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.     

Sieve-element plastids ofCyrillaceae,Erythroxylaceae andRhizophoraceae: Description and significance of subtype PV plastids

A new subtype (PV) of protein-containing sieve-element plastids was found to contain a uniquely large number of polygonal protein crystals, sometimes with (PVcf) and sometimes without (PVc) protein filaments. These plastids do not accumulate starch. The PVcf-plastids occur inCyrillaceae only, while the PVc-plastids are limited toErythroxylaceae andRhizophoraceae. The significance of the new P-subtype with respect to the systematic position of the three families is discussed.     

Sieve-element plastids,exine sculpturing and the systematic affinities of theBuxaceae

The sieve-element plastids of members of several genera in theBuxaceae (Buxus, Pachysandra andSarcococca) were found to be of the specific subtype PVI, which contains a central globular protein crystal.Simmondsia (Simmondsiaceae) andDaphniphyllum (Daphniphyllaceae), on the other hand, were found to contain S-type sieve-element plastids. The occurrence of the highly restricted PVI plastids in theBuxaceae mitigates against a close relationship between theBuxaceae andSimmondsia, Daphniphyllum andEuphorbiaceae. Exine sculpturing of theBuxaceae andSimmondsiaceae also shows no close similarities. Both of these EM characters are discussed in connection with other available data and with respect to earlier systematic treatment of these families.     

Sequence diversity of a gene encoding a putative primary sigma factor among Borrelia burgdorferi sensu lato strains

Twenty-six strains of Borrelia burgdorferi sensu lato were subjected to polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) analysis for assessing the sequence divergence of rpoD gene encoding the primary sigma factor. Four and five RFLP patterns were observed from two fragments of rpoD gene. Sequence analysis of a subgenic fragment covering region 1 through 4 from 13 strains of Borrelia burgdorferi s. l. revealed that 21 of 450 deduced amino acid residues were diverged. These results indicate that the sequence heterogeneity of rpoD is present in different strains of Borrelia burgdorferi s. l., and agreed well with the current classification of genospecies.     

The higher‐level phylogenetic relationships of the Eumeninae (Insecta,Hymenoptera, Vespidae), with emphasis on Eumenes sensu lato

Cladistic analyses were carried out to infer the phylogenetic relationships among taxa that were originally part of the large genus Eumenes. Terminals belonging to other eumenine lineages were also included, as well as terminals from other vespid subfamilies. Analyses under equal weights and implied weights were carried out, and better results were obtained with the latter. The results corroborated the monophyly of Eumeninae, and recovered Zethini sensu lato as the sister‐lineage to the remaining eumenines. Eumenes sensu lato as originally recognized is paraphyletic relative to Odynerus sensu lato. A natural classification at the tribal level congruent with the phylogenetic results may be proposed, and the names Zethini, Odynerini, and Eumenini are already available. This is the most comprehensive phylogeny of the Eumeninae to date. A new generic synonymy is Alfieria Giordani Soika, 1934 = Delta de Saussure, 1855.     

Taxonomic update of Clitocybula sensu lato with a new generic classification

The taxonomy and phylogeny of the hydropoid clade (genera Clitocybula s.l., Megacollybia, Leucoinocybe gen. nov., Hydropus, Trogia, Gerronema, Porotheleum and Lignomphalia gen. nov.) in Europe is studied using morphological and molecular approaches; the first three genera in detail including all known European species. Only two European species remain in Clitocybula s.str., Clitocybula lacerata and Clitocybula familia. The European C. lacerata is a species complex which should be treated as C. lacerata agg. at the current state of knowledge. A neotype originating from type area was designated to fix the application of the name. The presence of American species Clitocybula abundans in Europe is insufficiently proved. “Clitocybula dryadicola ? belongs to the genus Hydropus, and Clitocybula tilieti has an unclear systematic position. The results showed that Megacollybia and Leucoinocybe represent independent genera separated from Clitocybula. The genus Leucoinocybe is validly published with two European species, Leucoinocybe lenta and Leucoinocybe taniae. “Clitocybula flavoaurantia” proved to be conspecific with the latter species. The genus Lignomphalia is published for “Pseudoomphalina lignicola”, a lignicolous omphalinoid species. The Indian “Clitocybula sulcata” is transferred to Leucoinocybe and “Clitocybula atrialba” to Gerronema. The first European records of Megacollybia marginata are published.     

