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.     

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.     

基于16S rDNA部分序列探讨中国近海30种石斑鱼类的分子系统进化关系

石斑鱼因其种类繁多、分布广泛及缺乏显著的形体特征,使其系统分类的研究颇为困难。为探讨中国近海石斑鱼类的系统进化关系,通过PCR扩增获得了石斑鱼亚科(Epinephelinae)6属30个种类的线粒体16SrDNA基因片段序列。采用多个生物软件对序列变异和碱基组成进行分析,计算了Kimura2parameter遗传距离、转换/颠换比等遗传信息指数,并结合GenBank石斑鱼属的同源序列,以多纹长尾(Pronotogrammusmultifasciatus)和皮氏叫姑鱼(Johniusbelengerii)为外群构建NJ、MP和ML系统树。根据所得分子依据并结合形态学特征,推论如下:1)在本研究的30种石斑鱼中,鳃棘鲈属(Plectropomus)最先分化,并呈明显单系性;九棘鲈属(Cephalopholis)是一个单系群,并且较石斑鱼属(Epinephelus)原始;侧牙鲈属(Variola)的进化地位介于鳃棘鲈属与九棘鲈属之间;2)宽额鲈(Promicropslanceolatus)可以归入石斑鱼属,而驼背鲈(Cromileptesaltivelis)也与石斑鱼属有很近的亲缘关系,甚至可能是石斑鱼属内的特化类群;3)石斑鱼属内部存在两个平行进化的姐妹分支,分支内部的种类组成与地理分布无关,暗示了石斑鱼属早期的分化模式。     

Phylogenetic Study of Complete Cytochrome b Genes in Musk Deer (Genus Moschus) Using Museum Samples

As an endangered animal group, musk deer (genus Moschus) are not only a great concern of wildlife conservation, but also of special interest to evolutionary studies due to long-standing arguments on the taxonomic and phylogenetic associations in this group. Using museum samples, we sequenced complete mitochondrial cytochrome b genes (1140 bp) of all suggested species of musk deer in order to reconstruct their phylogenetic history through molecular information. Our results showed that the cytochrome b gene tree is rather robust and concurred for all the algorithms employed (parsimony, maximum likelihood, and distance methods). Further, the relative rate test indicated a constant sequence substitution rate among all the species, permitting the dating of divergence events by molecular clock. According to the molecular topology, M. moschiferus branched off the earliest from a common ancestor of musk deer (about 700,000 years ago); then followed the bifurcation forming the M. berezovskii lineage and the lineage clustering M. fuscus, M. chrysogaster, and M. leucogaster (around 370,000 years before present). Interestingly, the most recent speciation event in musk deer happened rather recently (140,000 years ago), which might have resulted from the diversified habitats and geographic barriers in southwest China caused by gigantic movements of the Qinghai-Tibetan Plateau in history. Combining the data of current distributions, fossil records, and molecular data of this study, we suggest that the historical dispersion of musk deer might be from north to south in China. Additionally, in our further analyses involving other pecora species, musk deer was strongly supported as a monophyletic group and a valid family in Artiodactyla, closely related to Cervidae.     

Molecular phylogenetic relationship of Epinephelus based on sequences of mtDNA Cty b

The mtDNA Cyt b gene was sequenced partially for Variola louti of Serranidae, Epinephelinae and seven endemic species of groupers—Epinephelus awoara, E. brunneus, E. coioides, E. longispinis, E. sexfasciatus, E. spilotoceps and E. tauvina in China. The seven endemic species and other seven foreign species of groupers—E. aeneus, E. caninus, E. drummondhayi, E. haifensis, E. labriformis, E. marginatus and E. multinotatus from the GenBank were combined and analysed as ingroup, while Variola louti was used as outgroup. We compared the 420 bp sequences of Cyt b among the 15 species and constructed two types of molecular phylogenetic trees with maximum parsimony method (MP) and neighbor-joining method (NJ) respectively. The results were as follows: (1) As to the base composition of mtDNA Cyt b sequence (402 bp) of 14 species of Epinephelus, the content of (A + T) was 53.6%, higher than that of (G + C) (46.4%). The transition/transversion ratio was 4.78 with no mutation saturation. (2) The cluster relationships between E. awoara and E. sexfasciatus, E. coioides and E. tauvina, E. longispinis and E. spilotoceps were consistent with phenotypes in taxonomy. (3) In the phylogenetic tree, the species in the Atlantic Ocean were associated closely with those in the Pacific Ocean, which suggested that the Cyt b sequences of Epinephelus were highly conserved. This may be attributed to the coordinate evolution. (4) In wel1-bred mating or heredity management, mating Epinephelus of the same branch should be avoided. It is likely to be an effective way to mate the species of the Atlantic Ocean with those of the Pacific Ocean to improve the inheritance species. __________ Translated from Acta Hydrobiologica Sinica, 2006, 30(4): 432–438 [译自: 水生生物学报]     

