Multiple origins of anural development in ascidians inferred from rDNA sequences

Ascidians exhibit two different modes of development. A tadpole larva is formed during urodele development, whereas the larval phase is modified or absent during anural development. Anural development is restricted to a small number of species in one or possibly two ascidian families and is probably derived from ancestors with urodele development. Anural and urodele ascidians constitute a model system in which to study the evolution of development, but the phylogeny of anural development has not been resolved. Classification based on larval characters suggests that anural species are monophyletic, whereas classification according to adult morphology suggests they are polyphyletic. In the present study, we have inferred the origin of anural development using rDNA sequences. The central region of 18S rDNA and the hypervariable D2 loop of 28S rDNA were amplified from the genomic DNA of anural and urodele ascidian species by the polymerase chain reaction and sequenced. Phylogenetic trees inferred from 18S rDNA sequences of 21 species placed anural developers into two discrete groups corresponding to the Styelidae and Molgulidae, suggesting that anural development evolved independently in these families. Furthermore, the 18S rDNA trees inferred at least four independent origins of anural development in the family Molgulidae. Phylogenetic trees inferred from the D2 loop sequences of 13 molgulid species confirmed the 18S rDNA phylogeny. Anural development appears to have evolved rapidly because some anural species are placed as closely related sister groups to urodele species. The phylogeny inferred from rDNA sequences is consistent with molgulid systematics according to adult morphology and supports the polyphyletic origin of anural development in ascidians. Correspondence to: W.R. Jeffery     

Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early‐branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schi‐sandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well‐supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well‐supported eudicot clade, the early‐diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise six well‐supported subclades: (1) Berberidopsidaceae/Aextoxicaceae; (2) Myrothamnaceae/ Gunneraceae; (3) Saxifragales, which are the sister to Vitaceae (including Leea) plus a strongly supported eurosid clade; (4) Santalales; (5) Caryophyllales, to which Dilleniaceae are sister; and (6) an asterid clade. The relationships among these six subclades of core eudicots do not receive strong support. This large data set has also helped place a number of enigmatic angiosperm families, including Podostemaceae, Aphloiaceae, and Ixerbaceae. This analysis further illustrates the tractability of large data sets and supports a recent, phylogenetically based, ordinal‐level reclassification of the angiosperms based largely, but not exclusively, on molecular (DNA sequence) data.     

Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences

The Haptophyta is a common algal group in many marine environments, but only a few species have been observed in freshwaters, with DNA sequences available from just a single species, Crysochromulina parva Lackey, 1939. Here we investigate the haptophyte diversity in a high mountain lake, Lake Finsevatn, Norway, targeting the variable V4 region of the 18S rDNA gene with PCR and 454 pyrosequencing. In addition, the freshwater diversity of Pavlovophyceae was investigated by lineage-specific PCR-primers and clone library sequencing from another Norwegian lake, Lake Svaersvann. We present new freshwater phylotypes belonging to the classes Prymnesiophyceae and Pavlovophyceae, as well as a distinct group here named HAP-1. This is the first molecular evidence of a freshwater species belonging to the class Pavlovophyceae. The HAP-1 and another recently detected marine group (i.e. HAP-2) are separated from both Pavlovophyceae and Prymnesiophyceae and may constitute new higher order taxonomic lineages. As all obtained freshwater sequences of haptophytes are distantly related to the freshwater species C. parva, the phylogeny demonstrates that haptophytes colonized freshwater on multiple independent occasions. One of these colonizations, which gave rise to HAP-1, took place very early in the history of haptophytes, before the radiation of the Prymnesiophyceae.     

Flatworm phylogeny from partial 18S rDNA sequences

Partial 18S rDNA sequences from 29 flatworms and 2 outgroup taxa were used in a cladistic analysis of the Platyhelminthes. Support for the clades in the resulting single most parsimonious tree was estimated through bootstrap analysis, jack-knife analysis and decay indices. The Acoelomorpha (Acoela and Nemertodermatida) were absent from the most parsimonious tree. The Acoela and the Fecampiidae form a strongly supported clade, the sister group of which may be the Tricladida. There is some support for monophyly of the rhabdocoel taxon Dalyellioida, previously regarded as paraphyletic. The sister group of the Neodermata remains unresolved. This revised version was published online in July 2006 with corrections to the Cover Date.     

