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.     

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.     

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 African Killifishes in the GeneraAphyosemionandFundulopanchaxInferred from Mitochondrial DNA Sequences

We have analyzed the phylogenetic relationships of 52 species representing all defined species groups (J. J. Scheel, 1990, Atlas of Killifishes of the Old World, 448 pp.) of the African aplocheiloid fish generaAphyosemionandFundulopanchaxin order to examine their interrelationships and to reveal trends of karyotypic evolution. The data set comprised 785 total nucleotides from the mitochondrial 12S rRNA and cytochromebgenes. The molecular-based topologies analyzed by both maximum parsimony and neighbor-joining support the monophyly of most previously defined species groups within these two killifish genera. The genusAphyosemionis monophyletic except for the nested position ofFundulopanchax kunzi(batesigroup; subgenusRaddaella) within this clade, suggesting that this taxon was improperly assigned toFundulopanchax.The remainingFundulopanchaxspecies sampled were supported as being monophyletic in most analyses. Relationships among the species groups in both genera were not as strongly supported, suggesting that further data will be required to resolve these relationships. Additional sampling from the 16S rRNA gene allowed further resolution of relationships withinFundulopanchax,more specifically identifying the nonannualscheeligroup as the basal lineage of this otherwise annual genus. Chromosomal evolution withinAphyosemionhas been episodic, with the evolution of a reducedn= 9–10 metacentric complement having occurred in multiple, independent lineages. Polarity of chromosomal reductions within theelegansspecies group appears to support previous hypotheses concerning mechanisms of karyotypic change within the genusAphyosemion.     

山羊草属二倍体物种核rDNA ITS区序列及其系统发育关系分析

测定了山羊草属（Ａｅｇｉｌｏｐｓ）二倍物种核ｒＤＮＡ ＩＴＳ区序列,发现其碱基粉介于６０１－６０７之间,比报道的小ｒｉｕｃｅａｅ）其他属的ＩＴＳ区我略长,Ｇ＋Ｃ含量达６１．１％～６２．９％,序列间的分化距离为０．００５０～０．０４６８。用ＰＨＹＬＩＰ３．５ｅ软件包对所测得的ＤＮＡ数据进行聚类分析,结果显示：１．Ａｅ．ｓｐｅｌｔｏｉｄｅｓ与该组其他种相距很远,支持将其从Ｓｉｔｏｐｓｉｓ组中独立出来,     

六种灵猫科动物的分子系统关系研究

对六种灵猫科物种线粒体12 S rRNA基因及其中四种的Cytb基因部分序列进行了测定,并从Gen-Bank获得斑林狸(Prionodon pardicolor)、熊狸(Arctictis binturong)的Cytb基因同源序列。两基因整合序列比对后长755 bp,12 S rRNA基因序列中有70个变异位点,31个简约信息位点,在Cytb基因序列中,共有120个位点呈现变异,60个简约信息位点,Cytb基因的碱基变异百分比高于12 S rRNA基因的碱基变异百分比。使用邻接法(NJ)、最大似然法(ML)重建的分子系统树显示:斑林狸从灵猫亚科中分离出来,支持灵猫亚科的多系起源,而且斑林狸可能是中国起源最早且最特化的灵猫科动物。另外,同属于灵猫亚科的大灵猫(Viverra zibe-tha)、小灵猫(Viverricula indica)聚为一支,同属于棕榈狸亚科的果子狸(Viverricula indica)、熊狸聚为姐妹群,这些与传统形态学分类观点一致。     

Complete Mitochondrial DNA Sequences of Six Snakes: Phylogenetic Relationships and Molecular Evolution of Genomic Features

Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNA^Leu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences.[Reviewing Editor: Dr. Bill Ballard]     

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.     

Phylogenetic Relationships Among Xiphinema and Xiphidorus Nematode Species from Brazil Inferred from 18S rDNA Sequences

Maximum likelihood trees produced from 18S rDNA sequences separated 14 Xiphinema and five Xiphidorus nematode species from Brazil into distinct groups that concurred with their current morphological taxonomic status. Species belonging to the X. americanum group (X. brevicolle, X. diffusum, X. oxycaudatum, and X. peruvianum) formed a single group that was clearly separated from the other Xiphinema species. As with previous taxonomic studies that noted only minor morphological differences between putative X. americanum group species, separation of these species based upon 18S rDNA sequences was inconclusive. Thus it is probable that instead of comprising distinct species, the X. americanum group may in fact represent numerous morphotypes with large inter- and intra- population morphological variability that may be environmentally driven. Within the cluster representing non X. americanum group species, there was little statistical support to clearly separate species. However, three subgroups, comprising (i) the X. setariae/vulgare complex, (ii) X. ifacolum and X. paritaliae, and (iii) X. brasiliense and X. ensiculiferum were well resolved.     

