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.     

Phylogeny and distribution of crested gibbons (genus Nomascus) based on mitochondrial cytochrome b gene sequence data

Crested gibbons, genus Nomascus, are endemic to the Indochinese bioregion and occur only in Vietnam, Laos, Cambodia, and southern China. However, knowledge about the number of species to be recognized and their exact geographical distributions is still limited. To further elucidate the evolutionary history of crested gibbon species and to settle their distribution ranges, we analyzed the complete mitochondrial cytochrome b gene from 79 crested gibbon individuals from known locations. Based on our findings, crested gibbons should be classified into seven species. Within N. concolor, we recognize two subspecies, N. concolor concolor and N. concolor lu. Phylogenetic reconstructions indicate that the northernmost species, N. hainanus, N. nasutus, and N. concolor branched off first, suggesting that the genus originated in the north and successively migrated to the south. The most recent splits within Nomascus occurred between N. leucogenys and N. siki, and between Nomascus sp. and N. gabriellae. Based on our data, the currently postulated distributions of the latter four species have to be revised. Our study shows that molecular methods are a useful tool to elucidate phylogenetic relationships among crested gibbons and to determine species boundaries. Am. J. Primatol. 72:1047–1054, 2010. © 2010 Wiley‐Liss, Inc.     

Phylogenetic affinities and species limits within the genus Megadontomys (Rodentia: Cricetidae) based on mitochondrial sequence data

The evolutionary history of the genus Megadontomys, a group of mice allopatrically distributed along the cool‐humid forest in the highlands of México, is controversial. In this study, we examined phylogenetic relationships within the genus using sequences data from the complete mitochondrial cytochrome b gene. This information also allowed us to corroborate species limits, geographic boundaries of taxonomic entities and assess genetic variation within each taxon. The results of the phylogenetic analyses based on maximum likelihood, Bayesian inference and maximum parsimony were largely congruent in that M. nelsoni and M. thomasi were more closely related relative to M. cryophilus. These results are concordant with previous studies based on morphology and allozyme variation. However, testing of the alternative hypothesis of a closer evolutionary affinity between M. nelsoni–M. cryophilus did not produce a significantly less likely tree. The lack of unambiguous support towards one of these previously proposed contending hypotheses is congruent with the alternative scenario of an almost simultaneous diversification of the three species. Application of the phylogenetic species concept and the genetic species concept supports the recognition of three distinct taxonomic entities at the specific level. M. nelsoni inhabits the Sierra Madre Oriental (Hidalgo, Veracruz, and Puebla) including the Sierra Mazateca (Oaxaca); M. cryophilus is restricted to the Sierra de Juárez (Oaxaca); and M. thomasi occurs in portions of the Sierra Madre del Sur (Guerrero) and the Sierra Mixteca (Oaxaca). Our data show that M. thomasi is formed by two genetically distinct lineages that potentially may represent distinct Evolutionary Significant Units.     

Relationships among didelphid marsupials based on sequence variation in the mitochondrial cytochrome B gene

Variation in the mitochondrial cytochrome b gene (nucleotide and amino acid sequences) is evaluated for 9 genera and 15 species of American opossums in the family Didelphidae, using the American caenolestid rat opossumLestoros and the New Guinean peroryctid bandicootEchimypera as outgroups. Phylogenetic analyses (parsimony and distance) strongly support the monophyly of the Didelphidae and delineate two major clades; (1)Didelphis andPhilander are strongly aligned sister taxa, withMetachirus weakly but consistently associated with them, and (2)Marmosa plusMicoureus, withMonodelphis falling outside that pair. The generaMarmosops, Caluromys, andGlironia exhibit varied relationships, depending upon the method of analysis and data (DNA or amino acid sequences) used, but generally are placed individually or in combinations near or at the base of the didelphid radiation. Some aspects of these relationships are consistent with current taxonomic views, but others are in marked contrast. Specifically, a clade comprised of the mouse opossumsMarmosa, Micoureus, andMarmosops is strongly rejected by log-likelihood analysis, contrary to expectations from some current classifications. Also, the woolly opossumsCaluromys andGlironia also do not form a sister-taxon relationship, as suggested by their placement in a subfamily separate from the remaining didelphids examined. However, such a relationship cannot be rejected from log-likelihood analyses. The relationships suggested fromcyt-b sequences are strongly concordant with those based on DNA-DNA hybridization analyses. In addition to systematic and phylogenetic properties, molecular evolution of the didelphid cytochrome b gene sequence is characterized according to nucleotide bias and rate differentials at each codon position and across the entire sequence.To whom correspondence should be addressed.     