New insights into polychaete phylogeny (Annelida) inferred from 18S rDNA sequences

Annelid systematics and the ingroup relationships of polychaete annelids are matter of ongoing debates in recent analyses. For the investigation of sedentary polychaete relationships a molecular phylogenetic analysis was conducted based on 94 sequences of 18S rDNA, including unpublished sequences of 13 polychaete species. The data set was analyzed with maximum parsimony and maximum likelihood methods, as wells as Bayesian inference. As in previous molecular analyses the monophyly of many traditional polychaete families is confirmed. No evidence has been found for a possible monophyly of Canalipalpata or Scolecida. In all analyses a placement of the Echiura as a derived polychaete ingroup with a close relationship to the Capitellidae is confirmed. The orbiniids appear paraphyletic with regard to Questa. Travisia is transferred from Opheliidae to Scalibregmatidae. The remaining opheliids include a yet undescribed ctenodrilid species from Elba, whereas the other investigated ctenodrilid Ctenodrilus serratus groups with the Cirratulidae and shows a close affinity to the cirratulid genus Dodecaceria. A common ancestry of Branchiomaldane and Arenicola, which has been predicted on morphological data, is confirmed by the analysis and a sistergroup relationship between Arenicolidae and Maldanidae is also recovered. These results support our assumption that on the basis of a broader taxon sampling the phylogenetic position of controversially discussed taxa can be inferred by using 18S rDNA sequence data.     

The syndermatan phylogeny and the evolution of acanthocephalan endoparasitism as inferred from 18S rDNA sequences

The phylogeny of the Syndermata (Rotifera: Monogononta, Bdelloidea, Seisonidea; Acanthocephala: Palaeacanthocephala, Eoacanthocephala, Archiacanthocephala) is key to understanding the evolution of acanthocephalan endoparasitism from free-living ancestors. In the present study, maximum likelihood, distance/neighbor-joining, and maximum parsimony analyses have been carried out based on 18S rDNA data of 22 species (four new sequences). The results suggest a monophyletic origin of the Eurotatoria (Monogononta+Bdelloidea). Seison appears as the acanthocephalan sistergroup. Palaeacanthocephala split into an "Echinorhynchus"-and a "Leptorhynchoides"-group, the latter sharing a monophyletic origin with the Eoacanthocephala and Archiacanthocephala. As inferred from the phylogeny obtained acanthocephalan endoparasitism evolved from a common ancestor of Seison and Acanthocephala that lived epizoically on an early mandibulate. Probably, an acanthocephalan stem species invaded the mandibulate host, thus establishing an endoparasitic lifestyle. Subsequently, vertebrates (or gnathostomes) became part of the parasite's life cycle. In the stem line of the Archiacanthocephala, a terrestrial life cycle has evolved, with an ancestor of the Tracheata (Insecta, Myriapoda) acting as intermediate host.     

基于部分18S rDNA, 28S rDNA和COI基因序列的索科线虫亲缘关系

通过PCR扩增获得我国常见昆虫病原索科线虫6属10种18S rDNA、28S rDNA(D3区)和COI基因序列,结合来自GenBank中6属10种索科线虫的18S rDNA同源序列,用邻接法和最大简约法构建系统进化树。结果显示:12属索科线虫分为三大类群,第一大类群是三种罗索属线虫(Romanomermis)先聚在一起,再与两索属(Amphimermis)和蛛索属(Aranimermis)线虫聚为一支;在第二大类群中,六索属(Hexamermis)、卵索属线虫(Ovomermis)和多索属(Agamermis)亲缘关系最近,先聚在一起,再与八腱索属(Octomyomermis)和Thaumamermis线虫聚为一支。第三大类群由索属(Mermis)和异索属(Allomermis)线虫以显著水平的置信度先聚在一起,再与蠓索属(Heleidomermis)和施特克尔霍夫索属(Strelkovimermis)线虫聚为一支。从遗传距离看,基于3个基因的数据集均显示索科线虫属内种间差异明显小于属间差异,武昌罗索线虫(R.wuchangensis)和食蚊罗索线虫(R.culicivorax)同属蚊幼寄生罗索属线虫,其种间的遗传距离最小。     

