Phylogenetic relationships among major species of japanese coleoid cephalopods (Mollusca: Cephalopoda) using three mitochondrial DNA sequences

Phylogenetic relationships among 36 species of major coleoid cephalopods from Japanese waters were studied using partial sequences of three mitochondrial genes, 16S rDNA, 12S rDNA, and cytochrome c oxidase subunit I gene. Octopoda and Decapoda were monophylic groups. Within Sepioidea, Sepiadariidae and Sepiolidae were not closely related to Sepiidae, but rather related to Teuthoidea. Sepiidae with a distinct calcareous shell formed a single cluster. Myopsida was closely related to Oegopsida. Within Octopoda, Opisthoteuthis depressa and Argonauta argo diverged earlier than Octopodiidae. The common octopuses in Japanese waters were separated into three clusters. The first cluster occupied a basal position, and includes large-sized octopuses, such as Enteroctopus dofleini and Octopus (Paroctopus) conispadiceus from the continental shelf and upper slope. The second cluster consisted of long-armed octopuses, such as O. ornatus, O. minor, and O. sasakii. The third cluster contained small- to medium-sized octopus, such as Amphioctopus fangsiao, A. areolatus, O. cyaneus, and O. vulgaris, in which several species possess ocelli on the web. The second cluster formed the sister group to the third cluster.     

Evolutionary relationships among the true vipers (Reptilia: Viperidae) inferred from mitochondrial DNA sequences

Nucleotide sequences of mitochondrial cytochrome b and 16S rRNA genes, totaling 946 bp, were used to reconstruct a molecular phylogeny of 42 species of the subfamily Viperinae representing 12 of the 13 recognized genera. Maximum-parsimony and maximum-likelihood were used as methods for phylogeny reconstruction with and without a posteriori weighting. When representatives of the Causinae were taken as outgroup, five major monophyletic groups were consistently identified: Bitis, Cerastes, Echis, the Atherini (Atheris s.l.), and the Eurasian viperines. Proatheris was affiliated with Atheris, and Adenorhinos clustered within Atheris. The African Bitis consisted of at least three monophyletic groups: (i) the B. gabonica group, (ii) the B. caudalis group, and (iii) the B. cornuta group. B. worthingtoni and B. arietans are not included in any of these lineages. Eurasian viperines could be unambiguously devided into four monophyletic groups: (i) Pseudocerastes and Eristicophis, (ii) European vipers (Vipera s.str.), (iii) Middle East Macrovipera plus Montivipera (Vipera xanthina group), and (iv) North African Macrovipera plus Vipera palaestinae and Daboia russelii. These evolutionary lineages are consistent with historical biogeographical patterns. According to our analyses, the viperines originated in the Oligocene in Africa and successively underwent a first radiation leading to the five basal groups. The radiation might have been driven by the possession of an effective venom apparatus and a foraging startegy (sit-wait-strike) superior in most African biomes and might have been adaptive. The next diversifications led to the Proatheris-Atheris furcation, the basal Bitis splitting, and the emergence of the basal lineages within the Eurasian stock. Thereafter, lineages within Echis, Atheris, and Cerastes evolved. The emergence of three groups within Vipera s.l. might have been forced by the existence of three land masses during the early Miocene in the area of the Paratethys and the Mediterranean Seas. Taxonomic consequences of these findings are discussed.     

Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from three mitochondrial and six nuclear loci: a comparison of alignment, implied alignment and analysis methods

Recent molecular studies investigating higher-level phylogeneticsof coleoid cephalopods (octopuses, squids and cuttlefishes)have produced conflicting results. A wide range of sequencealignment and analysis methods are used in cephalopod phylogeneticstudies. The present study investigated the effect of commonlyused alignment and analysis methods on higher-level cephalopodphylogenetics. Two sequence homology methods: (1) eye alignment,(2) implied alignment, and three analysis methods: (1) parsimony,(2) maximum likelihood, (3) Bayesian methodologies, were employedon the longest sequence dataset available for the coleoid cephalopods,comprising three mitochondrial and six nuclear loci. The datawere also tested for base composition heterogeneity, which wasdetected in three genes and resolved using RY coding. The Octopoda,Argonautoidea, Oegopsida and Ommastrephidae are monophyleticin the phylogenies resulting from each of the alignment andanalysis combinations. Furthermore, the Bathyteuthidae are thesister taxon of the Oegopsida in each case. However many relationshipswithin the Coleoidea differed depending upon the alignment andanalysis method used. This study demonstrates how differencesin alignment and analysis methods commonly used in cephalopodphylogenetics can lead to different, but often highly supported,relationships. (Received 15 December 2006; accepted 1 September 2007)     

