Molecular systematics of the Malagasy babblers (Passeriformes: timaliidae) and warblers (Passeriformes: sylviidae), based on cytochrome b and 16S rRNA sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy "babblers" are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy "babblers" are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Phylogenetic analyses of some genera in Oedipodidae （Orthoptera： Acridoidea） based on 16S mitochondrial partial gene sequences

Basedonthe 16S mitochondrial partial gene sequences of 29 genera, containing 26 from Oedipodidae and one each from Tanaoceridae, Pyrgomorphidae and Tetrigidae （as outgroups）, the homologus sequences were compared and phylogenetic analyses were performed. A phylogenetic tree was inferred by neighbor-joining （N J）. The results of sequences compared show that： （i） in a total of 574 bp of Oedipodidae, the number of substituted nucleotides was 265 bp and the average percentages ofT, C, A and G were 38.3%, 11.4%, 31.8% and 18.5%, respectively, and the content of A＋T （70.1%） was distinctly richer than that of C＋G （29.9%）; and （ii） the average nucleotide divergence of 16S rDNA sequences among genera of Oedipodidae were 9.0%, among families of Acridoidea were 17.0%, and between superfamilies （Tetrigoidea and Acridoidea） were 23.9%, respectively. The phylogenetic tree indicated： （i） the Oedipodidae was a monophyletic group, which suggested that the taxonomic status of this family was confirmed; （ii） the genus Heteropternis separated from the other Oedipodids first and had another unique sound-producing structure in morphology, which is the type-genus of subfamily Heteropterninae; and （iii） the relative intergeneric relationship within the same continent was closer than that of different continents, and between the Eurasian genera and the African genera, was closer than that between Eurasians and Americans.     

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 leaf monkeys (Presbytis; Colobinae) based on cytochrome b and 12S rRNA genes

Little is known about the classification and phylogenetic relationships of the leaf monkeys (Presbytis). We analyzed mitochondrial DNA sequences of cytochrome b (Cyt b) and 12S rRNA to determine the phylogenetic relationships of the genus Presbytis. Gene fragments of 388 and 371 bp of Cyt b and 12S rRNA, respectively, were sequenced from samples of Presbytis melalophos (subspecies femoralis, siamensis, robinsoni, and chrysomelas), P. rubicunda and P. hosei. The genus Trachypithecus (Cercopithecidae) was used as an outgroup. The Cyt b NJ and MP phylogeny trees showed P. m. chrysomelas to be the most primitive, followed by P. hosei, whereas 12S rRNA tree topology only indicated that these two species have close relationships with the other members of the genus. In our analysis, chrysomelas, previously classified as a subspecies of P. melalophos, was not included in either the P. m. femoralis clade or the P. m. siamensis clade. Whether or not there should be a separation at the species level remains to be clarified. The tree topologies also showed that P. m. siamensis is paraphyletic with P. m. robinsoni, and P. m. femoralis with P. rubicunda, in two different clades. Cyt b and 12S rRNA are good gene candidates for the study of phylogenetic relationships at the species level. However, the systematic relationships of some subspecies in this genus remain unclear.     

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 five extant Rhinoceros species (Rhinocerotidae, Perissodactyla) based on mitochondrial cytochrome b and 12S rRNA genes

A major question in rhinocerotid phylogenetics concerns the position of the Sumatran rhinoceros (Dicerorhinus sumatrensis) with regard to the other extant Asian (Rhinoceros unicornis and R. sondaicus) and African (Diceros bicornis and Ceratotherium simum) species. We have examined this particular question through the phylogenetic analysis of the complete sequences of the mitochondrial 12S rRNA and cytochrome b genes. Three additional perissodactyls (one tapir and two equids) plus several outgroup cetartiodactyls were included in the analysis. The analysis identified a basal rhinocerotid divergence between the African and the Asian species, with the Sumatran rhinoceros forming the sister group of the genus Rhinoceros. We estimate the Asian and African lineages to have diverged at about 26 million years before present.     

