Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles

Molecular data had consistently recovered monophyletic classes for the heterokont algae, however, the relationships among the classes had remained only partially resolved. Furthermore, earlier studies did not include representatives from all taxonomic classes. We used a five-gene (nuclear encoded SSU rRNA; plastid encoded rbcL, psaA, psbA, psbC) analysis with a subset of 89 taxa representing all 16 heterokont classes to infer a phylogenetic tree. There were three major clades. The Aurearenophyceae, Chrysomerophyceae, Phaeophyceae, Phaeothamniophyceae, Raphidophyceae, Schizocladiophyceae and Xanthophyceae formed the SI clade. The Chrysophyceae, Eustigmatophyceae, Pinguiophyceae, Synchromophyceae and Synurophyceae formed the SII clade. The Bacillariophyceae, Bolidophyceae, Dictyochophyceae and Pelagophyceae formed the SIII clade. These three clades were also found in a ten-gene analysis. The approximately unbiased test rejected alternative hypotheses that forced each class into either of the other two clades. Morphological and biochemical data were not available for all 89 taxa, however, existing data were consistent with the molecular phylogenetic tree, especially for the SIII clade.     

基于核内核糖体小亚基序列的蝗总科系统发育关系分析

用核糖体SSURdna全序列对蝗总科（Acridoidea）进行了分子系统学研究。依据测定的8种蝗虫的SSU Rdna全序列 (平均 1.844 bp),并从GenBank中选取了6种内群种类和2种外群种类的SSU Rdna同源序列,进行序列分析。利用Clustal、MEGA 和 PHYLIP 软件构建分子系统树（距离邻接法Neighbor-Joining,NJ;最小进化法 Minimum Evolution）。结果显示： (1) 蝗总科是一个单系类群;(2) 锥头蝗科（Chrotogonidae）和瘤锥蝗科（Pyrgomorphidea）亲缘关系较近,为蝗总科最原始的类群;(3) 网翅蝗科（Arcypteridae）和槌角蝗科（Gomphoceridae）有较近的亲缘关系; (4) 斑翅蝗科 （Oedipodidae）为最进化的类群; (5) SSU Rdna序列保守性强,转换transition）取代的速率大于或接近颠换（transversion）取代的速率;(6) 在系统树中,总科首先分离,大多数同科不同属的类群以高置信度聚合在一起,说明SSU Rdna序列适合用于蝗总科的系统发育关系分析。     

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…     

真核生物系统发育和多样性概观

Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eukaryotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predominantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the proposed relationships of these groups to each other.     

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 phylogenetic study of the malagasy couas with insights into cuckoo relationships

The avian family Cuculidae (cuckoos) is a diverse group of birds that vary considerably in behaviors of interest to behavioral ecologists, e.g., obligate brood parasitism and cooperative breeding. The taxonomy of this group has historically been relatively stable but has not been extensively evaluated using molecular methods. The goal of this study was to evaluate phylogenetic relationships within the ecologically diverse genus Coua and the placement of Coua among major cuckoo lineages. We sequenced 429 bp of cytochrome b (cyt b) and 522 bp of ND2, both mitochondrial genes, for 26 species of cuckoos spanning 13 genera. We also included the enigmatic hoatzin (Opisthocomus hoazin) and used two Tauraco species as outgroups. ND2 exhibited higher rates of DNA sequence and amino acid substitution than cyt b; however, this did not greatly affect the overall levels of phylogenetic resolution and support provided by these two genes. Combined analyses produced two alternative phylogenies, depending on weighting scheme, both of which were fully resolved and were characterized by high bootstrap support. These phylogenies recovered monophyly for all of the traditional cuckoo subfamilies and indicated, with strong support, that the hoatzin is outside of Cuculidae. Within Coua, an arboreal and a terrestrial clade were identified. In contrast, habitat choice of Coua species did not greatly reflect the phylogeny.     

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.     

