The Phylogenetic Relationships of the Gobioninae (Teleostei: Cyprinidae) Inferred from Mitochondrial Cytochrome b Gene Sequences

The Gobioninae are a group of morphologically and ecologically diverse Eurasian freshwater cyprinid fishes. The intergeneric relationships of this group are unresolved and the possible monophyly of this subfamily remains to be established. We used complete mitochondrial cytochrome b gene sequences from most genera within the gobionine group, in addition to a selection of cyprinid outgroups, to investigate the possible monophyly of this group and resolve the interrelationships within the group. Our results support the monophyly of the Gobioninae and identify four monophyletic groups within the subfamily; the Hemibarbus group, the Sarcocheilichthys group, the Gobio group, and the Pseudogobio group. The morphologically aberrant genera Gobiobotia, Xenophysogobio and Gobiocypris are included in the Gobioninae, with the latter a sister group of Gnathopogon.     

Phylogenetic Relationships of the Macaques (Cercopithecidae: Macaca), Inferred from Mitochondrial DNA Sequences

To study the phylogenetic relationships of the macaques, five gene fragments were sequenced from 40 individuals of eight species: Macaca mulatta, M. cyclopis, M. fascicularis, M. arctoides, M. assamensis, M. thibetana, M. silenus, and M. leonina. In addition, sequences of M. sylvanus were obtained from Genbank. A baboon was used as the outgroup. The phylogenetic trees were constructed using maximum-parsimony and Bayesian methods. Because five gene fragments were from the mitochondrial genome and were inherited as a single entity without recombination, we combined the five genes into a single analysis. The parsimony bootstrap proportions we obtained were higher than those from earlier studies based on the combined mtDNA dataset. Excluding M. arctoides, our results are generally consistent with the classification of Delson (1980). Our phylogenetic analyses agree with earlier studies suggesting that the mitochondrial lineages of M. arctoides share a close evolutionary relationship with the mitochondrial lineages of the fascicularis group of macaques (and M. fascicularis, specifically). M. mulatta (with respect to M. cyclopis), M. assamensis assamensis (with respect to M. thibetana), and M. leonina (with respect to M. silenus) are paraphyletic based on our analysis of mitochondrial genes.     

从细胞色素b基因序列变异分析中国鲇形目鱼类的系统发育

采用PCR技术获得中国鲇形目鱼类11科24属27个代表种类细胞色素b基因1138bp全序列,比较分析了来自北美洲、非洲的部分鲇形目鱼类同一基因序列,并选取脂鲤目、鲤形目和鲱形目鱼类作外类群,采用Bayesian方法和最大简约法(MP)构建分子系统树。结果表明：(1)鲇形目鱼类细胞色素b基因序列中,与脂鲤目、鲤形目以及鲱形目鱼类相比存在3bp的缺失;(2)鲇形目鱼类各科代表种类形成一单系群;(3)两种建树方法均支持铫科、粒鲇科和钝头鮠科形成一单系群;而胡子鲇科、刀鲇科、海鲇科、鮰科、长臀鮠科、鲢科、鲇科、棘脂鲿科、鲿科形成一大的单系群;但鳗鲇科的系统位置两种建树方法没有取得一致结果;而其中长臀鲍科与北美的鮰科形成姐妹群,胡子鲇、鮰科、鲇科、鲿科和鮡科是较明显的单系群。     

Phylogenetic Relationships among Bufonoid Frogs (Anura: Neobatrachia) Inferred from Mitochondrial DNA Sequences

Nucleotide sequences of portions of the mitochondrial 12S and 16S ribosomal RNA genes were used to extend a recent study of anuran phylogeny (Hayet al., Mol. Biol. Evol.12: 928–937, 1995) and to further evaluate phylogenetic relationships within the Neobatrachia. An analysis of almost 900 nucleotides from each of 8 new representatives of the Dendrobatidae, Hylidae, Leptodactylidae, and Myobatrachidae, plus 14 available members of the Neobatrachia provides support for 2 major lineages (Bufonoidea and Ranoidea) within this anuran suborder. The neotropical Bufonoidea and their derivatives are monophyletic. There is an interesting association of the 2 Australian myobatrachids with the South African Heleophrynidae, and the Sooglossidae is one of the basal bufonoid lineages. Within the New World bufonoid frogs, a monophyletic Dendrobatidae is strongly supported. An Australian hylid (Pelodryadinae) shows close affinity with the South American hylid Phyllomedusinae. A group composed of Hylinae (HylaandSmilisca), Centrolenidae, Bufonidae, and the hylid Hemiphractinae, with the latter two clustered, was supported significantly. The addition of new taxa has more clearly defined some relationships within the suborder Neobatrachia and has indicated that the families Hylidae, Leptodactylidae, and Myobatrachidae may not be monophyletic.     