Phylogenetic Relationships of Species of the Genus Kluyveromyces van der Walt (Saccharomycetaceae) Deduced from the Partial Sequences of 18S and 26S Ribosomal RNAs

In order to clarify the phylogenetic relationships of the species classified in the genus Kluyveromyces (Saccharomycetaceae), three partial base sequences of 18S and 26S rRNAs of eighteen strains were determined. The regions determined of the strains corresponded to positions 1451 through 1618 (168 bases) of 18S rRNA and to positions 1611 through 1835 (225 bases) and 493 through 622 (130 bases) of a strain (IFO 2376) of Saccharomyces cerevisiae. The analyses of the partial base sequences suggested that the genus Kluyveromyces is phylogenetically heterogeneous, ranging from the strains that are quite close to the strain of S. cerevisiae to the strains that are distinct enough to be classified in genera separate from the genus Saccharomyces. From our sequence data, we concluded that the extent of the genus Kluyveromyces should be restricted to only one species, K. polysporus, the type species of the genus. Kluyveromyces phaffii was also distinct enough to deserve another genus. Kluyveromyces cellobiovorus was not close to any of the strains of Kluyveromyces species examined, and should be excluded from the genus. Most of the strains of the species examined were fairly close to the strain of S. cerevisiae.     

基于12S rRNA和16S rRNA基因序列探讨中国蚤蝇科部分属间的系统发育关系

基于线粒体12S rRNA和16S rRNA基因序列联合分析,采用最大简约法、最大似然法和贝叶斯法分别构建了中国蚤蝇科14属的系统发育树.结果表明:联合分析序列总长度为819 bp,其中可变位点277个,简约信息位点200个;A+T平均含量为77.7%,具A、T偏倚性.系统发育分析显:中国蚤蝇科为单系发生,分为蚤蝇亚科和裂蚤蝇亚科两个单系群.蚤蝇亚科内脉蚤蝇属、锥蚤蝇属和刺蚤蝇属亲缘关系较近,栅蚤蝇属与栓蚤蝇属亲缘关系较近;裂蚤蝇亚科中虼蚤蝇属与裂蚤蝇属互为姐妹群,寡蚤蝇属与伐蚤蝇属互为姐妹群.     

Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences

Species in the genus Oryza (Poaceae) contain 10 genomic types and are distributed in pan-tropics of the world. To explore phylogenetic relationships of Oryza species having the AA-genome, DNA sequences of the chloroplast trnL intron and trnL-trnF spacer, mitochondrial nad1 intron 2, and nuclear internal transcribed spacer were analyzed, based on materials from 6 cultivated (O. sativa and O. glaberrima) and 13 wild accessions, in addition to a CC-genome species (O. officinalis) that was used as an outgroup. Analyses of the combined sequence data set from different sources provide a much better resolution of the AA-genome species than the individual data set, indicating the limitation of a single gene in phylogenetic reconstruction. The phylogeny based on the combined data set demonstrated an apparent grouping of the AA-genome Oryza species that was well associated with their geographic origin, although the Australian O. meridionalis showed its affinity with the African species. The geographic pattern of the phylogenetic relationship was probably attributed to the frequent genetic exchange and introgression among the AA-genome species from the same continents. In addition, Asian cultivated rice O. sativa showed its close relation to O. rufipogon and O. nivara, whereas African cultivated rice O. glaberrima was closely linked to O. barthii and O. longistaminata, indicating the independent domestication of the two cultivated species in different geographic locations.     

Phylogenetic Relationships and Species Delimitation in Pinus Section Trifoliae Inferrred from Plastid DNA

Recent diversification followed by secondary contact and hybridization may explain complex patterns of intra- and interspecific morphological and genetic variation in the North American hard pines (Pinus section Trifoliae), a group of approximately 49 tree species distributed in North and Central America and the Caribbean islands. We concatenated five plastid DNA markers for an average of 3.9 individuals per putative species and assessed the suitability of the five regions as DNA bar codes for species identification, species delimitation, and phylogenetic reconstruction. The ycf1 gene accounted for the greatest proportion of the alignment (46.9%), the greatest proportion of variable sites (74.9%), and the most unique sequences (75 haplotypes). Phylogenetic analysis recovered clades corresponding to subsections Australes, Contortae, and Ponderosae. Sequences for 23 of the 49 species were monophyletic and sequences for another 9 species were paraphyletic. Morphologically similar species within subsections usually grouped together, but there were exceptions consistent with incomplete lineage sorting or introgression. Bayesian relaxed molecular clock analyses indicated that all three subsections diversified relatively recently during the Miocene. The general mixed Yule-coalescent method gave a mixed model estimate of only 22 or 23 evolutionary entities for the plastid sequences, which corresponds to less than half the 49 species recognized based on morphological species assignments. Including more unique haplotypes per species may result in higher estimates, but low mutation rates, recent diversification, and large effective population sizes may limit the effectiveness of this method to detect evolutionary entities.     

