Phylogenetic analysis in chicken breeds inferred from complete cytochrome b gene information

Complete cytochrome b (cyt b) gene (1140 bp) nucleotide sequences were used to investigate characteristics of the genetic constitution of Chunky broiler chickens, and these were compared with the Hy-Line and WL-GM (Garber) line of White Leghorn, the GSP line of Fayoumi, the BM-C line of Black Minorca (egg-chickens), and an outgroup of wild-origin Japanese quail. A high genetic difference (five haplotypes) was observed at the cytochrome b region in the Chunky broiler in contrast to the high homologies observed among the other chicken breeds (egg-purpose). Chunky broilers can be distinguished from the other breeds (White Leghorn, Fayoumi, and Black Minorca) at positions 552 and 779. The molecular phylogenetic tree exhibited genetic differences within Chunky broilers, and between Chunky broilers and the other three chicken breeds. As a result, some chicken strains or breeds apparently different from the other egg-chickens may have contributed to the Chunky broiler formation. Artificial selection may be one of the biggest factors causing nucleotide diversity in the chicken breeds.     

Phylogenetic analysis of hampala fishes (subfamily Cyprininae) in Malaysia inferred from partial mitochondrial cytochrome B DNA sequences

This study examined 396 base pairs of the mitochondrial cytochrome b gene from 110 individuals belonging to the genus Hampala, a group of freshwater cyprinids that inhabit Southeast Asia. The samples were taken from various locations throughout Sarawak, Sabah, and peninsular Malaysia. The nucleotide sequences were subjected to phylogenetic analyses by using the neighbor-joining, maximum parsimony, and maximum likelihood methods. All three methods revealed the reciprocally monophyletic relationship of Hampala macrolepidota to the other Hampala forms, thus strongly supporting its status as a distinct species. Phylogenetic analysis also discovered the existence of two H. bimaculata lineages endemic to Borneo: (1) a newly identified species from the southern and central part of Sarawak assigned as H. bimaculata Type A and (2) the previously described H. bimaculata from northern Sarawak and the west coast of Sabah assigned as H. bimaculata Type B. However, the status of H. sabana and an intermediate form were not elucidated. The results suggest that the intermediate form from the Tawau population is actually a subpopulation of H. sabana, while the highly divergent intermediate form from Kalabakan could represent a cryptic species. The sharing of H. macrolepidota haplotypes in the southern peninsular Malaysia and southern and central Sarawak samples (Hm1 and Hm2) reflected the recent disconnection of the two regions, during the late Pleistocene. Overall, the partial sequence of the mitochondrial cytochrome b gene was useful for resolving the phylogenetic relationships among Hampala fishes in Malaysia.     

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。     

Phylogenetic relationships of four species of floating gobies (Gymnogobius) as inferred from partial mitochondrial cytochrome b gene sequences

 To clarify the intra- and interspecific relationships of four Gymnogobius species, G. urotaenia, G. isaza, Gymnogobius sp. 1 (sumiukigori), and Gymnogobius sp. 2 (shimaukigori), partial mitochondrial cytochrome b gene sequences of 639 bp were obtained for a total of 31 specimens from Japan and Korea, plus 2 outgroup specimens. Twenty-nine haplotypes were identified in the ingroup, with a total of 122 variable sites (19.1%). The individuals regarded as the same species morphologically were monophyletic genetically. Sequence differences between amphidromous individuals of three species distributed in both Japan and Korea were relatively small (0.16–1.25%). The largest intraspecific sequence difference was observed between individuals of G. urotaenia from Lake Biwa and those from other localities (1.25–2.19%). Interspecific sequence differences ranged from 4.07% to 13.46%; neighbor-joining, maximum-parsimony, and maximum-likelihood methods indicated that Gymnogobius sp. 2 diverged first, followed by G. isaza, with Gymnogobius sp. 1 and G. urotaenia being monophyletic. The estimated divergence time of each species, based on estimated divergence rates for mitochondrial protein-coding genes already reported (0.8–2.8%/my), suggested that speciation occurred mainly in the Pliocene (possibly Miocene), with G. isaza (a Lake Biwa endemic) diverging significantly earlier (probably Lake Kouga stage) than estimated in previous studies. In contrast, according to the previous hypothesis, the substitution rates were highly overestimated to about 12–20%/my. Received: November 19, 2001 / Revised: May 20, 2002 / Accepted: June 18, 2002 Acknowledgments Special thanks are due to Katsutoshi Watanabe and Yuji Yamazaki for valuable advice and providing fish samples. We also thank Kouji Nakayama, Toshiyuki Ohkawa, Motoomi Yamaguchi, and members of the Laboratory of Marine Biology, Fukui Prefectural University, and members of the Laboratory of Molecular Marine Biology, Ocean Research Institute, University of Tokyo, and the Laboratory of Marine Stock Enhancement, University of Kyoto, for their help and advice during the present study. Correspondence to:Shigeo Harada     

