57 Systematics of hydropuntia montagne (gracilariaceae,gracilariales, rhodophyta) based on comparative morphology and rbcL sequence analysis

The taxonomic validity of the genus Hydropuntia Montagne (1843) (including Polycavernosa) within the Gracilariaceae (Gracilariales, Rhodophyta) is controversial. Morphological characters that define species of Hydropuntia are said to be variable and to overlap with those of Gracilaria. Here we present a global phylogenetic study of the family based on a Bayesian analysis of a large rbcL DNA sequence dataset indicating that the genus Hydropuntia forms a well supported monophyletic clade within the family, and recognize Hydropuntia as a genus distinct from Gracilaria. We also conducted smaller phylogenetic analyses in which thirty four Hydropuntia rbcL sequences resulted in two major clades within the genus, comprising a Caribbean clade and an Indo‐Pacific clade. Diagnostic reproductive stages that separate these two clades will be illustrated.     

SPECIES PHYLOGENY OF COSMARIUM AND STAURASTRUM (DESMIDIACEAE) BASED ON RBC L SEQUENCES

Cosmarium and Staurastrum are the two most diverse genera of placoderm desmids (Family Desmidiaceae), with approximately 1100 and 800 species, respectively. Phylogenetic analysis of relationships of species has been extremely difficult. In a monograph of North American placoderm desmids, Prescott et al. described early phylogenetic work that concluded Staurastrum to be polyphyletic and certainly polymorphic. Likewise, Cosmarium has also been viewed as polyphyletic, and a number of workers have proposed splitting these genera. The classical view of West and West grouped species within each genus into two divisions and 6–8 sections based on wall features and semicell shape. We sequenced rbc L from 18 species of Cosmarium (2 divisions, 7 sections) and 12 species of Staurastrum (2 divisions and 7 sections) and performed a phylogenetic analysis (parsimony, maximum likelihood, bootstrap) using other placoderm desmids and Zygnematales as outgroups. The results exhibit little support for the monophyly of sections or divisions of the two genera. Furthermore, although there is support for the monophyly of clades within each genus, there is also support for a separate clade containing species from both genera.     

Polyphyly of Limoniastrum (Plumbaginaceae): evidence from DNA sequences of plastid rbcL, trnL intron and trnL-F intergene spacer

Phylogenetic relationships of Limoniastrum and other genera of subfamily Staticoideae (Plumb-aginaceae) were studied using parsimony analysis of the plastid gene rbc L, the intron of trn L and the intergene spacer of trnL-trn F. Our analysis showed that Limoniastrum was polyphyletic. Limoniastrum ifniense , in both rbc L and combined data analyses, is sister to Armeria and Psylliostachys , whereas in the trn L-F (intron and spacer combined) analysis it is sister to a clade composed of Acantholimon, Dictyolimon and the remaining species of Limoniastrum . In all analyses, the five remaining species of Limoniastrum (excluding Limoniatrum ifniense ) formed a clade with two groups of species: L. monopetalum+L. guyonianum and those sometimes considered as the segregate genus Bubania ( L.feei, L. weygandiorum and L. rechingeri ). Levels of sequence divergence among these three groups of Limoniatrum were greater than for other well supported genera in the family and, in combination with morphological differences and paucity of synapomorphies, led us to conclude that separate generic status for each of the three clades is warranted.     

基于叶绿体TrnL- F序列和联合数据分析木通科的分子系统发育(英文)

基于叶绿体trnL_F序列单独分析以及trnL_F和rbcL序列联合分析重建了木通科的分子系统发育。本研究的系统发育拓扑结构与覃海宁和塔赫他间的族划分系统非常一致。猫儿屎族和串果藤族在系统发育树上位于本科的基部。由分布于南美的勃奎拉藤属和拉氏藤属组成的拉氏藤族得到了trnL_F序列分析 (10 0 % )和联合序列分析 (99% )的很好支持。木通族在两个分析里都得到了 10 0 %的靴带支持率。新建立的长萼木通属在trnL_F树上嵌套在木通属内 ;然而 ,在联合分析的树上 ,它与木通属形成姐妹群并得到很高的支持率。在系统发育上关系密切的 3个属 :牛藤果属、八月瓜属和野木瓜属之间的关系仍未解决。牛藤果与八月瓜在两个分析里都形成姐妹群 ,但支持率低。小花鹰爪枫嵌套在野木瓜属内 ,并与西南野木瓜形成姐妹群。木通族内这 3个属可能都不是单系 ,它们的属间界限和属的界定需要更多的分子和形态数据的进一步研究。     