Phylogenetic relationships among cirrate octopods (Mollusca: Cephalopoda) resolved using mitochondrial 16S ribosomal DNA sequences

PHYLOGENETIC RELATIONSHIPS AMONG THE CIRRATE OCTOPODS (MOLLUSCA: Cephalopoda) were investigated using partial sequences of the 16S rRNA mitochondrial gene. The derived phylogeny supports the traditional separation of cirrate families based on web form. Genera with a single web (Opisthoteuthis, Grimpoteuthis, Luteuthis, and Cirroctopus) are clearly distinct from those with an intermediate or secondary web (Cirroteuthis, Cirrothauma, and Stauroteuthis). The cirrates with a single web are separated into three groups. The first group is represented by Opisthoteuthis species, the second by Grimpoteuthis and Luteuthis, and the third by members of the genus Cirroctopus. There is no support for the isolation of Luteuthis in a separate family (Luteuthidae). There is, however, evidence of two groupings within the genus Opisthoteuthis. The data suggest the following revisions in the systematic classification of the cirrates: (1) Cirrothauma, Cirroteuthis, and Stauroteuthis be united in the Cirroteuthidae; (2) Grimpoteuthis and Luteuthis be placed in the Grimpoteuthidae; (3) Opisthoteuthis in the Opisthoteuthidae, and; (4) Cirroctopus be considered sufficiently distinct from both Opisthoteuthidae and Grimpoteuthidae to warrant placement in a new family.     

Molecular phylogenetic analysis of the squid family Mastigoteuthidae (Mollusca, Cephalopoda) based on three mitochondrial genes

Mastigoteuthid squids are ecologically important, being prey to many apex predators, yet the diversity and systematics of the family remain poorly understood. Delicate by nature, they are often damaged during capture; there is a need to accurately identify incomplete mastigoteuthid specimens from collections and stomach contents. This study aimed to test a morphological hypothesis for the division of the genera Mastigoteuthis (Mt.), Idioteuthis, Mastigopsis (Mp.), Echinoteuthis, and Magnoteuthis (Mg.) and to assess the utility of DNA barcodes to discriminate species. Three mitochondrial genes (16S rRNA, 12S rRNA, and cytochrome c oxidase subunit I) were analysed for eight different species, representing the largest phylogenetic assessment of the family to date. Evidence was found for a potentially new species in New Zealand that has been previously misidentified as the morphologically similar species Mg. magna. Each species analysed herein exhibited unique mitochondrial DNA haplotypes for all loci, and the morphological distinction between the five proposed genera was strongly supported using a combined Bayesian and maximum-likelihood phylogenies. Of the three loci examined, the DNA barcode region shows the greatest divergence between species and should be used in future systematic work on the Mastigoteuthidae.     

Phylogenetic relationships of Nembrothinae (Mollusca: Doridacea: Polyceridae) inferred from morphology and mitochondrial DNA

Within the Polyceridae, Nembrothinae includes some of the most striking and conspicuous sea slugs known, although several features of their biology and phylogenetic relationships remain unknown. This paper reports a phylogenetic analysis based on partial sequences of two mitochondrial genes (cytochrome c oxidase subunit I and 16S rRNA) and morphology for most species included in Nembrothinae. Our phylogenetic reconstructions using both molecular and combined morphological and molecular data support the taxonomic splitting of Nembrothinae into several taxa. Excluding one species (Tambja tentaculata), the monophyly of Roboastra was supported by all the phylogenetic analyses of the combined molecular data. Nembrotha was monophyletic both in the morphological and molecular analyses, always with high support. However, Tambja was recovered as para- or polyphyletic, depending on the analysis performed. Our study also rejects the monophyly of "phanerobranch" dorids based on molecular data.     

