a molecular phylogeny of apiaceae subfamily Apioideae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences

Phylogenetic relationships among 40 New World and Old World members of Apiaceae subfamily Apioideae, representing seven of the eight tribes and eight of the ten subtribes commonly recognized in the subfamily, were inferred from nucleotide sequence variation in the internal transcribed spacer (ITS) regions of 18-26S nuclear ribosomal DNA. Although the sequences are alignable, with only 11% of sites excluded from the analyses because of alignment ambiguity, divergence values in pairwise comparisons of unambiguous positions among all taxa were high and ranged from 0.5 to 33.2% of nucleotides in ITS 1 and from 0 to 33.2% of nucleotides in ITS 2. Average sequence divergence across both spacer regions was 18.4% of nucleotides. Phylogenies derived from ITS sequences estimated using neighbor-joining analysis of substitution rates, and maximum likelihood and parsimony methods give trees of essentially similar topology and indicate that: (1) there is little support for any existing system of classification of the subfamily that is based largely on morphological and anatomical features of the mericarp; (2) there is a major phylogenetic division within the subfamily, with one clade comprising the genus Smyrnium and those taxa belonging to Drude's tribes Dauceae, Scandiceae, and Laserpitieae and the other clade comprising all other examined taxa; and (3) the genera Arracacia, Coaxana, Coulterophytum, Enantiophylla, Myrrhidendron, Prionosciadium, and Rhodosciadium, all endemic to Mexico and Central America, comprise a clade but their relationships to other New World taxa are equivocal. A phylogeny derived from parsimony analysis of chloroplast DNA rpoC1 intron sequences is consistent with, but considerably less resolved than, relationships derived from these ITS regions. This study affirms that ITS sequences are useful for phylogenetic inference among closely related members of Apioideae but, owing to high rates of nucleotide substitution, are less useful in resolving relationships among the more ancestral nodes of the phylogeny.     

基于28S rDNA D2基因片段与形态特征的优茧蜂亚科系统发育研究

本研究选取优茧蜂亚科Euphorinae(膜翅目Hymenoptera:茧蜂科Braconidae)的8族19属23种作为内群,茧蜂其它6个亚科的8属8种作外群,首次结合同源核糖体28S rDNA D2基因序列片段和41个形态学特征对该亚科进行了系统发育学研究。利用"圆口类"的内茧蜂亚科Rogadinae、茧蜂亚科Braconinae、矛茧蜂亚科Doryctinae的3个亚科为根,以PAUP*4.0和MrBayes3.0B4软件分别应用最大简约法(MP)和贝叶斯法对优茧蜂亚科的分子数据和分子数据与非分子数据的结合体进行了分析;并以PAUP*4.0对优茧蜂亚科的28S rDNA D2基因序列的片段的碱基组成与碱基替代情况进行了分析。结果表明:优茧蜂亚科的28S rDNA D2基因序列片段的GC%含量在40.00%~49.25%之间变动,而对于碱基替代情况来讲,优茧蜂亚科各个成员间序列变异位点上颠换(transversion)大于转换(transition);不同的分析和算法所产生的系统发育树都表明目前根据形态定义出的优茧蜂亚科Euphorinae不是一个单系群,而是一个与蚁茧蜂亚科Neoneurinae和高腹茧蜂亚科Cenocoelinae混杂在一起的并系群;在优茧蜂亚科内部,悬茧蜂族Meterorini和食甲茧蜂族Microctonini(排除猎户茧蜂属Orionis)为单系群,而宽鞘茧蜂族Centistini、大颚茧蜂族Cosmophorini、优茧蜂族Euphorini、瓢虫茧蜂族Dinocampini为并系群;悬茧蜂族Meterorini在优茧蜂亚科Euphorinae内位于基部位置的观点得到部分的支持,同时食甲茧蜂族Microctonini被判定为相对进化的类群。此外对于优茧蜂亚科内各属之间的相互亲缘关系,不同算法所得到的系统发育属的结果不完全一致,这表明优茧蜂亚科内(属及族)的系统发育关系还有待于进一步研究。     