Paraphyly of Homoptera and Auchenorrhyncha inferred from 18S rDNA nucleotide sequences

Evolutionary affiliations of eighteen families of Hemiptera (s.l.) are inferred using molecular phylogenetic analysis of nucleotide (nt) sequences of 18S rDNAs. Exemplar taxa include: Archaeorrhyncha (=Fulgoromorpha): flatid, issid, dictyopharid, cixiid and delphacid; Prosorrhyncha (=Heteropterodea): Peloridiomorpha (=Coleorhyncha) -peloridiid, Heteroptera gerrid, lygaeid and mirid; Clypeorrhyncha [=extant (monophyletic) cicadomorphs]: cicadid, cercopoids (cercopid, aphrophorid), membracid and cicadellids (deltocephaline and cicadelline); and Sternorrhyncha: psyllid, aleyrodid, diaspidid and aphid. Analysed sequences encompass a region beginning ?550 nucleotides (nts) from the 5'-end to ?200 nts upstream from the 3'-end of the gene [?1150 base pairs (bp) in euhemipteran to >1400 bp in sternorrhynchan taxa]. Maximum parsimony and bootstrap analyses (PAUP) identify four principal hemipteran clades, Stenorrhyncha, Clypeorrhyncha, Archaeorrhyncha and Prosorrhyncha. These lineages are identified by synapomorphies distributed throughout the gene. Sternorrhyncha is a sister group to all other Hemiptera (i.e. Euhemiptera sensu Zrzavy), rendering Homoptera paraphyletic. Within Euhemiptera, clades Clypeorrhyncha, Archaeorrhyncha, Prosorrhyncha and Heteroptera are supported by one, three, two and three synapomorphic sites, respectively. There is equitable parsimonious inference for Archaeorrhyncha as the sister group to Prosorrhyncha (Neoherriiptera sensu Sorensen et al.) or Clypeorrhyncha, in either case rendering Auchenorrhyncha paraphyletic. Neohemiptera is supported by one synapomorphy. Within Clypeorrhyncha, clade cicada + cercopoids is the sister group of the clade cicadellids + membracid (Membracoidea sensu Dietrich & Deitz). Among archaeorrhynchans, clade delphacid + cixiid is the sister group of the clade dictyopharid + flatid + issid. Within Prosorrhyncha, the peloridiid is sister to the Heteroptera. Within Heteroptera, gerrid is the sister group of the clade mirid + lygaeid (Panheteroptera sensu Schuh). Based on secondary structure of synonymous 18S rRNA, two synapomorphies each of Sternorrhyncha, Prosorrhyncha and Heteroptera are compensatory substitutions on stem substructures. All other synapomorphies identifying major lineages of Hemiptera are noncompensatory substitutions on either bulges or stems. Short basal internodal distances suggest radiation of hemipteran lineages at the suborder level occurred rapidly. Morphological, palaeoentomological and eco-evolutionary factors supporting the 18S rDNA-based phylogenetic tree are discussed.     

Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences

SUMMARY Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.     

