Phylogenetic relationships,subdivision, and biogeography of the cyprinid tribe Labeonini (sensu ) (Teleostei: Cypriniformes), with comments on the implications of lips and associated structures in the labeonin classification

The Labeonini (sensu Rainboth, 1991) is a tribe of the subfamily Cyprininae, the largest subfamily of Cypriniformes. With around 400 species in 34 genera, this tribe is widely distributed in the freshwaters of tropical Africa and Asia. Most species are adapted to fast-flowing streams and rivers, and exhibit unique morphological modifications associated with their lips and other structures around the mouth. The monophyly of this tribe has been tested and generally accepted in previous morphological and molecular studies. The major objectives of this study were to reconstruct the phylogenetic relationships within the tribe Labeonini, test its monophyly and explore the taxonomic subdivisions, intrarelationships and biogeography of the group. The value of the morphological characters associated with the lips and other associated structures in the taxonomic classification of labeonins was also discussed. Nucleotide sequences (3867 bp) of four unlinked nuclear loci were obtained from 51 species in 18 Labeonini genera from throughout the range of the tribe. Maximum parsimony, partitioned maximum likelihood and partitioned Bayesian analyses were used for phylogenetic inference from combined and separate gene data sets. Based on our results, the monophyly of Labeonini was well supported. Two major clades could be recovered within the tribe. Three subclades could further be recognized from the first clade. These clades/subclades are not consistent with groupings of any of previous workers using either morphological or molecular characters for phylogenetic inference. Only five currently recognized genera in this analysis are monophyletic. The similarity between some lips and associated structures (e.g. suctorial discs) of labeonins may due to convergence or parallelism instead of common ancestry. Labeonins of Southeast Asia, India and China are closely related to each other; the multiple clades of African taxa do not form a single monophyletic group, indicating multiple, independent dispersal events of labeonins into Africa from Asia.     

Phylogenetic relationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA gene sequences

The small subunit rDNAs of five species belonging to the Euplotidae and eight species of the Oxytrichidae were sequenced to obtain a more detailed picture of the phylogenetic relationships within the Spirotrichea (Ciliophora). Various tree reconstruction algorhythms yielded nearly identical topologies. All Euplotidae were separated from the other Spirotrichea by a deep split. Further, a large genetic distance between the marine genus Moneuplotes and the freshwater species of Euplotoides was found. Differences between the methods used occurred only within the Oxytrichidae. Whereas the monophyly of the Stylonychinae was supported in all trees, the monophyly of the Oxytrichinae was not. However, the molecular data support the morphological and ontogenetic evidence that the pattern of 18 frontal-ventral-transversal cirri evolved in the stemline of the Oxytrichidae and was modified several times independently. Our results are also in agreement with taxonomic revisions: the separation of both Sterkiella nova from Oxytricha and Tetmemena pustulata from Stylonychia.     

Molecular tests of phylogenetic taxonomies: a general procedure and example using four subfamilies of the lizard family Iguanidae

A general procedure is described for examining when results of molecular phylogenetic analyses warrant formal revision of taxonomies constructed using morphological characters. We illustrate this procedure with tests of monophyly for four subfamilies in the lizard family Iguanidae using 1561 aligned base positions (838 phylogenetically informative) of mitochondrial DNA sequences, representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Ten new sequences ranging in length from 1732 to 1751 bases are compared with 12 previously reported sequences and 67 morphological characters (54 phylogenetically informative) from the literature. New morphological character states are provided for Sator. Phylogenies derived from the molecular and combined data are in agreement but both conflict with phylogenetic inferences from the morphological data alone. Strong support is found for the monophyly of the subfamilies Crotaphytinae and Phrynosomatinae. Monophyly of the Iguaninae is weakly supported in each analysis. All analyses suggest that the Tropidurinae is not monophyletic but the hypothesis of monophyly cannot be rejected. A phylogenetic taxonomy is proposed in which the Tropidurinae* is maintained as a metataxon (denoted with an asterisk), for which monophyly has not been demonstrated. Within the Phrynosomatinae, the close relationship of Sator and Sceloporus is questioned and an alternative hypothesis in which Sator is the sister taxon to a clade comprising Petrosaurus, Sceloporus, and Urosaurus is presented. Statistical tests of monophyly provide a powerful way to evaluate support for taxonomic groupings. Use of the metataxon prevents premature taxonomic rearrangements where support is lacking.     

Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents.