Evolutionary and taxonomic relationships among Far-Eastern salmonid fishes inferred from mitochondrial DNA divergence

Mitochondrial DNA (mtDNA) restriction analysis was used to examine the evolutionary and taxonomic relationships among 11 taxa of the subfamily Salmoninae. The genera Brachymystax and Hucho were closely related, diverging by sequence divergence estimates of 3.1%. Because the mtDNA sequence divergence between blunt- and sharp-snouted forms of Brachymystax (2.24%) was similar to divergence level of Brachymystax and Hucho , then taking into account the distinct morphological, ecological and allozyme differences between them, it is possible to recognize these forms as two separate species. The subgenus Parahucho formed a very distinct group differing by 6.35–7.08% (sequence divergence estimate) from both Brachymystax and Hucho and must be considered as a valid genus. The UPGMA and neighbour-joined phenograms showed that the five genera studied are divided into two main groupings: (1) Hucho, Brachymystax and Salvelinus ; and (2) Oncorhynchus and Parahucho species. The mtDNA sequence divergence estimates between these groupings were about 8.1%. However, the subsequent bootstrap analysis of mtDNA RFLP data did not support the monophyly of the latter grouping. The concordance of morphological and mtDNA phylogenetic patterns is discussed.     

The cells that secrete the beaks in octopods and squids (Mollusca,Cephalopoda)

A single layer of cell secrets the hard cephalopod beaks. The beccublasts are tall columnar cells that separate the beak from the surrounding buccal muscles, and must serve to attach these muscles to the beak. Within the cell layer there are three types of cells. The first, and most frequently found contain cell-long fibrils. These fibrils may have contractile and tensile properties. Complex trabeculae extend from the beccublasts into the matrix of the beak. The fibrils are attached to these trabeculae and at the other end of the cells they are anchored near to the beccublast-muscle cell interface, closely associated with the muscles that move the beak. The second group of cells contain masses of endoplasmic reticulum the cysternae of which are arranged along the long axis of the cell. These cells also contain dense granules and are probably the major source of beak hard tissue. It is probable that each cell secretes its own column of beak hard tissue. The third group of cells cells contains a mixture of fibrils and secretory tissue. In the beccublast layer there are changes in the proportion of the three types of cells depending upon the region sampled. In the region where growth is most active there are mostly secretory cells, whereas near the biting and wearing tip there are mainly anchoring type cells.     

Identification, distribution and relative abundance of paralarval gonatid squids (Cephalopoda: Oegopsida: Gonatidae) from the Gulf of Alaska, 2001 2003

Paralarvae of the family Gonatidae were sampled in the Gulfof Alaska during spring 2001–2003. Taxonomic characterswere determined to allow identification of the specimens tospecies. The dorsal head chromatophore pattern (DHCP) was themost robust character and allowed identification to speciesfor the first time without requiring the removal and examinationof the radula. Six different DHCPs were found among the sixspecies in the study area. The 1140 specimens collected consistedof the following six species: Berryteuthis anonychus (759),Berryteuthis magister (71), Gonatopsis borealis (155), Gonatuskamtschaticus (1), Gonatus madokai (4) and Gonatus onyx (143).The specimens had a size range of 3.0–20.63 mm dorsalmantle length with the majority of specimens smaller than 10 mm.All species showed an increasing trend in abundance from theshelf (0–200 m) to the slope (200–1000 m)to the basin (>1000 m) except G. onyx in 2001 and 2002.Wide variation in distribution and abundance was found for thefour most abundant species; however, in general, B. anonychuswas most abundant and widely distributed, followed by Gonatopisborealis, Gonatus onyx and B. magister. (Received 28 April 2006; accepted 1 February 2007)     

The statocysts of cranchiid squids (Cephalopoda)

The statocysts of Cranchiidae are unlike those of all other squids. They are very varied: at one extreme is Bathothauma with a very large sac unique in having no internal interruptions. Conversely Egea has more of these anticristae than any other cephalopod. They are arranged in patterns that are different from those of other squids and they are sometimes very long and thin. The anticristae are large and numerous in the cranchiids that are perhaps more rapid swimmers and more active in hunting their prey, for example Mesonychoteuthis, Megalocranchia, Egea or Taonius. However, in the moderately large cranchiids Teuthowenia and Galiteuthis the statocyst cavities are little interruped by anticristae.
The conditions of the statocysts are found to correspond well with the cladistic analyses of relationship within the family performed by N.A. and R.S. Voss, except for those of Teuthowenia and Galiteuthis which stand apart, having relatively uninterrupted cavities. Other genera showing this condition are mostly small animals and form a group of presumably neotenous forms as suggested by N. Voss. It is discussed whether these may be the more primitive genera in the group. Possibly the Cranchiidae arose as neotenous buoyant squids with a peculiar mantle cavity and coelom and uninterrupted statocysts. Later genera exploited these characters and when they became more active swimmers they developed anticristae with an original pattern, allowing monitoring of more rapid turns.     

