Towards resolving the identities of the Graphium butterflies (Lepidoptera: Papilionidae) of Peninsular Malaysia

Graphium butterflies are famous in Peninsular Malaysia for their colourful wings, yet their taxonomy remains unresolved. The popular guides to Malaysian butterflies, place the species in one, two or three genera and identification to species using obscure morphological characters can be difficult, especially for the closely related species, G. bathycles bathycloides and G. chironides malayanum. We sequenced the COI mtDNA barcode for Graphium specimens in the Museum of Zoology, University of Malaya to test the utility of DNA barcoding for the identification of Graphium species. Additionally, we sequenced 28S rRNA to examine, in conjunction with COI, the phylogenetic relationships of these species and investigate the validity of Pathysa and Paranticopsis as distinct genera. We found that all species of Graphium possessed a distinctive cluster of DNA barcodes with the exception of specimens originally identified as G. bathycles bathycloides and G. chironides malayanum which shared DNA barcodes. On further examination we found that the morphological determinations were ambiguous as the specimens overlapped for diagnostic characters reported for each species. The COI and 28S rRNA phylogenetic trees showed a similar topology with Paranticopsis species forming a clade nested within a larger clade also comprising Pathysa species. Based on this topology, in order for Pathysa to be a valid genus, at least three other clades within Graphium s.l. would also have to be raised as genera.     

Evolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): insight from an expanded sampling of molecular data

Relative to its diversity (34 genera, 700 species), Scolopendromorpha has been undersampled in molecular phylogenetic analyses compared with the other chilopod orders. Previous analyses based on morphology have not resolved several key controversies in systematics and evolutionary morphology unambiguously. Here we apply new molecular and morphological data to scolopendromorph phylogenetics, with a focus on the evolution of blindness. The taxonomic sample includes 19 genera, many lacking previous molecular data, and diverse, cosmopolitan genera of Scolopendridae are sampled by multiple species. Phylogenetic analysis with Direct Optimization used 94 morphological characters and ca. 4.5 kb of sequence data from two nuclear (18S and 28S rRNA) and two mitochondrial (16S rRNA and COI) loci. A single most‐parsimonious cladogram selected after sensitivity analyses resolves Scolopendromorpha as monophyletic, and divides it into a blind clade of three families (Plutoniumidae, Cryptopidae, Scolopocryptopidae) and its ocellate sister group, Scolopendridae. Some species‐rich, cosmopolitan genera (Cormocephalus, Otostigmus, Scolopendra) in Scolopendridae are non‐monophyletic, and in several instances (e.g. New and Old World Scolopendra) relationships are more congruent with geographical distributions than with traditional classifications. The tribe Asanadini is particularly subject to parameter‐sensitivity, nesting in the combined analysis within Scolopendrini but as sister to all other Scolopendrinae for molecular data alone. The total‐evidence tree unambiguously optimizes trunk segmentation: a 23‐segmented trunk has a single origin in the blind clade. © The Willi Hennig Society 2011.     

Morphological and molecular description of new species of squat lobster (Crustacea: Decapoda: Galatheidae) from the Solomon and Fiji Islands (South‐West Pacific)

The family Galatheidae is among the most diverse families of anomuran decapod crustaceans, and the South‐West Pacific is a biodiversity hot spot for these squat lobsters. Attempts to clarify the taxonomic and evolutionary relationships of the Galatheidae on the basis of morphological and molecular data have revealed the existence of several cryptic species, differentiated only by subtle morphological characters. Despite these efforts, however, relationships among genera are poorly understood, and the family is in need of a detailed systematic review. In this study, we assess material collected in different surveys conducted in the Solomon Islands, as well as comparative material from the Fiji Islands, by examining both the morphology of the specimens and two mitochondrial markers (cytochrome oxidase subunit I, COI, and 16S rRNA). These two sources of data revealed the existence of eight new species of squat lobster, four of which were ascribed to the genus Munida, two to the genus Paramunida, one to the genus Plesionida, and the last species was ascribed to the genus Agononida. These eight species are described along with phylogenetic relationships at the genus level. Our findings support the taxonomic status of the new species, yet the phylogenetic relationships are not yet fully resolved. Further molecular analysis of a larger data set of species, and more conserved genes, will help clarify the systematics of this group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 465–493.     