Nucleotide sequences of exon 28 of the von Willebrand Factor (vWF) were analyzed for a representative sampling of rodent families and eutherian orders, with one marsupial sequence as outgroup. The aim of this study was to test if inclusion of an increased taxonomic diversity in molecular analyses would shed light on three uncertainties concerning rodent phylogeny: (1) relationships between rodent families, (2) Rodentia monophyly, and (3) the sister group relationship of rodents and lagomorphs. The results did not give evidence of any particular rodent pattern of molecular evolution relative to a general eutherian pattern. Base compositions and rates of evolution of vWF sequences of rodents were in the range of placental variation. The 10 rodent families studied here cluster in five clades: Hystricognathi, Sciuridae and Aplodontidae (Sciuroidea), Muridae, Dipodidae, and Gliridae. Among hystricognaths, the following conclusions are drawn: a single colonization event in South America by Caviomorpha, a paraphyly of Old World and New World porcupines, and an African origin for Old World porcupines. Despite a broader taxonomic sampling diversity, we did not obtain a robust answer to the question of Rodentia monophyly, but in the absence of any other alternative, we cannot reject the hypothesis of a single origin of rodents. Moreover, the phylogenetic position of Lagomorpha remains totally unsettled.     

Molecular systematics of Scaphirhynchinae: an assessment of North American and Central Asian Freshwater Sturgeon Species

The sturgeon subfamily Scaphirhynchinae contains two genera of obligate freshwater sturgeon: Scaphirhynchus and Pseudoscaphirhynchus, from North America and Central Asia, respectively. Both genera contain morphologically variable species. A novel data set containing multiple individuals representing four diagnosable morphological variants for two species of Pseudoscaphirhynchus, P. hermanni and P. kaufmanni, was generated. These data were used to test taxonomic hypotheses of monophyly for the subfamily Scaphirhynchinae, monophyly of both Scaphirhynchus and Pseudoscaphirhynchus, monophyly of P. hermanni and P. kaufmanni, and monophyly of the recognized morphological variants. Monophyly of the subfamily Scaphirhynchinae is consistently rejected by all phylogenetic reconstruction methodologies with the molecular character set while monophyly of both river sturgeon genera is robustly supported. The molecular data set also rejects hypotheses of monophyly for sampled species of Pseudoscaphirhynchus as well as monophyly for the recognized intraspecific morphological variants. Interestingly both Scaphirhynchus and Pseudoscaphirhynchus demonstrate the same general pattern in reconstructed topologies; a lack of phylogenetic structure in the clade with respect to recognized diversity. Despite rejection of monophyly for the subfamily Scaphirhynchinae with molecular data, reconstructed hypotheses from morphological character sets consistently support monophyly for this subfamily. Disparities among the data sets, as well as reasons for rejection of monophyly for Scaphirhynchinae and species of Scaphirhynchus and Pseudoscaphirhynchus with molecular characters are examined and a decreased rate of molecular evolution is found to be most consistent with the data.     

Phylogenetic Relationships among Deep-Sea and Chemosynthetic Sea Anemones: Actinoscyphiidae and Actinostolidae (Actiniaria: Mesomyaria)

Sea anemones (Cnidaria, Actiniaria) are present in all marine ecosystems, including chemosynthetic environments. The high level of endemicity of sea anemones in chemosynthetic environments and the taxonomic confusion in many of the groups to which these animals belong makes their systematic relationships obscure. We use five molecular markers to explore the phylogenetic relationships of the superfamily Mesomyaria, which includes most of the species that live in chemosynthetic, deep-sea, and polar sea habitats and to test the monophyly of the recently defined clades Actinostolina and Chemosynthina. We found that sea anemones of chemosynthetic environments derive from at least two different lineages: one lineage including acontiate deep-sea taxa and the other primarily encompassing shallow-water taxa.     

Rapid radiation and cryptic speciation in squat lobsters of the genus Munida (Crustacea, Decapoda) and related genera in the South West Pacific: molecular and morphological evidence

Squat lobsters (genus Munida and related genera) are among the most diverse taxa of western Pacific crustaceans, though several features of their biology and phylogenetic relationships are unknown. This paper reports an extensive phylogenetic analysis based on mitochondrial DNA sequences (cytochrome c oxidase subunit I and 16S rRNA) and the morphology of 72 species of 12 genera of western Pacific squat lobsters. Our phylogenetic reconstruction using molecular data supports the recent taxonomic splitting of the genus Munida into several genera. Excluding one species (M. callista), the monophyly of the genus Munida was supported by Bayesian analysis of the molecular data. Three moderately diverse genera (Onconida, Paramunida, and Raymunida) also appeared monophyletic, both according to morphological and molecular data, always with high support. However, other genera (Crosnierita and Agononida) seem to be para- or polyphyletic. Three new cryptic species were identified in the course of this study. It would appear that the evolution of this group was marked by rapid speciation and stasis, or certain constraints, in its morphological evolution.     