The use of ribosomal ITS to determine phylogenetic relationships within Sorghum

 For the first time, a combined analysis of the ITS1 regions of all twenty-five Sorghum species has been undertaken. Parsimony analysis revealed a distinct lineage of Sorghum consisting of the cultivated species and their progenitors plus S. angustum, S. brachypodum, S. ecarinatum, S. macrospermum, S. laxiflorum and Saccharum officinarum. A second unsupported lineage consists of the Parasorghum and Stiposorghum species S. grande, S. leiocladum, S. nitidum, S. purpureosericeum, S. timorense, S. versicolor, S. amplum, S. bulbosum, S. interjectum, S. plumosum, S. stipoideum and the African grass Cleistachne sorghoides. Three Australian endemic species, S. angustum, S. brachypodum and S. ecarinatum, are closely related to S. bicolor, with S. angustum showing no difference to S. bicolor in ITS1 sequence. Sorghum macrospermum and S. laxiflorum form a strong clade within the Eusorghum branch indicating closer relationships to this group than to any of the Parasorghum or Stiposorghum species. Saccharum officinarum has shown closer relationships to Sorghum than to Zea mays, while the close relationship of Cleistachne sorghoides to Sorghum has been confirmed. These relationships between Sorghum species provide an important guide for plant breeders to exploit the wider Sorghum genepool through crosses between wild and cultivated species in an effort to improve sorghum production. Received April 30, 2001 Accepted July 10, 2001     

Mitochondrial DNA polymorphism and phylogenetic relationships inHevea brasiliensis

Using fourteen random mitochondrial DNA probes, we have examined restriction fragment length polymorphism (RFLP) in wild and cultivatedHevea brasiliensis. A total of 395 accessions, including 345 from various prospectings collected in Brazil, Colombia and Peru and 50 cultivated clones, were analyzed. Two other species (H. benthamiana andH. pauciflora) were also included in the study for comparison. The high level of mitochondrial polymorphism allowed us to divide all the accessions analyzed into 212 distinct genotypes. The genetic variability of cultivated clones was limited to four genotypes forming two clusters. In contrast, considerable genetic variation was found in the wild collections. In almost all cases, accessions displaying the same RFLP profile were restricted to the same geographical area (same or neighbor administrative districts). In addition, accessions whose genetic closeness was predicted by RFLP profiles were also clustered according to geographical origin. In a few cases, however, similar RFLP profiles were found for accessions originating from geographically distant districts. This discrepancy can be explained either by seed dispersion (by river) or possibly by similar genetic events occurring independently in different geographical locations. Chloroplast DNA RFLP was also analyzed in 217 accessions, representative of 126 distinct mitochondrial genotypes. Very few differences were found, indicating that the chloroplast genome is more highly conserved than the mitochondrial genome.     

Rapidly evolving lineages impede the resolution of phylogenetic relationships among Clitellata (Annelida)

The phylogenetic relationships of the Clitellata were investigated using a data set with published and new complete or partial 18S rRNA and mtCOI gene sequences of 13 and 49 taxa representing 8 and 14 families, respectively. Three different alignments were considered for 18S, and the possible influence of departures from rate constancy among sites was evaluated by analyses using a Gamma model of rate heterogeneity. Maximum-likelihood estimates of the shape parameter alpha of the Gamma distribution were very low, whatever the alignment or the gene considered, suggesting that phylogenetic reconstructions taking into account the rate heterogeneity among sites are likely to be the most reliable. Analyzed separately, the two genes did not resolve the relationships among the Clitellata, but the consensus tree was congruent with the morphology-based relationships. Our data suggest the inclusion of the Euhirudinea, Acanthobdellida, and Branchiobdellida in the Oligochaeta and suggest the Lumbriculidae as the link between both assemblages. Although separate analyses of both genes, as well as different alignments for the 18S rRNA sequences, yielded conflicting results concerning the phylogenetic position of leeches and leech-like worms vis-à-vis the Oligochaeta, subsequent analyses using the Gamma model greatly reduced the observed inconsistencies. Our analyses show that among the Clitellata, the leeches and the leech-like and gutless worms represent significantly faster evolving lineages. It is suggested that the observed higher mutation rates may be explained by the fact that these lineages contain almost exclusively commensal and/or parasitic taxa.     