Molecular phylogenetic relationships of China Seas groupers based on cytochrome b gene fragment sequences

The classification and evolutionary relationships are important issues in the study of the groupers. Cytochrome b gene fragment of twenty-eight grouper species within six genera of subfamily Epinephelinae was amplified using PCR techniques and the sequences were analyzed to derive the phylogenetic relationships of the groupers from the China Seas. Genetic information indexes, including Kimura-2 parameter genetic distance and Ts/Tv ratios, were generated by using a variety of biology softwares. With Niphon spinosus, Pagrus major and Pagrus auriga as the designated outgroups, phylogenetic trees, which invoke additional homologous sequences of other Epinephelus fishes from GenBank, were constructed based on the neighbor-joining (NJ), maximum-parsimony (MP), maximum-likelihood (ML) and minimum-evolution (ME) methods. Several conclusions were drawn from the DNA sequences analysis: (1) genus Plectropomus, which was early diverged, is the most primitive group in the subfamily Epinephelinae; (2) genus Variola is more closely related to genus Cephalopolis than the other four genera; (3) genus Cephalopolis is a monophyletic group and more primitive than genus Epinephelus; (4) Promicrops lanceolatus and Cromileptes altivelis should be included in genus Epinephelus; (5) there exist two sister groups in genus Epinephelus.     

从细胞色素b基因序列探讨笛鲷属的分子系统发生关系

测定了9种中国南海的笛鲷属鱼类的细胞色素b基因的部分序列,结合来自GenBank中1种分布于菲律宾和9种分布于美国大西洋的笛鲷属鱼类的相应同源序列,用邻接法和最大简约法构建分子系统树。结果显示:红鳍笛鲷(Lutjanuserythropterus)与红笛鲷(L.sanguineus)之间的同源序列碱基差异百分率只有0.32%,支持二者是同种异名的观点;中国南海的笛鲷属鱼类间的平均碱基差异要高于美国大西洋笛鲷属鱼类。在MP和NJ树中,美国大西洋笛鲷表现为亲缘关系较近,来源于中国南海的笛鲷鱼类相对集中在树的基部,分歧较大。这与所研究的笛鲷地理分布和地理隔离基本相一致,同时也说明中国南海笛鲷分化较早并且分歧较大。     

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。     

Molecular phylogeny of Pamphagidae (Acridoidea,Orthoptera) from China based on mitochondrial cytochrome oxidase II sequences

Abstract Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II (COII) mtDNA sequences (684 bp). Twenty‐seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%–11.1% between genera within subfamilies, and 8.8%–12.3% between subfamilies. Amino acid sequence diverged 0–6.1% between genera within subfamilies, and 0.4%–7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.     

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp – Cyprinus carpio haematopterus , Yuanjiang River wild common carp – Cyprinus carpio rubrofuscus and Volga River wild common carp – Cyprinus carpio carpio ) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus , C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus , most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus ) to 1.47%(between C. c. carpio and C. c. rubrofuscus ). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus . Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus .     

A mtDNA phylogeny of sea eagles (genus Haliaeetus) based on nucleotide sequences of the cytochrome b-gene

The mitochondrial cytochrome b gene of seven species of sea eagles H. albicilla, H. leucocephalus, H. leucoryphus, H. leucogaster, H. sanfordi, H. pelagicus and H. vocifer was amplified by PCR and sequenced (1026 bp). Phylogeny reconstructions by the Maximum Parsimony and Neighbour-Joining methods produced similar trees in which sea eagles represent a monophyletic group. In addition, the clade H. albicilla/H. leucocephalus groups with the clade H. pelagicus/H. leucoryphus in a monophyletic boreal group while H. vocifer clusters with the H. leucogaster/H. sanfordi clade in a monophyletic tropical clade. The nearest relatives of sea eagles are the kites (genus Milvus) and buzzards (genus Buteo), whereas ‘booted’ eagles (genus Aquila) and vultures (genera Gyps and Aegypius) have diverged earlier from the accipitrid branch. Honey bussards (genus Pernis) and vultures of the genera Gypaetus and Neophron represent basal taxa of the accipitrid lineage. Falcons, New World vultures and the secretary bird (Sagittarius) appear in separate clades outside the Accipitridae.     