Floral morphology and embryo sac development in Burretiodendron kydiifolium Y. C. Hsu et R. Zhuge (Tiliaceae) and their systematic significance

Phylogenetic analysis of rbc L and atp B gene sequences from Biebersteinia Stephan (represented by B. orphanidis Boiss.) and from selected taxa of the rosids I and II clades does not support traditional grouping of this genus in Geraniaceae s. s. nor in Geraniales, but indicates strong support for a position nested within Sapindales (as recently delimitated). The rbc L and atp B phylogenies obtained were congruent but differently resolved and do not link Biebersteinia to any other clade within Sapindales. Biebersteinia is on a long branch on its own which, given the particular combination of apomorphic morphological characters, justifies familial status.     

Phylogeny and taxonomy of Macrolepiota (Agaricaceae)

The position and composition of Macrolepiota within the Agaricaceae and its phylogenetic relationships with other members of the family were investigated, using both molecular (ITS and LSU rDNA sequences) and morphological characters. The molecular data separate the genus into two clades. The first clade comprises M. procera, M. mastoidea, M. clelandii and allies and is a sister group of Leucoagaricus and Leucocoprinus. The second, more diverse, clade, with M. rachodes and allies, M. globosa, Chlorophyllum molybdites, Leucoagaricus hortensis and Endoptychum agaricoides, is a sister group of Agaricus. The separation of the two clades is supported by morphological characters, such as the structure of the pileus covering, the stipitipellis and the shape of the germ pore and the spore apex. The two clades are regarded as genera for which the names Macrolepiota and Chlorophyllum are proposed. Macrolepiota nympharum does not belong to either clade but is assigned to the genus Leucoagaricus, close to L. leucothites. Endoptychum depressum is transferred to the genus Agaricus as A. inapertus.     

CLONING AND CHARACTERIZATION OF NITRATE TRANSPORTER GENES FROM THE DIATOM CYLINDROTHECA FUSIFORMIS

Molecular phylogenetic analysis of the conjugating green algae (Class Zygnemophyceae) using nuclear (SSU rDNA) and chloroplast ( rbcL ) gene sequences has resolved hypotheses of relationship at the class, order, and family levels, but several key questions will require data from additional genes. Based on SSU and rbc L sequences, the Zygnemophyceae and Desmidiales are monophyletic, and families of placoderm desmids are distinct clades (Desmidiaceae, Peniaceae, Closteriaceae, and Gonatozygaceae). In contrast, the Zygnemataceae and Mesotaeniaceae are paraphyletic, although whether these two traditional families constitute a clade is uncertain. In addition, relationships of genera within families have proven resistant to resolution with these two oft-used genes. We have sequenced the cox III gene from the mitochondrial genome to address some of these ambiguous portions of the phylogeny of conjugating green algae. The cox III gene is more variable than rbc L or SSU rDNA and offers greater resolving power for relationships of genera. We present preliminary analyses of coxIII sequences from each of the traditional families of Zygnemophyceae and contrast the resulting topologies with those derived from nuclear and chloroplast genes.     