Molecular evolution of tephritid fruit flies in the genus Bactrocera based on the cytochrome oxidase I gene

Fruit flies of the genus Bactrocera (Diptera: Tephritidae) are one of the major economically important insects in Asia and Australia. Little attention has been given to analyses of molecular phylogenetic relationships among Bactrocera subgenera. By using mitochondrial cytochrome oxidase I gene (COI) sequences, the phylogenetic relationships among four subgenera, Asiadacus, Bactrocera, Hemigymnodacus, and Zeugodacus, were investigated. Nucleotide diversity within subgenera ranged from 11.7 to 12.4%, and the net divergence among subgenera ranged from 11.2 to 15.7%. Phylogenetic trees calculated from both maximum parsimony and neighbor-joining phylogenetic analysis methods were highly congruent in terms of tree topologies. Phylogenetic analysis of mitochondrial COI sequences suggests that tephritid fruit fly species, which attack cucurbit plants, that is, Asiadacus, Hemigymnodacus and Zeugodacus, were more closely related to each other than to fruit fly species of the subgenus Bactrocera, which attack plants of numerous families. Our data supports previous classification of Bactrocera based on morphological characters. However, the phylogenetic tree showed the polyphyletic of fruit flies in subgenus Zeugodacus. Possible causes of speciation among fruit flies species in this genus were also discussed.     

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 Systematics of Selene (Perciformes: Carangidae) Based on Cytochrome b Sequences

The marine fishes of the genus Selene are morphologically unique, although little is known about how these species are related to other members of the family Carangidae (Perciformes). In addition, questions remain about the potential validity of two putative species and how species groups with unique body forms within Selene are related. We used DNA sequences of the mitochondrial cytochrome b gene to reconstruct the phylogeny of the seven species of Selene along with five additional species of carangids. Maximum-likelihood and maximum-parsimony analyses were used to examine the sequence data and both phylogenetic methods were compared. Maximum-likelihood produced a monophyletic Selene, whereas parsimony analyses did not. Both maximum-likelihood and maximum-parsimony produced similar support for species groups within Selene. Maximum-likelihood produced two monophyletic subgroups within the genus Selene, the "long-finned" and "short-finned" Selene. Maximum-parsimony produced the same monophyletic "long-finned" group but a paraphyletic "short-finned" group. Both analyses confirm that S. brownii and S. setapinnis are distinct species, expunging the question of conspecificity. The phylogenetic placement of the most basal taxon within Selene, S. orstedii, was problematic and differed among analyses. More data are needed to resolve with confidence its correct phylogenetic placement and, thus, the monophyly of the genus Selene.     

Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences

Cyprinidae, the largest fish family, comprises ap-proximately 210 recognized genera and 2010 species that are distributed widely in Eurasia, East Indian Is-land, Africa, and North America[1]. Species richness of this family is the greatest in East Asia, for example, China has 122 genera and more than 600 species. It is difficult to build a comprehensive phylogeny of Cy-prinidae due to the large number of genera and species. The classification of this family has been subject to revisions an…     

Genetic diversity and the biogeographical process of Acheilognathus macropterus revealed by sequence variations of mitochondrial cytochrome b gene

In this study, thirty-six individuals of Acheilognathus macropterus were collected from the Heilongjiang River, the Yangtze River, and the Nandujiang River. Partial mitochondrial cytochrome b gene region (636 base pair) was sequenced to these samples and 22 haplotypes were found. With A. chankaensis and A. tokinensis as outgroups, their relationships were analyzed. The p-distances were calculated with Mega software and a molecular phylogenetic tree was constructed using the neighbor-joining (NJ) method. The proportions of main morphological characters were compared as well. P-distances showed that the genetic differences in A. macropterus samples were far smaller than those between these samples and the outgroups. The molecular phylogenetic tree shows that samples with barbels and those without barbels were intermingled. There was no distinctive difference in proportions of morphological characteristics among them. These results suggested that samples with barbels and those without barbels (formally identified as A. taenianalis) are the same species; A. taenianalis is synonymous with A. macropterus. The thirtysix individuals were grouped into five clades and the positions of the samples in the clades were correspondingly grouped within their geographical distributions. Among the five clades, clades 1 and 5 included samples from the Heilongjiang River and Nandujiang River respectively. The samples from the Yangtze River scattered into clades 2, 3, and 4. There were distinctive genetic differences (>5%) among them. Interestingly, the distributions of the 21 samples in these three clades were not correlated to their geographical distributions. It is postulated that these genetic differences were due to the bitterlings’ mating choice mechanism, the prozygotic isolation. The genetic differences between the fish from Nandujiang River and those from the mainland indicated that they were separated early. However, the small genetic differences among the samples and the positions of the fish from the Heilonjiang River in the molecular phylogenetic tree indicate that fish in Heilongjiang River might have dispersed from the Yangtze River to that area much later. __________ Translated from Acta Hydrobiologica Sinica, 2006, 39(2): 134–140 [译自: 水生生物学报]     