Molecular phylogeny of rootworms and related galerucine beetles (Coleoptera: Chrysomelidae)

The Galerucinae (Coleoptera: Chrysomelidae) sensu stricto (true galerucines) comprise a large assemblage of diverse phytophagous beetles containing over 5000 described species. Together with their sister taxon, the flea beetles, which differ from true galerucines by having the hind femora usually modified for jumping, the Galerucinae sensu lato comprises over 13 000 described species and is the largest natural group within the Chrysomelidae. Unlike the flea beetles, for which robust hierarchical classification schemes have not been erected, an existing taxonomic structure exists for the true galerucines, based mostly on the works of the late John Wilcox. In the most recent taxonomic list of the Galerucinae sensu stricto, five tribes were established comprising 29 sections housing 488 genera. The majority of the diversity within these tribes is found within the tribe Luperini, in which two genera, Monolepta and Diabrotica, are known to contain over 500 described species. Here, we extend the work from previous phylogenetic studies of the Galerucinae by analysing four amplicons from three gene regions (18S and 28S rRNA; COI) representing 249 taxa, providing the largest phylogenetic analysis of this taxon to date. Using two seven‐state RNA models, we combine five maximum likelihood models (RNA + DNA for the rRNAs; three separate DNA models for the COI codon positions) for these partitions and analyse the data under likelihood using Bayesian inference. The results of these two analyses are compared with those from equally weighted parsimony. Instead of choosing the results from one optimality criterion over another, either based on statistical support, tree topology or philosophical predisposition, we elect to draw attention to the similar results produced by all three analyses, illustrating the robustness of the data to these different analytical methods. In general, the results from all three analyses are consistent with each other and previous molecular phylogenetic reconstructions for Galerucinae, except that increased taxon sampling for several groups, namely the tribes Hylaspini and Oidini, has improved the phylogenetic position of these taxa. As with previous analyses, under‐sampled taxa, such as the Old World Metacyclini and all sections of the subtribe Luperina, continue to be unstable, with the few taxa representing these groups fluctuating in their positions based on the implemented optimality criterion. Nonetheless, we report here the most comprehensive phylogenetic estimation for the Galerucinae to date.     

Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 5′ End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic

The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.     

Phylogenomic species delimitation and host‐symbiont coevolution in the fungus‐farming ant genus Sericomyrmex Mayr (Hymenoptera: Formicidae): ultraconserved elements (UCEs) resolve a recent radiation

Ants in the Neotropical genus Sericomyrmex Mayr cultivate fungi for food. Both ants and fungi are obligate, coevolved symbionts. The taxonomy of Sericomyrmex is problematic because the morphology of the worker caste is generally homogeneous across all of the species within the genus, species limits are vague, and the relationships between them are unknown. We used ultraconserved elements (UCEs) as genome‐scale markers to reconstruct evolutionary history and to infer species boundaries in Sericomyrmex. We recovered an average of ～990 UCE loci for 88 Sericomyrmex samples from across the geographical range of the genus as well as for five outgroup taxa. Using maximum likelihood and species‐tree approaches, we recovered nearly identical topologies across datasets with 50–95% matrix completeness. We identify nine species‐level lineages in Sericomyrmex, including two new species. This is less than the previously described 19 species, even accounting for two species for which we had no UCE samples, which brings the total number of Sericomyrmex species to 11. Divergence‐dating analyses recovered 4.3 Ma as the crown‐group age estimates for Sericomyrmex, indicating a recent, rapid radiation. We also sequenced mitochondrial cytochrome oxidase subunit I (COI) for 125 specimens. Resolution and support for clades in our COI phylogeny are weak, indicating that COI is not an appropriate species‐delimitation tool. However, taxa within species consistently cluster together, suggesting that COI is useful as a species identification (‘DNA barcoding’) tool. We also sequenced internal transcribed spacer (ITS) and large subunit (LSU) for 32 Sericomyrmex fungal cultivars. The fungal phylogeny confirms that Sericomyrmex fungi are generalized higher‐attine cultivars, interspersed with Trachymyrmex‐associated fungal species, indicating cultivar sharing and horizontal transfer between these two genera. Our results indicate that UCEs offer immense potential for delimiting and resolving relationships of problematic, recently diverged species.     