Phylogenetic Relationships of Bears (the Ursidae) Inferred from Mitochondrial DNA Sequences

The phylogenetic relationships among some bear species are still open questions. We present here mitochondrial DNA sequences of D-loop region, cytochrome b, 12S rRNA, tRNA^Pro, and tRNA^Thr genes from all bear species and the giant panda. A series of evolutionary trees with concordant topology has been derived based on the combined data set of all of the mitochondrial DNA sequences, which may have resolved the evolutionary relationships of all bear species: the ancestor of the spectacled bear diverged first, followed by the sloth bear; the brown bear and polar bear are sister taxa relative to the Asiatic black bear; the closest relative of the American black bear is the sun bear. Primers for forensic identification of the giant panda and bears are proposed. Analysis of these data, in combination with data from primates and antelopes, suggests that relative substitutional rates between different mitochondrial DNA regions may vary greatly among different taxa of the vertebrates.     

(行鸟)形目12种鸟类线粒体细胞色素b基因序列差异及其系统发育关系

采用PCR直接测序方法首次对Hang形目(Charadriiformes)12种鸟类：蒙古沙Hang(Charadrius mongolus)、环颈Hang(Charadrius alexandrinus)、大杓鹬(Numenius madagascariensis)、白腰杓鹬(Numenius arquata)、中杓鹬（Numenius phaeo-pus）、红脚鹬（Trina totanus）、林鹬（Trina alareola）、翘嘴鹬（Xenus cineres）、翻石鹬（Arenaria interpres）、大滨鹬（Calidris teruarostris)、反嘴鹬（Recurvirostra avosetts)和砺鹬（Haematopus ostralensis)线粒体cyt b基因全序列进行测定,并以白鹳（Ciconia ciconia)的同序列作为外群杓建系统发生树。经比对,Hang形目12种鸟类线粒体cyt b基因全序列均包括1143bp,序列间未见有插入和缺失,共有381个变异位点,种间序列差异值为5．16％—16．01％。重建的系统树将Hang形目12种鸟类分为2个支系：第1支系包括红脚鹬、林鹬、翻石鹬、大滨鹬、翘嘴鹬、中杓鹬、大杓鹬和白腰杓鹬,其中红脚鹬、林鹬、翻石鹬、大滨鹬、翘嘴鹬聚为一支,中杓鹬、大杓鹬和白腰杓鹬聚为另一支;第2支系包括蒙古沙Hang、环颈Hang、反嘴鹬和硕鹬,其中反嘴鹬与砺鹬互为姐妹群,然后再与Hang属的两个种蒙古沙Jamg和环Hang组成的姐妹群构成并系群。分子证据提示：第1支系中各属问及种间的系统关系与形态学研究结果相吻合;第2支系中的反嘴鹬与Hang鹬之间的亲缘关系较近,两者聚为姐妹群,提示将这两个类群合并为一个亚科——反嘴葫亚科更为合理,与码亚科共同组成Hang科,与核型研究结果和Sibley在新分类体系中将码科分为反嘴鹬亚科和Hang亚科、反嘴鹬族和砺鹬族属于反嘴鹬亚科的观点相一致。     