Floral development of dioecious species and trends of floral evolution in Piper sensu lato

The initiation of the floral parts (mainly stamens and carpels) is described for the four dioecious species of Piper: Piper polysyphorum C. DC, P. bavinum C. DC., P. pedicellatum C. DC., P. pubicatulum C. DC. The initiation order resembles that in the perfect flowers of some species, such as P. amalago. The carpels are initiated simultaneously, in most cases, as three primordia. In P. polysyphorum , carpel tips split into two lobes, so that finally a four- or five-lobed stigma will be formed when the ovary is fully developed. The staminodes (exactly, staminodial primordia) in the female flowers are initiated in the same order as the stamens in the male flowers and remain until the ovaries are enclosed. The unisexual flowers have stamens reduced to three or two. The reduction of stamen or staminode (staminodial primordium) number is accompanied by the change of their positions from opposite the carpels to alternate. After the initiation of the staminodes, or, exactly staminodial primordia, in the female flowers, the central part of the floral apex forms a ring meristem which is triangular. The carpel primordia (often three) are initiated on the three points of the ring meristem. The evolutionary trends of the flowers of Piper sensu lato are discussed.     

Phylogenetic analyses and chromosome evolution in Convallarieae (Ruscaceae sensu lato), with some taxonomic treatments

The tribe Convallarieae, comprising 10 genera and 95 species, has recently been transferred from its own family to Ruscaceae sensu lato. In this study, sequence data from trnK and rbcL were analyzed for 19 species in 8 genera, and chromosome morphology was analyzed for 17 species in 7 genera. The parsimony analysis of trnK and rbcL sequences showed that Convallarieae are monophyletic. Although early branches did not receive strong bootstrap support, Convallaria diverged at the first branch, followed by Speirantha. The rest of the tribe was split into three, well-supported clades: one with Reineckea, the second with Campylandra and Rohdea, and the third with Tupistra, Tricalistra, and Aspidistra. Two monotypic genera, Rohdea and Tricalistra, were embedded in a clade of Campylandra and of Tupistra, respectively. Three karyotypes were distinguished in the tribe on the basis of the basic number and morphology of metaphase chromosomes: Convallaria type (with x=19 and unimodal chromosome length), Tupistra type (with x=19 and trimodal chromosome length), and Aspidistra-elatior type (with x=18 and trimodal chromosome length). The character-state distribution in the molecular tree showed that the Convallaria type is plesiomorphic, from which was derived the Tupistra type and subsequently the Aspidistra-elatior type. Taxonomic treatments to transfer Campylandra to Rohdea and Tricalistra to Tupistra are also given.     

Chromosomal and protein evolution in morphologically similar species of Praomys sensu lato (Rodentia, Muridae)

Evidence of extensive chromosomal evolution in a biologically and economically important group of African murids of the Praomys/Mastomys complex was provided by examination of G- and C-band chromosomal data on P. coucha (2n = 32), P. fumatus (2n = 38), P. hildebrandti (2n = 32), P. jacksoni (2n = 28), P. misonnei (2n = 36), and P. cf. tullbergi (2n = 35). A coding system was developed for the chromosomal characters, and analyses were performed by a computer program to find the shortest tree with a minimum of 35 autosomal rearrangements (pericentric inversions, complex translocations, centric fusions, centric fissions, tandem fusions, euchromatic additions, and heterochromatic additions). The resulting phylogenetic hypothesis differs from traditionally accepted hypotheses regarding this complex group of rodents. The cytogenetic data show that 1) there is no support for the dichotomy of Mastomys/Praomys previously based on morphology, 2) the 2n = 32 species from eastern Africa (P. hildebrandti) is distinct from the 2n = 32 species from southern Africa (P. natalensis), and 3) there is a close association between P. jacksoni and P. cf. tullbergi. Polyacrylamide gel electrophoresis of liver membrane proteins demonstrated few differences in protein mobilities between species and even fewer between individuals of the same species taken from different habitats and localities in Kenya. Monoclonal antibodies produced against liver proteins of one species and tested for reactivity to other species confirmed the evolutionary similarity of species of this complex. This immunologic approach may provide a robust data set for future phylogenetic studies of muroid rodents.(ABSTRACT TRUNCATED AT 250 WORDS)     

Cryptic goldfields: a molecular phylogenetic reinvestigation of Lasthenia californica sensu lato and close relatives (Compositae: Heliantheae sensu lato)

Maximum parsimony analysis of DNA sequence data from the internal and external transcribed spacer (ITS and ETS) regions of 18S-26S nuclear ribosomal DNA and the 3' trnK intron of chloroplast DNA from over 60 populations of Lasthenia sect. Amphiachaenia yielded a well-supported tree showing that the most common species of Lasthenia, L. californica sensu lato (s.l.), is not monophyletic. Members of Lasthenia californica s.l. belong to two well-supported but morphologically cryptic clades. One clade includes members of L. macrantha; the other represents a basally divergent lineage in L. sect. Amphiachaenia. Members of each clade can be diagnosed by pappus morphology and by geographic distribution, except for epappose plants that occur in a broad region of sympatry in central California. Overall diversification in the clade corresponding to L. sect. Amphiachaenia has been accompanied by minimal morphological divergence, which has resulted in previously underappreciated cryptic diversity.     