The molecular phylogeny of the sea star Echinaster (Asteroidea: Echinasteridae) provides insights for genus taxonomy

In this study, we used sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and 16S rRNA, and one nuclear gene, 28S rRNA, to test the monophyly of the sea star genus Echinaster, and understand the phylogenetic relationships among species and subgenera within this genus. Phylogenetic analyses based on Bayesian inference and maximum likelihood methods revealed three clades with high values of genetic divergence among them (K2P distances for COI over 23%). One of the clades grouped all Echinaster (Othilia) species, and the other two clades included Echinaster (non‐Othilia) species and Henricia species, respectively. Although the relationships among Henricia, Othilia, and Echinaster could not be completely clarified, the Othilia clade was a well‐supported group with shared diagnostic morphological characters. Moreover, the approximately unbiased test applied to the phylogenetic reconstruction rejected the hypothesis of the genus Echinaster as a monophyletic group. According to these results, we suggest the revalidation of Othilia as a genus instead of a subgenus within Echinaster. Our study clarifies important points about the phylogenetic relationships among species of Echinaster. Other important systematic questions about the taxonomic classification of Echinaster and Henricia still remain open, but this molecular study provides bases for future research on the topic.     

Taxonomy and biogeography of Diapensia (Diapensiaceae) based on chloroplast genome data

Diapensia L. is the second largest genus of Diapensiaceae. The taxonomic treatment within Diapensia and relationships within Diapensiaceae have been disputed. Chloroplast genome sequence data have proved to be useful for plant phylogenetic analyses and species delimitation. In this study, we de novo sequenced and assembled 22 chloroplast genomes of 15 species of Diapensiaceae, including all recognized species of Diapensia with multiple samples. A super‐matrix containing a total of 107 genes and 18 taxa was constructed for phylogenetic analyses to resolve phylogenetic relationships among genera of the family and within Diapensia. The resulting phylogenetic tree showed the following strongly supported relationships: (Galax, (Pyxidanthera, (Berneuxia, ((Schizocodon, Diapensia), and Shortia s.s.)))). The dated phylogeny and reconstructed lineage‐through‐time plot for the family indicated rapid diversification in the Neogene and an acceleration of diversification rate after c. 8 Ma. Biogeographic analysis suggested that Diapensia originated in the Northeast Asian mountains approximately 6.06 Ma, followed by northward dispersal to the Arctic and southwestward dispersal to the Himalaya–Hengduan Mountains. Phylogenetic relationships within Diapensia were well resolved. Based on the phylogenetic results, we proposed to reinstate the species status of Diapensia bulleyana Forrest ex Diels, and raised D. purpurea f. albida to the species rank (D. albida [W. E. Evans] J. F. Ye comb. & stat. nov.). The distribution ranges of all species delineated based on the phylogenetic results were revised accordingly based on specimen occurrences. Our study adds new examples for the power of plastid genome data for resolving phylogenetic relationships and clarifying taxonomic disputes among closely related species.     

The Relationship between the Number of Loci and the Statistical Support for the Topology of UPGMA Trees Obtained from Genetic Distance Data

An analysis of the relationship between the number of loci utilized in an electrophoretic study of genetic relationships and the statistical support for the topology of UPGMA trees is reported for two published data sets. These are Highton and Larson (Syst. Zool.28: 579-599, 1979), an analysis of the relationships of 28 species of plethodonine salamanders, and Hedges (Syst. Zool., 35: 1-21, 1986), a similar study of 30 taxa of Holarctic hylid frogs. As the number of loci increases, the statistical support for the topology at each node in UPGMA trees was determined by both the bootstrap and jackknife methods. The results show that the bootstrap and jackknife probabilities supporting the topology at some nodes of UPGMA trees increase as the number of loci utilized in a study is increased, as expected for nodes that have groupings that reflect phylogenetic relationships. The pattern of increase varies and is especially rapid in the case of groups with no close relatives. At nodes that likely do not represent correct phylogenetic relationships, the bootstrap probabilities do not increase and often decline with the addition of more loci.     