Phylogeny and phylogeography of squirrel monkeys (genus Saimiri) based on cytochrome b genetic analysis

Squirrel monkeys (genus Saimiri) are distributed over a wide area encompassing the Amazon Basin: French Guiana, Suriname, and Guyana, together with Western Panama and Western Costa Rica. The genus Saimiri includes a complex of species and subspecies displaying considerable morphological variation. Taxonomic and systematic studies have identified, in this genus, one to seven species comprising up to 16 subspecies. The phylogenetic relationships between these taxa are poorly understood. Molecular markers have yielded a consistent framework for the systematics of Central and South American Saimiri, identifying four distinct clades: S. oerstedii, S. sciureus, S. boliviensis, and S. ustus. Here, we reconsider the phylogenetic and biogeographic history of Saimiri on the basis of mitochondrial (mtDNA) sequence data, focusing mostly on individuals originating from the Amazon Basin. We studied 32 monkeys with well‐defined geographic origins and inferred the phylogenetic relationships between them on the basis of full‐length cytochrome b gene nucleotide sequences. The high level of gene diversity observed (0.966) is consistent with the high level of behavioral and morphological variation observed across the geographic range of the genus: 20 mtDNA haplotypes were identified with a maximum divergence of 4.81% between S. b. boliviensis and S. ustus. In addition to confirming the existence of the four clades previously identified on the basis of molecular characters, we suggest several new lineages, including S. s. macrodon, S. s. albigena, S. s. cassiquiarensis, and S. s. collinsi. We also propose new patterns of dispersion and diversification for the genus Saimiri, and discuss the contribution of certain rivers and forest refuges to its structuring. Am. J. Primatol. 72:242–253, 2010. © 2009 Wiley‐Liss, Inc.     

Phylogenetic relationships of the sea eagles (genus Haliaeetus): reconstructions based on morphology, allozymes and mitochondrial DNA sequences

The relationships of eight extant species of sea eagles (genus Haliaeetus ) and some potentially related Accipitrid genera were investigated. A phylogenetic hypothesis is developed based on morphological characters and allozyme data, which is then contrasted with a reconstruction based on 1071 nucleotides of mitochondrial DNA (cytochrome b and part of one tRNA gene). Phylogenies derived from the three data sets are largely congruent, although several aspects are supported by only one kind of evidence (but not contradicted by the others). Only with regard to the position of south-east Asian H. leucogaster and its closely related sister species H. sanfordi was there conflict between allozyme and mtDNA data. The position of H. pelagicus relative to H. leucoryphus or H. albicilla/leucocephalus could not be resolved with the mtDNA sequence data, suggesting that some speciation events occurred in relatively quick succession during the early Pliocene or late Miocene periods. Available evidence suggests that extant sea eagles originated at tropical latitudes, the northernmost species appearing most derived.     

Phylogeography of Peromyscus furvus (Rodentia; muridae) based on cytochrome b sequence data

We conducted phylogenetic analyses of cytochrome b sequence data to assess genetic variation within and among the three allopatric segments of the distribution of Peromyscus furvus from the Sierra Madre Oriental in eastern Mexico. We identified 24 unique haplotypes among the 54 individuals examined and genetic distances ranged up to 0.078 substitutions per site. Populations from the central portion of the range formed a monophyletic unit, whereas samples from the southern distributional unit were polyphyletic. Furthermore, the southernmost population sampled may represent a distinct species. This high degree of genetic differentiation among populations, currently recognized as conspecific, mirrors the result of other genetic studies of highland rodents in Mesoamerica. Together these studies indicate that the region, already considered hyperdiverse on the basis of species diversity and endemism, may contain considerably greater diversity than is currently appreciated.     

Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences

Cyprinidae, the largest fish family, comprises ap-proximately 210 recognized genera and 2010 species that are distributed widely in Eurasia, East Indian Is-land, Africa, and North America[1]. Species richness of this family is the greatest in East Asia, for example, China has 122 genera and more than 600 species. It is difficult to build a comprehensive phylogeny of Cy-prinidae due to the large number of genera and species. The classification of this family has been subject to revisions an…     

基于线粒体Cyt b基因的全长序列探讨闭壳龟类的系统进化

采用PCR技术对淡水龟科具闭壳结构的黄缘盒龟、黄额盒龟、金头闭壳龟、潘氏闭壳龟、锯缘龟和白腹摄龟的线粒体Cytb基因的全长序列进行了PCR扩增和序列测定,并结合GenBank中16种淡水龟科物种的同源序列,进行了序列变异和系统发生分析。经C lustalX1.8软件对位排列后共有1154个位点,其中可变位点413个,简约信息位点301个;A＋T的平均含量（56.5%）高于G＋C（43.5%）。在氨基酸密码子中,第一位富含A,第二位富含T,第三位富含C;碱基转换/颠换率为5.97,碱基替换多发生在密码子第三位。以中华鳖和马来鳖为外群,通过最大简约法,最大似然法和贝叶斯法重建了分子系统树,均具有一致的拓扑结构,结果表明：金头闭壳龟和潘氏闭壳龟最先聚成一支,再和三线闭壳龟聚成一组,说明形态上相似的三种闭壳龟亲缘关系最近;闭壳龟属、盒龟属和单种锯缘龟属聚成一个单系的闭壳龟群,建议合并为闭壳龟属;齿缘龟属和果龟属聚为一支,它们与新的闭壳龟属关系较远,揭示闭壳结构的形成不是由一个共同祖先分化而来;乌龟属、花龟属和拟水龟属三属为并系起源,建议三属可以合并为一属。     