形目12种鸟类线粒体细胞色素b基因序列差异及其系统发育关系

采用PCR直接测序方法首次对形目 (Charadriiformes) 12种鸟类 :蒙古沙 (Charadriusmongolus)、环颈(Charadriusalexandrinus)、大杓鹬 (Numeniusmadagascariensis)、白腰杓鹬 (Numeniusarquata)、中杓鹬 (Numeniusphaeo pus)、红脚鹬 (Tringatotanus)、林鹬 (Tringaglareola)、翘嘴鹬 (Xenuscineres)、翻石鹬 (Arenariainterpres)、大滨鹬 (Calidristenuirostris)、反嘴鹬 (Recurvirostraavosetts)和砺鹬 (Haematopusostralensis)线粒体cytb基因全序列进行测定 ,并以白鹳(Ciconiaciconia)的同源序列作为外群构建系统发生树。经比对 ,形目 12种鸟类线粒体cytb基因全序列均包括1143bp ,序列间未见有插入和缺失 ,共有 381个变异位点 ,种间序列差异值为 5 16 %～ 16 0 1%。重建的系统树将形目 12种鸟类分为 2个支系 :第 1支系包括红脚鹬、林鹬、翻石鹬、大滨鹬、翘嘴鹬、中杓鹬、大杓鹬和白腰杓鹬 ,其中红脚鹬、林鹬、翻石鹬、大滨鹬、翘嘴鹬聚为一支 ,中杓鹬、大杓鹬和白腰杓鹬聚为另一支 ;第 2支系包括蒙古沙、环颈、反嘴鹬和砺鹬 ,其中反嘴鹬与砺鹬互为姐妹群 ,然后再与属的两个种蒙古沙和环颈组成的姐妹群构成并系群。分子证据提示 :第 1支系中各属间及种间的系统关系与形态学研     

基于matR基因序列分析的山茶科系统关系

通过线粒体matR基因序列分析探讨了山茶科的分类学范围和系统演化关系。结果显示,传统山茶科的两个核心——山茶亚科（Theoideae或Camellioideae）和厚皮香亚科（Ternstroemioideae）不构成姐妹群关系,山茶亚科是一个支持率很高的单系类群,厚皮香亚科没有形成单系;山茶亚科下可区分出3个明显的分支,基部的分支由紫茎属（Stewartia）和舟柄茶属（Hartia）组成,木荷属（Schima）、美洲荷属（Franklirda）和美国大头茶属（Gordonia）构成第2个分支,该分支与由山茶属（Camellia）、核果茶属（Pyrenaria）、多瓣核果茶属（Parapyrenaria）、石笔木属（Tutcheria）、大头荣属（Polyspora）和圆籽荷属（Aptersperma）组成的第3个分支互为姐妹群。研究结果很好地支持了Prince和Parks等学者提出的的狭义山茶科（仅含山茶亚科）和狭义大头茶属的概念以及科下3个族（紫茎族Stewartieae、大头茶族Gordonieae和山茶族Theeae）的划分。但本研究更为清晰地揭示了科下3个族间的系统关系,即紫茎族是最基部的分支,山茶族与大头茶族间有更近的亲缘关系。同时,本文认为,厚皮香（亚）科是否为单系类群值得进一步研究。     

Phylogenetic Relationships among Higher Nemertean (Nemertea) Taxa Inferred from 18S rDNA Sequences

We estimated the phylogenetic relationships of 15 nemertean (phylum Nemertea) species from the four subclasses Hoplo-, Hetero-, Palaeo-, and Bdellonemertea with 18S rDNA sequence data. Three outgroup taxa were used for rooting: Annelida, Platyhelminthes, and Mollusca. Parsimony and maximum-likelihood analyses supported the monophyletic status of the Heteronemertea and a taxon consisting of hoplonemerteans and Bdellonemertea, while indicating that Palaeonemertea is paraphyletic. The monophyletic status of the two nemertean classes Anopla and Enopla is not supported by the data. The unambiguous clades are well supported, as assessed by a randomization test (bootstrapping) and branch support values.     

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.     

川陕哲罗鲑Cyt b基因克隆及其在鲑亚科中的系统发育关系

采用聚合酶链式反应克隆川陕哲罗鲑Hucho bleekeri线粒体细胞色素b基因 (Cyt b),首次报道该基因的全长序列(1140 bp,GenBank 登录号FJ597623),并与鲑亚科中其他5属14个物种的Cyt b基因进行同源性比较,分析了碱基组成和变异情况,以白鲑亚科的白鲑Coregonus lavaretus作为外群构建了ML、NJ和MP系统发育树.遗传距离和分子系统学分析表明,川陕哲罗鲑与细鳞鲑属的细鳞鱼Brachymystax lenok之间的遗传距离相对较小(8.47%),在系统发育树上两者聚在一起,提示川陕哲罗鲑与细鳞鱼存在较近的亲缘关系,该结果与以往的形态学分类不相符.     