Phylogenetic signal and the utility of 12S and 16S mtDNA in frog phylogeny

Genes selected for a phylogenetic study need to contain conserved information that reflects the phylogenetic history at the specific taxonomic level of interest. Mitochondrial ribosomal genes have been used for a wide range of phylogenetic questions in general and in anuran systematics in particular. We checked the plausibility of phylogenetic reconstructions in anurans that were built from commonly used 12S and 16S rRNA gene sequences. For up to 27 species arranged in taxon sets of graded inclusiveness, we inferred phylogenetic hypotheses based on different a priori decisions, i.e. choice of alignment method and alignment parameters, including/excluding variable sites, choice of reconstruction algorithm and models of evolution. Alignment methods and parameters, as well as taxon sampling all had notable effects on the results leading to a large number of conflicting topologies. Very few nodes were supported in all of the analyses. Data sets in which fast evolving and ambiguously aligned sites had been excluded performed worse than the complete data sets. There was moderate support for the monophyly of the Discoglossidae, Pelobatoidea, Pelobatidae and Pipidae. The clade Neobatrachia was robustly supported and the intrageneric relationships within Bombina and Discoglossus were well resolved indicating the usefulness of the genes for relatively recent phylogenetic events. Although 12S and 16S rRNA genes seem to carry some phylogenetic signal of deep (Mesozoic) splitting events the signal was not strong enough to resolve consistently the inter‐relationships of major clades within the Anura under varied methods and parameter settings.     

Phylogenetic analyses of Cloeodes Traver and related genera (Ephemeroptera: Baetidae)

Cloeodes Traver is atypical among Baetidae (Ephemeroptera) because it seems to possess a unique Pantropical distribution. Thirty‐nine species have been described to date, 26 from the Neotropics, four from the Southern Nearctic, seven from the Afrotropics and two from the Oriental region. Several genera have been considered related to Cloeodes during the last decades, of which the following remain valid: Crassabwa Lugo‐Ortiz & McCafferty, Dabulamanzia Lugo‐Ortiz & McCafferty (both Afrotropical), Bungona Harker (Australasian) and Chopralla Waltz & McCafferty (Oriental). Despite their supposed relationship, a phylogenetic analysis between all of these genera has never been performed. In the present paper, based on an extensive analysis of all genera that have been considered related to Cloeodes, a phylogenetic analysis using morphological characters (continuous and discrete) was performed in order to address the monophyly of the genus Cloeodes within the Cloeodes complex of genera. According to our results, Cloeodes and the complex are paraphyletic. Based on this, Cloeodes is restricted to the New World, Potamocloeon is revalidated to include most representatives of Afrotropical Cloeodes and is divided into two subgenera: Potamocloeon (Africa) and the new Aquaediva (Madagascar). In addition, the concept of Bungona is expanded to include Australasian and Oriental taxa – namely the subgenera Chopralla and the revalidated Centroptella – and finally the new genus Crassolus is established to include C. inzingae comb.n. from Africa. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:C416090E-C43D-481A-9A3D-F3B1EEE41176 .     

基于Cytb和COⅠ基因部分序列的15种麻蝇之间的系统发育关系(双翅目：麻蝇科)

本研究通过测序Cytb基因和COⅠ基因的部分序列来推定15种麻蝇之间的系统发育关系。在世界麻蝇名录中,本研究的15种麻蝇能够代表麻蝇属Sarcophaga的6个亚属。连接序列（972 bp）被用于系统发育分析;分析方法包括了了最大简约法、最大似然法以及贝叶斯法。我们的结果提示了亚麻蝇亚属Parasarcophaga、别麻蝇亚属Boettcherisca以及红麻蝇亚属Liopygia的单系性,同时也表明蛇麻蝇亚属Liosarcophaga和德麻蝇亚属Pandelleisca并不是单源的。不过,目前的研究并不能分辨野德麻蝇S. (Pandelleisca) similis和峨眉叉麻蝇S. (Robineauella) coei的系统发育位置。此外,最大简约分析和似然功能分析在scopariiformis-iwuensis进化枝和polystylata-hui进化枝的关系上产生了不一致的系统发育推断。因此,后续研究不仅需要其他的分子标记,也需要更多的分类取样。     

