Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences

Aim To test a vicariant speciation hypothesis derived from geological evidence of large‐scale changes in drainage patterns in the late Miocene that affected the drainages in the south‐eastern Tibetan Plateau. Location The Tibetan Plateau and adjacent areas. Methods The cytochrome b DNA sequences of 30 species of the genus Schizothorax from nine different river systems were analysed. These DNA sequences were analysed using parsimony, maximum likelihood and Bayesian methods. The approximately unbiased and Shimodaira–Hasegawa tests were applied to evaluate the statistical significance of the shortest trees relative to alternative hypotheses. Dates of divergences between lineages were estimated using the nonparametric rate smoothing method, and confidence intervals of dates were obtained by parametric bootstrapping. Results The phylogenetic relationships recovered from molecular data were inconsistent with traditional taxonomy, but apparently reflected geographical associations with rivers. Within the genus Schizothorax, we observed a divergence between the lineages from the Irrawaddy–Lhuit and Tsangpo–Parlung rivers, and tentatively dated this vicariant event back to the late Miocene (7.3–6.8 Ma). We also observed approximately simultaneous geographical splits within drainages of the south‐eastern Tibetan Plateau, the Irrawaddy, the Yangtze and the Mekong–Salween rivers in the late Miocene (7.1–6.2 Ma). Main conclusions Our molecular evidence tentatively highlights the importance of palaeoriver connections and the uplift of the Tibetan Plateau in understanding the evolution of the genus Schizothorax. Molecular estimates of divergence times allowed us to date these vicariant scenarios back to the late Miocene, which agrees with geological suggestions for the separation of these drainages caused by tectonic uplift in south‐eastern Tibet. Our results indicated the substantial role of vicariant‐based speciation in shaping the current distribution pattern of the genus Schizothorax.     

Molecular phylogeny of the chipmunks inferred from Mitochondrial cytochrome b and cytochrome oxidase II gene sequences

There are currently 25 recognized species of the chipmunk genus Tamias. In this study we sequenced the complete mitochondrial cytochrome b (cyt b) gene of 23 Tamias species. We analyzed the cyt b sequence and then analyzed a combined data set of cyt b along with a previous data set of cytochrome oxidase subunit II (COII) sequence. Maximum-likelihood was used to further test the fit of models of evolution to the cyt b data. Other sciurid cyt b sequence was added to examine the evolution of Tamias in the context of other sciurids. Relationships among Tamias species are discussed, particularly the possibility of a current sorting event among taxa of the southwestern United States and the extreme divergences among the three subgenera (Neotamias, Eutamias, and Tamias).     

Molecular phylogeny of five species of Dremomys (Rodentia: Sciuridae), inferred from cytochrome b gene sequences

Analyses of the mitochondrial cytochrome b gene (1140 bp) showed that Dremomys lokriah , D. pernyi , D. pyrrhomerus , D. rufigenis and D. gularis all are separate species. Dremomys pyrrhomerus showed 8.5% sequence variation from D. rufigenis, and the level of estimated sequence divergence observed among D. gularis , D. lokriah and D. pernyi was > 11%. With Tamiops and Callosciurus as the outgroup taxa, in both maximum likelihood and Bayesian analyses, the five Dremomys species formed one strongly supported monophyletic group and D. pyrrhomerus is closely related to D. rufigenis . The derived divergence times and fossil record suggested that the present geographical distributions of Dremomys owe much to the uplifting of the Himalayas and the successive glacial and interglacial in the Pliocene–Pleistocene.     

Molecular phylogeny of the genus Oryzomys (Rodentia: Sigmodontinae) based on cytochrome b DNA sequences

The genus Oryzomys comprises 40 species arranged in several species groups. To test the monophyly of three Oryzomys species groups ("capito," nitidus, and subflavus), we analyzed, by distance, parsimony, and maximum-likelihood (ML), 801 bp of the mitochondrial gene cytochrome b. Our results did not sustain the monophyly of Oryzomys nor of the nitidus and subflavus species groups. Within the "capito" species group, O. perenensis appeared as a valid species, as a sister branch of the clade formed by O. megacephalus and O. laticeps. Within the nitidius species group, only the association between O. nitidus and O. lamia was well supported.The subflavus species group split into two clades: one with O. subflavus karyomorphotypes and another grouping O. angouya with species of different genera in the parsimony, distance, and ML trees.     