猕猴属6个种的rDNA变异及其系统进化关系

以人２８Ｓ,１８Ｓ,ｒＤＮＡ为探针,用１５种限制性内切酶构建了猕猴属６个种（Ｍ．ｍｕｌａｔｔａ,Ｍ．ｆａｃｓｉｃｕｌａｒｉｓｆＭ．ａｒｃｔｏｉｄｅｓ,Ｍ．ａｓｓａｍｅｎｓｉｓ．Ｍ．ｔｈｉｂｅｔａｎａ．Ｍ。ｎｅｍｅｓｔｒｉｎａ）和滇金丝猴Ｒｈｉｎｏｐｉｔｈｅｃｕｓｂｉｅｔｉ）,白颊长臂猿（Ｈｙｌｏｂａｔｅｓｌｅｕｃｏｇｅｎｙｓ）核糖体ＤＮＡ重复单位的限制性内切酶图谱,红面猴（Ｍ．ａｒｃｔｏｉｅｓ）与     

基于ND4和ND5基因序列分析的鳅超科鱼类系统发育关系

ND4和ND5是线粒体基因组中编码NADH脱氢酶亚基4和亚基5的两个蛋白质编码基因.该研究以鳅超科鱼类为研究对象,新测定了10个物种的ND4和ND5基因全序列以及中间的3个tRNA基因共212 bp的序列,结合从GenBank 下载的15个物种的15条序列进行序列比较和系统发育关系分析.结果显示:鳅超科鱼类ND4基因全长1380～1387 bp,以ATG为起始密码子,终止密码子为不完全终止信号;ND5基因全长1821～1839bp,同样起始密码子为ATG,终止密码子为TAA或TAG;ND4和ND5基因之间插入了3个tRNA基因,分别编码携带组氨酸、丝氨酸、亮氨酸的tRNA.ND4和ND5基因(包含3个tRNA基因)中A、T、G、C的平均含量分别为30.4%、27.3%、14.2%、28.1%,A+T(57.7%)的含量高于G+C(42.3%)的含量.转换与颠换比(Ti/Tv)平均值为1.586.选取斑马鱼和鲤鱼作为外类群,采用最大简约法(MP)、最大似然法(ML)和贝叶斯推断法(BI)进行系统发育树的重建.三种方法的系统发育分析结果都显示:花鳅亚科、条鳅亚科、沙鳅亚科、平鳍鳅科及Vaillantellidae分别构成单系;它们的系统发育关系为:(Vaillantellidae+(沙鳅亚科+(花鳅亚科+(条鳅亚科+平鳍鳅科).这与线粒体全基因组和某些核基因(如RAG1基因)的研究结果类似,且支持率较高,表明ND4和ND5基因用于鳅超科鱼类的系统发育分析是可行的;但是该研究的结果有别于其他线粒体基因的分析结果,如基于cytb和D-loop基因进行的系统发育分析表明,条鳅亚科和花鳅亚科聚为姐妹群,再和平鳍鳅科聚在一起.这种差异可能是由于使用的基因长度差异造成的,长度越长,信息量越大,所反映的系统发育结果可能更加接近真实情况.     

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 among Asian species of Petaurista (Rodentia, Sciuridae), Inferred from Mitochondrial Cytochrome b Gene Sequences

To elucidate the phylogenetic relationships among four species belonging to the genus Petaurista (P. alborufus castaneus, P. alborufus lena, P. leucogenys leucogenys, P. leucogenys nikkonis, P. petaurista melanotus, and P. philippensis grandis), we investigated the partial sequences (1,068 bp) of the mitochondrial cytochrome b gene for these giant flying squirrels. Phylogenetic trees (NJ, MP, and ML trees) constructed from cytochrome b sequences indicated that P. leucogenys was grouped independently with other species, and that P. philippensis was most closely related to P. petaurista with 99-100% bootstrap values. In addition, two subspecies of P. alborufus did not form a single clade: P. alborufus castaneus from China was most distantly related to the other species, whereas P. alborufus lena from Taiwan was closely related to P. petaurista and P. philippensis with 82-90% bootstrap values. This result suggests that it is reasonable to regard P. alborufus lena as a distinct species from P. alborufus castaneus.     

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。     

(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。