从rbcL序列探讨单室茱萸属的系统位置

为了探讨单室茱萸属Mastixia的系统位置,本文对八蕊单室萸（Mastixia euony moides),云南单室茱萸（M.pentandra subsp,chinensis)及近缘物种云南紫树（Nyssa yunnanensis)和毛八角枫（Alangium kurzii)的cpDNA中编码1,5－二磷酸核酸糖羧化酶大亚基的rbcL基因序列进行了双脱氧测定。通过对这些序列与广义山茱萸科Cornaceae和Mastixia曾被归入的科的类群的rbcL序列进行PAUP（Phylogenetic Analysis Using Parsimony)分析,得到24棵最简约的分支树图。PAUP分析表明单室茱萸属与马蹄参属Diplopanax,紫树属Nyssa,喜树属Camptotheca和珙桐属Davidia的亲缘关系最近,并由分支图支持可以将Mastixia提升为山茱萸目Cornales中的一个科－单室萸科Masstixiaceae。     

Phylogenetic placement of the enigmatic and critically endangered genus Saniculiphyllum (Saxifragaceae) inferred from combined analysis of plastid and nuclear DNA sequences

Saniculiphyllum, a monotypic genus distributed in Southwest China, was thought to be extinct before our recent rediscovery. The taxonomic position of this genus has been enigmatic ever since its publication. It was originally treated as the only member of a distinct tribe Saniculiphylleae in the family Saxifragaceae. Some proposed a new family, Saniculophyllaceae, to accommodate this genus, although its affinities are clearly with members of Saxifragaceae. Here we analyzed six DNA regions, the nuclear ribosomal ITS and 26S rDNA and the plastid rbcL, matK, trnL-trnF, psbA-trnH genes, spacers, and intron to explore the phylogenetic position of Saniculiphyllum within Saxifragaceae. The combined nuclear and chloroplast dataset includes 63 ingroup species, representing all genera but Hieronymusia in the family. Results from likelihood, parsimony and Bayesian phylogenetic methods corroborate earlier results. Two clades of Saxifragaceae, the Heucheroid and Saxifragoid clades, were recovered. The topologies obtained from different analyses confirm the placement of Saniculiphyllum in Saxifragaceae, but our analyses reveal that Saniculiphyllum is embedded within the large Heucheroid clade. However, the closest relatives of Saniculiphyllum within the Heucheroid clade remain unclear. Combined with morphological data, our results suggest that Saniculiphyllum should best be regarded as a highly distinctive lineage within the Heucheroid clade of Saxifragaceae. Morphological novelties and conservation status of Saniculiphyllum are also presented.     

Phylogeny of finescale shiners of the genus Lythrurus (Cypriniformes: Cyprinidae) inferred from four mitochondrial genes

We infer the phylogenetic relationships of finescale shiners of the genus Lythrurus, a group of 11 species of freshwater minnows widely distributed in eastern North America, using DNA sequences from the ND2 (1047 bp), ATPase8 and 6 (823 bp), and ND3 (421 bp) mitochondrial protein-coding genes. The topologies resulting from maximum parsimony, Bayesian, and maximum likelihood tree building methods are broadly congruent, with two distinct clades within the genus: the L. umbratilis clade (L. umbratilis + L. lirus + (L. fasciolaris + (L. ardens, L. matutinus))) and the L. bellus clade (L. fumeus + L. snelsoni + (L. roseipinnis + (L. atrapiculus + (L. bellus, L. algenotus)))). Support is weak at the base of several clades, but strongly supported nodes differ significantly from prior investigations. In particular, our results confirm and extend earlier studies recovering two clades within Lythrurus corresponding to groups with largely "northern" and "southern" geographic distributions. Several species in this genus are listed in the United States as threatened or of special concern due to habitat degradation or limited geographic ranges. In this study, populations assigned to L. roseipinnis show significant genetic divergence suggesting that there is greater genetic diversity within this species than its current taxonomy reflects. A full accounting of the biodiversity of the genus awaits further study.     