Phylogeny of the East Asian botiine loaches (Cypriniformes,Botiidae) inferred from mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> gene sequences

The Botiinae have traditionally represented a subfamily of the Cobitidae. At present, the classification and phylogenetic relationships of the Botiinae are controversial. To address systematic and phylogenetic questions concerning this group, we sequenced the complete cytochrome b gene from 34 samples, of which 24 represented 13 species of the East Asian botiine fishes, while the other 10 were non-botiine loach species. For the 1140 bp sequences determined, 494 sites were variable ones, of which 424 were parsimony informative. With Myxocyprinus asiaticus as an outgroup, molecular phylogenetic trees were constructed using the neighbor-joining, maximum parsimony, maximum likelihood and Bayesian methods. All molecular phylogenetic trees revealed that botiine fishes form a monophyletic group and are distantly related to other loaches, suggesting that the Botiinae should be placed in their own family. Within the Botiinae, there are three genera; Botia, Parabotia, andLeptobotia, each genus forming a monophyletic group, with the genus Botia as the most ancestral split. Our molecular results are in agreement with morphological analyses of botiines, suggesting that Botia is the ancestral genus, while Leptobotia and Parabotia were resolved as more derived sister groups.     

Phylogeographic relationships among worldwide populations of the cosmopolitan marine species, the striped gray mullet (Mugil cephalus), investigated by partial cytochrome b gene sequences

Several factors such as geographical barriers, demographic history, biological and ecological traits may contribute to delineate the evolutionary history of a species. The gray mullet, Mugil cephalus, represents an interesting case of a marine species with a coastal ecology and a cosmopolitan distribution. In this study, partial cytochrome b sequences were resolved for 177 M. cephalus specimens sampled from 14 different geographic sites, in order to investigate the genetic divergence and the phylogeographic relationship among populations at a global scale. Demographic parameters were also assessed. Analysis of partial cyt b sequences showed high levels of differentiation among populations from distant geographic areas as most populations harbored private alleles and showed reciprocal monophyly. Both phylogenetic trees and haplotype network indicate the East Australian haplotypes as the closest to the ancestor sequences, which leads to the hypothesis of an Indo-West Pacific center of origin for M. cephalus. The analyses of the molecular variance showed that the genetic variation in M. cephalus is mainly harbored among populations rather than within populations. The high variability indices (h, π) calculated on M. cephalus individuals pooled together and the very low variability indices detected at some geographic sampling sites suggest that gray mullet populations have undergone a long-term reproductive isolation characterized by events of population abundance reductions which may have favored genetic differentiation among populations.     

Molecular phylogenetic relationships of Melanthiaceae (Liliales) based on plastid DNA sequences

Melanthiaceae (Liliales) comprise 17 genera of rhizomatous or bulbous perennials and are distributed across the Northern Hemisphere. The relationships among the five tribes in this family have been evaluated in many molecular and morphological studies. In this study, we performed a phylogenetic analysis of the 17 genera, including 106 species of Melanthiaceae sensu APG III and nine related species as outgroups, based on sequences of five plastid regions (atpB, rbcL, matK, ndhF and trnL‐F). Support values for the monophyly of the family (BS_MP = 96%, BS_ML = 100%, PP_BI = 1.00) and each tribe were improved in comparison with previous studies. Among the tribes, Melanthieae were sister to the remainder of the family and sister relationships between Xerophylleae and Parideae (BS_MP = 96%, BS_ML = 100%, PP_BI = 1.00) and Chionographideae and Heloniadeae (BS_MP = 96%, BS_ML = 100%, PP_BI = 1.00) were confirmed. Notably, the generic concept of Veratrum s.l. including Melanthium was not supported in the present study and these genera should be treated as distinct. In the case of Parideae, the relationship of Trillium govanianum to the other species remains uncertain and requires further studies. Finally, we mapped seven representative morphological characters onto the molecular phylogenetic tree for Melanthiaceae.     

