Phylogenetic structure of the marsupial family dasyuridae based on cytochromeb DNA sequences

Archer provided the most recent and comprehensive suprageneric classification of dasyurid marsupials. Five extant subfamilies, two with constituent tribes, were recognized on the basis of morphological, serological, and allozyme data. Phylogenetic relationships among these groups, however, were totally unresolved. Subsequent molecular studies suggested that the endemic New Guinean subfamilies Muricinae and Phascolosoricinae are parts of larger Australian clades. Our objective in this study was to test the monophyly of Archer's seven groups and estimate relationships among them using DNA sequences from the mitochondrial cytochromeb (cyt-b) gene. We report 657 bp ofcyt-b from 32 dasyuroid species. Phylogenetic analysis of these data leads to the following conclusions: (1) muricines form a clade within Phascogalinae that includes endemic New GuineanAntechinus species; (2) the two genera of Phascolosoricinae are part of a more inclusive Dasyurinae; (3) Sminthopsinae is monophyletic, but the tribes Sminthopsini and Planigalini are not; and (4) the dasyurine tribes Dasyurini and Parantechini are probably not monophyletic. Relationships among Sminthopsinae, Dasyurinae (including phascolosoricines), and Phascogalinae (including muricines) remain unresolved.     

Phylogenetic relationships among deer in China derived from mitochondrial DNA cytochromeb sequences

The phylogenetic relationships of Cervidae and Moschidae were examined using partial sequence data of mitochondrial DNA (mtDNA) cytochromeb. Ten new sequences were obtained for six species of Cervidae and Moschidae, and aligned with those previously reported for other deer species. Our results demonstrated that the phylogenetic status of the taxa inferred from molecular data was congruent with taxonomy based on morphological studies. Cervidae formed a monophyletic group that consists of four subfamilies: Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. Moschidae occurred at the base of the Cervidae clade. On the basis of molecular clocks for genetic distance, the divergence time of mtDNA haplotypes within the subfamily Cervinae, among subfamilies in Cervidae, and between Moschidae and Cervidae was estimated to date 2–7 MYA, 6–10 MYA and 8–13 MYA, respectively.     

基于线粒体COI基因全序列的直翅目部分类群系统发育关系分析

该研究基于直翅目56种昆虫的COI基因全序列构建了该目部分类群间的系统发育关系,同时也分析了COI基因编码的氨基酸序列构建直翅目系统发育关系的可靠性。将COI序列按照密码子一、二、三位点划分,分别计算PBS(partioned Bremer support)值,评估蛋白质编码基因密码子不同位点的系统发生信号强度。分析结果支持螽亚目和蝗亚目的单系性;剑角蝗科、斑腿蝗科、斑翅蝗科、网翅蝗科和槌角蝗科5科均不是单系群,科间的遗传距离在0.107~0.153之间变化,与其他科相比遗传距离较小,符合将这5科合并为一科(即蝗科)的分类系统,瘤锥蝗科和锥头蝗科归为锥头蝗总科,癞蝗科单独成为一科,这也与Otte(1997)系统的划分一致。根据PBS值的大小推断密码子第三、第一位点对系统树分支的贡献比第二位点大,并且较长的序列含有较多的信息位点。研究也证实将各物种COI基因之间的遗传距离作为直翅目划分科级阶元的工具是可行的。     

Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences

A molecular phylogenetic analysis of the genus Phytophthora was performed, 113 isolates from 48 Phytophthora species were included in this analysis. Phylogenetic analyses were performed on regions of mitochondrial (cytochrome c oxidase subunit 1; NADH dehydrogenase subunit 1) and nuclear gene sequences (translation elongation factor 1alpha; beta-tubulin) and comparisons made to test for incongruence between the mitochondrial and nuclear data sets. The genus Phytophthora was confirmed to be monophyletic. In addition, results confirm that the classical taxonomic grouping as described by [Waterhouse (1963)] does not reflect true phylogenetic relations. Phytophthora species were redistributed into 8 clades, providing a more accurate representation of phylogenetic relationships within the genus Phytophthora. The evolution and transition of morphological, pathogenic, and reproductive traits was inferred from the cladogram generated in this study. Mating system was inferred to be a homoplasious trait, with at least eight independent transitions from homothallism to heterothallism observed.     