A Phylogenetic Analysis of the Plastid matK Gene with Emphasis on Melanthiaceae sensu lato

Abstract: The presented mat K tree primarily agrees well with the previously presented rbc L tree and combined rbc L + atp B + 18SrDNA tree. According to the mat K tree, the monocotyledons are monophyletic with 100 % bootstrap support. Acorus diverges first from all other monocotyledons (90 % bootstrap support) in which two major clades are recognized: one (89 %) consisting of Alismatanae and Tofieldia (Nartheciaceae), and the other (< 50 %) comprising Lilianae, Commelinanae and Nartheciaceae other than Tofieldia. Within the latter major clade, Petrosavia and Japonolirion (Nartheciaceae) (82 %) diverge first from the remaining taxa (< 50 %) in which two clades are formed: one (81 %) consisting of Pandanales, Dioscoreales and Nartheciaceae-Narthecioideae, and the other (< 50 %) comprising Liliales, Asparagales and Commelinanae. In the former clade, Dioscoreales and Narthecioideae are grouped together (88 %). In the latter clade, Asparagales and Commelinanae are grouped together (< 50 %). Differences between the mat K and rbc L tree topologies appear in the positions of Tricyrtis (Calochortaceae) and Dracaenaceae. Differences between the mat K and combined rbc L + atp B + 18SrDNA tree topologies exist in the positions of the Petrosavia-Japonolirion pair (Nartheciaceae) and Pandanales. The stop codon position of the mat K gene appears to be highly variable among the monocotyledons, especially in the Liliales.     

A fine line between sex and unisexuality: the phylogenetic constraints on parthenogenesis in lacertid lizards

A phylogeny of Caucasian rock lizards (genus Darevskia , formerly Lacerta ) was reconstructed using mitochondrial DNA sequence and allozyme data. All 15 bisexual species grouped into three major clades: the caucasica, saxicola and rudis clades. Unisexual Darevskia originate from inter-clade hybridization, never from within clades. Only two clades, the caucasica clade and the rudis clade, were involved in forming unisexuals; the saxicola clade was never involved. Furthermore, the hybridization is directional in that the caucasica clade contributed only maternal parents and the rudis clade only paternal parents. The formation of unisexual species is best explained by sexually directional phylogenetic constraints. We hypothesize that the causative agents are likely to be genes linked with the sex chromosomes within the parental sexual species.     

MODULATION OF VERY-LONG CHAIN (C28) HIGHLY UNSATURATED FATTY ACIDS IN PROROCENTRUM MININUM (DINOPHYCEAE) BY SELENIUM

Sargassum is one of the most species-rich genera in the brown algae with over 400 described species worldwide. The bulk of these species occurs in Pacific-Indian ocean waters with only a small portion found on the Atlantic side of the Isthmus of Panama. Sargassum also has one of the most subdivided and complex taxonomic systems used within the algae. Systematic distinctions within the genus are further complicated by high rates of phenotypic variability in several key morphological characters. Molecular analyses in such systems should allow testing of systematic concepts while providing insights into speciation and evolutionary patterns. Global molecular phylogenetic analyses using both conserved and variable regions of the Rubisco operon ( rbc L and rbc L-IGS-rbcS) were performed with species from the Gulf of Mexico, Caribbean, and Pacific basin. Results confirm earlier analyses based on rbc L-IGS- rbc S from Pacific species at the subgeneric and sectional level while providing additional insights into the systematics and phylogenetics on a global scale. For example, species east of the Isthmus of Panama form a distinct well-resolved clade within the tropical subgenus. This result in sharp contrast to traditional systematic treatments but provides a window into the evolutionary history of this genus in the Pacific and Atlantic Ocean basins and a possible means to time speciation events.     

A new phylogenetic tribal classification of the grape family (Vitaceae)