Phylogenetic Relationships among the Major Lineages of the Birds-of-Paradise (Paradisaeidae) Using Mitochondrial DNA Gene Sequences

Complete mitochondrial cytochromebgene sequences were determined from 12 species of the Australo-Papuan birds-of-paradise (Paradisaeidae) representing 9 genera. Phylogenetic analysis of these and 5 previously published sequences reveals a radiation of the main paradisaeinine lineages that took place over a relatively short evolutionary time scale. The core paradisaeinines are resolved as the monophyletic sister-group to the crow-like manucodines. The genusParotiais basal to other paradisaeinines and is not closely related to the morphologically similar generaPtilorisandLophorina.Three major clades within the paradisaeinine ingroup include: (1)CicinnurusandDiphyllodes,(2)PtilorisandLophorina,and (3) the genusParadisaea.The monotypic genusSeleucidisis apparently closely related to clades (1) and (2). Cytochromebsequences did not provide evidence for the monophyly of the sicklebill generaEpimachusandDrepanornis.The paradisaeid tree is characterized by short internodal distances. Thus, some clades cannot be strongly resolved by cytochromebsequences alone.     

鹳形目12种鸟类核c-mos 基因和线粒体12S rRNA基因序列分析及其系统发生研究

鹳形目鸟类的传统分类一直存在分歧,而近期的分子系统学研究大多只用单个基因,其结论的可信度需要进一步验证.本文通过核c-mos基因和线粒体12S rRNA基因序列分别和合并分析,采用分子系统学方法探讨了鹳形目6科12种鸟类的系统发生关系.文中测出鹳形目鸟类6种核c-mos基因的片断序列,结合来自Genebank的其他种类的c-mos和12S rRNA基因序列,分别经Clustal W软件对位排列后,以原鸡为外类群用最大似然法、邻接法和最大简约法建立系统树.系统树分析表明, 鹳形目6科之间的系统发生关系总结为：（鹭科,（（鹮科,美洲鹫科）,（鹳科,（鲸头鹳科,锤头鹳科））））.鹭科7个属之间的系统发生关系总结为：（麻（开鸟）属（夜鹭属（池鹭属（苍鹭属（中白鹭属（白鹭属,大白鹭属））））））.分别基于两个单基因的系统树有一定差异,而基于合并数据的系统树支持率和分辨率都高于基于单基因的系统树,表明使用在遗传上相对独立的分子数据合并建立系统树有较高的可信度和分辨率,是一种更好的研究方法.     

以Cytb基因部分序列分析大额牛系统地位及其种群现状

对12头大额牛Cytb基因部分序列447bp进行分析,共发现33个变异位点,定义了4种单倍型;结合GenBank中牛属普通牛、瘤牛、牦牛和印度褐牛4个近缘种的Cytb基因同源区序列进行分析,以水牛作为外群,分别采用邻接(NJ)法和最大简约(MP)法构建分子系统发育树,得到基本一致的拓扑结构,结果表明大额牛是独立于普通牛、瘤牛和印度褐牛之外的Bos属的一个独立的种。同时还指出目前我国有相当比例的大额牛受到外来物种的入侵,我国的大额牛保护工作正面临非常严峻的考验。     

Phylogenetic Relationships of Orders Within the Class Colpodea (Phylum Ciliophora) Inferred from Small Subunit rRNA Gene Sequences

