Phylogenetic and phylogeographic relationships in the crayfish genus Austropotamobius inferred from mitochondrial COI gene sequences

The present study explores the utility of mitochondrial COI gene sequences to reveal phylogenetic and phylogeographic relationships for the entire European freshwater crayfish genus Austropotamobius. The two traditional taxa, Austropotamobius pallipes and Austropotamobius torrentium, were monophyletic, showing similar genetic diversity, with 28 and 25 haplotypes, respectively, and an uncorrected average pairwise divergence of 0.059 and 0.041. A third distinct haplotype clade, in sister relation to A. torrentium, was discovered at the Upper Kolpa drainage in the northern Dinaric area. All populations north and west of the Alps are genetically impoverished (nucleotide diversity (pi)=0.000-0.001), while southern populations are more diverse (pi=0.001-0.034). A. pallipes reaches the highest diversity in the region of Istra, probably its primary center of radiation. The genetic diversity center for A. torrentium is the southern Balkan peninsula. Other potential glacial refugia were identified in Southern France, Northwestern Italy, the Apennine Peninsula, and in the northern Dinaric area. The Iberian Peninsula has been stocked artificially from Northern Italy. Three main periods of radiation were tentatively identified: late Miocene/early Pliocene for the divergence of species and main lineages, the Pleistocene for the divergence within populations south from Alps, and a postPleistocene expansion north and west from Alps.     

Phylogenetic relationships of the Chinese brown frogs (genus Rana) inferred from partial mitochondrial 12S and 16S rRNA gene sequences

Based on partial sequences of the 12S and 16S ribosomal RNA genes, we estimated phylogenetic relationships among brown frogs of the Rana temporaria group from China. From the phylogenetic trees obtained, we propose to include Rana zhengi in the brown frogs. Monophyly of the brown frogs was not unambiguously supported, but four well-supported clades (A, B, C, and D) always emerged, although relationships among them remained unresolved. Clade A contained brown frogs with 24 chromosomes and was split into two distinct subclades (Subclade A-1: R. chensinensis and R. huanrenensis; Subclade A-2: R. dybowskii). Polytomous relationships among populations of R. chensinensis and R. huanrenensis suggested the necessity of further taxonomic assessment. Rana kunyuensis proved to be the sister group to R. amurensis, and these two species formed Clade B. Clade C was composed of R. omeimontis and R. chaochiaoensis, and Clade D included R. sauteri, which has been placed in other ranid genera. These relationships did not change after adding published data, and monophyly of Subclade A-1, A-2, and other East Asian brown frogs with 24 chromosomes (R. pirica and R. ornativentris) was ascertained, though their relationships were unresolved. Clade C, together with R. japonica and R. longicrus, also formed a monophyletic group. Brown frogs related to Clades A and C were estimated to have dispersed from continental Asia to adjacent regions through multiple events.     

Phylogenetic relationships within the genus Jesogammarus (Crustacea, Amphipoda, Anisogammaridae) deduced from mitochondrial COI and 12S sequences

The genus Jesogammarus contains 16 species in two subgenera, Jesogammarus and Annanogammarus. To examine relationships among species in the genus, a molecular phylogenetic study including eight species of the former subgenus and four of the latter was conducted using partial DNA sequences of the mitochondrial COI and 12S rRNA genes. MP, NJ, and ML trees based on the combined COI and 12S data indicated monophyly of the subgenus Annanogammarus, though the monophyly of Jesogammarus was left unresolved. Consistent with few morphological differences, Jesogammarus (A.) naritai and J. (A.) suwaensis showed low genetic differentiation and did not show reciprocal monophyly, which suggests a close affinity of these taxa.     

Phylogenetic relationships among microgastrine braconid wasp genera based on data from the 16S, COI and 28S genes and morphology

Abstract Phylogenetic relationships among the genera of the large braconid wasp subfamily Microgastrinae were explored using DNA sequence data from the mitochondrial large ribosomal subunit (16S), nuclear large ribosomal subunit (28S) and mitochondrial cytochrome oxidase (COI) genes, along with morphological characters, both new and from previous studies. The taxonomic history of this group of wasps is reviewed, along with a critique of previous phylogenetic studies on the group. Molecular data were sampled from forty-six species representing twenty-six genera of microgastrines, plus three species representing the close outgroup taxa Cardiochilinae and Miracinae. Some 2300 base pairs of aligned sequence were obtained per taxon from the three genes. In addition, fifty-three morphological characters were coded for all known genera, including two undescribed genera, except Semionis Nixon (known from only a single male type specimen). Relationships among several groups of genera are clarified and challenge some major assumptions made in earlier classifications. In particular, it is clear that dependence on one or a few major morphological character systems oversimplifies relationships, and can lead to misleading results. Despite the large amount of data analysed, basal divergences within the subfamily remain poorly resolved and essentially unsupported in any rigorous statistical sense.     