从细胞色素b基因全序列探讨大额牛的分子系统发生

大额牛是一种半野生半家养的珍稀牛种, 有关其起源和系统地位一直存在争议。通过PCR扩增、测序等步骤共获得了11头大额牛细胞色素b(Cyt b)基因全序列(1 140 bp)。应用分析软件, 对大额牛11条Cyt b序列进行了分析, 并结合GenBank中牛属动物6个近缘种的同源序列, 以亚洲水牛(Bubalus bubalis)为外群, 分别采用邻接法(NJ)和最大简约法(MP)构建了牛属动物分子系统发育树。序列分析结果表明, 11条大额牛Cyt b序列1 140位点中, 共发现95个变异位点(占分析位点总数的8.33 %), 定义了6种单倍型, 表明大额牛群体的Cyt b基因遗传多态性比较丰富。构建的NJ和MP分子系统树均显示, 大额牛研究群体明显分为3支, 第1支与普通牛(Bos taurus)相聚, 第2支与瘤牛(Bos indicus)相聚, 第3支与印度野牛(Bos gaurus)相聚。系统发育分析表明, 大额牛很可能是印度野牛的家养型或驯化种, 我国大额牛群体可能曾受到其他牛种血缘的入侵。     

A salmon id phylogeny inferred from mitochondrial cytochrome b gene sequences

Partial mitochondrial cytochrome b gene sequences of eight salmonid species were used in a PAUP analysis to generate a phylogeny of the group. The four genera represented are Salmo, Salvelinus, Oncorhynchus and Thymallus . The inferred phylogenetic tree coincides well with the classically derived one for these genera. The recent reclassification of the rainbow trout as a member of the genus Oncorhynchus is supported. The assignment of grayling as the outgroup is vindicated. The utility of gene sequence data to infer the phylogenetic relationships of the Salmonidae is discussed.     

Molecular phylogeny and biogeography of woolly flying squirrel (Rodentia: Sciuridae), inferred from mitochondrial cytochrome b gene sequences

To investigate the genetic diversity between the populations of woolly flying squirrels (Eupetaurus) from the eastern and western extremes of the Himalayas, partial mitochondrial cytochrome b gene sequences (390-810 bp) that were determined from the museum specimens were analyzed using maximum parsimony (MP) and maximum likelihood (ML) methods. The molecular data reveal that the two specimens that were collected in northwestern Yunnan (China) are members of the genus Eupetaurus. Reconstructed phylogenetic relationships show that the populations of Eupetaurus in the eastern and western extremes of the Himalayas are two distinct species with significant genetic differences (12%) and diverged about 10.8 million years ago. Eupetaurus is significantly different from Petaurista and Pteromys. The level of estimated pairwise-sequence divergence observed between Eupetaurus and Petaurista or Pteromys is greater than that observed between Eupetaurus and Trogopterus, Belomys, Glaucomys, or Hylopetes. Considering the divergence time of the two Eupetaurus groups, the glaciations and the uplift of the Himalayas and Qinghai-Tibet plateau during the Pliocene-Pleistocene period might be the major factors affecting the present distribution of Eupetaurus along the Himalayas.     

Molecular phylogeny of the genus Alticola (Cricetidae, Rodentia) as inferred from the sequence of the cytochrome b gene

Central Asian mountain voles Alticola is one of the least known groups of voles both in evolution and life history. This genus includes three subgenera Alticola s.str., Aschizomys and Platycranius, and belongs to the tribe Clethrionomyini comprising also red‐backed voles Clethrionomys and oriental voles Eothenomys. In order to elucidate the phylogenetic relationships within Alticola and to examine its position within the tribe, mitochondrial cytochrome b (cyt b) gene variation was estimated, and the results were compared with morphological and palaeontological data. Maximum likelihood (ML), neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian phylogenetic analyses show that the genus Alticola does not appear to be a monophyletic group since the representatives of Aschizomys branch within Clethrionomys, whereas two other subgenera (Alticola and Platycranius) form a separate monophyletic clade. Flat‐headed vole Alticola (Platycranius) strelzowi is nested within the nominative subgenus showing close association with A. (Alticola) semicanus. Surprisingly, the two species of Aschizomys do not form a monophyletic group. The results of the relaxed‐clock analysis suggest that the Alticola clade splits from the Clethrionomys stem in early Middle Pliocene while basal cladogenetic events within Alticola s.str. dates back to the late Middle to early Late Pliocene. A scenario of evolution in Clethrionomyini is put forward implying rapid parallel morphological changes in different lineages leading to the formation of Alticola‐like biomorphs adapted to mountain and arid petrophilous habitats. Corresponding author: Vladimir S. Lebedev, Zoological Museum, Moscow State University, B. Nikitskaya 6, 125009 Moscow, Russia. E‐mail: wslebedev@hotmail.com Anna A. Bannikova, Lomonosov Moscow State University, Vorobievy Gory, 119992 Moscow, Russia. E‐mail: hylomys@mail.ru Alexey S. Tesakov, Geological Institute RAS, Pyzhevsky 7, 119017 Moscow, Russia. E‐mail: tesak@ginras.ru Natalia I. Abramson, Zoological Institute RAS, Universitetskaya nab. 1, 199034 St Petersburg, Russia. E‐mail: lemmus@zin.ru     