The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae

The phylogenetic utility of chloroplast (atpB-rbcL, petD, rps16, trnL-F) and nuclear (ETS, ITS) DNA regions was investigated for the tribe Spermacoceae of the coffee family (Rubiaceae). ITS was, despite often raised cautions of its utility at higher taxonomic levels, shown to provide the highest number of parsimony informative characters, in partitioned Bayesian analyses it yielded the fewest trees in the 95% credible set, it resolved the highest proportion of well resolved clades, and was the most accurate region as measured by the partition metric and the proportion of correctly resolved clades (well supported clades retrieved from a combined analysis regarded as “true”). For Hedyotis, the nuclear 5S-NTS was shown to be potentially as useful as ITS, despite its shorter sequence length. The chloroplast region being the most phylogenetically informative was the petD group II intron.We also present a phylogeny of Spermacoceae based on a Bayesian analysis of the four chloroplast regions, ITS, and ETS combined. Spermacoceae are shown to be monophyletic. Clades supported by high posterior probabilities are discussed, especially in respect to the current generic classification. Notably, Oldenlandia is polyphyletic, the two subgenera of Kohautia are not sister taxa, and Hedyotis should be treated in a narrow sense to include only Asian species.     

The phylogeny of Schistidium (Bryophyta, Grimmiaceae) based on primary and secondary structure study of nuclear rDNA internal transcribed spacers

The phylogeny of Schistidium (Bryophyta, Grimmiaceae) was studied on the basis of nucleotide sequences of internal transcribed spacers ITS1-2 of nuclear DNA and trnT-trnD region of chloroplast DNA. The consistency of phylogenetic trees constructed from nuclear and chloroplast sequences was shown. A basal grade and two large clades were resolved on the phylogenetic trees. Morphological characteristics specific for these clades were described. ITS1 and ITS2 secondary structures of Schistidium species were modeled using thermodynamic criteria. Four different structures of the longest ITS1 hairpin were identified. Possible paths of Schistidium evolution were considered based on the four types of ITS1 secondary structure and phylogenetic trees.     

Nuclear DNA Amounts in Palms (Arecaceae)

Nuclear DNA amounts are reported for 83 species and 53 genera of palms, covering all of the six subfamilies. 4C DNA contents range between 3.89 and 55.62 pg in diploids, showing an approximate 14.3-fold variation in genome size. Polyploids have DNA contents of up to 156.40 pg/4c which demonstrates a 40.2-fold variation. Diploids with high DNA contents occur in three subfamilies of palms (Coryphoideae, Calamoideae, Arecoideae), and seem to be further restricted to particular tribes or subtribes (Thrinacinae, Borasseae, Lepidocaryeae, Caryoteae, some subtribes of Areceae). Palms from the subfamilies Nypoideae and Phytelephantoideae have the lowest DNA amounts, followed by the Phoeniceae and the Corypheae: Livistoninae from the subfamily Coryphoideae. Although DNA amounts in some genera and subtribes are usually constant, e.g., in Phoenix, Phytelephas, the Livistoninae, Dypsidinae, diploid Butiinae), considerable variation occurs at the diploid level in some large and apparently actively evolving genera such as Chamaedorea, Pinanga, Cenoma and possibly Bactris. Formaldehyde fixation is recommended for palms, as conventional ethanol-acetic acid fixation has proved to be unsuitable for DNA estimation of Feulgen-stained nuclei by microdensitometry, since it can lead to errors up to 2.5-fold in extent. Chromosome counts are reported for 72 of the species studied, of which 42 are new.     

Phylogenetic relationships in Southern African chloridoid grasses (Poaceae) based on nuclear and chloroplast sequence data

Phylogenetic relationships in southern African members of chloridoid grasses were investigated using DNA sequences from the chloroplast trnL (UAA) 5’ exon‐ trnF (GAA) region and the nuclear ribosomal internal transcribed spacer regions. The two datasets were analysed separately before being combined into a matrix of 50 specimens, representing 38 species. The congruence between the individual data sets was assessed in a conditional combination approach and the congruent data sets were then combined into a single data set. In this analysis, the chloridoid grasses were monophyletic and two large groups, corresponding to the tribes Eragrostideae and Cynodonteae, were polyphyletic; Eragrostis, the largest genus in the subfamily, was polyphyletic. Otherwise, high support levels were found at species and generic level.     