Molecular phylogeny of cetaceans prompts revision of morphological transformations

The echolocating toothed whales and the filter-feeding baleen whales are traditionally considered as two monophyletic lineages that originated from the extinct cetacean suborder Archaeoceti. While current interpretation of the morphological and behavioural data sets supports toothed-whale monophyly, molecular phylogenies contradict this long-accepted taxonomic subdivision. The molecular data indicate that one group of toothed whales, the sperm whales, Is more closely related to the morphologically highly divergent baleen whales than to other odontocetes. Furthermore, these molecular analyses tentatively suggest a more recent origin of baleen whales than has been generally accepted. Although a thorough cladistic analysis of all relevant morphological data is still needed, reevaluation of some of the most important of these characters helps to reconcile the morphological and the molecular approaches.     

Molecular phylogeny of the Drosophila tripunctata and closely related species groups (Diptera: Drosophilidae)

We suggest a new phylogenetic hypothesis for the tripunctata radiation based on sequences of mitochondrial genes. Phylogenetic trees were reconstructed by parsimony, maximum likelihood and Bayesian methods. We performed tests for hypotheses of monophyly for taxonomic groups and other specific hypotheses. Results reject the monophyly for the tripunctata group whereas monophyly is not rejected for the tripunctata radiation and other specific groups within the radiation. Although most of the basal nodes were unresolved we were able to identify four clusters within the tripunctata radiation. These results suggest the collection of additional data before a proper taxonomic revision could be proposed.     

以演化时间为新增指标构建真菌分类系统

随着分子系统发育研究的普及,真菌各分类类群逐渐被修订为单系发生类群,通常结合形态学特征为代表的表型特征("单系+表型特征")对不同的分类等级命名是最为普遍的方法.历史上存在的大量多系名称被逐步修订、补充和完善,各个不同等级类群的分类系统变得更加合理、客观和趋于自然,这是分类学进程中巨大的进步.然而系统发育重建所揭示的单...     

Phylogenetic Relationships Between the Orders Artiodactyla and Cetacea: A Combined Assessment of Morphological and Molecular Evidence

A character analysis of selected conservative morphological traits from extant and fossil artiodactyls and cetaceans was combined with a similar analysis of conservative nucleotide positions from the complete mitochondrial cytochrome b sequences of available extant artiodactyls, cetaceans, sirenians, perissodactyls, and other mammals. This combined analysis focuses on the evidence that supports conflicting hypotheses of artiodactyl monophyly, including the affinities of hippopotamids and the monophyly or paraphyly of odontocete cetaceans. Highly conserved morphological traits of the astragalus and deciduous dentition provide strong corroboration of artiodactyl monophyly, including extant and fossil hippopotamids. In contrast, cytochrome b gene sequences are incapable of confirming this monophyly, due to excessive homoplasy of nucleotide and amino acid traits within extant Eutheria. In like manner, highly conserved and uniquely derived morphological features of the skull and auditory regions provide robust corroboration of Odontoceti monophyly, including extant and fossil physeteroids. Several nucleotide similarities do exist between physeteroids and mysticetes; however, most are either silent third-position transversions or occur also in two or more odontocete families. We suggest that increased taxon sampling, combined with functional considerations of amino acids and their secondary structure in protein-coding genes, are essential requirements for the phylogenetic interpretations of molecules at higher taxonomic levels, especially when they conflict with well-supported hypotheses of mammalian phylogeny, corroborated by uniquely derived morphological traits from extant and fossil taxa.     

Molecular phylogeny of the stromateoid fishes (Teleostei: Perciformes) inferred from mitochondrial DNA sequences and compared with morphology-based hypotheses

The phylogenetic relationships among 21 species of stromateoid fishes, representing five families and 13 genera, were reconstructed using 3263bp of mitochondrial DNA sequences, including the posterior half of the 16S rRNA and entire COI and Cytb genes. The resultant molecular phylogenies were compared with previous phylogenetic hypotheses inferred from morphological characters. Molecular phylogenetic trees were constructed using the maximum parsimony, maximum likelihood, and Bayesian methods. All three methods resulted in well-resolved trees with most nodes being supported by moderate to high support values. In contrast to previous morphological analyses, which resulted in non-monophyly of Centrolophidae, all three methods utilized for the present molecular analyses supported the monophyly of Centrolophidae, as well as the reciprocal monophyly of the other stromateoid families, previous morphological hypotheses being rejected by the Templeton and Shimodaira-Hasegawa tests. In addition, the three methods indicated a sister-group relationship between Ariommatidae and Nomeidae. The position of Tetragonuridae was, however, incongruent between the MP method and the ML and Bayesian methods, being placed in the most basal position of Stromateoidei in the former, but occupying a sister relationship to Stromateidae in the latter. Comparison of the molecular phylogenies to previous morphological hypotheses suggested that evolutionary changes in morphological characters have not occurred equally among the stromateoid lineages, the evolution of the centrolophids not having been accompanied by appreciable morphological changes, whereas other stromateoids have undergone considerable morphological changes during their evolutionary history. The molecular phylogenies also shed some light on the evolutionary pattern of the pharyngeal sac, two of the four types of sac corresponding to two main lineages of Stromateoidei. Some taxonomic implications were also discussed.     