Phylogenetic relationships of the Japanese minnows,Pseudorasbora (Cyprinidae), as inferred from mitochondrial 16S rRNA gene sequences

The phylogenetic relationships among threePseudorasbora fishes (Cyprinidae, Sarcocheiichthyinae) occurring in Japan (P. parva, P. pumila pumila andP. pumila subsp. sensu Nakamura [1963]) were inferred from nucleotide sequences of the mitochondrial 16S rRNA gene. The sequences. of 1240 bp, were determined and compared for 22 specimens from 2–8 populations for each taxon, with a singlePungtungia herzi specimen as an outgroup. A total of 171 sites (13.8%) were variable among the specimens, but only 0–2 sites within each population. The phylogenetic relationships estimated by neighbor-joining, maximum-parsimony and maximum-likelihood methods confirmed a sister relationship between the twoP. pumila subspecies, with a high level of confidence. However, their genetic distinction from each other (4.1±0.4SD % sequence difference on average) was at a level similar to that between them andP. parva (5.9±0.5%). The geographic distribution of the twoP. pumila subspecies, which are separated by the Fossa Magna region, suggests that the genetic divergence of the two subspecies originated from a vicariant process separating the freshwater ichthyofaunas of eastern and western Honshu.Pseudorasbora parva populations were divided into two genetic groups (1.8±0.2% sequence difference), one group comprising continental and part of the Japanese populations, and the other the remaining Japanese populations. This suggests that at least two genetically divergent lineages had been originally distributed in Japan, but a strong possibility remains that the present situation has resulted from artificial transplantation.     

Phylogenetic relationship of 16 Oedipodidae species （Insecta： Orthoptera） based on the 16S rRNA gene sequences

The sequences of the mitochondrial 16S rRNA gene of 16 Oedipodidae species were amplified and sequenced. All sequences were aligned and analyzed and the phylogenetic relationships were inferred. The properties of 16S gene in Oedipodidae showed typical patterns of many insects such as a high A＋T content and variable distance-dependent transition/transversion ratios. The 0.2 weight for sites of loops may be advisable for phylogeny reconstruction using the maximum parsimony method. The phylogenetic analysis results do not support the current subfamily classification systems of Oedipodidae. Bryodemellinae and Bryodeminae are closely related and should be merged as one subfamily. The status of Oedipodinae and Locustinae is also problematic.     

从线粒体16S rDNA序列探讨绒螯蟹类的系统发生关系

测定了绒螯蟹类各物种的线粒体16SrDNA部分片段的序列,构建了NJ树、ML树和MP树。序列歧异数据比较和各系统发生树都支持新绒螯蟹属(Neoeriocheir)为一个独立的属。在3种系统发生树中,直额绒螯蟹(Eriocheir recta)都是绒螯蟹属(Eriocheir)所有其它成员的姐妹群,并且广东珠江1只直额绒螯蟹标本的16SrDNA部分序列与台湾产台湾绒螯蟹(Eriocheir formasa)的相应序列相同。这些结果不支持平绒螯蟹属(Platyeriocheir)是一个有效的属,并表明E．formosa是E．recta的同物异名。绒螯蟹属(Eriocheir)所有其它成员聚为一个单系的分支,支持中华绒螯蟹、合浦绒螯蟹与日本绒螯蟹属于同一个物种Eriocheir japonica。16SrDNA部分序列的比对表明,产于台湾的日本绒螯蟹的此段序列与合浦绒螯蟹的相同,产于崇明岛的和产于美国旧金山海湾的中华绒螯蟹的此段序列与中华绒螯蟹单元型B的序列相同。     

Phylogenetic relationships of African microhylid frogs inferred from DNA sequences of mitochondrial 12S and 16S rRNA genes