Phylogenetic relationships among higher Nemertean (Nemertea) Taxa inferred from 18S rDNA sequences

A phylogeny was reconstructed for 23 populations of fringe-toed lizards (genus Uma) from the three most northern species of the genus, including the Mojave fringe-toed lizard U. scoparia, the Colorado Desert fringe-toed lizard U. notata, and the endangered Coachella Valley fringe-toed lizard U. inornata. The outgroup taxa were the zebra-tailed lizard, Callisaurus draconoides; the lesser earless lizard, Holbrookia maculata; and the greater earless lizard, Cophosaurus texanus. Evaluation of 1630 combined nucleotide sequence from the mitochondrial genes ATPase 6 and cytochrome b yielded 10 most parsimonious trees. Reweighting the characters using the rescaled consistency index eliminated eight of these trees. The remaining two trees differ only in the placement of two individuals from the Superstition Mountains which either formed a monophlyetic unit or grouped with one individual from the Anza-Borrego population. The preferred phylogeny, one more consistent with geography, had two primary clades: one consisting of U. scoparia and the other placing U. inornata inside the clade containing U. notata. Uma inornata was most closely related to nearby U. notata notata, as opposed to more distant U. notata rufopunctata.     

The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology

Phylogenetic relationships among the holometabolous insect orders were inferred from cladistic analysis of nucleotide sequences of 18S ribosomal DNA (rDNA) (85 exemplars) and 28S rDNA (52 exemplars) and morphological characters. Exemplar outgroup taxa were Collembola (1 sequence), Archaeognatha (1), Ephemerida (1), Odonata (2), Plecoptera (2), Blattodea (1), Mantodea (1), Dermaptera (1), Orthoptera (1), Phasmatodea (1), Embioptera (1), Psocoptera (1), Phthiraptera (1), Hemiptera (4), and Thysanoptera (1). Exemplar ingroup taxa were Coleoptera: Archostemata (1), Adephaga (2), and Polyphaga (7); Megaloptera (1); Raphidioptera (1); Neuroptera (sensu stricto = Planipennia): Mantispoidea (2), Hemerobioidea (2), and Myrmeleontoidea (2); Hymenoptera: Symphyta (4) and Apocrita (19); Trichoptera: Hydropsychoidea (1) and Limnephiloidea (2); Lepidoptera: Ditrysia (3); Siphonaptera: Pulicoidea (1) and Ceratophylloidea (2); Mecoptera: Meropeidae (1), Boreidae (1), Panorpidae (1), and Bittacidae (2); Diptera: Nematocera (1), Brachycera (2), and Cyclorrhapha (1); and Strepsiptera: Corioxenidae (1), Myrmecolacidae (1), Elenchidae (1), and Stylopidae (3). We analyzed approximately 1 kilobase of 18S rDNA, starting 398 nucleotides downstream of the 5' end, and approximately 400 bp of 28S rDNA in expansion segment D3. Multiple alignment of the 18S and 28S sequences resulted in 1,116 nucleotide positions with 24 insert regions and 398 positions with 14 insert regions, respectively. All Strepsiptera and Neuroptera have large insert regions in 18S and 28S. The secondary structure of 18S insert 23 is composed of long stems that are GC rich in the basal Strepsiptera and AT rich in the more derived Strepsiptera. A matrix of 176 morphological characters was analyzed for holometabolous orders. Incongruence length difference tests indicate that the 28S + morphological data sets are incongruent but that 28S + 18S, 18S + morphology, and 28S + 18S + morphology fail to reject the hypothesis of congruence. Phylogenetic trees were generated by parsimony analysis, and clade robustness was evaluated by branch length, Bremer support, percentage of extra steps required to force paraphyly, and sensitivity analysis using the following parameters: gap weights, morphological character weights, methods of data set combination, removal of key taxa, and alignment region. The following are monophyletic under most or all combinations of parameter values: Holometabola, Polyphaga, Megaloptera + Raphidioptera, Neuroptera, Hymenoptera, Trichoptera, Lepidoptera, Amphiesmenoptera (Trichoptera + Lepidoptera), Siphonaptera, Siphonaptera + Mecoptera, Strepsiptera, Diptera, and Strepsiptera + Diptera (Halteria). Antliophora (Mecoptera + Diptera + Siphonaptera + Strepsiptera), Mecopterida (Antliophora + Amphiesmenoptera), and Hymenoptera + Mecopterida are supported in the majority of total evidence analyses. Mecoptera may be paraphyletic because Boreus is often placed as sister group to the fleas; hence, Siphonaptera may be subordinate within Mecoptera. The 18S sequences for Priacma (Coleoptera: Archostemata), Colpocaccus (Coleoptera: Adephaga), Agulla (Raphidioptera), and Corydalus (Megaloptera) are nearly identical, and Neuropterida are monophyletic only when those two beetle sequences are removed from the analysis. Coleoptera are therefore paraphyletic under almost all combinations of parameter values. Halteria and Amphiesmenoptera have high Bremer support values and long branch lengths. The data do not support placement of Strepsiptera outside of Holometabola nor as sister group to Coleoptera. We reject the notion that the monophyly of Halteria is due to long branch attraction because Strepsiptera and Diptera do not have the longest branches and there is phylogenetic congruence between molecules, across the entire parameter space, and between morphological and molecular data.     