Possible imitation of jellyfish by the squid paralarvae of the family Gonatidae (Cephalopoda,oegopsida)

Paralarval behaviour of eight species of the family Gonatidae (Teuthoidea, Cephalopoda) was examined in small 3–1 aquaria on board ship during planktonic surveys, which were carried out above and off the continental slope of the western part of the Bering Sea. Undisturbed paralarvae moved in aquaria with an average frequency of 15–20 mantle contractions per minute. In response to a sudden disturbance (flash of light, impact to the aquarium wall) squids exhibited a defensive body posture, relaxing the mantle and pulling the head with tentacles and arms into the mantle cavity, thereby becoming similar in appearance, size and colour to small jellyfishesAglantha digitalis (Hydromedusae).     

Actin gene family evolution and the phylogeny of coleoid cephalopods (Mollusca: Cephalopoda)

Phylogenetic analysis conducted on a 784-bp fragment of 82 actin gene sequences of 44 coleoid cephalopod taxa, along with results obtained from genomic Southern blot analysis, confirmed the presence of at least three distinct actin loci in coleoids. Actin isoforms were characteri zed through phylogenetic analysis of representative cephalopod sequences from each of the three isoforms, along with translated actin cDNA sequences from a diverse array of metazoan taxa downloaded from GenBank. One of the three isoforms found in cephalopods was closely related to actin sequences expressed in the muscular tissues of other molluscs. A second isoform was most similar to cytoplasmic-specific actin amino acid sequences. The muscle type actins of molluscs were found to be distinct from those of arthropods, suggesting at least two independent derivations of muscle actins in the protostome lineage, although statistical support for this conclusion was lacking. Parsimony and maximum-likelihood analyses of two of the isoforms from which >30 orthologous coleoid sequences had been obtained (one of the cytoplasmic actins and the muscle actin) supported the monophyly of several higher-level coleoid taxa. These included the superorders Octopodiformes and Decapodiformes, the order Octopoda, the octopod suborder Incirrata, and the teuthoid suborder Myopsida. The monophyly of several taxonomic groups within the Decapodiformes was not supported, including the orders Teuthoidea and Sepioidea and the teuthoid suborder Oegopsida. Parametric bootstrap analysis conducted on the simulated cytoplasmic actin data set provided statistical support to reject the monophyly of the Sepioidea. Although parametric bootstrap analysis of the muscle actin isoform did not reject sepioid monophyly at the 5% level, the results (rejection at P: = 0.068) were certainly suggestive of sepioid nonmonophyly.     

Phylogenetic relationships within the Laridae (Charadriiformes: Aves) inferred from mitochondrial markers

Gulls (Aves: Laridae) constitute a recent and cosmopolite family of well-studied seabirds for which a robust phylogeny is needed to perform comparative and biogeographical analyses. The present study, the first molecular phylogeny of all Larids species (N=53), is based on a combined segment of mtDNA (partial cytochrome b and control region). We discuss our phylogenetic tree in the light of previous suggestions based on morphological, behavioral, and plumage characters. Although the phylogeny is not fully resolved, it highlights several robust species groups and confirms or identifies for the first time some sister relationships that had never been suggested before. The Dolphin Gull (Leucophaeus scoresbii) for instance, is identified as the sister species of the Grey Gull (Larus modestus) and the Ross's Gull (Rhodostethia rosea) forms a monophyletic group with the Little Gull (Larus minutus). Our results clearly demonstrate that the genus Larus as currently defined is not monophyletic, since current taxonomy of gulls is based on the use of convergent phenotypic characters. We propose a new systematic arrangement that better reflects their evolutionary history.     