Microsatellite polymorphisms reveal phylogenetic relationships in primates

We amplified, via PCR, DNA segments from intron 1 of the tyrosine hydroxylase gene (TH01) and intron 40 of the von Willebrand factor gene (VWA) in ten nonhuman primate genera. In humans both introns contain polymorphic microsatellites with tetrameric repeats. Compared to the allelic ranges in human populations relatively short repeat arrays could be detected for the nonhuman primates typed, presumably reflecting an ancient precursor state at both microsatellite loci. Furthermore, our results provide evidence for an association of the average number of repeats present in different primate genera and their divergence time from man. DNA sequencing of VWA orthologues revealed a relatively high variability in the arrangement of repeats in the 5-repeat arrays, the generation of which could probably be explained by polar mutational events. Correspondence to: B. Brinkmann     

New substitution models for rooting phylogenetic trees

The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made.     

Ribosomal DNA gene and phylogenetic relationships of Diplura and lower Hexapods

HennigdividedInsectas.lat.(=Hexapoda)intotwowelldefinedtaxonomicgroups:Entog-nathaandEctognatha[1].ThemostdistinctivecharacterofEntognatha(includingProtura,Col-lembolaandDiplura)liesintheenclosedmouthpartscondition,whereasthepresenceofexposedmouthpartsisthemainfeatureofEctognatha(includingMicrocoryphia,Zygentomaandtheptery-goteinsects).ControversiesaboutthephylogeneticrelationshipsofhightaxaEntognathahavekeptgrowinginrecentyears,withthemonophylyofDipluraandthephylogeneticpositionsofDiplur…     

Housekeeping genes for phylogenetic analysis of eutherian relationships

The molecular relationship of placental mammals has attracted great interest in recent years. However, 2 crucial and conflicting hypotheses remain, one with respect to the position of the root of the eutherian tree and the other the relationship between the orders Rodentia, Lagomorpha (rabbits, hares), and Primates. Although most mitochondrial (mt) analyses have suggested that rodents have a basal position in the eutherian tree, some nuclear data in combination with mt-rRNA genes have placed the root on the so-called African clade or on a branch that includes this clade and the Xenarthra (e.g., anteater and armadillo). In order to generate a new and independent set of molecular data for phylogenetic analysis, we have established cDNA sequences from different tissues of various mammalian species. With this in mind, we have identified and sequenced 8 housekeeping genes with moderately fast rate of evolution from 22 placental mammals, representing 11 orders. In order to determine the root of the eutherian tree, the same genes were also sequenced for 3 marsupial species, which were used as outgroup. Inconsistent with the analyses of nuclear + mt-rRNA gene data, the current data set did not favor a basal position of the African clade or Xenarthra in the eutherian tree. Similarly, by joining rodents and lagomorphs on the same basal branch (Glires hypothesis), the data set is also inconsistent with the tree commonly favored in mtDNA analyses. The analyses of the currently established sequences have helped examination of problematic parts in the eutherian tree at the same time as they caution against suggestions that have claimed that basal eutherian relationships have been conclusively settled.     

AFLP analysis of phylogenetic relationships among myrmecophytic species of Macaranga (Euphorbiaceae) and their allies

The palaeotropic pioneer tree genus Macaranga Thouars (Euphorbiaceae) is characterized by various types of mutualistic interactions with specific ant partners (mainly Crematogaster spp.). About 30 species are obligate ant-plants (myrmecophytes). We used amplified fragment length polymorphism (AFLP) markers to assess phylogenetic relationships among 108 Macaranga specimens from 43 species, including all available taxa from the three sections known to contain myrmecophytes. Eight primer combinations produced 426 bands that were scored as presence/absence characters. Banding patterns were analyzed phenetically, cladistically and by principal coordinates analysis. Monophyly of section Pruinosae is clearly supported. There is also good evidence for a monophyletic section Pachystemon that includes the puncticulata group. The monophyly of section Winklerianae and relationships between the three sections remain ambiguous. Section Pachystemon is subdivided into four well-supported monophyletic subclades that presumably correspond to taxonomic entities.We acknowledge the support by the Deutsche Forschungsgemeinschaft (DFG Fi606/4-1, DFG We1830/2-1, 4-1 and 4-2), which in part was granted in the frame of the DFG-SPP 1127 Radiations: origins of biological diversity. Part of the plant material was kindly supplied by Dr. H. Feldhaar (University of Würzburg), Dr. U. Moog (University of Kassel) and Dr. F. Slik (Leiden University Branch, Nationaal Herbarium Nederland). We thank the University of Malaysia (Dr. Rosli b. Hashim) and Taman Taman Sabah (Datuk Lamri Ali; Dr. J. Nais) for permits and logistic support, and EPU for permission to conduct research in Malaysia.     