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.     

Molecular Systematics of the Family Mormoopidae (Chiroptera) Based on Cytochrome b and Recombination Activating Gene 2 Sequences

We examined 1140 bp of the mitochondrial cytochrome b gene and 1398 bp of the nuclear RAG2 gene to investigate the systematics of the eight species of bats within the family Mormoopidae. It was concluded that within the genus Pteronotus there were four valid subgenera: Phyllodia, Chilonycteris, Pteronotus, and an undescribed subgenus. Within Pteronotus, P. parnellii either was part of an unresolved tetratomy with the other three subgenera (cytochrome b data) or was basal (RAG2 and combined data). For three species, P. gymnonotus, P. macleayii, and P. quadridens, our sample revealed little geographic variation. In P. davyi and P. parnellii, the magnitude of genetic distance suggests the possibility of two biological species existing within the currently recognized taxa. Within P. personatus, there was substantial geographic variation partitioned in a step-like fashion among our specimens. Neither of the species within the genus Mormoops showed the deep distance nodes present in P. davyi, P. parnellii, and P. personatus. Cytochrome b and RAG2 data indicated that M. megalophylla evolved recently from its common ancestor. Although there was considerable agreement among the branching patterns for the nuclear and mitochondrial genes, both genes failed to provide robust data concerning the evolutionary relationships among the subgenera.     

Multiphasic oxidation-reduction of cytochrome b in the succinate-cytochrome c reductase

The triphasic course previously reported for the reduction of cytochrome b in the succinate-cytochrome c reductase by either succinate or duroquinol has been shown to be dependent on the redox state of the enzyme preparation. Prior reduction with increasing concentrations of ascorbate leads to partial reduction of cytochrome c₁, and a gradual decrease in the magnitude of the oxidation phase of cytochrome b. At an ascorbate concentration sufficient to reduce cytochrome c₁ almost completely, the reduction of cytochrome b by either succinate or duroquinol becomes monophasic. Owing to the presence of a trace amount of cytochrome oxidase in the reductase preparation employed, the addition of cytochrome c makes electron flow from substrate to oxygen possible. Under such circumstances, the addition of a limited amount of either succinate or duroquinol leads to a multiphasic reduction and oxidation of cytochrome b. After the initial three phases as described previously, cytochrome b becomes oxidized before cytochrome c₁ when the limited amount of added substrate is being used up. However, at the end of the reaction when cytochrome c_a is being rapidly oxidized, cytochrome b becomes again reduced. The above observations support a cyclic scheme of electron flow in which the reduction of cytochrome b proceeds by two different routes and its oxidation controlled by the redox state of a component of the respiratory chain.     

A neonatal polyvisceral failure linked to a de novo homoplasmic mutation in the mitochondrially encoded cytochrome b gene

Mutations within the mitochondrially encoded cytochrome b (MTCYB) gene are heteroplasmic and lead to severe exercise intolerance. We describe an unusual clinical presentation secondary to a novel homoplasmic mutation within MTCYB. The m.15635T > C transition (S297P) was carried by a newborn who presented with a polyvisceral failure. This mutation was responsible for a complex III deficiency. It was homoplasmic in all tissues tested and was undetectable in patient’s mother. Functional analyses, including studies on patient’s cybrid cell lines, demonstrate the pathogenicity of this variant. Our data show that mutations within MTCYB can be responsible for severe phenotype at birth.     

Molecular Systematics of the Malagasy Babblers (Passeriformes: Timaliidae) and Warblers (Passeriformes: Sylviidae), Based on Cytochrome b and 16S rRNA Sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy “babblers” are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy “babblers” are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Molecular phylogeny of parasitic Platyhelminthes based on sequences of partial 28S rDNA D1 and mitochondrial cytochrome c oxidase subunit I

The phylogenic relationships existing among 14 parasitic Platyhelminthes in the Republic of Korea were investigated via the use of the partial 28S ribosomal DNA (rDNA) D1 region and the partial mitochondrial cytochrome c oxidase subunit 1 (mCOI) DNA sequences. The nucleotide sequences were analyzed by length, G + C %, nucleotide differences and gaps in order to determine the analyzed phylogenic relationships. The phylogenic patterns of the 28S rDNA D1 and mCOI regions were closely related within the same class and order as analyzed by the PAUP 4.0 program, with the exception of a few species. These findings indicate that the 28S rDNA gene sequence is more highly conserved than are the mCOI gene sequences. The 28S rDNA gene may prove useful in studies of the systematics and population genetic structures of parasitic Platyhelminthes.