Phylogenetic relationships of species of Crenicichla (Teleostei: Cichlidae) from southern South America based on the mitochondrial cytochrome b gene

Phylogenetic analysis using Bayesian inference, likelihood and parsimony methods was conducted on 60 complete mitochondrial cytochrome b sequences from 21 species of Crenicichla, including all species known from Uruguay (Crenicichla celidochilus, Crenicichla lepidota Crenicichla minuano, Crenicichla missioneira, Crenicichla punctata, Crenicichla scottii, Crenicichla vittata), Crenicichla compressiceps, Crenicichla empheres, Crenicichla geayi, Crenicichla iguassuensis, Crenicichla macrophthalma, Crenicichla menezesi, Crenicichla notophthalmus, Crenicichla regani, Crenicichla cf. regani, Crenicichla semifasciata, Crenicichla sveni, Crenicichla tendybaguassu, two unidentified species, and also two species of Teleocichla. Bayesian analysis resulted in a trichotomy with three major groups: (1) The C. missioneira species group (C. celidochilus, C. empheres, C. minuano, C. missioneira, C. tendybaguassu, and an undescribed species analyzed); (2) a group of southern species (C. iguassuensis, C. punctata, C. scottii, C. vittata); and (3) a rather heterogeneous group comprising the type species C. macrophthalma, members of the Crenicichla reticulata species group (C. geayi, C. semifasciata), members of the Crenicichla wallacii species group (C. compressiceps, C. notophthalmus, C. regani, C. cf. regani), members of the Crenicichla saxatilis species group (C. lepidota, C. menezesi, C. sveni, C. sp.), and two species of Teleocichla. Parsimony jackknifing resulted in a quadritomy with: (1) C. macrophthalma, (2) Teleocichla, (3) the saxatilis + wallacii group species, and (4) the rest, which include C. geayi and C. semifasciata as sister group to a dichotomy with the C. missioneira group and the remaining southern species. The sequence variation within the C. missioneira group is remarkably minor despite considerable morphological differences, supporting the conclusion that it forms an endemic species flock in the Uruguay River basin. Previously proposed species groups within the speciose genus Crenicichla (more than 90 species known) are partly corroborated. However, C. celidochilus was not previously associated with the C. missioneira species group, and C. vittata has not previously been associated with C. scottii, C. iguassuensis, or C. punctata. Crenicichla lepidota, C. sveni, C. menezesi and C. sp. represent the C. saxatilis group. Species of small size, representing the C. wallacii species group and Teleocichla are characterized by very long branches, and the position of Teleocichla differed considerably between the Bayesian and parsimony trees. This finding does not invalidate Teleocichla but rather suggests that the several monophyletic major clades within Crenicichla may need nominal recognition. A putative hybrid specimen with a morphology combining components from C. vittata and C. scottii, but with a cytochrome b sequence from C. scottii was found in a sample from the Rio Quaraí/Cuareim. Another putative hybrid specimen with a unique morphology but a cytochrome b sequence agreeing with C. scottii was found in a sample from Maldonado, but no other Crenicichla species than C. scottii is known from that locality.     

Phylogenetic relationships among four species and a sub-species of Mullidae (Actinopterygii; Perciformes) based on mitochondrial cytochrome B, 12S rRNA and cytochrome oxidase II genes

DNA sequence comparisons of three mitochondrial DNA genes were used to reveal phylogenetic relationships among four species and a sub-species of Mullidae family. This is the first report using mitochondrial DNA sequence data to infer intraspecific relationship among different populations of Mullus barbatus and Mullus surmuletus; phylogenetic relationships between M. barbatus and its sub-species; M. barbatus ponticus. Cytochrome b, 12S ribosomal RNA, and cytochrome oxidase II regions of 242 individuals belonging to species M. barbatus, M. surmuletus, Upeneus moluccensis, Upeneus pori and sub-species M. barbatus ponticus were sequenced and phylogenetic trees were constructed using four different algorithms. The phylogenetic trees constructed support the existing taxonomical data of two mullid genera (Mullus, Upeneus). Molecular data shows no significant difference between same species of different geographical populations. The results suggest that the molecular difference is not large enough between M. barbatus and M. barbatus ponticus to consider them as sub-species.