Phylogenetic relationships among Pneumocystis from Asian macaques inferred from mitochondrial rRNA sequences

The presence of Pneumocystis organisms was detected by nested-PCR at mitochondrial large subunit (mtLSU) rRNA gene in 23 respiratory samples from Asian macaques representing two species: Macaca mulatta and M. fascicularis. A very high level of sequence heterogeneity was detected with 18 original sequence types. Two genetic groups of Pneumocystis could be distinguished from the samples. Within each group, the extent of genetic divergence was low (2.5+/-1.4% in group 1 and 2.3+/-1.7% in group 2). Genetic divergences were systematically higher when macaque-derived sequence types were compared with Pneumocystis mtLSU sequences from other primate species (from 5.3+/-2.7% to 19.3+/-3.0%). The two macaque-derived groups may be considered as distinct Pneumocystis species. Surprisingly, these Pneumocystis species were recovered from both M. mulatta and M. fascicularis suggesting that host-species restriction may not systematically occur in the genus Pneumocystis. Alternatively, these observations question about the species concept in macaques.     

A new genus and three new species of decapodiform cephalopods (Mollusca: Cephalopoda)

We describe here two new species of oegopsid squids. The first is an Asperoteuthis (Chiroteuthidae), and it is based on 18 specimens. This new species has sucker dentition and a funnel–mantle locking apparatus that are unique within the genus. The second new species is a Promachoteuthis (Promachoteuthidae), and is based on a unique specimen. This new species has tentacle ornamentation which is unique within the genus. We also describe a new genus and a new species of sepioid squid in the subfamily Heteroteuthinae (Sepiolidae) and it is based on four specimens. This new genus and species exhibits unique modifications of the arms in males.     

A new dicyemid from Octopus hubbsorum (Mollusca:Cephalopoda:Octopoda)

A new species of dicyemid mesozoan is described from Octopus hubbsorum Berry, 1953, collected in the south of Bahia de La Paz, Baja California Sur, México. Dicyema guaycurense n. sp. is a medium-size species that reaches about 1,600 μm in length. It occurs in folds of the renal appendages. The vermiform stages are characterized as having 22 peripheral cells, a conical calotte, and an axial cell that extends to the base of the propolar cells. Infusoriform embryos consist of 39 cells; 1 nucleus is present in each urn cell and the refringent bodies are solid. This is the first of a dicyemid species from a host collected in the Gulf of California.     

Phylogenetic relationships among Syndermata inferred from nuclear and mitochondrial gene sequences

Phylogenetic relationships among Syndermata have been extensively debated, mainly because the sister-group of the Acanthocephala has not yet been clearly identified from analyses of morphological and molecular data. Here we conduct phylogenetic analyses on samples from the 4 classes of Acanthocephala (Archiacanthocephala, Eoacanthocephala, Polyacanthocephala, and Palaeacanthocephala) and the 3 Rotifera classes (Bdelloidea, Monogononta, and Seisonidea). We do so using small-subunit (SSU) and large-subunit (LSU) ribosomal DNA and cytochrome c oxidase subunit 1 (cox 1) sequences. These nuclear and mitochondrial DNA sequences were obtained for 27 acanthocephalans, 9 rotifers, and representatives of 6 phyla that were used as outgroups. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian analyses were conducted on the nuclear rDNA(SSU+LSU) and the combined sequence dataset(SSU+LSU+cox 1 genes). Phylogenetic analyses of the combined rDNA and cox 1 data uniformly provided strong support for a clade including rotifers plus acanthocephalans (Syndermata). Strong support was also found for monophyly of Acanthocephala in analyses of the combined dataset or rDNA sequences alone. Within the Acanthocephala the monophyletic grouping of the representatives of each class was strongly supported. Our results depicted Archiacanthocephala as the sister-group to the remaining acanthocephalans. Analyses of the combined dataset recovered a sister-group relationship between Acanthocephala and Bdelloidea by parsimony, likelihood, and Bayesian methods. Support for this clade was generally strong. Alternative topologies that depicted a different rotifer sister-group of Acanthocephala (or monophyly of Rotifera) were significantly worse. In this paraphyletic assemblage of rotifers, the relative positions of Seisonidea and Monogononta to the clade Bdelloidea+Acanthocephala were inconsistent among trees based on different inference methods. These results indicate that Bdelloidea is the free-living sister-group to acanthocephalans, which should prove key for comparative investigations of the morphological, molecular, and ecological changes accompanying the evolution of parasitism.