Phylogenetic Analysis of Different Breeds of Domestic Chickens in Selected Area of Peninsular Malaysia Inferred from Partial Cytochrome b Gene Information and RAPD Markers

The present investigation was carried out in an attempt to study the phylogenetic analysis of different breeds of domestic chickens in Peninsular Malaysia inferred from partial cytochrome b gene information and random amplified polymorphic DNA (RAPD) markers. Phylogenetic analysis using both neighbor-joining (NJ) and maximum parsimony (MP) methods produced three clusters that encompassed Type-I village chickens, the red jungle fowl subspecies and the Japanese Chunky broilers. The phylogenetic analysis also revealed that majority of the Malaysian commercial chickens were randomly assembled with the Type-II village chickens. In RAPD assay, phylogenetic analysis using neighbor-joining produced six clusters that were completely distinguished based on the locality of chickens. High levels of genetic variations were observed among the village chickens, the commercial broilers, and between the commercial broilers and layer chickens. In this study, it was found that Type-I village chickens could be distinguished from the commercial chickens and Type-II village chickens at the position of the 27th nucleotide of the 351 bp cytochrome b gene. This study also revealed that RAPD markers were unable to differentiate the type of chickens, but it showed the effectiveness of RAPD in evaluating the genetic variation and the genetic relationships between chicken lines and populations.     

Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences

To explore phylogenetic relationships among glyptosternoid fishes, we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1138 base pair). Thirteen species of glyptosternoid fishes and six species of non-glyptosternoids represent 10 sisorid genera were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, minimum evolution, maximum likelihood, and Bayesian methods. Bayesian and maximum likelihood analyses support the monophyly of glyptosternoids, but our hypothesis of internal relationships differs from previous hypothesis. Results indicated that glyptosternoid is a monophyletic group and genera Glyptosternum and Exostoma are two basal species having a primitive position among it. Genera Euchiloglanis and Pareuchiloglanis form a sister-group. Then they form a sister-group with Pseudexostoma plus Oreoglanis. Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.     

Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences

The conifers, which traditionally comprise seven families, are the largest and most diverse group of living gymnosperms. Efforts to systematize this diversity without a cladistic phylogenetic framework have often resulted in the segregation of certain genera and/or families from the conifers. In order to understand better the relationships between the families, we performed cladistic analyses using a new data set obtained from 28S rRNA gene sequences. These analyses strongly support the monophyly of conifers including Taxaceae. Within the conifers, the Pinaceae are the first to diverge, being the sister group of the rest of conifers. A recently discovered Australian genus Wollemia is confirmed to be a natural member of the Araucariaceae. The Taxaceae are nested within the conifer clade, being the most closely related to the Cephalotaxaceae. The Taxodiaceae and Cupressaceae together form a monophyletic group. Sciadopitys should be considered as constituting a separate family. These relationships are consistent with previous cladistic analyses of morphological and molecular (18S rRNA, rbcL) data. Furthermore, the well-supported clade linking the Araucariaceae and Podocarpaceae, which has not been previously reported, suggests that the common ancestor of these families, both having the greatest diversity in the Southern Hemisphere, inhabited Gondwanaland.     