Molecular analyses have been used recently to refine our knowledge of phylogenetic relationships within the ciliated protozoa (phylum Ciliophora). A current Hennigian phylogeny of the orders in the class Colpodea, based on light and electron microscopic analyses, makes three important assumptions with regard to apomorphic character states, namely, (1) that the kreyellid silver line evolved early in colpodean phylogeny, separating bryometopids, such as Bryometopus, from all other colpodeans; (2) that the macro–micronuclear complex is an autapomorphy of the cyrtolophosidids, such as Platyophrya; and (3) that merotelokinetal stomatogenesis is an apomorphic character of colpodids, such as Colpoda, Bresslaua, and Pseudoplatyophrya. These predictions of relationships within the class Colpodea were investigated by determining the complete small subunit rRNA gene sequences for the colpodid Bresslaua vorax, the grossglockneriid Pseudoplatyophrya nana, and the cyrtolophosidid Platyophrya vorax and a partial sequence for the bryometopid Bryometopus sphagni. These sequences were combined with the previously published complete SSrRNA sequences for the colpodid Colpoda inflata and the bursariomorphid Bursaria truncatella. The affiliations were assessed using both distance matrix and maximum-parsimony analyses. The tree topologies for the class Colpodea were identical in all analyses, with bootstrap support for bifurcations always exceeding 60%. The results suggest the following. (1) Since the clade including Bryometopus and its sister taxon, Bursaria, is never basal, the kreyellid silver-line system evolved later in colpodean phylogeny and does not separate bryometopids from all other colpodeans. (2) Since Platyophrya is always the sister taxon to the other five genera, there is a fundamental phylogenetic significance for its macro–micronuclear complex. (3) Since the colpodids, Colpoda, Bresslaua, and Pseudoplatyophrya, always group in one clade, merotelokinetal stomatogenesis appears to be a derived character state. Received: 30 June 1998 / Accepted: 3 December 1998     

Formation of the Japanese Carabina Fauna Inferred from a Phylogenetic Tree of Mitochondrial ND5 Gene Sequences (Coleoptera, Carabidae)

Phylogenetic analyses based on the mitochondrial ND5 gene comparisons and the geohistory of the Japanese Islands suggest that each Japanese species belonging to the subtribe Carabina has its own history for the establishment of its present habitat in the Japanese Islands. It can be roughly classified into two categories: (1) species which were derived from the ancestry that inhabited ancient Japan at the time of its split from the Eurasian Continent [ca. 15 million years ago (MYA)], followed by diversification within the Japanese Islands; and (2) species which invaded Hokkaido from the Eurasian Continent through land-bridges from Sakhalin and/or the Kuriles or from western Japan from the Korean Peninsula during the glacial era (<2 MYA). Received: 28 September 1999 / Accepted: 25 February 2000     

基于线粒体16S rRNA基因对中国狼蛛科(Lycosidae)系统发育研究

将自测的中国狼蛛科Lycosidae4亚科6属26种和从GenBank中检索到的北美2种豹蛛的mtD-NA-16S rRNA序列进行比较;以漏斗蛛科1种蜘蛛作为外群,对碱基序列的组成和遗传距离进行了分析,采用Bayesian方法和最大简约法(MP)构建分子系统树。研究结果表明:16SrRNA基因的部分序列为340bp到360bp,A T含量平均为75%,存在较强的A T含量偏向性;序列共有157个碱基存在变异,其中79个简约信息位点。狼蛛科各属间的遗传距离介于0.026￣0.200之间。2种建树方法均表明:科内的属及属内的种优先聚在一起;水狼蛛属相对马蛛属是狼蛛科中较为原始的类群,分化较早;獾蛛属作为1个单系群与熊蛛属合为1个并系,属于狼蛛亚科。狼蛛科6属间的分子系统关系为(Pirata(Hippasa(Trochsa Arctosa(Pardosa Wadicosa))))。     

Phylogeny of Snub-Nosed Monkeys Inferred from Mitochondrial DNA,Cytochrome B,and 12S rRNA Sequences

Snub-nosed monkeys (Rhinopithecus spp.) are confined to isolated mountainous regions in China and North Vietnam. Their systematic classification and phylogenetic relationship has been controversial. The structures of mitochondrial DNA cytochrome b and 12S rRNA show that the 4 species of Rhinopithecus are quite different from other colobines. It is reasonable to regard them as an independent genus, as determined by external features, morphometric characters and behavior. However, whether or not there should be a subdivision between the Vietnamese and Chinese species at the subgeneric level remains to be clarified; more evidence from a large range of Asian colobine species is needed. The Guizhou species, Rhinopithecus brelichi, is a valid species, which is more closely related to Pygathrix than the other species ( R. roxellana, R. bieti and R. avunculus) are. Results also indicate that 3 species—Rhinopithecus roxellana, R. bieti and R. avunculus—might have diverged from R. brelichi, but the phylogenetic relationship of R. avunculus is not clear.