Phylogenetic relationships between Hapalemur species and subspecies based on mitochondrial DNA sequences

Background  

Phylogenetic relationships of the genus Hapalemur remains controversial, particularly within the Hapalemur griseus species group. In order to obtain more information on the taxonomic status within this genus, and particularly in the cytogenetic distinct subspecies group of Hapalemur griseus, 357 bp sequence of cytochrome b and 438 bp of 12S mitochondrial DNAs were analyzed on a sample of animals captured in areas extending from the north to the south-east of Madagascar. This sample covers all cytogenetically defined types recognized of the genus Hapalemur.     

Phylogenetic relationships among Lactuca (Asteraceae) species and related genera based on ITS-1 DNA sequences

Internal transcribed spacer (ITS-1) sequences from 97 accessions representing 23 species of Lactuca and related genera were determined and used to evaluate species relationships of Lactuca sensu lato (s.l.). The ITS-1 phylogenies, calculated using PAUP and PHYLIP, correspond better to the classification of Feráková than to other classifications evaluated, although the inclusion of sect. Lactuca subsect. Cyanicae is not supported. Therefore, exclusion of subsect. Cyanicae from Lactuca sensu Feráková is proposed. The amended genus contains the entire gene pool (sensu Harlan and De Wet) of cultivated lettuce (Lactuca sativa). The position of the species in the amended classification corresponds to their position in the lettuce gene pool. In the ITS-1 phylogenies, a clade with L. sativa, L. serriola, L. dregeana, L. altaica, and L. aculeata represents the primary gene pool. L. virosa and L. saligna, branching off closest to this clade, encompass the secondary gene pool. L. virosa is possibly of hybrid origin. The primary and secondary gene pool species are classified in sect. Lactuca subsect. Lactuca. The species L. quercina, L. viminea, L. sibirica, and L. tatarica, branching off next, represent the tertiary gene pool. They are classified in Lactuca sect. Lactucopsis, sect. Phaenixopus, and sect. Mulgedium, respectively. L. perennis and L. tenerrima, classified in sect. Lactuca subsect. Cyanicae, form clades with species from related genera and are not part of the lettuce gene pool.     

Phylogenetic relationship of 16 Oedipodidae species （Insecta： Orthoptera） based on the 16S rRNA gene sequences

The sequences of the mitochondrial 16S rRNA gene of 16 Oedipodidae species were amplified and sequenced. All sequences were aligned and analyzed and the phylogenetic relationships were inferred. The properties of 16S gene in Oedipodidae showed typical patterns of many insects such as a high A＋T content and variable distance-dependent transition/transversion ratios. The 0.2 weight for sites of loops may be advisable for phylogeny reconstruction using the maximum parsimony method. The phylogenetic analysis results do not support the current subfamily classification systems of Oedipodidae. Bryodemellinae and Bryodeminae are closely related and should be merged as one subfamily. The status of Oedipodinae and Locustinae is also problematic.     

Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences

The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.     

Phylogenetic relationships among the black fly species (Diptera: Simuliidae) of Thailand based on multiple gene sequences

Simulium is a very speciose genus of the black fly family Simuliidae that includes many important pests of humans and animals. Cytotaxonomic and morphological studies have made substantial progress in Simulium systematics. 16S rRNA and ITS-1 DNA sequence studies have assisted this progress. Intensive multi-gene molecular systematic investigations will, however, be required for a comprehensive understanding of the genus’ taxonomy and evolution. Our research was conducted to investigate the relationships of Thai Simulium at the subgeneric, species group and species levels. We also examined the possibility of using mitochondrial DNA sequences to facilitate Simulium species identification. Data were collected from three mitochondrial genes (COI, ND4 and 16S rRNA) and two segments of the nuclear 28S ribosomal RNA (the D1 to D2 and the D4 expansion regions). The subgenera Simulium and Gomphostilbia were monophyletic in most analyses. Nevermannia included Montisimulium but was otherwise monophyletic in multigene analyses. In most analyses, Simulium and Nevermannia were more closely related to each other than to Gomphostilbia which was usually basal. Species groups were generally monophyletic. Within Gomphostilbia, however, the batoense species group was always paraphyletic to the other two species groups found in Thailand. Three species groups in Simulium were not monophyletic. The tendency to gill filament number reduction for some species groups in the subgenus Simulium was associated with a derived position in multigene analyses. Most species were monophyletic with two exceptions that probably represent species complexes and will present difficulties for rapid mitochondrial DNA identification.     

Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences

Many attempts to resolve the phylogenetic relationships of higher groups of insects have been made based on both morphological and molecular evidence; nonetheless, most of the interordinal relationships of insects remain unclear or are controversial. As a new approach, in this study we sequenced three nuclear genes encoding the catalytic subunit of DNA polymerase delta and the two largest subunits of RNA polymerase II from all insect orders. The predicted amino acid sequences (In total, approx. 3500 amino acid sites) of these proteins were subjected to phylogenetic analyses based on the maximum likelihood and Bayesian analysis methods with various models. The resulting trees strongly support the monophyly of Palaeoptera, Neoptera, Polyneoptera, and Holometabola, while within Polyneoptera, the groupings of Isoptera/"Blattaria"/Mantodea (Superorder Dictyoptera), Dictyoptera/Zoraptera, Dermaptera/Plecoptera, Mantophasmatodea/Grylloblattodea, and Embioptera/Phasmatodea are supported. Although Paraneoptera is not supported as a monophyletic group, the grouping of Phthiraptera/Psocoptera is robustly supported. The interordinal relationships within Holometabola are well resolved and strongly supported that the order Hymenoptera is the sister lineage to all other holometabolous insects. The other orders of Holometabola are separated into two large groups, and the interordinal relationships of each group are (((Siphonaptera, Mecoptera), Diptera), (Trichoptera, Lepidoptera)) and ((Coleoptera, Strepsiptera), (Neuroptera, Raphidioptera, Megaloptera)). The sister relationship between Strepsiptera and Diptera are significantly rejected by all the statistical tests (AU, KH and wSH), while the affinity between Hymenoptera and Mecopterida are significantly rejected only by AU and KH tests. Our results show that the use of amino acid sequences of these three nuclear genes is an effective approach for resolving the relationships of higher groups of insects.     

Phylogenetic relationships of living and recently extinct bandicoots based on nuclear and mitochondrial DNA sequences

Bandicoots (Peramelemorphia) are a major order of australidelphian marsupials, which despite a fossil record spanning at least the past 25 million years and a pandemic Australasian range, remain poorly understood in terms of their evolutionary relationships. Many living peramelemorphians are critically endangered, making this group an important focus for biological and conservation research. To establish a phylogenetic framework for the group, we compiled a concatenated alignment of nuclear and mitochondrial DNA sequences, comprising representatives of most living and recently extinct species. Our analysis confirmed the currently recognised deep split between Macrotis (Thylacomyidae), Chaeropus (Chaeropodidae) and all other living bandicoots (Peramelidae). The mainly New Guinean rainforest peramelids were returned as the sister clade of Australian dry-country species. The wholly New Guinean Peroryctinae was sister to Echymiperinae. The poorly known and perhaps recently extinct Seram Bandicoot (Rhynchomeles) is sister to Echymipera. Estimates of divergence times from relaxed-clock Bayesian methods suggest that living bandicoots originated in the late Oligocene or early Miocene, much earlier than currently thought based on fossils. Subsequent radiations within Peramelemorphia probably took place on the Australian mainland during the Miocene, with diversification of rainforest taxa on the newly emergent New Guinean landmasses through the middle-late Miocene and complete establishment of modern lineages by the early Pliocene.     

Phylogenetic relationships ofPythium species based on ITS and 5.8S sequences of the ribosomal DNA

The sequences of ITS regions in 30 species and two groups of the genusPythium were resolved. In the phylogenetic trees, the species were generally divided into two clusters, referred to here as the F and S groups. The species in the two groups correspond in terms of their sporangial morphology, with the F group being filamentous/lobulate and the S group being spherical. Genetic divergence within the F group was lower than that within the S group. Other morphological characteristics such as oogonial structure and sexual nature appeared to be unrelated to the groupings in these trees. An alignment analysis revealed common sequences to all the species and arrangements specific to each F or S group. It was found that the ITS region was a good target in designing species-specific primers for the identification and detection ofPythium species. In the tree based on 5.8S rDNA sequences, oomycetes are distantly related to other fungi but separated from algae in Chromista.     