A taxonomic review of the Neoserica (sensu lato) abnormis group (Coleoptera,Scarabaeidae, Sericini)

The present paper revises the species belonging to the Neoserica (sensu lato) abnormis group, so far known only with two nominal species. Twenty new species are herein described from Indochina and southern China: N. abnormoides sp. n. (Vietnam, China), N. allolaotica sp. n., N. namthaensis sp. n., N. simplicissima sp. n. (Laos), N. thailandensis sp. n. (Thailand), N. alloputaoana sp. n., N. kanphantensis sp. n., N. natmatoungensis sp. n., N. putaoana sp. n., N. taunggyiana sp. n. (Myanmar), N. lamellosa sp. n., N. tonkinea sp. n. (Vietnam), N. bairailingshanica sp. n., N. euyunnanica sp. n., N. huangi sp. n., N. jiangxiensis sp. n., N. trifida sp. n., N. yaoi sp. n., N. yingjiangensis sp. n. (China), N. cardamomensis sp. n. (Indochina and southern China). One new combination is established: Neoserica ponderosa Arrow, 1946, comb. n. The lectotypes of Neoserica abnormis Moser, 1908 and the taxonomically uncertain N. inclinata Brenske, 1898, which very likely also belongs to this species group, are designated herein. A key to the species and to species groups is given, the genitalia of all species including their habitus are illustrated. Maps of species distribution are included.     

A taxonomic review of the Neoserica (sensu lato) septemlamellata group (Coleoptera,Scarabaeidae, Sericini)

In the present paper the species belonging to the Neoserica (sensu lato) septemlamellata group, that included so far only four known species, are revised. Here we describe eleven new species originating mainly from Indochina and Southern China: N. daweishanica sp. n., N. gaoligongshanica sp. n., N. guangpingensis sp. n., N. igori sp. n., N. jiulongensis sp. n., N. plurilamellata sp. n., N. weishanica sp. n., N. yanzigouensis sp. n. (China) N. sapaensis sp. n. (China, Vietnam), N. bansongchana sp. n., N. takakuwai sp. n. (Laos). The lectotypes of Neoserica septemlamellata Brenske, 1898 and N. septemfoliata Moser, 1915 are designated. Keys to the species and species groups are given, the genitalia of all species and their habitus are illustrated and distribution maps are included.     

A taxonomic revision of the Neoserica (sensu lato) pilosula group (Coleoptera,Scarabaeidae, Sericini)

Nine new species of the Neoserica (sensu lato) pilosula Moser, 1915, group are described from China: Neoserica curvipenis sp. n., N. emeishanensis sp. n., N. lincangensis sp. n., N. ludingensis sp. n., N. lushuiana sp. n., N. rangshuiensis sp. n., N. shennongjiaensis sp. n., N. tianeana sp. n., and N. weibaoshanica sp. n. The lectotype of Neoserica pilosula Moser, 1915, is designated. Habitus and male genitalia are illustrated, a key to the species of the group and a map of species distribution are given.     

Molecular support for a sister group relationship between Pici and Galbulae (Piciformes sensu Wetmore 1960)

Woodpeckers, honeyguides, barbets, and toucans form a well-supported clade with approximately 355 species. This clade, commonly referred to as Pici, share with the South American clade Galbulae (puffbirds and jacamars) a zygodactyls foot with a unique arrangement of the deep flexor tendons (Gadow's Type VI). Based on these characters, Pici and Galbulae are often considered sister taxa, and have in traditional classification been placed in the order Piciformes. There are, however, a wealth of other morphological characters that contradicts this association, and indicates that Pici is closer related to the Passeriformes (passerines) than to Galbulae. Galbulae, in turn, is considered more closely related to the rollers and ground-rollers (Coracii). In this study, we evaluate these two hypotheses by using DNA sequence data from exons of the nuclear RAG-1 and c- myc genes, and an intron of the nuclear myoglobin gene, totally including 3400 basepairs of aligned sequences. The results indicate a sister group relationship between Pici and Galbulae, i.e. monophyly of the Piciformes, and this association has high statistical support in terms of bootstrap values and posterior probabilities. This study also supports several associations within the traditional order Coraciiformes, including a sister group relationship between the kingfishers (Alcedinidae) and a clade with todies (Todidae) and motmots (Momotidae), and with the bee-eaters (Meropidae) placed basal relative to these three groups.     