Phylogenetic relationships of Steinernema Travassos, 1927 (Nematoda: Cephalobina: Steinernematidae) based on nuclear, mitochondrial and morphological data

Entomopathogenic nematodes of the genus Steinernema are lethal parasites of insects that are used as biological control agents of several lepidopteran, dipteran and coleopteran pests. Phylogenetic relationships among 25 Steinernema species were estimated using nucleotide sequences from three genes and 22 morphological characters. Parsimony analysis of 28S (LSU) sequences yielded a well-resolved phylogenetic hypothesis with reliable bootstrap support for 13 clades. Parsimony analysis of mitochondrial DNA sequences (12S rDNA and cox 1 genes) yielded phylogenetic trees with a lower consistency index than for LSU sequences, and with fewer reliably supported clades. Combined phylogenetic analysis of the 3-gene dataset by parsimony and Bayesian methods yielded well-resolved and highly similar trees. Bayesian posterior probabilities were high for most clades; bootstrap (parsimony) support was reliable for approximately half of the internal nodes. Parsimony analysis of the morphological dataset yielded a poorly resolved tree, whereas total evidence analysis (molecular plus morphological data) yielded a phylogenetic hypothesis consistent with, but less resolved than trees inferred from combined molecular data. Parsimony mapping of morphological characters on the 3-gene trees showed that most structural features of steinernematids are highly homoplastic. The distribution of nematode foraging strategies on these trees predicts that S. hermaphroditum, S. diaprepesi and S. longicaudum (US isolate) have cruise forager behaviours.     

Phylogenetic relationships within the New World subfamily Larreoideae (Zygophyllaceae) confirm polyphyly of the disjunct genus Bulnesia

The Larreoideae subfamily is the major representative of the family Zygophyllaceae in South America, where several of its members are common to dominant in arid regions of the Southern Cone. However, there are currently no phylogenetic analyses of the subfamily that may help to understand its origin and diversification. Additionally, there are taxonomic discrepancies around Bulnesia Gay (1845), one of its more important genera. Accordingly, we performed a phylogenetic analysis combining chloroplast (rbcL and trnL-F) and nuclear (ITS) DNA sequences. Bayesian and Parsimony analyses were performed to highlight the intergeneric relationships within Larreoideae. All genera with the exception of Bulnesia are monophyletic and we propose to redefine Bulnesia, dividing it in two genera. Furthermore, other taxonomic issues of the remaining genera are solved. This study represents the first approximation to clarify the phylogenetic relationships amongst all Larreoideae genera, producing a phylogenetic framework that can be used in future macro-ecological studies.     

基于28S rDNA D2基因片段与形态特征的矛茧蜂亚科系统发育研究（膜翅目：茧蜂科）

本研究选取矛茧蜂亚科Doryctinae（昆虫纲Insecta：膜翅目Hymenoptera：茧蜂科Braconidae）的6族15属18种做内群,茧蜂科其它7亚科11属11种做外群,首次结合同源核糖体28S rDNA D2基因序列片段和100个形态学和解剖学特征对该亚科进行了系统发育学研究。利用“非圆口类"的小腹茧蜂亚科Microgastrinae为根,以PAUP*4.0和MrBayes 3.0B4软件分别应用最大简约法（MP）和贝叶斯法对矛茧蜂亚科的分子数据和分子数据与非分子数据的结合体进行了运算分析;并以PAUP*4.0对矛茧蜂亚科的28S rDNA D2基因序列片段的碱基组成与碱基替代情况进行了分析。结果表明：矛茧蜂亚科的28S rDNA D2基因序列片段的GC含量在39.33%～48.28%之间变动,而对于碱基替代情况来讲,矛茧蜂亚科各成员间序列变异位点上颠换（transversion）大于转换（transition）。不同的分析算法所产生的系统发育树都表明矛茧蜂亚科是一个界限分明的单系群;在矛茧蜂亚科内,除了吉丁茧蜂族Siragrini为单系群外,其他族（矛茧蜂族Doryctini和方头茧蜂族Hecabolini）都是并系群。对于矛茧蜂亚科内各属之间的相互亲缘关系,不同算法所得的系统发育树的拓扑结构不完全一致,表明矛茧蜂亚科内（属及族）的系统发育关系还有待于进一步研究。     