Vitaceae (the grape family) consist of 16 genera and ca. 950 species primarily distributed in tropical regions. The family is well‐known for the economic importance of grapes, and is also ecologically significant with many species as dominant climbers in tropical and temperate forests. Recent phylogenetic and phylogenomic analyses of sequence data from all three genomes have supported five major clades within Vitaceae: (i) the clade of Ampelopsis, Nekemias, Rhoicissus, and Clematicissus; (ii) the Cissus clade; (iii) the clade of Cayratia, Causonis, Cyphostemma, Pseudocayratia, Tetrastigma, and an undescribed genus “Afrocayratia”; (iv) the clade of Parthenocissus and Yua; and (v) the grape genus Vitis and its close tropical relatives Ampelocissus, Pterisanthes and Nothocissus, with Nothocissus and Pterisanthes nested within Ampelocissus. Based on the phylogenetic and morphological (mostly inflorescence, floral and seed characters) evidence, the new classification places the 950 species and 16 genera into five tribes: (i) tribe Ampelopsideae J.Wen & Z.L.Nie, trib. nov. (47 species in four genera; Ampelopsis, Nekemias, Rhoicissus and Clematicissus); (ii) tribe Cisseae Rchb. (300 species in one genus; Cissus); (iii) tribe Cayratieae J.Wen & L.M.Lu, trib. nov. (370 species in seven genera; Cayratia, Causonis, “Afrocayratia”, Pseudocayratia, Acareosperma, Cyphostemma and Tetrastigma); (iv) tribe Parthenocisseae J.Wen & Z.D.Chen, trib. nov. (ca. 16 spp. in two genera; Parthenocissus and Yua); and (v) tribe Viteae Dumort. (ca. 190 species in two genera; Ampelocissus and Vitis).     

Nuclear and mitochondrial sequence data reveal the major lineages of starlings, mynas and related taxa

We investigated the phylogenetic relationships among the major lineages of the avian family Sturnidae and their placement within the Muscicapoidea clade using two nuclear (RAG-1 and myoglobin) and one mitochondrial gene (ND2). Among Muscicapoidea, we recovered three clades corresponding to the families Cinclidae, Muscicapidae and Sturnidae (sensu [Sibley, C.G., Monroe Jr., B.L., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT]). Within the sturnoid lineage Mimini and Sturnini are sister groups, with Buphagus basal to them. We identified three major lineages of starlings: the Philippine endemic genus Rhabdornis, an Oriental-Australasian clade (genera Scissirostrum, Gracula, Mino, Ampeliceps, Sarcops, Aplonis), and an Afrotropical-Palaearctic clade (all African taxa, Sturnus and Acridotheres). We discuss the biogeographic implications of our findings and suggest an Asiatic origin for this family. The congruence between the age of major clades, estimated by NPRS, and palaeoclimatic data present evidence for the role of climatic changes in shaping present day distribution of the group.     

Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales)

Approximately 3000 bp across 84 taxa have been analyzed for variable regions of RPB1, RPB2, and nLSU-rDNA to infer phylogenetic relationships in the large ectomycorrhizal mushroom genus Inocybe (Agaricales; Basidiomycota). This study represents the first effort to combine variable regions of RPB1 and RPB2 with nLSU-rDNA for low-level phylogenetic studies in mushroom-forming fungi. Combination of the three loci increases non-parametric bootstrap support, Bayesian posterior probabilities, and resolution for numerous clades compared to separate gene analyses. These data suggest the evolution of at least five major lineages in Inocybe-the Inocybe clade, the Mallocybe clade, the Auritella clade, the Inosperma clade, and the Pseudosperma clade. Additionally, many clades nested within each major lineage are strongly supported. These results also suggest the family Crepiodataceae sensu stricto is sister to Inocybe. Recognition of Inocybe at the family level, the Inocybaceae, is recommended.     

Evidence for the Polyphyly of Haworthia (Asphodelaceae Subfamily Alooideae; Asparagales) Inferred from Nucleotide Sequences of rbcL, matK, ITS1 and Genomic Fingerprinting with ISSR-PCR

Abstract: Four molecular markers have been studied to examine the phylogenetic position of the South African plant genus Haworthia Duval within the succulent Asphodelaceae. Sequence data of the chloroplast genes mat K and rbc L were compared to the nuclear markers ITS1 and ISSR (Inter Simple Sequence Repeat) analysis. Both lines of molecular data, chloroplast and nuclear DNA, indicate that Haworthia is polyphyletic, forming two distinct clades. Most taxa previously combined as Haworthia subgenus Haworthia branch off early in the alooid chloroplast trees forming a strongly monophyletic group, whereas subgenus Hexangulares forms a polyphyletic assemblage comprising other alooid genera. The nuclear markers ITS1 and ISSR fingerprinting support the two groups as distinctly different, therefore confirming the division seen in chloroplast DNA. The practical implication is that the generic concept of Haworthia may have to be restricted to H. subgenus Haworthia or alternatively, that the groups of Haworthia be treated as infrageneric taxa within a broadened (Linnaean) concept of Aloe.     