基于Cytb基因序列探讨蝽亚科11种昆虫的系统发育关系

对蝽亚科6属11种昆虫线粒体DNA细胞色素b基因部分序列进行PCR扩增和序列测定。比较其同源性,统计密码子使用频率并应用生物学软件构建分子系统树。在获得的432bp序列中,碱基T,C,A和G的平均含量分别是38．1,18．2,31．9和11．8％,表现出强烈的AT偏向性;就每个氨基酸密码子来看,第3位点的A＋T含量较高,达到85．5％。该序列片段中共有162个核甘酸位点发生变异（约占37．5％）,种间序列差异范围为0．9％～19．4％,平均为16．6％,变异较大。以筛豆龟蝽Megaeopta cribraria为外群,通过多种方法构建的系统发育树拓扑结构一致,这6属11种昆虫大致形成4个分支：珀蝽属、碧蝽属、菜蝽属3属的关系最接近,形成一个分支;真蝽属的3种聚为1支,与第1支形成姊妹群;曼蝽属的2种形成1支;麻皮蝽位于系统树的基部,为分化较早的1支,是蝽亚科中较为原始的类群。     

10种披碱草属植物的RAPD分析及其系统学意义

利用随机扩增多态性DNA(RAPD)技术分析了10种披碱草属植物,即：Elymus sibiricus L.,E． caninus(L．)L¨E．lanceolatus(Scribner et Smith)Gould,E．nutans Griseb,E．dahuricus Turcz,, E．tangutorum(Nevski)Hand．-Mazz., E．brachyaristatus ALöve,E.submuticus(Keng)Keng f.,E． cylidricus(Franch)Honda和E．excelsus Turcz. 。对34个OPRON公司十聚体随机引物进行多态性筛 选,25个(75．53％)能产生多态性。16个引物产生的136个DNA片断,用于计算种间Nei氏遗传相似 性系数分析,在NTSYS程序中利用UPGMA构建系统发育树状图。分析结果表明：(1)四倍体和六倍体 物种各自聚为一支,它们之间的亲缘关系较远;(2)E．sibiricus和E. caninus;亲缘关系较近,支持把 Roegneria caninus (L．)Nevski归入Elymus;(3)E．nutans和E．dahuricus亲缘关系密切;(4)形态相 似、地理分布一致的E．brachyaristatus和E．submuticus存在着一定程度的核苷酸序列的差异,它们与 E．nutans和E．dahuricus有一定的亲缘关系;(5)E．excelsus 与 E．cylindricus的亲缘关系较近,它们 又与E．tangutorum有亲缘关系;(6)RAPD结果与形态学和细胞学等分析结果基本一致,RAPD分析方法将为Elymus系统分类提供DNA水平上丰富的资料。     

Phylogenetic relationships among ten Elymus species based on random amplified polymorphic DNA

Ten species of Elymus (Poaceae: Triticeae) were analyzed using random amplilied polymorphic DNA (RAPD) markers. Thirty-four decamer oligonucleotide random primers from Opron Technologies were used for polymorphic selection. 25 (73.53%) produced polymorphic products. A total of 136 bands amplified from 16 primers were selected for RAPD analyses. The data were used to generate Nei's similarity coefficients and to construct a dendrogram using UPGMA in NTSYS programs. The result showed that: (1) Three tetraploid species, E. sibiricus L., E. caninus (L.) L. and E. lanceolatus (Scribner et Smith) Gould, were clustered in one group, while seven hexaploid species, E. nutans Griseb., E. dahuricusTurcz., E. brachyaristatus A Löve, E. submuticus (Keng) Keng f., E. tangutorum (Nevski)Hand.-Mazz., E. excelsus Turcz. and E. cylindricus (Franch) Honda, were clustered in another group. 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利用多基因序列探讨稻属药稻复合体二倍体物种的系统发育关系