Internal phylogeny of the Chilopoda (Myriapoda, Arthropoda) using complete 18S rDNA and partial 28S rDNA sequences

The internal phylogeny of the 'myriapod' class Chilopoda is evaluated for 12 species belonging to the five extant centipede orders, using 18S rDNA complete gene sequence and 28S rDNA partial gene sequence data. Equally and differentially weighted parsimony, neighbour-joining and maximum-likelihood were used for phylogenetic reconstruction, and bootstrapping and branch support analyses were performed to evaluate tree topology stability. The results show that the Chilopoda constitute a monophyletic group that is divided into two lines, Notostigmophora (= Scutigeromorpha) and Pleurostigmophora, as found in previous morphological analyses. The Notostigmophora are markedly modified for their epigenic mode of life. The first offshoot of the Pleurostigmophora are the Lithobiomorpha, followed by the Craterostigmomorpha and by the Epimorpha s. str. (= Scolopendromorpha + Geophilomorpha), although strong support for the monophyly of the Epimorpha s. lat. (= Craterostigmomorpha + Epimorpha s. str.) is only found in the differentially weighted parsimony analysis.     

Phylogenetic relationships among the Braconidae (Hymenoptera: Ichneumonoidea) inferred from partial 16S rDNA, 28S rDNA D2, 18S rDNA gene sequences and morphological characters

Phylogenetic relationships among the Braconidae were examined using homologous 16S rDNA, 28S rDNA D2 region, and 18S rDNA gene sequences and morphological data using both PAUP* 4.0 and MRBAYES 3.0B4 from 88 in-group taxa representing 35 subfamilies. The monophyletic nature of almost all subfamilies, of which multiple representatives are present in this study, is well-supported except for two subfamilies, Cenocoelinae and Neoneurinae that should probably be treated as tribal rank taxa in the subfamily Euphorinae. The topology of the trees generated in the present study supported the existence of three large generally accepted lineage or groupings of subfamilies: two main entirely endoparasitic lineages of this family, referred to as the "helconoid complex" and the "microgastroid complex," and the third "the cyclostome." The Aphidiinae was recovered as a member of the non-cyclostomes, probably a sister group of Euphorinae or Euphorinae-complex. The basal position of the microgastroid complex among the non-cyclostomes has been found in all our analyses. The cyclostomes were resolved as a monophyletic group in all analyses if two putatively misplaced groups (Mesostoa and Aspilodemon) were excluded from them. Certain well-supported relationships evident in this family from the previous analyses were recovered, such as a sister-group relationships of Alysiinae+Opiinae, of Braconinae+Doryctinae, and a close relationship between Macrocentrinae, Xiphozelinae, Homolobinae, and Charmontinae. The relationships of "Ichneutinae + ((Adeliinae + Cheloninae) + (Miracinae + (Cardiochilinae + Microgastrinae)))" was confirmed within the microgastroid complex. The position of Acampsohelconinae, Blacinae, and Trachypetinae is problematic.     