Phylogenetic relationships in genus Niviventer (Rodentia: Muridae) in China inferred from complete mitochondrial cytochrome b gene

Chinese species of the genus Niviventer, predominantly distributed in the southeastern Tibetan Plateau and in Taiwan, are a diverse group and have not yet received a thorough molecular phylogenetic analysis. Here, we reconstructed the phylogenetic relationships of 32 specimens representing nine Chinese species of Niviventer, based on sequences of the complete mitochondrial cytochrome b gene. Maximum parsimony, maximum likelihood and Bayesian analysis resulted in three consistent trees, each supported by high bootstrap values. The results showed that the Niviventer species included here are monophyletic. The nine species were classified into three distinct clades: clade A with Niviventer brahma, N. confucianus, N. coxingi, N. culturatus, N. eha and N. fulvescens; clade B with N. andersoni and N. excelsior; clade C with N. cremoriventer. Our results also suggested that N. culturatus should be a valid species rather than a subspecies of N. confucianus. Divergence times among species were calibrated according to the middle-late Pleistocene (1.2-0.13 Mya) fossil records of N. confucianus. The results demonstrated that the first radiation event of the genus Niviventer occurred in early Pleistocene (about 1.66 Mya), followed by the divergence of clades A and B at about 1.46 Mya. Most of the extant Niviventer species appeared during early to middle Pleistocene (about 1.29-0.67 Mya). These divergence times are coincidental with the last uplift events of the Tibetan Plateau, Kun-Huang movement, Pleistocene glaciations and the vicariant formation of Taiwan Strait. Consequently geographical events and Pleistocene glaciations have played a great role in the diversification of Niviventer.     

Genetic diversity and differentiation of Russian common carp (Cyprinus carpio L.) breeds inferred from RAPD markers

Polymorphic components of the common carp Cyprinus carpio L. genome were examined by means of polymerase chain reaction with random primers (RAPD-PCR). Using four primers, genetic diversity estimates were obtained for 12 populations and seven strains of Russian common carp breeds, as well as for European Hungarian common carp and Amur wild common carp (N = 87). The highest number of polymorphic loci was revealed in Angelinskii common carp, as well as in the samples of Altai common carp and Amur wild common carp (P = 23.8-18.7%), while the lowest number of polymorphic loci was in the BB strain of Ropsha common carp. The index of genetic diversity, H, was high (11%) in Amur wild common carp, as well as in Altai and Angelinskii common carps. In the remaining breeds, the value of this index varied from 4 to 8%. Based on summarized RAPD profile (132 bands), a dendrogram of genetic differences was constructed. In this dendrogram, all breeds examined grouped into two clusters. One of the clusters was formed by Hungarian and Angelinskii common carps, and the three samples of Altai common carp. The second cluster was formed by the group consisting of the representatives of Cherepetskskii, Stavropol, and Ropsha common carps, along with the differing from them Amur wild common carp. The observed differentiation was confirmed by the analysis of the polymorphic markers variance by the method of principle components. Evolutionary history and the reasons for genetic differentiation of Russian common carp breeds are discussed.     

Genetic diversity and differentiation of Russian common carp (Cyprinus carpio L.) breeds inferred from RAPD markers

Polymorphic components of the common carp Cyprinus carpio L. genome were examined by means of polymerase chain reaction with random primers (RAPD-PCR). Using four primers, genetic diversity estimates were obtained for 12 populations and seven strains of Russian common carp breeds, as well as for European Hungarian common carp and Amur wild common carp (N = 87). The highest number of polymorphic loci was revealed in Angelinskii common carp, as well as in the samples of Altai common carp and Amur wild common carp (P = 23.8?18.7%), while the lowest number (12.8%) of polymorphic loci was in the BB strain of Ropsha common carp. The index of genetic diversity, H, was high (11%) in Amur wild common carp, as well as in Altai and Angelinskii common carps. In the remaining breeds, the value of this index varied from 4 to 8%. Based on summarized RAPD profile (132 bands), a dendrogram of genetic differences was constructed. In this dendrogram, all breeds examined grouped into two clusters. One of the clusters was formed by Hungarian and Angelinskii common carps, and the three samples of Altai common carp. The second cluster was formed by the group consisting of the representatives of Cherepetskskii, Stavropol, and Ropsha common carps, along with the differing from them Amur wild common carp. The observed differentiation was confirmed by the analysis of the polymorphic markers variance by the method of principle components. Evolutionary history and the reasons for genetic differentiation of Russian common carp breeds are discussed.     

Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences

We examined intra-specific phylogenetic relationships in leatherside chub, Gila copei. The complete mitochondrial (mt) cytochrome b gene (1140 bp) was sequenced for 30 individuals from 10 populations that span the geographical distribution of this species. Traditional phylogenetic analyses revealed two deeply divergent and evolutionarily distinct mtDNA clades that are geographically separated in northern and southern drainage basins. Interpopulation sequence variation between clades ranged from 7.7 to 8.1%. The northern clade was genetically more similar and phylogenetically more closely related to the selected out-group Lepidomeda m. mollispinus than to the southern clade, suggesting that the taxonomy of this species may require revision. Sequence variation among populations within clades ranged from 0 to 0.3% in the north and from 0 to 0.7% in the south. Statistical parsimony was used to construct phylogenetic networks of haplotypes within clades. Nested clade analysis revealed that geographical fragmentation has played an important role in genetic structuring within northern and southern clades.     

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。     

Phylogenetic relationships among Southern Balkan Rutilus species inferred from cytochrome b sequence analysis: Micro-geographic resolution and taxonomic implications

The phylogenetic relationships and geographic distribution of Greek roaches (Rutilus spp.) were investigated by analyzing the complete mitochondrial cytochrome b gene sequence of 84 specimens collected from 15 southern Balkan lakes. Phylogenetic analysis revealed the existence of five highly divergent haplotype groups with mean pairwise sequence divergence between them ranging from 4.1 to 9%, namely at the level of values reported for different species. These five groups correspond to four species namely Rutilus rutilus, Rutilus prespensis, Rutilus panosi and Rutilus ylikiensis. On the other hand, the existence of two highly divergent haplotype groups, which are currently attributed to R. rutilus, suggests the re-examination of the current taxonomic status of this species.     

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.     

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).     

蜂猴属（Nycticebus）D-loop控制区和Cyt b基因遗传学研究

测定了蜂猴属线粒体DNA中的D-loop控制区部分序列和细胞色素b基因全序列（1140 bp）,对其变异情况进行了分析,并采用Mega 4.0软件中构建了分子系统树。无论是基于D-loop控制区部分序列构建的系统树,还是基于细胞色素b基因序列构建的分子系统树的拓扑结构图,都清晰地表明蜂猴属由两个分支组成,分支置信度较高,一支由N．pygmaeus聚成,另一支由N．coucang聚成,即支持蜂猴属由N．coucang和N．pygmaeus两物种组成。     

Phylogenetic relationships of mormyrid electric fishes (Mormyridae; Teleostei) inferred from cytochrome b sequences

The nasute termite genus Nasutitermes is widely distributed over all tropical regions. The phylogenetic relationships among 17 Nasutitermes species from the Pacific tropics were inferred from sequences of mitochondrial cytochrome oxidase II and 16S ribosomal RNA genes. Several methods of analysis yielded phylogenetic trees showing almost the same topology and in good agreement with reconstructions based on morphological or behavioral characters. Neotropical and Australian species came out as separate, apical clades. Asian species split between an apical branch, appearing as sister group to the neotropical clade, and basal taxa. New Guinean species were spread among several clades, suggesting a derivation from multiple origins. A well-supported clade includes the neotropical, Australian, and New Guinean species, with the southeast Asian N. takasagoensis and N. matangensis. It excludes the Asian species N. regularis, N. parvonasutus, and N. longinasus, which might deserve to be removed from Nasutitermes, as well as the long-legged Asian genera Hospitalitermes and Longipeditermes. A Gondwanan origin is proposed for the former clade, although an Old World origin of Nasutitermes followed by dispersal to Australia and South America cannot be excluded.     

