Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome <Emphasis Type="Italic">b</Emphasis> sequences

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily “Danioninae” did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the “Leuciscinae” in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leuciscinae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.     

Molecular phylogenetic relationships of China Seas groupers based on cytochrome <Emphasis Type="Italic">b</Emphasis> 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 T _S/T _V 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.     

犬科的线粒体细胞色素b DNA序列及其分子系统学研究

通过对犬科的赤狐、蓝狐、貉和狼４种的线粒体细胞色素ｂ约３７２ｂｐＤＮＡ片段序列分析,结合ＧｅｎＢａｎｋ中狗、西门豺和非洲野犬３种的该区段ＤＮＡ序列的比较,共发现１１３个核苷酸位点存在变异（约３０％）。ＮＪ法构建的分子系统树显示,非洲野犬最先从犬科动物中分化出来;犬属的我狼、狗和西门豺等３种为系统树上独立的一支,且其分歧的时间较赤狐、蓝狐和貉早;赤狐和蓝狐具有较近的亲缘关系。上述结果与形态的观点基本     

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.     

Biogeography of Sulawesian Shrews: Testing for their Origin with a Parametric Bootstrap on Molecular Data

In order to identify the zoogeographic origin of shrews (genusCrocidura) living on the oceanic island of Sulawesi, 15 taxa from Southeast Asia and 1 from Europe were examined for sequence variation in a segment (617 bp) of the mitochondrial cytochromebgene. The null hypothesis of a monophyletic origin of all Sulawesian shrews was investigated by a phylogenetic reconstruction using maximum parsimony. According to a parametric bootstrap which simulated sequence evolution for these taxa, the null hypothesis could be rejected as highly unlikely (P < 0.01). Therefore, the molecular phylogeny strongly suggests that overwater colonization of Sulawesi by shrews succeeded on at least two occasions. The first, relatively ancient wave of colonizers radiated and gave rise to a surprizingly diverse assemblage of at least five species which now coexist in perfect sympatry on Sulawesi. The second wave, of more recent origin, gave rise toCrocidura nigripes,a species which retained close genetic affinities with other Malay shrews.     

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.     

Genotypic and phenotypic evaluation of Rutilus spp. from Skadar, Ohrid and Prespa Lakes supports revision of endemic as well as taxonomic status of several taxa

One mtDNA gene (cytochrome b), one nuclear DNA fragment, five microsatellites and a suite of morphological characters were evaluated in samples of Rutilus spp. from Skadar, Ohrid and Prespa Lakes. Both genetic and phenotypic data supported two sympatric taxa in Lake Skadar, whereby Prespa and Ohrid Lakes revealed only a single taxon each. One of the taxa from Lake Skadar was similar to samples from Lake Prespa, whereas the second taxon was the most divergent in the data set. The estimated time to the most recent common ancestor of these two sympatric taxa in Lake Skadar was between 125 000 and 500 000 years. The data did not support existing taxonomic schemes for Rutilus in these lakes. This study poses the following working hypothesis: (1) Rutilus prespensis lives both in Lake Prespa and Lake Skadar and therefore is not endemic to Lake Prespa, (2) Rutilus ohridanus lives in Lake Ohrid only and therefore could be considered an endemic if its species status is retained and (3) a third recently described taxon (Rutilus albus) sympatric to R. prespensis lives in Lake Skadar.     

Molecular phylogeny and ecological diversification in a clade of New World songbirds (genus Vireo)

We constructed a molecular phylogeny for a clade of eye-ringed vireos ( Vireo flavifrons and the V . solitarius complex) to examine existing hypotheses of speciation and ecological diversification. Complete sequences of the mtDNA cytochrome b gene were obtained from 47 individuals of this group plus four vireonid outgroups. Mean levels of sequence divergence in the clade varied from 0.29% to 5.7%. Differences were greatest between V . flavifrons and four taxa of ' V . solitarius '. The latter separated into three taxonomic, geographical and ecological groups: V . plumbeus plumbeus, V . cassinii cassinii , and V . solitarius solitarius plus V . solitarius alticola . These differed by an average of 2.6–3.2%. Populations within each group revealed low levels of sequence variation ( x- = 0.20%) and little geographical structuring. The mtDNA data generally corroborate results from allozymes. V. plumbeus shows a loss of yellow-green carotenoid pigmentation from the ancestral condition. The occupancy of relatively dry habitats by this species and V . cassinii represents a derived ecological shift from more-humid environments occupied by other species of vireonids. Ecological divergence in this clade occurred in allopatry and is associated with generic-level stability in morphometrics and foraging styles. Migratory behaviour and seasonal habitat shifts apparently evolved multiple times in vireos breeding in temperate environments. Present geographical and ecological distributions, and low levels of intrataxon genetic divergence, are hypothesized to be the result of postglacial regionalization of climate–plant associations and rapid northward expansion of breeding ranges.     

从细胞色素b基因序列差异分析神农架白熊的系统进化关系

神农架白熊的分类地位从它被发现后就一直存在着争议。文章测定了神农架白熊一个个体的Cyt b基因从423~1 140共718 bp的序列, 结合亚洲黑熊(Selenarctos thibetanus)、美洲黑熊(Euarctos americanus)、马来熊(Helarctos malayanus)、棕熊(Ursus arctos)、北极熊(Thalarctos maritimus)、懒熊(Melursus ursinus)、眼镜熊(Tremarctos ornatus)、大熊猫(Ailuropoda melanoleuca)、小熊猫(Ailurus fulgens)、浣熊(Procyon lotor)同源DNA序列进行比较, 分析了碱基组成频率、替代数、变异位点、简约信息位点数、转换/颠换比率、相似指数和分化指数。用邻接法( NJ)和最大节约法(MP)构建了分子系统树, 得到了基本相同的拓扑结构。结果显示, 神农架白熊与亚洲黑熊的亲缘关系最近, 与大熊猫的亲缘关系较远。     

板角山羊mtDNA Cyt b基因变异特点及系统进化研究

测定了板角山羊品种13个个体的细胞色素b基因全序列(1140 bp),比较分析了群体中细胞色素b基因的碱基组成和序列间碱基的变异情况,结果显示:在该品种(群体)中细胞色素b基因序列中6个变异位点上观察到11次T-C间和2次A-G间的碱基转换,除了有2次T-C间碱基转换发生在密码子第2位点为非同义突变以外,其余的11次碱基转换发生在密码子第3位点,均为同义突变;有1次T-G间碱基颠换发生在密码子第2位点,为非同义突变;观察到5种单倍型,单倍型多样度为0.8077.并以绵羊为外群,与山羊属其他种的同源区序列构建系统发生树.结果显示, 在系统地位上板角山羊与胃石山羊有较近的亲缘关系.     

Weak phylogenetic effects on ecological niches of Sylvia warblers

To understand the evolution of ecological niches it is important to know whether niche evolution is constrained by phylogeny. We approached this question for Sylvia warblers by testing if closely related species are more similar in 20 ecologically relevant morphological traits than distantly related species. Phylogenetic relatedness was quantified using a molecular phylogeny based on the mitochondrial cytochrome b gene. By Principal Component Analysis (PCA) two major niche axes were extracted. We tested the individual ecomorphological traits and the positions of the species on the PCA axes for phylogenetic effects using Mantel tests. The results demonstrated small but significant phylogenetic effects only for the length of the middle toe, a trait probably correlated with locomotion. In general, however, phylogenetic effects were very weak. This suggests that ecological niches in passerine birds have the potential to evolve rapidly and are not subject to major phylogenetic constraints.