18S rDNA sequences and the holometabolous insects

The Holometabola (insects with complete metamorphosis: beetles, wasps, flies, fleas, butterflies, lacewings, and others) is a monophyletic group that includes the majority of the world's animal species. Holometabolous orders are well defined by morphological characters, but relationships among orders are unclear. In a search for a region of DNA that will clarify the interordinal relationships we sequenced approximately 1080 nucleotides of the 5' end of the 18S ribosomal RNA gene from representatives of 14 families of insects in the orders Hymenoptera (sawflies and wasps), Neuroptera (lacewing and antlion), Siphonaptera (flea), and Mecoptera (scorpionfly). We aligned the sequences with the published sequences of insects from the orders Coleoptera (beetle) and Diptera (mosquito and Drosophila), and the outgroups aphid, shrimp, and spider. Unlike the other insects examined in this study, the neuropterans have A-T rich insertions or expansion regions: one in the antlion was approximately 260 bp long. The dipteran 18S rDNA evolved rapidly, with over 3 times as many substitutions among the aligned sequences, and 2-3 times more unalignable nucleotides than other Holometabola, in violation of an insect-wide molecular clock. When we excluded the long-branched taxa (Diptera, shrimp, and spider) from the analysis, the most parsimonious (minimum-length) trees placed the beetle basal to other holometabolous orders, and supported a morphologically monophyletic clade including the fleas+scorpionflies (96% bootstrap support). However, most interordinal relationships were not significantly supported when tested by maximum likelihood or bootstrapping and were sensitive to the taxa included in the analysis. The most parsimonious and maximum-likelihood trees both separated the Coleoptera and Neuroptera, but this separation was not statistically significant.(ABSTRACT TRUNCATED AT 250 WORDS)     

单子叶植物高级分类阶元系统演化: matK、rbcL和18S rDNA序列的证据

基于两个叶绿体基因（matK和rbcL）和一个核糖体基因（18S rDNA）的序列分析,对代表了基部被子植物和单子叶植物主要谱系分支的86科126属151种被子植物（单子叶植物58科86属101种）进行了系统演化关系分析。研究结果表明由胡椒目Piperales、樟目Laurales、木兰目Magnoliales和林仙目Canellales构成的真木兰类复合群是单子叶植物的姐妹群。单子叶植物的单系性在3个序列联合分析中得到98％的强烈自展支持。联合分析鉴定出9个单子叶植物主要谱系（广义泽泻目Alismatales、薯蓣目Dioscorcales、露兜树目Pandanales、天门冬目Asparagalcs、百合目Liliales、棕榈目Arecales、禾本目Poales、姜目Zingiberales、鸭跖草目Commelinales）和6个其他被子植物主要谱系（睡莲目Nymphaeales、真双子叶植物、木兰目、樟目、胡椒目、林仙目）。在单子叶植物内,菖蒲目Acorales（菖蒲属Acorus）是单子叶植物最早分化的一个谱系,广义泽泻目（包括天南星科Araceae和岩菖蒲科Toficldiaccae）紧随其后分化出来,二者依次和其余单子叶植物类群构成姐妹群关系。无叶莲科Petrosaviaceac紧随广义的泽泻目之后分化出来,无叶莲科和剩余的单子叶植物类群形成姐妹群关系,并得到了较高的支持率。继无叶莲科之后分化的类群形成两个大的分支：一支是由露兜树目和薯蓣目构成,二者形成姐妹群关系：另一支是由天门冬目、百合目和鸭跖草类复合群组成,三者之间的关系在单个序列分析和联合分析中不稳定,需要进一步扩大取样范围来确定。在鸭跖草类复合群分支内,鸭跖草目和姜目的姐妹群关系在3个序列联合分析和2个序列联合分析的严格一致树中均得到强烈的自展支持,获得的支持率均是100％。但是,对于棕榈目和禾本目在鸭跖草类中的系统位置以及它们和鸭跖草目-姜目之间的关系,有待进一步解决。值得注意的是,无叶莲科与其他单子叶植物类群（除菖蒲目和泽泻目外）的系统关系在本文中获得较高的自展支持率,薯蓣目和天门冬目的单系性在序列联合分析中都得到了较好的自展支持,而这些在以往的研究中通常支持率较低。鉴于菖蒲科和无叶莲科独特的系统演化位置,本文支持将其分别独立成菖蒲目和无叶莲目Petrosavialcs的分类学界定。     