The phylogenetic relationships of microhylid frogs are poorly understood. The first molecular phylogeny for continental African microhylids is presented, including representatives of all subfamilies, six of the eight genera, and the enigmatic hemisotid Hemisus. Mitochondrial 12S and 16S rRNA sequence data were analysed using parsimony, likelihood and Bayesian methods. Analyses of the data are consistent with the monophyly of all sampled subfamilies and genera. Hemisus does not nest within either brevicipitines or non-brevicipitines. It is possibly the sister group to brevicipitines, in which case brevicipitines might not be microhylids. Phrynomantis and Hoplophryne potentially group with non-African, non-brevicipitine microhylids, in agreement with recent morphological and molecular data. Within brevicipitines, Breviceps is recovered as the sister group to a clade of Callulina+Spelaeophryne+Probreviceps. The relationships among the genera within this latter clade are unclear, being sensitive to the method of analysis. Optimal trees suggest the Probreviceps macrodactylus subspecies complex might be paraphyletic with respect to P. uluguruensis, corroborating preliminary morphological studies indicating that P. m. rungwensis may be a distinct species. P. m. loveridgei may be paraphyletic with respect to P. m. macrodactylus, though this is not strongly supported. Some biogeographic hypotheses are examined in light of these findings.     

Phylogenetic relationships in West Mediterranean Scaritina (Coleoptera: Carabidae) inferred from mitochondrial COI sequences and karyotype analysis

The phylogenetic relationships of the West Mediterranean lineages of the subtribe Scaritina have been investigated by studying the mitochondrial cytochrome oxidase gene (COI) and the mitotic and meiotic chromosomes, including the localization of rDNA genes by fluorescence in situ hybridization. These sources of data are congruent and suggest the following conclusions: (1) the subgenus Parallelomorphus (genus Scarites ) is a monophyletic group according to molecular and karyotypic data, in agreement with its geographical distribution and morphological characters; (2) in the same genus, the subgenus Scallophorites seems to be monophyletic but includes two well-separated lineages – one represented by Scarites buparius (Forster, 1771) and Scarites occidentalis (Bedel, 1895) (both with multiple sex chromosomes), and one represented by Scarites hespericus (Dejean, 1831); (3) the nominal subgenus Scarites s.s . represented by Scarites eurytus (Fischer, 1828), is cladistically more closely related to subgenus Scallophorites than to subgenus Parallelomorphus ; (4) Distichus planus (Bonelli, 1813) belongs to a distinct clade that is well separated from Scarites, and shows more plesiomorphic states of COI sequence and chromosome number. In addition, the presence of two autapomorphies, such as rDNA sites located in the X chromosome, and an A + T rich intergenic spacer of about 120 bp between the stop codon of the COI gene and the tRNAleu, agree with the ranking of Distichus as a separate genus from Scarites .     

Phylogenetic relationships of rodent pinworms (genus Syphacia) in Japan inferred from 28S rDNA sequences

The 28S rDNA from nine species of the genus Syphacia collected in Japan was sequenced, and the phylogenetic relationship was inferred from multiple sequence alignment of 28S rDNA by the MAFFT program. Phylogenetic tree indicates that S. petrusewiczi, which was the only species belonging to the subgenus Seuratoxyuris, has diverged earlier than other rodent pinworms examined and was distantly separated from the others genetically. It was revealed that S. agraria and S. vandenbrueli, whose subgeneric status has not been specified, belonged to the subgenus Syphacia together with other 6 species. Syphacia montana from Clethrionomys, Eothenomys and Microtus was very closely related to S. obvelata from Mus, and that S. frederici from Apodemus and S. vandenbrueli from Micromys were comparatively closely related to the former two species. The phylogenetic relationship among the three species of Syphacia found in Japanese Apodemus was inconsistent with the biogeography of host rodents. The co-evolutionary relationship between pinworm species and their host rodents may not be so strict and host switching has probably occurred frequently during the course of evolution.     

Phylogenetic relationships of Central European wolf spiders (Araneae: lycosidae) inferred from 12S ribosomal DNA sequences

We have analyzed a sequence dataset of a portion of mitochondrial 12S rRNA gene of the ribosomal small subunit for 27 species of the family Lycosidae (wolf spiders) from Central Europe, belonging to six genera (Alopecosa, Arctosa, Pardosa, Pirata, Trochosa, and Xerolycosa) and four subfamilies (Evippinae, Lycosinae, Pardosinae and Venoniinae). Phylogenetic analyses were performed in two steps and corroborate the monophyly of all the genera analyzed with strong bootstrap support. In the first step focusing on the most ancestral splits the genus Pirata consistently emerged as the most ancestral branch, followed by the two genera Arctosa and Xerolycosa, with conflicting branching order, however. The second step of analysis placed Xerolycosa more ancestral than Arctosa. Arctosa appeared as sister group to the genera Alopecosa, Trochosa, and Pardosa. The palearctic genus Xerolycosa was not yet included in previous studies derived from morphological characters, but its placement based on mtDNA sequences is in good agreement to that according to current diagnostic morphological features. Further, the single representative of the genus Arctosa examined in our study was placed at a more ancestral position than in a previous investigation based on phenotypic characters. The superimposition of the currently used diagnostic phenotypic characters on the DNA-based phylogeny shows that both character sets are widely congruent; only 3 out of 16 phenotypic characters were resolved as homoplasious, suggesting their parallel evolution and/or reversal. Among the three different styles of predation found in the Lycosids, tube builders appear to be the most ancestral from which burrow dwellers descended and from which two groups of vagrant hunters evolved in parallel.     