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 structure of the genera Flexibacter,Flexithrix, and Microscilla deduced from 16S rRNA sequence analysis

The 16S rDNA sequences of 40 strains of 17 species in the genus Flexibacter, 5 strains of 4 species in the genus Microscilla, and 1 strain of Flexithrix dorotheae, including all type strains of approved and validated species in these genera, were determined to reveal their phylogenetic relationships. The 16S rRNA sequence analysis demonstrated the extreme heterogeneity of the genera Flexibacter and Microscilla. The strains examined diverged into 24 distinct lines of descent (1 group included both flexibacteria and flexithrix, and 1 group included both flexibacteria and microscilla) that were remote from each other at the genus level or higher. Flexibacter strains were scattered across the cytophaga-flavobacteria-bacteroides phylum and divided into 20 phylogenetic groups, and the genus Microscilla was separated into 5 groups. Flexibacter flexilis, the type species of the genus Flexibacter, and Microscilla marina, the type species of the genus Microscilla, were isolated from other organisms in their respective genera. This means that each genus should be restricted to only the type species. Flexithrix dorotheae, the type species of the genus Flexithrix, clustered with Flexibacter aggregans. The heterogeneity was found not only within genera but also within species. Flexibacter aggregans, Flexibacter aurantiacus, Flexibacter flexilis, Flexibacter roseolus, Flexibacter tractuosus, and "Microscilla sericea" each contained phylogenetically distant strains. The taxonomic concept of the genera Flexibacter, Flexithrix, and Microscilla should be reorganized in accordance with the natural relationships revealed in this study.     

A broad-host-range, generalized transducing phage (SN-T) acquires 16S rRNA genes from different genera of bacteria

Genomic analysis has revealed heterogeneity among bacterial 16S rRNA gene sequences within a single species; yet the cause(s) remains uncertain. Generalized transducing bacteriophages have recently gained recognition for their abundance as well as their ability to affect lateral gene transfer and to harbor bacterial 16S rRNA gene sequences. Here, we demonstrate the ability of broad-host-range, generalized transducing phages to acquire 16S rRNA genes and gene sequences. Using PCR and primers specific to conserved regions of the 16S rRNA gene, we have found that generalized transducing phages (D3112, UT1, and SN-T), but not specialized transducing phages (D3), acquired entire bacterial 16S rRNA genes. Furthermore, we show that the broad-host-range, generalized transducing phage SN-T is capable of acquiring the 16S rRNA gene from two different genera: Sphaerotilus natans, the host from which SN-T was originally isolated, and Pseudomonas aeruginosa. In sequential infections, SN-T harbored only 16S rRNA gene sequences of the final host as determined by restriction fragment length polymorphism analysis. The frequency of 16S rRNA gene sequences in SN-T populations was determined to be 1 x 10(-9) transductants/PFU. Our findings further implicate transduction in the horizontal transfer of 16S rRNA genes between different species or genera of bacteria.     

Phylogenetic analysis of the genera Pseudonocardia and Actinobispora based on 16S ribosomal DNA sequences

The 16S rDNA sequences of 11 strains, nine type strains of validated Pseudonocardia species and Actinobispora yunnanensis, and two strains of unnamed Pseudonocardia species, were determined and compared with those of representatives of the family Pseudonocardiaceae. The phylogenetic analysis indicated that all of the validated species of the genera Pseudonocardia and Actinobispora consistently formed a monophyletic unit and separated well from the other genera of the family Pseudonocardiaceae. One unnamed Pseudonocardia strain was related to members of the genus Pseudonocardia, whereas the other unnamed Pseudonocardia strain formed a distinct clade within the radiation of the genus Amycolatopsis.     

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.     