Phylogeny of the Trichostrongylina (Nematoda) inferred from 28S rDNA sequences

We produced a molecular phylogeny of species within the order Strongylida (bursate nematodes) using the D1 and D2 domains of 28S rDNA, with 23 new sequences for each domain. A first analysis using Caenorhabditis elegans as an outgroup produced a tree with low resolution in which three taxa (Dictyocaulus filaria, Dictyocaulus noerneri, and Metastrongylus pudendotectus) showed highly divergent sequences. In a second analysis, these three species and C. elegans were removed and an Ancylostomatina, Bunostomum trigonocephalum, was chosen (on the basis of previous morphological analyses) as the outgroup for an analysis of the phylogenetic relationships between and within the Strongylina (strongyles) and Trichostrongylina (trichostrongyles). A very robust tree was obtained. The Trichostrongylina were monophyletic, but the Strongylina were paraphyletic, though this requires confirmation. Within the Trichostrongylina, the three superfamilies defined from morphological characters are confirmed, with the Trichostrongyloidea sister group to a clade including the Molineoidea and Heligmosomoidea. Within the Trichostrongyloidea, the Cooperiidae, Trichostrongylidae, and Haemonchidae were polytomous, the Haemonchinae were monophyletic, but the Ostertagiinae were paraphyletic. The sister-group relationships between Molineoidea and Heligmosomoidea were unsuspected from previous morphological analysis. No unequivocal morphological synapomorphy could be found for the grouping Molineoidea + Heligmosomoidea, but none was found which contradicted it.     

Evolutionary history of free-swimming and sessile lifestyles in urochordates as deduced from 18S rDNA molecular phylogeny

Whether the ancestral chordates were free-swimming or sessile is a longstanding question that remains to be settled. Vertebrates and amphioxi are free-swimming, but the most basal chordate subphylum (the urochordates) includes both sessile and free-swimming species. Here, 1 report molecular phylogenetic analyses of 18S rDNA of urochordates to deduce which lifestyle is ancestral. This revealed a close relationship between salps and doliolids and paraphyly of the ascidians. An early divergence of larvaceans, which show a tadpole-like body plan throughout life, is also supported by the analyses. Based on this phylogeny, a free-swimming ancestor for chordates is more parsimonious than a sessile ancestor. The evolutionary history of various lifestyles of chordates from this ancestral form is proposed.      

Molecular phylogeny of the Caryophyllaceae (Caryophyllales) inferred from chloroplast matK and nuclear rDNA ITS sequences

Caryophyllaceae is a principally holarctic family including around 2200 species often classified into the three subfamilies Alsinoideae, Caryophylloideae, and Paronychioideae. Complex and possibly homoplasious morphological characters within the family make taxa difficult to delimit and diagnose. To explore part of the morphological evolution within the family, we investigated the phylogeny of the Caryophyllaceae by means of analyzing plastid and nuclear sequence data with parsimony and Bayesian methods. We describe a mode of tracing a stable phylogenetic signal in ITS sequences, and a significant common signal is shared with the plastid data. Parsimony and Bayesian analyses yield some differences in tree resolution. None of the subfamilies appear monophyletic, but the monophyly of the Caryophylloideae is not contradicted. Alsinoideae are paraphyletic, with Arenaria subg. Eremogone and Minuartia subg. Spergella more closely related to the Caryophylloideae. There is strong support for the inclusion of Spergula-Spergularia in an Alsinoideae-Caryophylloideae clade. Putative synapomorphies for these groupings are twice as many stamens as number of sepals and a caryophyllad-type of embryogeny. Paronychioideae form a basal grade, where tribe Corrigioleae are sister to the rest of the family. Free styles and capsules with simple teeth are possibly plesiomorphic for the family.