Anatomy and systematics of the minute syrnolopsine gastropods from Lake Tanganyika (Caenogastropoda, Cerithioidea, Paludomidae)

The minute syrnolopsine gastropods endemic to Lake Tanganyika have been allied to a number of freshwater, marine and terrestrial groups as a consequence of superficial conchological similarity. Although early anatomical studies confirmed the cerithioid organization of this clade, their close relationship to other lake species was not consistently recognized. In several recent cladistic analyses based on molecular data, the higher taxonomic placement and sister group relationships of syrnolopsines have been unstable. The present analysis confirms that syrnolopsines possess a spermatophore-forming organ – a synapomorphy of the Paludomidae – corroborating their placement in this family. Consistent with the molecular data, syrnolopsine monophyly is supported by two characters that occur exclusively in this group (salivary gland ducts that bypass the nerve ring and a linear albumen gland). Several characters in Martelia tanganyicensis – the most diminutive syrnolopsine – are only evident in the smallest lake species thus far investigated ( Bridouxia , Stormsia ) namely reduction of ctenidial leaflets, sorting area, intestine length and number of statoconia. These features are interpreted as being correlated with reduction in size. Nevertheless, close examination reveals differences in detail that allow more refined hypotheses of homology and are consistent with their independent origin.     

Phylogeny of Antarctic dragonfishes (Bathydraconidae,Notothenioidei, Teleostei) and related families based on their anatomy and two mitochondrial genes

Although Antarctic teleosts of the suborder Notothenioidei are well studied, the status of some families remains unclear because of limited taxonomic sampling and sometimes poor statistical support from molecular phylogenies. It is true for the Bathydraconidae, the sister-family of the famous haemoglobin-less icefishes, the Channichthyidae. The present study is aimed at clarifying bathydraconid phylogeny and the interrelationships of higher notothenioid families, taking nototheniids as the outgroup. For this purpose, about 300 positions in the mitochondrial control region, 750 positions in the cytochrome b, and a matrix of morphological characters were employed for separate and simultaneous phylogenetic analyses. We conclude that (1) molecular data strongly support the split of bathydraconids into three clades, here called the Bathydraconinae (Bathydraco, Prionodraco, Racovitzia), the Gymnodraconinae (Gymnodraco, Psilodraco, Acanthodraco), and the Cygnodraconinae (Cygnodraco, Gerlachea, Parachaenichthys). Interrelationships between these three and the Channichthyidae remain unclear. Molecular data support neither paraphyly nor monophyly of the bathydraconids, while morphology leads to the monophyly of the family based on the synapomorphic loss of the spinous dorsal fin; (2) The Channichthyidae, the Harpagiferidae, and the Artedidraconidae are monophyletic families; (3) the phylogeny of the haemoglobin-less channichthyids is completely resolved and congruent with the conclusions of based on anatomical characters; (4) The present molecular results as well as other molecular studies favour the hypothesis that harpagiferids are the sister-group of artedidraconids, though our morphological matrix puts harpagiferids as the sister-group of all other families on the basis of a single character. With regard to harpagiferid relationships, it is interesting to notice that, when analysed simultaneously, morphological characters are not automatically "swamped" within molecular ones: in the tree based on the simultaneous analysis of all available data, morphological characters impose their topology on molecules.     

Molecular phylogeny of solitary shell-bearing Polycystinea (Radiolaria)

The phylogeny of the Family Spongodiscidae (polycystine Radiolaria), which includes Dictyocoryne profunda Ehrenberg, Dictyocoryne truncatum (Ehrenberg) and Spongaster tetras Ehrenberg, was examined using 18S ribosomal DNA (small-subunit ribosomal DNA) sequence analysis. Three types of tree construction methods, the neighbor joining (NJ), maximum parsimony (MP), and maximum likelihood (ML) methods, were used to infer the phylogenetic relationships of the polycystine and acantharian Radiolaria among eukaryotes. The obtained 18S rDNA molecular phylogenetic tree argues for the monophyly of the two groups. Furthermore, the Polycystinea is divided into at least two distinct lineages consisting of: (1) colonial and skeletonless Polycystinea, including Thalassicollidae, Collospaeridae, and Sphaerozoidae; and (2) shell-bearing solitary Polycystinea, including Spongodiscidae. The Polycystinea thus show a paraphyly among Radiolaria. Moreover, the monophyly of the clade including the acantharians and the spongodiscid polycystines was supported by bootstrap values, which were 94%, 53%, and 59% in the NJ, MP, and ML analyses, respectively. This lineage is characterized by having latticed or spongy skeletons of different chemical composition, namely SiO₂ (Class Polycystinea) or SrSO₄ (Class Acantharea). According to the present taxonomic scheme, the Acantharea and the Polycystinea have not been placed in different classes, but the results of our molecular study show the opposite. We therefore suggest, based on the monophyly of the two clades, that a new taxonomic group of Radiolaria can be established. Our molecular data also suggest that the currently used radiolarian taxonomic system may need serious revisions.     

Reproductive structures and phylogenetic framework of the rosids - progress and prospects

With ca 70.000 species the rosids contain more than a quarter of the total angiosperm species diversity. This taxonomic richness is reflected in a tremendous variety of floral organization and architecture. Rosids have received extensive molecular phylogenetic study. As a result, the monophyly and taxonomic composition of the group are well established. In addition, many subclades at the order level are now apparent. Deeper relationships, however, are still largely equivocal. As in many other parts of the plant tree of life, it will be impossible to reach an adequate understanding of the evolutionary history of the rosids without taking into account information from comparative morphological studies of extant and, in particular, also of fossil taxa. The fossil record of rosids is rich in well-preserved reproductive structures, and together with recent results from comparative studies of extant rosids, provides a wealth of floral structural data. Although much remains to be done at all levels, fresh attempts to synthesize and possibly reconcile results from molecular phylogenetics, comparative floral morphology, and palaeobotany, seem timely.     

Molecular phylogeny of grapsoid crabs (Decapoda, Brachyura) and allies based on two mitochondrial genes and a proposal for refraining from current superfamily classification

Grapsoid and ocypodoid crabs receive a lot of attention in the literature due to their predominance and important role as primary and secondary consumers in intertidal as well as supratidal marine habitats. They are especially species‐rich in the tropics, where they have been found to repeatedly invade terrestrial and freshwater habitats. However, the systematics of the crabs belonging to these two superfamilies is still not settled, despite recent steps clarifying phylogenetic relationships and introducing new taxa. In this study, a molecular phylogeny of grapsoid crabs primarily based on East African representatives is constructed based on DNA sequences of the mitochondrial small and large ribosomal subunits (12S and 16S rRNA), thus complementing previous molecular taxonomic studies that had been carried out with the American and East Asian fauna. In addition, selected representatives of all ocypodoid families and subfamilies were included. The monophyly of Grapsidae, Ocypodidae (sensu stuctu), Sesarmidae and Varunidae is well confirmed, if the genera Cyclograpsus, Helice are considered Varunidae and Euchirograpsus a Plagusiidae, as previously suggested. The monophyly of the family Gecarcinidae cannot be supported with our data. The family Plagusiidae in its present composition is polyphyletic. Special attention was given to the large family Sesarmidae, which has many endemic genera in the Indo‐West Pacific. According to this study, two of the most speciose genera, Chiromantes and Parasesarma, are not monophyletic and need to be redefined. On the higher taxonomic level, it becomes evident that both superfamilies, Grapsoidea and Ocypodoidea, are not monophyletic in their current composition, as exemplified by a proposed sister group relationship of Varunidae and Macrophthalmidae. These results confirm those from previous molecular studies and we therefore propose to refrain from the traditional use of the Grapsoidea and Ocypodoidea as monophyletic superfamilies and treat the constituent families separately.     

安徽麝线粒体DNA细胞色素b基因全长序列分析

自80年代安徽麝[Moschus (moschiferus/berezovskii)anhuiensis]被发现以来,其分类地位一直众说纷纭。在本研究中,我们对安徽麝模式皮张标本进行了线粒体DNA细胞色素b基因全长序列分析。研究结果表明,安徽麝同麝属中其他种的遗传分化已经相当明显.分子系统学的分析表明,安徽麝是一个单系群,它同麝属其他种的DNA序列差异已达到种间分化的程度。因此,线粒体DNA序列的证据支持将安徽麝列为麝属中一有效种（Moschus anhuiensis),而不是前人认为的原麝或林麝的亚种。