Molecular phylogeny of the Acre clade (Crassulaceae): Dealing with the lack of definitions for Echeveria and Sedum

The phylogenetic relationships within many clades of the Crassulaceae are still uncertain, therefore in this study attention was focused on the “Acre clade”, a group comprised of approximately 526 species in eight genera that include many Asian and Mediterranean species of Sedum and the majority of the American genera (Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Villadia, and Thompsonella). Parsimony and Bayesian analyses were conducted with 133 species based on nuclear (ETS, ITS) and chloroplast DNA regions (rpS16, matK). Our analyses retrieved four major clades within the Acre clade. Two of these were in a grade and corresponded to Asian species of Sedum, the rest corresponded to a European–Macaronesian group and to an American group. The American group included all taxa that were formerly placed in the Echeverioideae and the majority of the American Sedoideae. Our analyses support the monophyly of three genera – Lenophyllum, Thompsonella, and Pachyphytum; however, the relationships among Echeveria, Sedum and the various segregates of Sedum are largely unresolved. Our analyses represents the first broad phylogenetic framework for Acre clade, but further studies are necessary on the groups poorly represented here, such as the European and Asian species of Sedum and the Central and South American species of Echeveria.     

Phylogeny of the water strider genus Gerris Fabricius (Heteroptera: Gerridae) based on COI mtDNA, EF-1α nuclear DNA and morphology

Phylogenetic relationships between water striders (Heteroptera: Gerridae) of genus Gerris Fabricius were examined using molecular and morphological characters. The molecular dataset was 820 bp DNA from the 3′ half of the mitochondrial gene encoding cytochrome oxidase subunit I and 515 bp DNA from the nuclear gene encoding elongation factor 1 alpha. The morphological dataset was a slightly modified version of a previously published dataset. Representatives from all eight recognized species groups of Gerris, as well as six species from three related genera, including Gigantometra gigas, Limnoporus esakii, L. rufoscutellatus, Aquarius najas, A. conformis and A. paludum, were included. Unweighted parsimony analyses of the COI sequences gave a topology with strong support for only those nodes that were already recognized as closely related based on morphological characters. Similar analyses of EF‐1α gave a cladogram with a topology quite different from that based on morphology and COI. Unweighted parsimony analyses of the ‘total evidence’ dataset largely supports the traditional view of Gerris phylogeny. Finally, the implications of the reconstructed phylogeny in relation to biogeography and ecological phylogenetics of Gerris is discussed.     

A species-level total evidence phylogeny of the microteiid lizard family Alopoglossidae (Squamata: Gymnophthalmoidea)

Alopoglossidae is a family of Neotropical lizards composed of 23 species allocated in two genera (Alopoglossus and Ptychoglossus). There is a lack of knowledge about the phylogenetic relationships and systematics of this family. Published phylogenies that include alopoglossid species have very low taxon coverage within the family, and are usually based on limited character sampling. Considering these shortcomings, we infer the phylogenetic relationships of Alopoglossidae—including all but one species in the family—based on the combined analyses of DNA sequences and morphological characters. We use four loci (the mitochondrial 12S, 16S and ND4; the nuclear C-mos) and a matrix of 143 phenotypic characters from scutellation, tongue morphology, hemipenis morphology, and osteology. The dataset is analyzed with Maximum Parsimony, with four alternative weighting schemes: three under Extended Implied Weighting, and one with equal weighting. The respective resulting topologies are compared in a sensitivity analysis framework. Our analyses support the paraphyly of Ptychoglossus, with Alopoglossus nested within it. We provide an updated classification for the family, where Ptychoglossus Boulenger, 1890 is considered a junior synonym of Alopoglossus Boulenger, 1885.     

Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

Nemacheilidae, in the superfamily Cobitoidea, is comprised of many of morphologically similar fish species that occur in Eurasian water bodies. This large group shows inconsistencies between traditional morphological taxonomy and molecular phylogenetic data. We used mitochondrial genomes, recombinase‐activating gene proteins 1 (RAG1) and the mitochondrial cytochrome c oxidase I gene (COI) to study the phylogenetic relationships among Nemacheilidae species using Bayesian inference and maximum likelihood approaches. Phylogenetic analyses based on mitogenomes provided support for two clades (I and II). The mitogenomes, RAG1, and COI results indicated that several species and genera were not consistent with the traditional morphological subdivisions. The two clades inferred from mitogenomes showed clear geographical patterns. The Tibetan Plateau, Hengduan Mountains, and the Iran Plateau may act as a barrier dividing the clades. The estimated timing of clades separation (36.05 million years ago) coincides with the first uplift of the Tibetan Plateau. We conclude that the geological history of the Tibetan Plateau played a role in the diversification and distribution of the Nemacheilidae taxa. These results provided a phylogenetic framework for future studies of this complex group.     

Molecular phylogeny of sea snakes reveals a rapidly diverged adaptive radiation

Evolutionary relationships within and between the marine hydrophiine sea snake groups have been inferred primarily using morphological characters, and two major groups traditionally are recognized. The Aipysurus group comprises nine species in two genera, and the taxonomically chaotic Hydrophis group comprises as many as 40 species, of which 27 are generally allocated to the genus Hydrophis and 13 to ten additional genera. In addition to these two major groups are three putatively ‘primitive’ monotypic genera, Hydrelaps darwiniensis, Ephalophis greyi and Parahydrophis mertoni. The present study investigated the evolutionary relationships of 23 representative species of marine hydrophiines, comprising 15 species from the Hydrophis group, six species from the Aipysurus group, and H. darwiniensis and P. mertoni, to address two broad aims. First, the aim was to provide a robust phylogeny for sea snakes to test previous phylogenetic hypotheses based on morphology, and thus provide some taxonomic stability to the group. Second, there was interest in evaluating the hypothesis that the Hydrophis group might represent a rapidly diverged adaptive radiation. A large mitochondrial DNA data set based on the cytochrome b gene (1080 bp, 401 parsimony informative) and the 16S rRNA gene (510 bp, 57 parsimony informative) was assembled and these data were analysed using parsimony, maximum‐likelihood and Bayesian approaches. All analyses yielded virtually the same optimal tree, confirming that hydrophiine sea snakes comprise at least three lineages. The Aipysurus group formed a strongly supported and well‐resolved monophyletic clade. The Hydrophis group also formed a strongly supported clade; however, resolution among the genera and species was very poor. Hydrelaps darwiniensis and P. mertoni formed a sister clade to the Hydrophis lineage. Our phylogeny was used to test the validity of previous taxonomic and phylogenetic hypotheses, and to demonstrate that the genus Hydrophis is not monophyletic. Genetic diversity relative to phenotypic diversity is four to seven times greater in the Hydrophis lineage compared with the Aipysurus lineage. The topology of our phylogenetic hypothesis, combined with the levels of genetic divergence relative to morphological diversity, demonstrate that the Hydrophis lineage represents a rapidly diverged adaptive radiation. The data are consistent with the hypothesis that this adaptive radiation may be due to historical sea level fluctuations that have isolated populations and promoted speciation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89 , 523–539.     

Chasing ghosts: the phylogeny of Amaurobioidinae ghost spiders (Araneae,Anyphaenidae)

The family Anyphaenidae, also known as ghost spiders, includes a diverse array of nocturnal cursorial spiders that actively hunt on vegetation. The family is mostly distributed in the Americas and has been traditionally divided into three subfamilies. The mostly tropical and North American Anyphaeninae and the Amaurobioidinae, primarily distributed in southern South America, hold the bulk of the diversity, while the Malenellininae includes a single Chilean species. Here, we use a combined morphological and molecular approach to infer the relationships of the subfamily Amaurobioidinae and examine the delimitation of contentious genera. The morphological characters include both genitalic and somatic morphology, whereas molecular data include four markers, two mitochondrial (COI, 16S) and two nuclear (28S, H3). All our analyses agree on the monophyly of Amaurobioidinae, Amaurobioidini, Gayennini, the genera Negayan, Amaurobioides, Josa, Araiya, Arachosia and Monapia, as well as the paraphyly of Anyphaeninae. The total evidence analysis supports the novel placement of Josa as the sister group of both tribes Amaurobioidini and Gayennini, most of the previously known intergeneric relationships within Gayennini, and a clade of Amaurobioidini with a projecting ocular area, including Aysenoides, Axyracrus, Amaurobioides and Aysenia. The sequence data solve the puzzling placement of Philisca puconensis, here transferred to Tomopisthes, and Tasata chiloensis, transferred to Oxysoma. The advantages of the total evidence phylogenetic approach and the evolution of the male copulatory organ are discussed.     