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

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

Phylogenetic relationships of the fox-like canids: mitochondrial DNA restriction fragment, site and cytochrome b sequence analyses

The fox-like canids include taxa from the genera Alopex, Otocyon, Fennecus, Urocyon and Vulpes . Previous morphological analysis indicated that species from the latter three genera are very similar and should be included in the same genus whereas Alopex and Otocyon are sufficiently different to be included in separate genera. Using phylogenetic methods, we analyse mitochondrial DNA (mtDNA) restriction fragment and restriction site data, and 402 bp of cytochrome b sequence variation in fox-like canids. Our results suggest that Alopex lagopus , the arctic fox, is actually a very close relative of the swift fox, a species in the genus Vulpes . Similarly, the fennec, Fennecus zerda is related to the co-existing desert species, the Blanford's fox, Vulpes cana . The grey fox, Urocyon cinereoargenteus , and the bat-eared fox, Otocyon megalotis , are not closely related to each other or to any of the sampled fox taxa. Our results indicate that desert adaptations have evolved independently at least twice in the Canidae, and that Pleistocene glaciations and character divergence may be important causes of morphological change in canids.     

Phylogenetic relationships of Eurasian and American cyprinids using cytochrome b sequences

Neighbour-joining and parsimony analyses identified five lineages of cyprinids: (1) European leuciscins (including Notemigonus )+North American phoxinins (including Phoxinus phoxinus ); (2) European gobionins+Pseudorasbora ; (3) primarily Asian groups [cultrins+acheilognathins+ gobionins (excluding Abbotina )+xenocyprinins]; (4) Abbottina+Sinocyclocheilus+Acrossocheilus ; (5) cyprinins [excluding Sinocyclocheilus and Acrossocheilus ]+barbins+labeonins. Relationships among these lineages and the enigmatic taxa Rhodeus were not well-resolved. Tests of monophyly of subfamilies and previously proposed relationships were examined by constraining cytochrome b sequences data to fit previous hypotheses. The analysis of constrained trees indicated that sequence data were not consistent with most previously proposed relationships. Inconsistency was largely attributable to Asian taxa, such as Xenocypris and Xenocyprioides . Improved understanding of historical and taxonomic relationships in Cyprinidae will require further morphological and molecular studies on Asian cyprinids and taxa representative of the diversity found in Africa.     

Phylogenetic relationships in the genus Agathemera (Insecta: Phasmatodea) inferred from the genes 16S,COI and H3

We present a phylogenetic analysis that includes all known species of Agathemera, using as outgroup four species of the genera Heteronemia, Spinonemia, Monticomorpha, and Anisomorpha. Phylogenetic inference was based on three genes, 16S, COI (mitochondrial markers) and H3 (nuclear marker), based on the maximum‐parsimony, maximum‐likelihood and Bayesian inference methods. Our results show that the genus Agathemera is monophyletic; six of its eight species showed phylogenetic support, while the group A. claraziana + A. millepunctata was not resolved. The resulting topology shows two major clades, the first with A. maculafulgens, A. luteola, A. crassa, A. millepunctata, and A. claraziana, and the second including A. grylloidea, A. mesoauriculae, and A. elegans. Species of the first clade have large mesonotal processes and are found mainly east of the Andes, except for A. crassa. Members of the second clade have small or absent mesonotal processes and are distributed mainly to the west of the Andes. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 63–72.     

Phylogenetic relationships among genera of Aphidiinae (Hymenoptera: Braconidae) based on DNA sequence of the mitochondrial 16S rRNA gene

Phylogenetic relationships among forty‐nine taxa representing twenty‐four genera of Aphidiinae (Hymenoptera: Braconidae) were investigated using DNA sequence of a portion of the mitochondrial 16S rRNA gene and parsimony analysis. Seven species in six other subfamilies of Braconidae were used as outgroup. The results suggested that members of Aphidiinae are monophyletic. The basal lineage of Aphidiinae was Aclitus in weighted and unweighted parsimony analyses and Praini was basal relative to Ephedrini. With the exception of Pauesia and Aphidius, all genera were monophyletic. The results support generic status for Euaphidius, but not for Lysaphidus. Diaeretus leucopterus was internal to a clade composed of three Pauesia species, suggesting that the latter genus may be paraphyletic. A combined analysis that included DNA sequence of 16S rRNA, NADH1 dehydrogenase and 28S rRNA resulted in more robust cladograms with topologies similar to those inferred from the 16S rRNA gene sequence alone. The results are compared to previously proposed phylogenies of Aphidiinae based on morphological and molecular characters.