A molecular phylogeny of Oxya (Orthoptera: Acridoidea) in China inferred from partial cytochrome b gene sequences

The grasshoppers of the genus Oxya are well known to damage rice, sugar cane, and other crops, yet their phylogenetic relationships have not been examined with molecular data. In this study, we obtained the 432 bp DNA sequences of the mitochondrial cytochrome b gene from 91 individuals of nine Oxya species and two outgroups (Gesonula punctifrons and Acrida cinerea). Phylogenetic analyses for the molecular data set were then carried out using the maximum parsimony and neighbor-joining methods. The results showed that the nine Oxya species form four well-supported clades, which include (1) O. intricata and O. flavefemura; (2) O. japonica and O. bicingula; (3) O. agavisa; and (4) O. chinensis, O. brachyptera, O. adentata, and O. hainanensis, respectively. In particular, the monophyly of O. hainanensis and O. agavisa is strongly supported, respectively. However, O. flavefemura and O. intricata, O. bicingula, and O. japonica form paraphyletic groups, respectively, and O. chinensis, O. adentata, and O. brachyptera form a polyphyletic group, suggesting that they should be merged as few as three species.     

Phylogeny of the genus Chironomus (Diptera) inferred from DNA sequences of mitochondrial cytochrome b and cytochrome oxidase I

Two mitochondrial genes, Cytochrome b (Cytb) and Cytochrome c oxidase subunit I (COI), have been used as phylogenetic markers in Chironomids. The nucleotide sequences of 685 bp from Cytb and 596 bp from COI have been determined for 36 Chironomus species from the Palearctic, or Holarctic, and Australasia. The concatenated sequence of 1281 bp from both genes was used to investigate the phylogenetic relationships among these species. The nucleotide sequence alignments were used for construction of phylogenetic trees based on maximum-parsimony and neighbor-joining methods. Both techniques produced similar phylogenies. Monophyly of the genus Chironomus is supported by a bootstrap value of 100% at the basal branch. Six clusters of species have been revealed with high bootstrap values supporting both monophyly of each cluster and the validity of the branching order within each cluster. Four species, C. circumdatus, C. nepeanensis, C. dorsalis, and C. crassiforceps, cannot be placed into any cluster. Cytological phylogenies were constructed using the same set of species, except for C. biwaprimus. These trees showed many similarities to that obtained from the mitochondrial (mt) sequence analysis, but also a number of significant differences. When compared with the tree constructed from the sequence of 23 species available for one of the globin genes, globin 2b (gb2b), there was better support for the mt tree than for the cytological trees. An intron, which varies in its occurrence and position in gb2b, was also investigated and the distribution of the introns supports the phylogenetic history of the genus Chironomus obtained with mt data. The differences observed in the cytological trees seem to be attributable more to the retention of the same chromosome banding sequence across several species, rather than convergent evolutionary events. An important question is the determination of the position of the subgenus Camptochironomus in relation to the representatives of the nominal subgenus Chironomus, since it has been suggested that this is a separate genus. The Camptochironomus species are internal to the trees and have arisen more recently than some of the species of the subgenus Chironomus, indicating that they are not sufficiently differentiated to be considered more than a subgenus.     

Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences

Voles of the genus Microtus represent one of the most speciose mammalian genera in the Holarctic. We established a molecular phylogeny for Microtus to resolve contentious issues of systematic relationships and evolutionary history in this genus. A total of 81 specimens representing ten Microtus species endemic to Europe as well as eight Eurasian, six Asian and one Holarctic species were sequenced for the entire cytochrome b gene (1140 bp). A further 25 sequences were retrieved from GenBank, providing data on an additional 23, mainly Nearctic, Microtus species. Phylogenetic analysis of these 48 species generated four well-supported monophyletic lineages. The genus Chionomys, snow voles, formed a distinct and well-supported lineage separate from the genus Microtus. The subgenus Microtus formed the strongest supported lineage with two sublineages displaying a close relationship between the arvalis species group (common voles) and the socialis species group (social voles). Monophyly of the Palearctic pitymyid voles, subgenus Terricola, was supported, and this subgenus was also subdivided into two monophyletic species groups. Together, these groupings clarify long-standing taxonomic uncertainties in Microtus. In addition, the "Asian" and the Nearctic lineages reported previously were identified although the latter group was not supported. However, relationships among the main Microtus branches were not resolved, suggesting a rapid and potentially simultaneous radiation of a widespread ancestor early in the history of the genus. This and subsequent radiations discernible in the cytochrome b phylogeny, show the considerable potential of Microtus for analysis of historical and ecological determinants of speciation in small mammals. It is evident that speciation is an ongoing process in the genus and that the molecular data provides a vital insight into current species limits as well as cladogenic events of the past.     

Molecular phylogeny of the clariid fishes of Lake Victoria,Tanzania, inferred from cytochrome b DNA sequences

Mitochondrial DNA cytochrome b (cyt b) sequence variation among the clariid fishes of Lake Victoria and the Malagarasi wetland Tanzania were studied between August 2003 and February 2005. Seven species were sampled and together with 26 cyt b sequences from GenBank were used to reconstruct phylogenetic relationships in the family Clariidae. The study revealed two clades: one consisting of the big‐head species, Clarias gariepinus and Heterobranchus longifilis, and the other of small‐sized species, Clarias werneri, Clarias alluaudi, Clarias liocephalus and Clariallabes petricola. The study further revealed that the genus Clarias is paraphyletic and that H. longifilis clusters deeply inside the Clarias group. Although H. longifilis is thought to be the oldest in evolutionary age in Tanzania, it is not close to the ancestor of the Clariidae family. The results also showed that C. werneri and C. alluaudi are genetically distinct from each other.     

Molecular phylogeny of Sinocyclocheilus (Cypriniformes: Cyprinidae) inferred from mitochondrial DNA sequences

More than 10 species within the freshwater fish genus Sinoncyclocheilus adapt to caves and show different degrees of degeneration of eyes and pigmentation. Therefore, this genus can be useful for studying evolutionary developmental mechanisms, role of natural selection and adaptation in cave animals. To better understand these processes, it is indispensable to have background knowledge about phylogenetic relationships of surface and cave species within this genus. To investigate phylogenetic relationships among species within this genus, we determined nucleotide sequences of complete mitochondrial cytochrome b gene (1140 bp) and partial ND4 gene (1032 bp) of 31 recognized ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony, Bayesian, and maximum likelihood analyses. Our phylogenetic results showed that all species except for two surface species S. jii and S. macrolepis clustered as five major monophyletic clades (I, II, III, IV, and V) with strong supports. S. jii was the most basal species in all analyses, but the position of S. macrolepis was not resolved. The cave species were polyphyletic and occurred in these five major clades. Our results indicate that adaptation to cave environments has occurred multiple times during the evolutionary history of Sinocyclocheilus. The branching orders among the clades I, II, III, and IV were not resolved, and this might be due to early rapid radiation in Sinocyclocheilus. All species distributed in Yunnan except for S. rhinocerous and S. hyalinus formed a strongly supported monophyletic group (clade V), probably reflecting their common origins. This result suggested that the diversification of Sinocyclocheilus in Yunnan may correlate with the uplifting of Yunnan Plateau.     

Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences

The taxonomy of clupeiforms has been extensively studied, yet phylogenetic relationships among component taxa remain controversial or unresolved. Here we test current and new hypotheses of relationships among clupeiforms using mitochondrial rRNA genes (12S and 16S) and nuclear RAG1 and RAG2 sequences (total of 4749bp) for 37 clupeiform taxa representing all five extant families and all subfamilies of Clupeiformes, except Pristigasterinae, plus seven outgroups. Our results, based on maximum parsimony, maximum likelihood, and Bayesian analyses of these data, show that some traditional hypotheses are supported. These include the monophyly of the families Engraulidae, consisting of two monophyletic subfamilies, Engraulinae (Engraulis and Anchoa) and Coilinae (Coilia and Setipinna), and Pristigasteridae (here represented only by Ilisha and Pellona). The basal position of Denticeps among clupeiforms is consistent with the molecular data when base compositional biases are accounted for. However, the monophyly of Clupeidae was not supported. Some clupeids were more closely related to taxa assigned to Pristigasteridae and Chirocentridae (Chirocentrus). These results suggest that a major revision in the classification of clupeiform fishes may be necessary, but should await a more complete taxonomic sampling and additional data.     

Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences

The origin of the anomalodesmatan bivalves and the relationships of the constituent families are far from being settled. Phylogenetic uncertainties result from the morphological heterogeneity of the Anomalodesmata and from parallel/convergent evolution of several character complexes due to similar life habits. Here, we assess these problems with 26 near-complete anomalodesmatan 18S rRNA sequences from 12 out of 15 families and a selection of heteroconch outgroup taxa. The robustly monophyletic Anomalodesmata share insertions in the V2 and V4 expansion regions. Both parsimony and maximum-likelihood analyses confirm their position among the basal heterodonts rooting between Carditidae and Lucinidae or, together with the latter, between Carditidae and the remaining Heterodonta. There is no support for monophyletic Myoida, nor for a close relationship of Anomalodesmata with any myoid taxon. At the base of the Anomalodesmata is an unstable cluster of long-branch species belonging to the Poromyidae, Verticordiidae, Lyonsiellidae and Thraciidae. The remaining Anomalodesmata split consistently but with varying branch support into three major clades: the Cuspidariidae excluding Myonera ; a 'thraciid' clade consisting of (Euciroidae, ( Myonera ( Thracia, Cleidothaerus , Myochamidae))); and a 'lyonsiid' clade with Laternulidae, Pandoridae, diphyletic Lyonsiidae due to a robust clade of Lyonsia norwegica and the clavagellid Brechites vaginiferus . Tests of various alternative topologies showed that all are significantly longer but optimal likelihood trees with monophyletic carnivorous taxa and/or Thraciidae are not significantly less likely. These results differ greatly from previous morphological studies. Palaeontological data and homology decisions for selected characters are evaluated in the light of the molecular trees.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 229–246.     

New insights into the taxonomy and phylogeny of social voles inferred from mitochondrial cytochrome b sequences

We sequenced the entire cytochrome b gene in Microtus paradoxus from Turkmenistan and Microtus socialis from Crimea and Kalmykia. Phylogenetic relationships among social voles were reconstructed by the inclusion into analyses of a further 23 published haplotypes belonging to six species. The two probabilistic methods which were used in phylogenetic analyses, the Bayesian inference and Maximum Likelihood, yielded very similar results. Both trees showed two highly divergent lineages which were further subdivided into seven species. The socialis lineage encompassed four species (M. socialis, M. irani, M. anatolicus, and M. paradoxus), and the remaining three species clustered into the guentheri lineage (M. guentheri, M. hartingi, M. dogramacii). The ranges for nucleotide divergences between seven species of social voles (4.95–9.28% and 4.18–8.81% for mean and net divergences, respectively) mainly exceeded 4.3%, which is frequently regarded as the conservative cut-off between sibling species in the specious genus Microtus.     

Phylogeny of the genus Aleochara inferred from mitochondrial cytochrome oxidase sequences (Coleoptera: Staphylinidae)

The phylogeny of the genus Aleochara was previously poorly understood due to difficulties with phylogenetic reconstruction by morphological characters. We present here a phylogeny based on the sequences of a 2022-bp fragment of the COI/II genes; 50 Aleochara and 10 outgroup species were included in the analysis. We used parsimony, minimum-evolution, and maximum-likelihood analyses to infer the phylogeny of the group. Our data do not support the commonly assumed sister group relationship between Aleocharini and Hoplandriini. Aleochara is resolved as a monophylum, although A. clavicornis might not belong to the genus. Within Aleochara, there are two large monophyletic clades. Many of the existing subgenera are shown to be para- or polyphyletic; others are likely to be monophyletic. Tinotus morion, previously assigned to the Hoplandriini, is strongly supported as belonging to Aleochara. According to our data, the mesosternal carina that has been used as an important character for classification has arisen and been reduced independently in several clades within Aleochara.     

Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences

The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e. , represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau. On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister taxa of one steppe dweller and one shrub dweller is very low. These findings support the hypothesis that pikas have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution.