Nearly complete mitochondrial genome of Polyascus gregaria and the phylogenetic relationships among maxillopodans

We determined for the first time the nearly complete mitochondrial genome sequence of the entozoic Polyascus gregaria, a representative of Rhizocephala, Cirripedia. The nearly complete mitogenome was 15, 465 bp in length, consisting of 11 protein-coding genes, two rRNA genes, 22 tRNA genes and one major incomplete noncoding region. In total there are 73 overlapping nucleotides and 17 spacers between genes. All genes sequenced in P. gregaria mtDNA (including RNAs) were encoded on the same strand of the DNA, and the gene arrangement differed from that of other metazoan animals. The mitochondrial genome rearrangements included translocation of at least 8 genes and even inversion of the coding polarity of at least 2 genes. Comparative analysis of the gene orders with other maxillopodan mtDNAs showed that the unique characteristics of the thoracican cirripeds lineage were not observed in this representative of rhizocephalan. Phylogenetic analyses supported a close affinity of Rhizocephala to Thoracica. By adding the mitochondrial genomes from 4 copepods, the reciprocally monophyletic cirripeds and copepods clustered as sister groups, refusing the close relationship between Cirripedia and Remipedia. However, the monophyly of Maxillopoda was not supported in this study.     

Morphological evolution and phylogenetic relationships of the European ground voles (Arvicolidae, Rodentia)

Brunet-Lecomte, P. & Chaline, J. 1991 01 15: Morphological evolution and phylogcnctic relationships of the European ground voles (Arvicolidae. Rodentia). Lethaia. Vol. 24. pp. 45–53. Oslo. ISSN 0024–1164. A new morphological study of the first lower molar M₁ of European Quaternary ground voles (Arvicolidac. Rodcntia. Microtus (Terricola)) by means of multivariate analysis renews the systematics. phylogenetic relationships and their evolutionary group history. An Allophaiomyan origin of ground voles has been confirmed and the evolution of Mediterranean and middle Europcan groups has now been clarified. Primitive species of middle European groups display plesiomorphics. except for M. (T.) arvalidens, which shows certain apomorphies of the present species. The occurrence of M. (T.) multiplex in France at the end of the middle Pleistocene before the appearance of M. (T.) suhterraneus completely reverses previous ideas which considered that M. (T.) multiplex was a sibling species derived from M. (T.) subterraneus during the Würmian glaciation. The Atlantic species M. (T.) pyrenaicus is probably derived from the middle Pleistocene species M. (T.) mariaclaudiue whose exact origin is unknown. M. (T.) sauii, M. (T.) tarentina. M. (T.) melirensis and M. (T.) henseli belong to the same geographic group. Perhaps M. (T.) savii derived from M. (T.) tarentina or shares the same ancestor with M. (T.) tarentina. M. (T.) duodecimcostarus probably indirectly derived from an Iberian specics of Allophuiomys such as A. chalinei, while M. (T.) lusitanicus was separated from M. (T.) duodecimcostutus about 60,000 years ago. A sketch of the stratigraphical records and geographical distribution of the Terricola species in Western Europe showing their phylogenetic relationships and migrations during the middle and upper Pleistocene is included. Morphometry, variance analysis, phylogeneric relationships. Mammalia. Rodentia. Arvicolidae. Microtus, Terricola.     

p-SINE1-like intron of the CatA catalase homologs and phylogenetic relationships among AA-genome Oryza and related species

 Intron-2 of the Oryza sativa CatA catalase gene is similar in nucleotide sequence to p-SINE1, a retroposon, and seems to have been added to the ancestral genome of rice. To examine when the p-SINE1-like intron was inserted into CatA during the evolutionary divergence of Oryza species, and to elucidate the evolutionary relationships among Oryza species using the sequence of the intron as a marker, we performed polymerase chain reaction (PCR) analyses of 32 accessions of 17 Oryza species with various genome types. Agarose-gel electrophoresis of the PCR products revealed that all the Oryza species with an AA genome have the CatA homolog with the intron, whereas other Oryza species have the CatA homolog without the intron. These results indicate that intron-2 of CatA is a good marker for distinguishing species with an AA genome among Oryza species. Sequencing of the PCR products showed that all the introns are similar to p-SINE1, though with slight variations in length. We also performed PCR analyses using four accessions of three species in genera related to Oryza, and found that there is an intron in the CatA homolog of Leersia perrieri. On the other hand, the CatA homolog of Porteresia coarctata has no intron. Sequence data showed that the L. perrieri homolog has a p-SINE1-like intron similar to that in Oryza species with an AA genome. These results suggest that the p-SINE1-like intron was already present in the common ancestor of Oryza and L. perrieri and was then lost in the ancestors of P. coarctata and of the Oryza species other than those with an AA genome. The phylogenetic tree of Oryza species with an AA genome based on the nucleotide sequences of the introns leads us to propose that Oryza species with an AA genome evolved from an ancestor of Oryza longistaminata. Received: 29 August 1998 / Accepted: 2 November 1998     

Molecular identification and phylogenetic relationships among the species of the genus Oligoryzomys (Rodentia, Cricetidae) present in Argentina, putative reservoirs of hantaviruses

The systematics and geographical distribution of the species of Oligoryzomys present in Argentina are poorly known. From some of the species different hantavirus genotypes have been recovered. In order to contribute to the accurate identification of those species and to infer their phylogenetic relationships, we analysed data of restriction sites and sequences of the mtDNA d -loop region. The samples used represent almost all Oligoryzomys species known to occur in Argentina. The trees obtained with the two types of data were similar, showing high bootstrap values for the majority of the nodes. Our results support the idea that the specific name Oligoryzomys longicaudatus should be applied only to individuals from the south of Argentina and Chile and confirm that O. nigripes and O. delticola are conspecific. Specimens identified as O. flavescens conform three related clades, probably belonging to a species complex. This study also emphasises that the use of a DNA fragment characterised by a high evolutionary rate compare with other mitochondrial segments as the d -loop, was appropriate to infer the phylogenetic relationships in a group originated by a rapid speciation process. We also suggest the following modifications in the rodent–hantavirus relationships: the only viral genotype associated to O. longicaudatus would be Andes Sout, while O. chacoensis would be the natural host of the genotype Oran. One of the forms of the O. flavescens complex would be the natural host of the genotype Bermejo. Our data are consistent with the hypothesis that each hantavirus genotype is associated with a specific rodent host.     

Genetic diversity and phylogenetic relationships in the zokor subfamily myospalacinae (Rodentia,Muridae) inferred from RAPD-PCR

Zokors (Myospalacinae) is a group of rodents specialized for underground life, endemics of eastern Asia, which is taxonomically and evolutionarily poorly studied. We examined genetic diversity and phylogenetic relationships among zokors (Myospalax myospalax, Myospalax aspalax, Myospalax armandii, Myospalax psilurus, Myospalax smithii) using RAPD-PCR. The subfamily Myospalacinae was shown to be monophyletic and contain four evolutionary branches: M. myospalax, M. aspalax-M. armandii, M. smithii and M. psilurus. Genetic differences and high differentiation were found among the species and between two geographic forms of Manchurian zokor M. psilurus from the marginal parts of the range, Transbaikalia and Primorye. The psiluris phylogroup was shown to be dichotomically divided into two clades according to the geographical distribution of animals from Transbaikalia and Primorye. The genetic differentiation between the geographic forms of M. psilurus corresponded to the differentiation between morphologically similar species M. aspalax and M. armandii. M. armandii is a sister taxon with regard to M. aspalax. This new evidence on the evolutionary relationships among zokors does not contradict the traditional views inferred from morphological, karyological, and allozyme data, on apartness of M. myospalax and the character of evolution in this group. The species status of Myospalax psilurus Milne-Edwards, 1874, M. epsilanus Thomas, 1912, and M. armandii Milne-Edwards, 1867, which had been suggested earlier on the basis of biochemical and karyological data, was confirmed.     

Phylogenetic relationships among Robertsonian karyomorphs of Graomys griseoflavus (Rodentia,Muridae) by mitochondrial cytochrome b DNA sequencing

Graomys griseoflavus (Waterhouse 1837) is a phyllotine murid rodent with a Robertsonian autosomal polymorphism, having been described 2n = 42, 41, 38, 37, 36, 35 and 34 karyomorphs, and proposed a chromosomal divergence pathway accounted by four sequential Robertsonian fusions. Sequences of a fragment (422 bp long) of the cytochrome b (cyt b) mitochondrial gene and its 5' flanking region (tRNA Glu) were obtained for 19 Graomys griseoflavus from different karyomorphs to infer phylogenetic relationships by using maximum parsimony. Outgroups considered for this analysis were the phyllotine rodents Phyllotis xanthopygus and Eligmodontia typus cyt b sequences. Three trees were produced showing the 2n = 38-34 karyomorphs grouped in a single clade while the 2n = 42-41 animals formed a different one. This is in agreement with a hypothesis of a single origin for 2n = 38-34 Robertsonian karyomorphs from the ancestral 2n = 42.     

尼罗鳄线粒体基因组全序列分析及鳄类系统发生关系的探讨

大多数脊椎动物的线粒体基因组（约16—18kb）的组成是相对较稳定的,但在不同类群中,线粒体基因组在基因结构和基因排列方式等方面均显示了极大的多样性,这种多样性可能反映了真核细胞不同的进化路线（Saccone et al．,1999）。就目前的研究而言,线粒体基因组是惟一一个能够从基因组水平上来分析动物系统发生的分子标记,可以从线粒体基因组序列信息、基因组成及基因排列方式等进行多方位的分子进化研究,因而线粒体基因组全序列将成为动物分子系统发生最有力的证据（Saccone et al．,1999）。     

On the phylogenetic relationships among tetraphyllidean,lecanicephalidean and diphyllidean tapeworm genera

This study had two main objectives: (1) to construct an extensive, explicit list of characters and character states that might serve as a starting point, and perhaps even a model, for the compilation of a more complete list of characters for all cestode taxa; and (2) to use this character list to generate a hypothesis of the phylogenetic relationships among species representing most of the tetraphyllidean, lecanicephalidean and diphyllidean genera. Specimens of one species in each of 48 genera of tetraphyllideans, eight genera of lecanicephalideans, the three genera of diphyllideans, two genera of proteocephalideans and two genera of trypanorhynchs, were examined as whole-mounts and sections, with light and scanning electron microscopy. A list of 120 morphological characters was compiled. Four phylogenetic analyses were conducted using PAUP* and/or NONA. The first was a comprehensive analysis with the 56 tetraphyllidean and lecanicephalidean species as ingroups and the remaining seven species as outgroups. The second was an analysis of the three diphyllidean species as ingroups and the two proteocephalidean and the two trypanorhynch species as outgroups. The third was an analysis of the eight lecanicephalidean species and the tetraphyllideans Echeneibothrium sp. and Pseudanthobothrium n. sp. as ingroups and an outgroup consisting of the seven species used as outgroups in the first analysis. In the fourth analysis, the ingroup consisted of the 14 hooked tetraphyllideans (onchobothriids), and the outgroup consisted of the seven species used as outgroups in the first analysis. The results of these analyses support the following phylogenetic hypotheses: The diphyllideans are monophyletic and Echinobothrium n. sp. and Macrobothridium sp. are more closely related to one another than either is to Ditrachybothridium macrocephalum. The tetraphyllideans, lecanicephalideans and proteocephalideans are more closely related to each other than they are to the diphyllideans or the trypanorhynchs. The ordinal status of the lecanicephalideans is dubious. The lecanicephalidean species are more closely related to some of the tetraphyllidean taxa than these tetraphyllidean taxa are to the remainder of the tetraphyllidean taxa. The proteocephalideans appear to belong within the tetraphyllidean clade. The tetraphyllidean species Echeneibothrium sp. and Pseudanthobothrium n. sp. are members of the lecanicephalidean clade. The position of Discobothrium n. sp. within the lecanicephalideans is dubious. Within the tetraphyllideans, the non-acetabulate species Litobothrium daileyi, Disculiceps galapagoensis and Cathetocephalus sp. are the most basal members of the group. The family Onchobothriidae is monophyletic, as it is currently defined. Within the onchobothriids, the uniloculate species are basal to the multiloculate species; the species with unipronged hooks are basal to the species with multipronged hooks. Although relationships among the phyllobothriids, as they are currently defined, remain poorly resolved, the family Phyllobothriidae is not monophyletic. These results suggest that some aspects of the classification of the lecanicephalidean and tetraphyllidean taxa require revision. However, such revision should be based on further analyses including a broader representation of the genera and species in these groups.     

The complete mitochondrial genome of Microtus fortis calamorum (Arvicolinae, Rodentia) and its phylogenetic analysis

Microtus fortis is a special resource of rodent in China. It is a promising experimental animal model for the study on the mechanism of Schistosome japonicum resistance. The first complete mitochondrial genome sequence for Microtus fortis calamorum, a subspecies of M. fortis (Arvicolinae, Rodentia), was reported in this study. The mitochondrial genome sequence of M. f. calamorum (Genbank: JF261175) showed a typical vertebrate pattern with 13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs and one major noncoding region (CR region).The extended termination associated sequences (ETAS-1 and ETAS-2) and conserved sequence block 1 (CSB-1) were found in the CR region. The putative origin of replication for the light strand (O(L)) of M. f. calamorum was 35bp long and showed high conservation in stem and adjacent sequences, but the difference existed in the loop region among three species of genus Microtus. In order to investigate the phylogenetic position of M. f. calamorum, the phylogenetic trees (Maximum likelihood and Bayesian methods) were constructed based on 12 protein-coding genes (except for ND6 gene) on H strand from 16 rodent species. M. f. calamorum was classified into genus Microtus, Arvcicolinae for the highly phylogenetic relationship with Microtus kikuchii (Taiwan vole). Further phylogenetic analysis results based on the cytochrome b gene ranged from M. f. calamorum to one of the subspecies of M. fortis, which formed a sister group of Microtus middendorfii in the genus Microtus.     

基于线粒体Cyt b 和核基因ZFY 探讨羊族物种之间的系统发生关系

为了阐明羊族物种之间的系统发生关系并解决岩羊属中矮岩羊物种的有效性问题,本文测定了来自金沙江河谷地区栖息于林线以上岩羊和林线以下矮岩羊共226 份粪便DNA 样品的线粒体Cyt b 基因全序列(1 140 bp)和核基因ZFY 部分序列(612 bp),结合从GenBank 中检索到的羊族物种同源DNA 序列进行比较,利用最大简约法和最大似然法构建分子系统发育树,根据获得的拓扑结构初步探讨它们的系统进化关系。结果表明,绵羊属的绵羊与山羊属、塔尔羊属、岩羊属各物种亲缘关系最远,喜马拉雅塔尔羊和岩羊属、山羊属的亲缘关系最近。在进化树的岩羊属这一分支中,金沙江河谷地带岩羊和矮岩羊与内蒙古、青海、四川其它地理种群的岩羊聚为一支,同时分布在这一区域的部分岩羊和矮岩羊在Cyt b 基因和ZFY 基因单倍型上存在共享现象。历史上的气候事件可能造成金沙江河谷地带岩羊和矮岩羊种群之间相互迁移,偏雄性扩散促进了各地理种群之间的基因交流。因此不支持矮岩羊为独立的物种,建议将金沙江河谷地带的岩羊和矮岩羊都划分到岩羊四川亚种(Pseudois nayaur szechuanensis)。由于它们的形态和生态上存在一定的分化,建议将林线以下矮岩羊作为一个独立的管理单元进行保护与管理。     

大头蛙和脆皮大头蛙线粒体3个基因的测定及两栖类亲缘关系研究

现存的两栖类系统发生关系一直存在争议,特别是3个目间的亲缘关系。本文设计了5对引物,扩增和测定了大头蛙和脆皮大头蛙线粒体12S和16S rRNA基因和Cytb基因的全序列。在对所测序列进行分析的同时,基于3个基因全序列的相加数据,运用MEGA 3.1和PHYLIP 3.64软件中的NJ法、MP法和ML法,对两爬类17个物种,以鱼类非洲肺鱼为外群,重建出3个树形完全一致的分子系统树。研究结果显示:现存两栖类中无尾目和有尾目为姐妹群关系,并推断有尾目内小鲵科和隐鳃鲵科亲缘关系较近。此外,在研究两栖类系统发生关系方面,作者分析前人研究中产生两种不同观点的可能原因,同时总结了在此类研究中产生偏差的几种影响因素。     

mtDNA variation and evaluation of phylogenetic relationships among karyotypically polymorphic populations of Microtus (Terricola) thomasi (Arvicolidae, Rodentia) from Greece

The Balkan endemic species Microtus (Terricola) thomasi – Thomas' vole – is widely distributed in the Greek mainland and presents regionally confined karyotypic forms. In order to test the significance of geographical isolation and/or karyological differences in microevolutionary processes at the intraspecific level we used restriction enzymes and partial sequencing to study the polymorphism of the mtDNA d -loop control region in ten Greek populations. An overall high rate of both inter- and intrapopulation polymorphism was observed. The mtDNA diversity was unevenly distributed so that most of the populations studied were very similar and closely related, and only a few of them were clearly differentiated from the others. The mtDNA analysis failed to reveal any clear variation pattern that could be correlated with karyotypic forms or geographical proximity of the populations studied. Instead, the mtDNA phylogeny gave evidence in support of the coexistence of non-polymorphic (2 n  = 44) and polymorphic (2 n  < 44) karyotypic forms within the ancestral Greek M. (T.) thomasi stock. Interestingly, only one population (Agios Stefanos) seemed to significantly diverge from all the others in both methods used, forming a well-supported paraphyletic clade. Allozymic studies have already reported similar results, corroborating the genetic peculiarity of this population.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 55–68.     

Comparative mitochondrial genomics and phylogenetic relationships of the Crossoptilon species (Phasianidae,Galliformes)

Background

Phasianidae is a family of Galliformes containing 38 genera and approximately 138 species, which is grouped into two tribes based on their morphological features, the Pheasants and Partridges. Several studies have attempted to reconstruct the phylogenetic relationships of the Phasianidae, but many questions still remain unaddressed, such as the taxonomic status and phylogenetic relationships among Crossoptilon species. The mitochondrial genome (mitogenome) has been extensively used to infer avian genetic diversification with reasonable resolution. Here, we sequenced the entire mitogenomes of three Crossoptilon species (C. harmani, C. mantchuricum and C. crossoptilon) to investigate their evolutionary relationship among Crossoptilon species.

Results

The complete mitogenomes of C. harmani, C. mantchuricum and C. crossoptilon are 16682 bp, 16690 bp and 16680 bp in length, respectively, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. C. auritum and C. mantchuricum are more closely related genetically, whereas C. harmani is more closely related to C. crossoptilon. Crossoptilon has a closer relationship with Lophura, and the following phylogenetic relationship was reconstructed: ((Crossoptilon + Lophura) + (Phasianus + Chrysolophus)). The divergence time between the clades C. harmani-C. crossoptilon and C. mantchuricum-C. auritum is consistent with the uplift of the Tibetan Plateau during the Tertiary Pliocene. The Ka/Ks analysis showed that atp8 gene in the Crossoptilon likely experienced a strong selective pressure in adaptation to the plateau environment.

Conclusions

C. auritum with C. mantchuricum and C. harmani with C. crossoptilon form two pairs of sister groups. The genetic distance between C. harmani and C. crossoptilon is far less than the interspecific distance and is close to the intraspecific distance of Crossoptilon, indicating that C. harmani is much more closely related to C. crossoptilon. Our mito-phylogenomic analysis supports the monophyly of Crossoptilon and its closer relationship with Lophura. The uplift of Tibetan Plateau is suggested to impact the divergence between C. harmani-C. crossoptilon clade and C. mantchuricum-C. auritum clade during the Tertiary Pliocene. Atp8 gene in the Crossoptilon species might have experienced a strong selective pressure for adaptation to the plateau environment.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1234-9) contains supplementary material, which is available to authorized users.     

Alignment and phylogenetic analysis of beta-fibrinogen intron 7 sequences among avian orders reveal conserved regions within the intron

We sequenced beta-fibrinogen intron 7 (beta-fibint 7) from 28 species of birds, representing 18 families in nine orders. Although the antiquity of the avian orders is estimated to be 55 to 90 Myr, and numerous indels have accrued among diverging lineages, the intron sequences were not difficult to align. However, alignment of avian sequences with mammal or snake sequences was difficult, and the residual phylogenetic signal was weak. beta-fibint 7 is an AT-rich intron, and its base composition varies little over the diversity of birds represented by our sample. Alignment of these anciently diverged sequences reveals at least five clusters of conserved nucleotides; at least two clusters appear to be in excess of the minimal set usually associated with intron excision, but their functions are unknown. Two equally most-parsimonious (MP) trees were found when indels were not included in the phylogenetic analysis, and six such trees were found when indels were included. The Neighbor-Joining and maximum-likelihood trees were identical to each other and to one of the MP trees in each MP analysis. Indels, as well as nucleotide substitutions, are phylogenetically informative, and bootstrap support exceeded 90% for 21 of 24 inferred nodes when indels were included in the MP analysis. All traditional orders represented by two or more species appear monophyletic. Relationships among avian orders are strongly supported with the exception of an inferred sister-group relationship between Caprimulgiformes and Columbiformes. A relatively close relationship between Piciformes and Passeriformes is inferred, at odds with earlier DNA-DNA hybridization studies but consistent with traditional classifications. Among Passeriformes, the traditional perspective of a sister-group relationship of suboscines and oscines is supported, as is the subsequent split of the oscines into a lineage representative of the Corvida before the diversification of the Passerida. The four species of owls divide into two strongly supported clades, corresponding to the widely accepted bifurcation of owls into two families, Tytonidae and Strigidae. A sister-group relationship between gallinaceous birds and waterfowl, the Galloanserae, is also strongly supported.     

Orthodox and unorthodox phylogenetic relationships among tunas revealed by the nucleotide sequence analysis of the mitochondrial DNA control region

A phylogeny of all eight recognized taxa of the genus Thunnus was constructed from approximately 400 base pairs of sequence of the mitochondrial DNA (mtDNA) control region. The PCR-amplified control region I segment studied contained a total of 186 variable sites and 159 phylogenetically informative sites. Diagnostic sequences for every taxon were identified. Neighbour-joining phylogenies supported monophyletic origins of the temperate subgenus Thunnus and of the tropical subgenus Neothunnus . Similar results were obtained by maximum parsimony analyses except that there was no support for a monophyletic origin of the subgenus Thunnus . Bigeye tuna, which have been difficult to place in either subgenus using conventional morphological data, was identified as the sister species of Neothunnus . Within the subgenus Thunnus , the Atlantic bluefin and Southern bluefin tunas were shown to be sister taxa of the highly divergent monophyletic clade formed by the Pacific northern bluefin and the Albacore tunas. The conspecific Atlantic ( T. thynnus thynnus ) and Pacific ( T. t. orientalis ) northern bluefin tunas were more divergent (Tamura-Nei distance 0·145 ± 0·019) from each other than the average distance separating most species-pairs within the genus. Thus, a re-examination of their status as subspecies of T. thunnus is warranted.     

Restriction fragment length polymorphism of mitochondrial DNA and phylogenetic relationships among five species of Indian freshwater turtles

DNA-based identification of species for phylogenetic analysis as well as forensic identification is widely being carried out with the help of polymerase chain reaction (PCR). In this study, a successful effort has been made to identify 5 species of Indian freshwater turtles, including 3 hard-shell turtles (Geoemydidae), i.e. Kachuga dhongoka, K. kachuga and Geoclemys hamiltoni, and 2 species of soft-shell turtles (Trionychidae), i.e. Aspideretes gangeticus and Lissemys punctata punctata, by using a well-optimized PCR-RFLP method. The analysis of nucleotide sequence variations in the PCR-amplified mitochondrial cyt-b genes (encoding cytochrome b) from the 5 species revealed its usefulness in the taxonomic differentiation of these species. On the basis of cyt-b sequence data and the PCR-RFLP pattern, a phylogeny was developed to resolve the genetic relationships between these species, living in the same habitat type. In comparison, the PCR-RFLP of mitochondrial 16S rDNA genes appeared less decisive in analysing phylogenetic relationships or even in species differentiation. Further, the molecular method (PCR-RFLP) developed here is simple, rapid, reliable and reproducible; hence it can be routinely applied for species identification, essential for conservation and management of endangered chelonian species.     

Comparison of complete mitochondrial DNA control regions among five Asian freshwater turtle species and their phylogenetic relationships

The complete mitochondrial DNA (mtDNA) control regions (CR), cytochrome b (Cyt b), NADH dehydrogenase subunit 4 (ND4) and cytochrome coxidase subunit I (CO I) genes of four Asian freshwater turtles, Mauremys japonica, Ocadia sinensis, M. mutica, and Annamemys annamensis, were sequenced using universal PCR and long-PCR techniques. Combined with CR sequences of Chinemys reevesii, the composition and structure of CR of the five species were compared and analyzed. Three functional domains (TAS, CD and CSB) in CR and their conserved sequences (TAS, CSB-F, CSB-1, CSB-2, and CSB-3) were identified based on sequence similarity to those of other turtles. At the 3' end of CSB, six type motifs of variable number of tandem repeats (VNTRs) of five species were recognized, in which the TTATATTA motif may be the VNTR motif of the ancestral species of these five turtles. Comparison of nucleotide divergences among Cyt b, ND4, CO I, and CR of 11 turtle species using transitions + transversions and transversions-only methods supported the conclusion that CR evolved 2.6- to 5.7-fold faster than the other mtDNA genes. After excluding VNTRs of CR, molecular phylogenetic trees were constructed with maximum parsimony, maximum likelihood and Bayesian inference methods. The results supported an expanded clade of Mauremys, which included species formerly in Ocadia, Chinemys, Mauremys, and Annamemys; this was also reflected in the results of VNTR analysis.     

Matrix representation in reconstructing phylogenetic relationships among the eukaryotes.

The application of the method of matrix representation (MRP) addresses several problems associated with reconstructing phylogenetic relationships among composite organisms such as the eukaryotes. By allowing multiple molecular-sequence and non-molecular data sets to be combined into a single, relatively compact matrix for joint analysis, MRP addresses problems associated with the depth, diversification and specialization of eukaryotic lineages. Characters whose distributions may have been affected by endosymbiotic lateral transfer can be identified by compatibility analysis of MRP-generated hybrid matrices. In conjunction with variant-filtering techniques, MRP can be used to map patterns of lateral transfer in a given phylogenetic tree. These applications are illustrated with molecular-sequence and non-molecular data sets for eukaryotes.     

The complete mitochondrial genome of Japanese sparrowhawk (Accipiter gularis) and the phylogenetic relationships among some predatory birds

Phylogenetic relationships among raptors, especially various groups are rather complex and controversial. We determined the complete mtDNA of Japanese sparrowhawk, and estimated phylogenetic trees based on the complete mtDNA alignment of it and 36 other raptor species, to clarify raptor phylogenetics. Phylogenetic trees were also estimated using a multiple sequence alignment of 12S rRNA and 16S rRNA from 81 typical species in GenBank, to further clarify the phylogenetic relationships of several groups among the raptors. The new mtDNA is a circular molecule, 17 917 bp in length, containing the 37 typical genes, with a pseudo-control region. ATG is generally the start codon, TAA is the most frequent stop codon. All tRNAs can be folded into canonical cloverleaf secondary structures except for tRNA^{Ser (AGY)} and tRNA^{Leu (CUN)}, which are missing the “DHU” arm. Phylogenetic relationships demonstrate that raptors can be divided into four branches: Accipitriformes, Falconiformes, Strigiformes and Caprimulgiformes in this study. We suggest that Accipitriformes should to be an independent order, Accipitriformes. The results also indicate that Accipitriformes contains three clades: Accipitridae, Pandionidae and Sagittariidae. Strigiformes includes species from Tytonidae and Strigidae. Caprimulgiformes contains Aegothelidae and Caprimulgidae.