Identifying the sister group to the bees: a molecular phylogeny of Aculeata with an emphasis on the superfamily Apoidea

Debevec, AH., Cardinal, S & Danforth, BN. Identifying the sister group to the bees: a molecular phylogeny of Aculeata with an emphasis on the superfamily Apoidea. —Zoologica Scripta, 41, 527–535. The hymenopteran superfamily Apoidea includes the bees (Anthophila) as well as four predatory wasp families (Heterogynaidae, Ampulicidae, Sphecidae and Crabronidae) collectively referred to as the “sphecoid” or “apoid” wasps. The most widely cited studies suggest that bees are sister to the wasp family Crabronidae, but alternative hypotheses have been proposed based on both morphological and molecular data. We combined DNA sequence data from previously published studies and newly generated data for four nuclear genes (28S, long‐wavelength rhodopsin, elongation factor‐1α and wingless) to identify the likely sister group to the bees. Analysis of our four‐gene data set by maximum likelihood and Bayesian methods indicates that bees most likely arise from within a paraphyletic Crabronidae. Possible sister groups to the bees include Philanthinae, Pemphredoninae or Philanthinae + Pemphredoninae. We used Bayesian methods to explore the robustness of our results. Bayes Factor tests strongly rejected the hypotheses of crabronid monophyly as well as placement of Heterogynaidae within Crabronidae. Our results were also stable to alternative rootings of the bees. These findings provide additional support for the hypothesis that bees arise from within Crabronidae, rather than being sister to Crabronidae, thus altering our understanding of bee ancestry and evolutionary history.     

A new combination of Bryum gossypinum with Synthetodontium (Bryophyta, Bryaceae sensu lato)

Synthetodontium gossypinum (X.J.Li & M.Zang) J.C.Zhao & Y.L.Niu,comb.nov. 绵毛合齿藓(S5-3.Fig.1,S5-4.Fig.2) Basionym:Bryum gossypinum X.J.Li & M.Zang in C.Gao & K.C.Zhang,Acta Phytotax.Sin.17 (4):116,t.1:34-39.1979. Type:China.Xizang:Gegyai County,in alpine meadow on the south slope of Alengshan Mountains,alt.5550 m,1976-08-16,Jin-Ting Wang 8 (holotype,IFP! (17285);isotypes,PE!,KUN!).     

Congruence and indifference between two molecular markers for understanding oral evolution in the Marynidae sensu lato (Ciliophora, Colpodea)

Our understanding of the evolution of oral structures within the Colpodida is confounded by the low number of morphological characters that can be used in constructing hypotheses, and by the low taxon and character sampling in molecular phylogenetic analyses designed to assess these hypotheses. Here we increase character sampling by sequencing the mitochondrial SSU-rDNA locus for three isolates of the Marynidae sensu lato. We show that the inferred mitochondrial and nuclear SSU-rDNA trees, as well as concatenated and constrained analyses, are congruent in not recovering a monophyletic Marynidae. However, due to low node support, the trees are indifferent to whether the morphological characters used to unite the Marynidae are the result of retention of ancestral states or convergence. In light of this indifference and an increased amount of nuclear and mitochondrial SSU-rDNA data, alternative hypotheses of oral evolution in the Colpodida are presented.     

Pangenome inventory of Burkholderia sensu lato,Burkholderia sensu stricto,and the Burkholderia cepacia complex reveals the uniqueness of Burkholderia catarinensis

Here the pangenome analysis of Burkholderia sensu lato (s.l.) was performed for the first time, together with an updated analysis of the pangenome of Burkholderia sensu stricto, and Burkholderia cepacia complex (Bcc) focusing on the Bcc B. catarinensis specific features of its re-sequenced genome. The pangenome of Burkholderia s.l., Burkholderia s.s., and of the Bcc was open, composed of more than 96% of accessory genes, and more than 62% of unknown genes. Functional annotations showed that secondary metabolism genes belonged to the variable portion of genomes, which might explain their production of several compounds with varied bioactivities. Taken together, this work showed the great variability and uniqueness of these genomes and revealed an underexplored unknown potential in poorly characterized genes. Regarding B. catarinensis 89^T, its genome harbors genes related to hydrolases production and plant growth promotion. This draft genome will be valuable for further investigation of its biotechnological potentials.