terrestrial snail genus Albinaria have caused a radical reassessment of its taxonomy. These studies, however, were limited to western species. This paper examines mitochondrial 12S sequences and nuclear ITS1 & 2 sequences of both eastern and western species, and demonstrates that Albinaria, in its most recent definition, is not monophyletic. Both molecular datasets place ' Albinaria ' hedenborgi from Lebanon in a well-supported clade with species of the genus Cristataria , distributed south-east of the vicariant range of Albinaria . The remaining species from Cyprus, Turkey and Greece constitute a well-supported monophyletic group. These two clades form geographical clusters, whereas Albinaria in the current definition (including ' A. '  hedenborgi ) has a disjunct distribution. ' A.' hedenborgi should therefore be classified with Cristataria , together with the morphologically similar and geographically close ' A. '  nadimi .  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 531−542.