谈系统发生树建立的分子标准

随着进化生物学以及生物信息学的发展 ,研究不同物种间进化关系的方法也有了新的进展。其中分子进化方法使得系统发生树的建立更加简便和精确。几种系统发生树的建树方法及相关分子标准目前比较流行。。     

Molecular markers for phylogenetic applications derived from comparative plastome analysis of Prunus species

Interspecific and intergeneric relationships of Prunus s.l. are still unclear due to low levels of genetic variation among species, and resulting partially unresolved phylogenetic inferences. Here we sequenced and compared six complete plastomes from two subgenera of Prunus in order to choose molecular markers to increase the amount of genetic variation suitable for inference of Prunus phylogeny. The plastomes range between 157 817 and 158 995 bp in length, and we found different levels of inverted repeat (IR) contraction among the three sampled subgenera of Prunus s.l. Most regions in Prunus plastomes considered individually provide low phylogenetic resolution at the subgenus or species level compared to a tree constructed using all 78 coding regions combined. We compared levels of variation among 206 coding regions and noncoding (intergenic and intron) plastid regions and inferred phylogenies from each region considered individually. We then chose using two regions together for future studies of relationships in Prunus, ycf1 and trnT-L, that display high to moderate levels of variation among coding and intergenic regions, respectively, and that individually permit inference of resolved species-level trees in Prunus with moderate to strong branch support. Considered together, these two regions allow inference of the same topology of Prunus inferred using all coding plastid regions combined, with comparable levels of tree support to the full plastome set. These two loci should therefore be useful as a plastid phylogenetic marker set for further inference of relationships within Prunus s.l.     

Molecular phylogenetic relationships reveal taxonomic and biogeographic clades in Dianella (flax lilies; Asphodelaceae,Hemerocallidoideae)

A phylogeny of Dianella is presented based on Bayesian and maximum parsimony analyses of a combined molecular data set using three chloroplast markers (trnQ^UUG–5'rps16, 3'rps16–5'trnK^(UUU) and rpl14–rps8–infA–rpl36) and two nuclear markers (ITS and ETS). Accessions included most Dianella species, including all species from Australia, the centre of diversity for the genus, and related outgroup genera Eccremis, Stypandra, Thelionema and Herpolirion. The phylogeny showed Stypandra sister to Herpolirion + Thelionema, and confirmed the monophyly of Dianella. Within Dianella, a number of clades were resolved that revealed biogeographic relationships. Accessions from south-western Australia (extending into South Australia) formed the earliest diverging clade, followed by D. serrulata from New Guinea, sister to all other clades of Dianella from Australia and other regions. Tropical North Queensland species, including the D. pavopennacea complex, were related to a clade of accessions from New Caledonia and the Hawaiian Islands in the Pacific, and a clade that included samples of D. carolinensis (Caroline Islands) and the widespread D. ensifolia from South-East Asia and across the Indian Ocean to Mauritius and Madagascar. However, D. ensifolia is not monophyletic, with accessions from Japan and Taiwan related to a clade of Queensland samples that are part of the D. revoluta complex. Three New Zealand species (diploid, 2n?=?16) were found to be related to Norfolk Island D. intermedia (type locality; octoploid, 2n?=?64). In contrast ‘D. intermedia’ from Lord Howe Island was resolved as sister to the eastern Australian D. caerulea complex. The phylogenetic results indicate the need for taxonomic revision, particularly revision of the species ‘complexes’ D. longifolia and D. caerulea in Australia, and recognition of more than one species within D. ensifolia and within D. sandwicensis on the Hawaiian Islands.