稻属药稻复合体Oryza officinalis complex中有5个二倍体物种,涉及B、C和E3个染色体组,分布在亚洲、非洲和大洋洲。其中,O.australiensis是稻属中惟一含E染色体组的物种;O.punctata则是惟一含B染色体组的物种。虽然O.officinalis、O.rhizomatis和O.eichingeri都含C染色体组,但由于它们间断分布在亚洲和非洲,可能在稻属异源多倍体成种中发挥了不同作用。染色体组B、C和E之间,以及上述二倍体物种之间的系统发育关系及其在稻属多倍体物种形成     

Phylogenetic relationships within Araucariaceae based on rbcL gene sequences

Phylogenetic relationships were determined in the Araucariaceae, which are now found mainly in the Southern Hemisphere. This conifer family was well diversified and widely distributed in both hemispheres during the Mesozoic era. The sequence of 1322 bases of the rbcL gene of cpDNA was determined from 29 species of Araucariaceae, representing almost all the species of the family. Phylogenetic trees determined by the parsimony method indicate that Araucariaceae are well defined by rbcL sequences and also that the monophyly of Agathis or Araucaria is well supported by high bootstrap values. The topology of these trees revealed that Wollemia had derived prior to Agathis and Araucaria. The rbcL phylogeny agrees well with the present recognition of four sections within Araucaria: Araucaria, Bunya, Eutacta, and Intermedia. Morphological characteristics of the number of cotyledons, position of male cone, and cuticular micromorphologies were evaluated as being phylogenetically informative. Section Bunya was found to be derived rather than to be the oldest taxon. Infrageneric relationships of Agathis could not be well elucidated because there are few informative site changes in the rbcL gene, suggesting the more recent differentiation of the species as their fossil records indicate. The New Caledonian Araucaria and Agathis species each formed a monophyletic group with very low differentiation in rbcL sequences among them, indicating rapid adaptive radiation to new edaphic conditions, i.e., ultramafic soils, in the post-Eocene era.     

Phylogenetic relationship between Dermanyssus gallinae populations in European countries based on mitochondrial COI gene sequences

Phylogenetic analysis of Dermanyssus gallinae mites originating from UK, France and Italy was performed using partial amplification of the mitochondrial COI gene. Results showed that UK samples reveal the greatest variation and diversity and are linked to one of the French populations highlighting North–South genetic transitions in European red mite populations. Intra-farm variations between mite samples highlighted the diversity between national populations and possibly its origin from the different chemical strategies used in each country.     

Phylogenetic relationships of colubroid snakes based on mitochondrial DNA sequences

We used a 694 bp length of the mitochondrial ND4 gene from 40 genera to infer phylogenetic relationships among colubroid snakes. The goals of this study were to identify conserved subsets of ND4 sequence data that could be used to address (1) which nominal higher-level colubroid taxa are monophyletic, and (2) the relationships among the monophyletic lineages identified. Use of transversions only proved the most reliable and efficient means of retrieving colubroid relationships. Transversion parsimony and neighbour-joining analyses identify similar monophyletic higher-level taxa, but relationships among these lineages differ considerably between the two analyses. These differences were affected by the inclusion/exclusion of (1) transitions, (2) autapomorphies, and (3) the boid outgroups. Saturation effects among the transitions, uninformativeness of autapomorphies for clustering taxa, and long-branch and base-compositional problems among the boids lead us to regard the tree resulting from transversion parsimony analysis rooted with Acrochordus as the best current estimate of colubroid phylogenetic relationships. However, several aspects of this proposed phylogeny need further testing (e.g. the apparent diphyly of Natricinae is especially controversial). Relationships retrieved using all colubroid taxa are not obtained when sparsely or unevenly sampled experimental subsets of taxa are used instead, suggesting that long-branch problems can severely compromise elucidation of colubroid relationships if limited taxonomic sampling strategies are followed. We discuss the importance of this finding for previous molecular attempts to assess colubroid relationships. Our analyses confirm the historical validity of several nominal colubroid families and subfamilies, establish polyphyly of a few, but generally fail to resolve relationships among the monophyletic taxa we identify. More conservative character information will be required to confidently resolve the last issue.