Phylogenetic relationships of xenodontine snakes inferred from 12S and 16S ribosomal RNA sequences

The phylogenetic relationships of xenodontine snakes are inferred from sequence analyses of portions of two mitochondrial genes (12S and 16S ribosomal RNA) in 85 species. Although support values for most of the basal nodes are low, the general pattern of cladogenesis observed is congruent with many independent molecular, morphological, and geographical data. The monophyly of xenodontines and the basal position of North American xenodontines in comparison with Neotropical xenodontines are favored, suggesting an Asian-North American origin of xenodontines. West Indian xenodontines (including endemic genera and members of the genus Alsophis) appear to form a monophyletic group belonging to the South American clade. Their mid-Cenozoic origin by dispersal using ocean currents is supported. Within South American mainland xenodontines, the tribes Hydropsini, Pseudoboini, and Xenodontini are monophyletic. Finally, our results suggest that some morphological and ecological traits concerning maxillary dentition, macrohabitat use, and foraging strategy have appeared multiple times during the evolution of xenodontine snakes.     

Phylogenetic relationships among four species of Mullidae (Perciformes) inferred from DNA sequences of mitochondrial cytochrome b and 16S rRNA genes

DNA sequence comparisons of two mitochondrial DNA genes were used to infer phylogenetic relationships among four species of mullids. Approximately 238 bp of the mitochondrial 16S ribosomal RNA (rRNA) and 261 bp of the cytochrome b (cytb) genes were sequenced from representatives of three mullid genera (Mullus, Upeneus, Pseudopeneus), present in the Mediterranean Sea. Trees were constructed using three methods: maximum likelihood (ML), neighbor joining (NJ) and parsimony (MP). The results of the analyses of these data together with published data of the same mtDNA segments of two other perciform species (Sparus aurata, Perca fluviatilis), support the previous taxonomic classification of the three genera examined, as well as the classification of the two red mullet species in the same genus.     

Phylogenetic relationships of the genus Chamaecyparis inferred from leaf essential oil

The species differentiation between Chamaecyparis formosensis, C. obtusa var. formosana, and C. obtusa, based on the composition of the leaf essential oils, was studied. The characterization of the oils by GC-FID and GC/MS analyses showed remarkable differences between these three essential oils. Cluster analysis (CA) and principal-component analysis (PCA) distinguished three groups of essential oils. The C. formosensis oil was dominated by α-pinene while those isolated from C. obtusa var. formosana and C. obtusa were characterized by high levels of (-)-thujopsene and α-terpinyl acetate, respectively. Moreover, the phylogenetic relationships of the genus Chamaecyparis were in agreement with previous findings based on morphological and molecular evidence. In addition, the essential oils from C. obtusa var. formosana could be classified into three chemical types, according to their different characteristic main compounds (β-elemol, (-)-thujopsene, and cis-thujopsenal). The biochemical correlations between the major constituents of the Chamaecyparis species were examined and their relationship is discussed.     

Phylogenetic relationships among the species of the genus Testudo (Testudines: Testudinidae) inferred from mitochondrial 12S rRNA gene sequences

To test phylogenetic relationships within the genus Testudo (Testudines: Testudinidae), we have sequenced a fragment of the mitochondrial (mt) 12S rRNA gene of 98 tortoise specimens belonging to the genera Testudo, Indotestudo, and Geochelone. Maximum likelihood and neighbor-joining methods identify two main clades of Mediterranean tortoises, one composed of the species Testudo graeca, Testudo marginata, and Testudo kleinmanni and a second of Testudo hermanni, Testudo horsfieldii, and Indotestudo elongata. The first clade, but not the second, was also supported by maximum parsimony analysis. Together with the genus Geochelone, a star-like radiation of these clades was suggested, as a sister-group relationship between the two Testudo clades could not be confirmed. The intraspecies genetic variation was examined by sequencing the mt 12S rRNA fragment from 28 specimens of T. graeca and 49 specimens of T. hermanni from various geographic locations. Haplotype diversity was found to be significantly larger in T. graeca compared with T. hermanni, suggestive of reduced genetic diversity in the latter species, perhaps due to Pleistocene glaciations affecting northern and middle Europe or other sources of lineage reduction. No ancient mt 12S rRNA gene haplotypes were identified in T. graeca and/or T. hermanni originating from islands in the Mediterranean Sea, suggesting that these islands harbor tortoise populations introduced from the European and African mainland.     

Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences

The phylogenetic relationships of nine species of freshwater sponges, representing the families Spongillidae, Lubomirskiidae, and Metaniidae, were inferred from analyses of 18S rDNA, cytochrome oxidase subunit I (COI) mtDNA, and internal transcribed spacer 2 (ITS2) rDNA sequences. These species form a strongly supported monophyletic group within the Demospongiae, with the lithistid Vetulina stalactites as the sister taxon. Within the freshwater sponge clade, the basal taxon is not resolved. Depending upon the method of analysis and sequence, the metaniid species, Corvomeyenia sp., or the spongillid species, Trochospongilla pennsylvanica , emerges as the basal species. Among the remaining freshwater sponge species, the spongillids, Spongilla lacustris and Eunapius fragilis , form a sister group to a clade comprised of the spongillid species, Clypeatula cooperensis , Ephydatia fluviatilis , and Ephydatia muelleri , and the lubomirskiid species, Baikalospongia bacillifera and Lubomisrkia baicalensis . C. cooperensis is the sister taxon of E. fluvialitis , and E. muelleri is the sister taxon of ( B. bacillifera + L. baicalensis ). The family Spongillidae and the genus Ephydatia are thus paraphyletic with respect to the lubomirskiid species; Ephydatia is also paraphyletic to C. cooperensis . We suggest that C. cooperensis be transferred to the genus Ephydatia and that the family Lubomirskiidae be subsumed into the Spongillidae.     

Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (trnL-F region) showed Bulbostylis as monophyletic, although they only incorporated four species of Bulbostylis and none of Nemum. In this work, we presented a phylogenetic hypothesis of Bulbostylis based on a comprehensive sampling, including species from different continents for the first time. New sequences of Abildgaardia, Crosslandia, Fimbristylis, and Nemum were included to test the monophyly of Bulbostylis. In total, 84 sequences of both ITS and trnL regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, Bulbostylis resulted paraphyletic as Nemum atracuminatum is nested within it. Most American species of Bulbostylis grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of Bulbostylis, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the Bulbostylis.     

Phylogenetic relationships of the helical-shaped bacteria in the alpha Proteobacteria inferred from 16S rDNA sequences

16S ribosomal RNA gene sequences from seven strains of Aquaspirillum peregrinum, Aqu. itersonii, Aqu. polymorphum, and Oceanospirillum pusillum were compared with homologous sequences from other members of helical-shaped bacteria. The bootstrapped neighbor-joining tree, inferred from 887 aligned sites, placed the spirillum taxa assigned to Aquaspirillum, Oceanospirillum, Azospirillum, Magnetospirillum, Rhodospirillum, and Rhodocista of the Proteobacteria in seven clusters of alpha Proteobacteria separately from other shapes of bacteria. Aqu. peregrinum and Aqu. itersonii grouped together in 88% bootstrap support. They were more related to Rhodospirillum rubrum and Rsp. photometricum than Aqu. polymorphum. Aqu. polymorphum was close to Magnetospirillum gryphiswaldense, Mag. magnetotacticum, Rsp. fulvum, and Rsp. molischianum, and more close to Mag. gryphiswaldense. Oce. pusillum was not related to other spirillum taxa and was placed in a separate branch. Rhodocista was very closely related to Azospirillum. Photosynthesis and magnetotaxis, as phenotypic characters, were not important in the classification of helical bacteria.     

Re: Phylogenetic relationships in Sphingidae (Insecta: Lepidoptera): initial evidence from two nuclear genes

Partial DNA sequences from two mitochondrial (mt) and one nuclear gene (cytochrome b, 12S rRNA, and C-mos) were used to estimate the phylogenetic relationships among the six extant species of skinks endemic to the Cape Verde Archipelago. The species form a monophyletic unit, indicating a single colonization of the islands, probably from West Africa. Mabuya vaillanti and M. delalandii are sister taxa, as indicated by morphological characters. Mabuya fogoensis and M. stangeri are closely related, but the former is probably paraphyletic. Mabuya spinalis and M. salensis are also probably paraphyletic. Within species, samples from separate islands always form monophyletic groups. Some colonization events can be hypothesized, which are in line with the age of the islands. C-mos variation is concordant with the topology derived from mtDNA.