PHYLOGENETIC RELATIONSHIPS OF THE BROWN ALGAL ORDERS ECTOCARPALES, CHORDARIALES, DICTYOSIPHONALES, AND TILOPTERIDALES (PHAEOPHYCEAE) BASED ON RUBISCO LARGE SUBUNIT AND SPACER SEQUENCES

Phylogenetic relationships among 23 species of morphologically simple brown algae belonging to the Ectocarpales sensu stricto , Chordariales, Dictyosiphonales, and Tilopteridales sensu stricto , Phaeophyceae (Fucophyceae), were analyzed using chloroplast-encoded RUBISCO large subunit gene sequences ( rbc L) and the associated RUBISCO spacer sequences. Comparison of the observed and expected sequence divergence at the three codon positions of rbc L showed that the level of mutational saturation within the brown algae is minor. Thus, rbc L is well suited for phylogenetic studies in this group. Unweighted parsimony analyses and a neighbor-joining distance analysis were performed using unambiguously aligned rbc L sequences from the above four orders, one marine raphidophyte and two Tribophyceae (Xantophyceae). Polyphyly of Tilopteridales sensu lato (i.e. including Dictyosiphonales) is verified; we therefore recommend the use of Tilopteridales in the strict sense. The Ectocarpales, Chordariales, and Dictyosiphonales are paraphyletic with respect to each other, forming a highly interwoven clade. A separate parsimony analysis of the RUBISCO spacer as well as a combined rbc L and spacer analysis supported the close relationship among the latter three orders, adding to the evidence that they should be subsumed into the Ectocarpales sensu lato.     

Local origin and diversification among Lampornis hummingbirds: a Mesoamerican taxon

The huge biodiversity found in Mesoamerica is often explained by its geographic situation as a natural bridge between two large biogeographic regions. Often overlooked, however, are the high levels of speciation and diversification in the area. Here we assess the phylogenetic relationships within a Mesoamerican group of hummingbirds (Lampornis). We sequenced both mtDNA (1,143 bp of cyt b and 727 bp of ND5) and nuclear genes (505 bp of AK-5 intron and 567 bp of c-mos) for each of the seven recognised species and outgroups. We find two or three clades of similar age within this genus: L. clemenciae and L. amethystinus (singly or as each other's sister taxa) and a Central American clade. This Central-American clade presents a clear bipartition between northern (L. viridipallens and L. sybillae) and southern Mesoamerica, which is shared with many other Mesoamerican organisms. Our analyses suggest that L. hemileucus does not belong in the genus Lampornis. While we refrain to apply a time-scale to our data because of the lack of an appropriate calibration, our results indicate that the genus Lampornis predates the uprising of the Panama land-bridge, and that diversification among the isthmian species (L. castaneoventris and L. calolaema) is a very recent event. Our results strongly suggest a local Mesoamerican origin for this genus.     

Phylogenetic analysis of the Silurian Retiolitidae

A cladistic, phylogenetic analysis of the Retiolitidae, using 18 genera and parataxa and 23 characters, reveals that two distinct clades can be recognized within this family, as well as a primitive stem-group that includes the genus Pseudoretiolites . One of the derived clades includes Pseudo-plegmatograptus, Stomatograptus and Retiolites , which are assigned to the revised subfamily Retiolitinae. The other derived clade, the early part of which shows a paraphyletic relationship, includes the remaining known genera Rotaretiofites s.l., Paraplectograptus s.l., Sokolovograptus, Plectograptus, Agastograptus, Spinograptus, Gothograptus, Eisenackograptus, Neogothograptus, Semiplectograptus, Plectodinemagraptus and Holoretiolites . These genera are all included within an expanded Plectograptinae. The biostratigraphic distribution of these taxa suggests that these two clades diverged from a Pseudoretiolites-like ancestor in mid-Aeronian time.