The phylogeny of <Emphasis Type="Italic">Schistidium</Emphasis> (Bryophyta,Grimmiaceae) based on the primary and secondary structure of nuclear rDNA internal transcribed spacers

Phylogeny of Schistidium (Bryophyta, Grimmiaceae) was studied by comparing the nucleotide sequences of internal transcribed spacers ITS1-2 of nuclear rDNA and the trnT-trnD region of chloroplast DNA. Phylogenetic trees constructed based on nuclear and chloroplast sequences were consistent, comprising a basal grade and two large clades. Morphological characteristics specific for these clades were described. Secondary structures of ITS1 and ITS2 Schistidium species were modeled using thermodynamic criteria. Four different structures of the longest ITS1 hairpin were identified. These results were used to analyze possible paths of Schistidium evolution. Characteristics of the ITS2 secondary structure support the two major clades recognized in the phylogenetic trees.     

Molecular phylogeny of Omaliinae (Coleoptera: Staphylinidae) and its implications for evolution of atypically long elytra in rove beetles

Staphylinidae, or rove beetles, are a megadiverse family known for their typically very short elytra exposing most of the abdomen, but the putatively early-derived subfamily Omaliinae and its relatives have been known to include multiple taxa with unusually long elytra. The ancestral elytral length of the family and of this subfamily have long been debated. We present a phylogenetic analysis of Omaliinae based on partial mitochondrial COI (1488 bp), COII (366 bp), 12S rDNA (353 bp), nuclear 18S rDNA (1814 bp), 28S rDNA (876 bp) and CAD (869 bp) data. In all, 51 species in 31 genera and four outgroup species were included. The concatenated sequences were analysed by both parsimony- and model-based (Bayesian and maximum likelihood) methods. The subfamily Omaliinae was not supported as a monophyletic group. The model-based analyses (Bayesian and maximum likelihood trees) showed Empelinae nested within Omaliinae (excluding Corneolabiini), whereas parsimony analysis found all three putative ingroup subfamilies, Empelinae, Glypholomatinae and Microsilphinae, grouped within Omaliinae. Within the Omaliinae, the tribes Coryphiini and Eusphalerini were each supported as monophyletic, whereas Anthophagini and Omaliini were each nonmonophyletic. We hypothesize that there have been at least four independent origins of long elytra from short elytra in the omaliine lineage.     

Phylogeny,taxonomy, and evolution of Neotropical cichlids (Teleostei: Cichlidae: Cichlinae)

Despite recent progress on the higher‐level relationships of Cichlidae and its Indian, Malagasy, and Greater Antillean components, conflict and uncertainty remain within the species‐rich African, South American, and Middle American assemblages. Herein, we combine morphological and nucleotide characters from the mitochondrial large ribosomal subunit, cytochrome c oxidase subunit I, NADH dehydrogenase four, and cytochrome b genes and from the nuclear histone H3, recombination activating gene two, Tmo‐4C4, Tmo‐M27, and ribosomal S7 loci to analyse relationships within the Neotropical cichlid subfamily Cichlinae. The simultaneous analysis of 6309 characters for 90 terminals, including representatives of all major cichlid lineages and all Neotropical genera, resulted in the first well‐supported and resolved generic‐level phylogeny for Neotropical cichlids. The Neotropical subfamily Cichlinae was recovered as monophyletic and partitioned into seven tribes: Astronotini, Chaetobranchini, Cichlasomatini, Cichlini, Geophagini, Heroini, and Retroculini. Chaetobranchini + Geophagini (including the “crenicichlines”) was resolved as the sister group of Heroini + Cichlasomatini (including Acaronia). The monogeneric Astronotini was recovered as the sister group of these four tribes. Finally, a clade composed of Cichlini + Retroculini was resolved as the sister group to all other cichlines. The analysis included the recently described ?Proterocara argentina, the oldest known cichlid fossil (Eocene), which was placed in an apical position within Geophagini, further supporting a Gondwanan origin for Cichlidae. These phylogenetic results were used as the basis for generating a monophyletic cichline taxonomy. © The Willi Hennig Society 2008.     