Phylogenetic relationships among bumble bees (Bombus, latreille) inferred from mitochondrial cytochrome b and cytochrome oxidase I sequences

We conducted a molecular study intending to derive an estimate of the relationships within the genus Bombus (bumble bees) by comparing the mitochondrial cytochrome b and cytochrome oxidase I (COI) genes from 19 species, spanning 10 of approximately 16 European subgenera and 3 subgenera from North and South America. Our trees differ from the most recent classifications of bumble bees. Although bootstrap values for deep branches are low, our sequences show significant data structure and low homoplasy, and all trees share some groups and patterns. In all cases, the subgenus Bombus s. str. clusters among the most derived bumble bees, contrary to other molecular studies. In all trees, B. funebris is the sister taxon of B. robustus, and in five of the six trees, B. wurflenii is the sister taxon to this clade. B. nevadensis is basal to the other species in the analysis of the cytochrome b gene, but appears to be among the most derived according to the analysis of the COI region. The species representing the subgenera Thoracobombus and Fervidobombus are consistently among the earliest diverged. Species that appear in very different positions in different trees are B. nevadensis, B. mesomelas, B. balteatus, and B. hyperboreus. All subgenera with two representatives in our analysis are apparently monophyletic except Fervidobombus, Melanobombus, and Pyrobombus. The groups formed by pocket makers and non-pocket makers within Bombus also appear to be paraphyletic, and therefore some subgenera may not accurately reflect phylogeny.     

DNA fingerprinting of Pakistani buffalo breeds (Nili-Ravi, Kundi) using microsatellite and cytochrome b gene markers

Cytochrome b gene markers have been proved as an efficient and powerful tool for breed characterization and species identification of buffaloes. This study represents the substantial analysis of mitochondrial DNA variation in Pakistani buffalo breeds and provides information about their genetic diversity. In this study partial amplification of cytochrome b gene of 1,061 bp was done and sequencing results showed ten haplotypes. Comparing all fifty samples from two buffalo breeds of Pakistan, fifteen polymorphic sites were observed out of which, twelve codons 42, 71, 118, 120, 199, 235, 269, 297, 318, 327, 350, 355 of mitochondrial cytochrome b gene are monomorphic which translate same amino acids as in the reference protein sequence due to silent mutation while different in DNA sequence. Similarly three codons 163, 246, 337 of mitochondrial cytochrome b are polymorphic and different from the reference sequence with respect to DNA as well as protein sequence. For the further confirmation a panel of nine microsatellite markers was used with high polymorphism information content (PIC). The frequency distribution of these alleles varies from three to eight allele at locus CSSM66 and ILST029 respectively. The results obtained from this study may contribute to the establishment of routine genotyping service of buffalo breeds for buffalo farmers for animal forensic application in case of any dispute. Additionally this study may help for breed characterization and phylogeny of aforementioned breeds of buffalo.     

黄河裸裂尻鱼群体遗传结构和Cyt b序列变异

测定了来自黄河上游和柴达木盆地托索湖的裸裂尻鱼共16个个体的Cytb基因全序列(1141bp),探讨了种群结构和遗传多样性。用MEGA2.1软件分析了碱基组成和序列变异;以青海湖裸鲤、花斑裸鲤和极边扁咽齿鱼为外类群,用PAUP*4.0b10程序构建了单倍型NJ树;用Arlequin Ver.2000程序计算了群体间遗传变异值(Fst)和Nm值以及群体分化概率值。结果显示,来自柴达木水系托索湖的裸裂尻鱼没有形成单系群,Fst=0.204(P0.05),Nm=1.95。初步判断,黄河和柴达木水系托索湖的裸裂尻鱼未显著分化,支持将柴达木裸裂尻鱼(Schizopygopsis kessleri)归并入黄河裸裂尻鱼(Schizopygopsis pylzovi)的形态学结果。两种群核苷酸多样度()分别为0.0012和0.0026,表现为较低水平。根据校正的分子钟推测,黄河和托索湖裸裂尻鱼群体分歧时间为距今7万年左右的更新世末期,结合地理分布的资料和古地质事件,对黄河裸裂尻鱼群体分布水系间的历史联系进行了分析。