New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes

Background

Two deep-sea eels collected from the Western Pacific Ocean are described in this study. Based on their morphological characteristics, the two deep-sea eel specimens were assumed to belong to the cusk-eel family Ophidiidae and the cutthroat eel family Synaphobranchidae.

Methods and results

To accurately identify the species of the deep-sea eel specimens, we sequenced the mitochondrial genes (cytochrome c oxidase subunit I [COI] and 16S ribosomal RNA [16S rRNA]). Through molecular phylogenetic analysis based on mtDNA COI and 16S rRNA gene sequences, these species clustered with the genera Bassozetus and Synaphobranchus, suggesting that the deep-sea eel specimens collected are two species from the genera Bassozetus and Synaphobranchus in the Western Pacific Ocean, respectively.

Conclusions

This is the first study to report new records of the genera Bassozetus and Synaphobranchus from the Western Pacific Ocean based on COI and 16S rRNA genes

     

Molecular Phylogeny and Systematics of Anoplocephaline Cestodes in Rodents and Lagomorphs

A molecular phylogenetic hypothesis is presented for the anoplocephaline cestodes of placental mammals based on sequence data from the mitochondrial cytochrome c oxidase I (COI) gene, the nuclear-encoded 28S rRNA gene and the internal transcribed spacer region I of rRNA (ITS1). The material consists of 35 species representing nine genera of cestodes, with emphasis on taxa parasitising rodents and lagomorphs in the Holarctic region. The resulting phylogenies show considerable disagreement with earlier systematic and phylogenetic hypotheses derived from morphology. Specifically, the results contradict the view of uterine morphology being the primary determinant of deeper phylogenetic splits within Anoplocephalinae. Also, the role of genital duplication as a means of generic divergence was not found to follow consistently the pattern suggested by earlier hypotheses. Colonisation of novel host lineages has evidently been the predominant mode of diversification in anoplocephaline cestodes of placental mammals; evidence for phyletic co-evolution was obscure. The phylogenies consistently distinguished a large monophyletic group including all species from arvicoline rodents (voles and lemmings), primarily representing the genera Anoplocephaloides Baer, 1923 and Paranoplocephala Lühe, 1910. Phylogenetic relationships within the “arvicoline clade” of cestodes were generally poorly resolved. Consistent support for nodes above and below the unresolved polytomy indicates a rapid radiation involving a nearly simultaneous diversification of many lineages, a scenario also proposed for the arvicoline hosts.     

The complete mitochondrial genome of the Sichuan taimen (Hucho bleekeri): repetitive sequences in the control region and phylogenetic implications for Salmonidae

The complete mitochondrial DNA genome of the Sichuan taimen (Hucho bleekeri) was determined by the long and accurate polymerase chain reaction (LA-PCR) and primer walking sequence method. The entire mitochondrial genome of this species is 16,997 bp in length, making it the longest among the completely sequenced Salmonidae mitochondrial genomes. It consists of two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one control region (CR). The gene arrangement, nucleotide composition, and codon usage pattern of the mitochondrial genome are similar to those of other teleosts. A T-type mononucleotide microsatellite and an 82 bp tandem repeat were identified in the control region, which were almost identical among the three H. bleekeri individuals examined. Both phylogenetic analyses based on 12 concatenated protein-coding genes of the heavy strand and on just the control region show that H. bleekeri is a basal species in Salmoninae. In addition, Salmo, Salvelinus and Oncorhynchus all represent monophyletic groups, respectively. All freshwater species occupied basal phylogenetic positions, and also possessed various tandem repeats in their mitochondrial control regions. These results support established phylogenetic relationships among genera in Salmonidae based on morphological and molecular analyses, and are consistent with the hypothesis that Salmonidae evolved from freshwater species.