Molecular phylogeny of selected Old World Astragalus (Fabaceae): incongruence among chloroplast trnL-F, ndhF and nuclear ribosomal DNA ITS sequences

This study reports maximum parsimony and Bayesian phylogenetic analyses of selected Old World Astragalus using two chloroplast fragments including trnL-F and ndhF and the nuclear ribosomal internal transcribed spacer (nrDNA ITS). A total of 52 taxa including 34 euploid Old World and New World Astragalus , one aneuploid species from the Neo-Astragalus clade as a representative and 14 other Astragalean taxa, plus Cheseneya astragalina and two species of Caragana as outgroups were analyzed for both trnL-F and nrDNA ITS regions. ndhF was analyzed in 30 taxa and the same number for the combination of these three datasets were examined. In general, the trnL-F dataset and the ndhF and nrDNA ITS datasets generated more or less the same clades within Astragalus . However, in the trnL-F and ndhF phylogenies, Astragalus species are not gathered in a single clade, the so-called Astragalus s.s., as indicated by the nrDNA ITS tree. Visual inspection of these three phylogenies revealed that they were inconsistent regarding the position and relationships of Astragalus hemsleyi , A. ophiocarpus , A. annularis–A. epiglottis / Astragalus pelecinus, A. echinatus and A. arizonicus . Incongruence length difference test suggested that the trnL-F , ndhF and nrDNA ITS datasets were incongruent. In spite of this, phylogenetic analyses of the combined datasets as one unit or as three partitions generated trees that were topologically similar as a mix of the cpDNA and the nrDNA ITS trees. However, the combined dataset provided more resolved and statistically supported clades. The recently described A. memoriosus appeared closely related to A. stocksii (both from sect. Caraganella ) based on both trnL-F and nrDNA ITS sequences.     

单种属弥勒苣苔属系统位置研究：基于分子和细胞学数据

弥勒苣苔属是苦苣苔科的单种属,仅分布于中国西南部。为探讨弥勒苣苔在苦苣苔亚科中的系统位置,我们选择了苦苣苔亚科116个类群,外类群为苦苣苔亚科以外的7个物种。用最大简约法（MP）和贝叶斯分析（BI）,对以上类群的核基因ITS以及两个叶绿体基因trnL-F、atpB-rbcL数据进行了独立和联合分析。在三个片段联合分析的结果中,弥勒苣苔与马铃苣苔属、后蕊苣苔属、金盏苣苔属、直瓣苣苔属以及川鄂粗筒苣苔构成一个强烈支持的分枝。MP树中,此分枝为并系,而在BI分析中,弥勒苣苔与川鄂粗筒苣苔、直瓣苣苔属互为姐妹类群。同时,第一次报道了弥勒苣苔的染色体数目（2n=34）。根据前人报道,马铃苣苔属、后蕊苣苔属、粗筒苣苔属和直瓣苣苔属的染色体数目同为2n=34,这进一步支持我们的分子系统发育分析。     

单种属弥勒苣苔属系统位置研究 基于分子和细胞学数据

弥勒苣苔属是苦苣苔科的单种属,仅分布于中国西南部。为探讨弥勒苣苔在苦苣苔亚科中的系统位置,我们选择了苦苣苔亚科116个类群,外类群为苦苣苔亚科以外的7个物种。用最大简约法（MP）和贝叶斯分析（BI）,对以上类群的核基因ITS以及两个叶绿体基因trnL-F、atpB-rbcL数据进行了独立和联合分析。在三个片段联合分析的结果中,弥勒苣苔与马铃苣苔属、后蕊苣苔属、金盏苣苔属、直瓣苣苔属以及川鄂粗筒苣苔构成一个强烈支持的分枝。MP树中,此分枝为并系,而在BI分析中,弥勒苣苔与川鄂粗筒苣苔、直瓣苣苔属互为姐妹类群。同时,第一次报道了弥勒苣苔的染色体数目（2n=34）。根据前人报道,马铃苣苔属、后蕊苣苔属、粗筒苣苔属和直瓣苣苔属的染色体数目同为2n=34,这进一步支持我们的分子系统发育分析。