Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters

The taxonomy of the coelomycetous fungus Pestalotiopsis and other closely related genera based on morphological characters has been equivocal. To gain insight in the phylogenetic relationships of Pestalotiopsis and its allies, part of the large subunit (28S) ribosomal DNA region was examined and compared with existing morphological information. Phylogenetic analyses were conducted using parsimony, distance, and likelihood criteria. Results of the analyses showed that Bartalinia, Pestalotiopsis, Seimatosporium, and Seiridium represent distinct monophyletic groups with high bootstrap support. However, Truncatella species are paraphyletic with Bartalinia, sharing a common ancestor. Pestalotia species sequenced clustered together with Pestalotiopsis. These genera should be recognized as distinct natural groups except for Monochaetia and Discosia, which need to be further resolved. Tree topologies are generally in concordance with previous morphological hypotheses, most notably the placement of all Pestalotia species, except the type P. pezizoides, in Pestalotiopsis. Well-supported clades corresponding to groupings based on conidial morphology were resolved and the relative importance of morphological characters for generic delimitation is discussed. Molecular data also provide further evidence to support the association of these coelomycetes with the Amphisphaeriaceae.     

A Phylogenetic Analysis of Heterorhabditis (Nemata: Rhabditidae) Based on Internal Transcribed Spacer 1 DNA Sequence Data

Internal transcribed spacer 1 sequences were used to infer phylogenetic relationships among 8 of the 9 described species and one putative species of the entomopathogenic nematode genus Heterorhabditis. Sequences were aligned and optimized based on pairwise genetic distance and parsimony criteria and subjected to a variety of sequence alignment parameters. Phylogenetic trees were constructed with maximum parsimony, cladistic, distance, and maximum likelihood algorithms. Our results gave strong support for four pairs of sister species, while relationships between these pairs also were resolved but less well supported. The ITS1 region of the nuclear ribosomal repeat was a reliable source of homologous characters for resolving relationships between closely related taxa but provided more tenuous resolution among more divergent lineages. A high degree of sequence identity and lack of autapomorphic characters suggest that sister species pairs within three distinct lineages may be mutually conspecific. Application of these molecular data and current morphological knowledge to the delimitation of species is hindered by an incomplete understanding of their variability in natural populations.     

Phylogenetic relationships within the genus Pimephales as inferred from ND4 and ND4L nucleotide sequences

In phylogenetic analyses, conducted on the ND4L gene and part of the ND4 gene from species of the genus Pimephales , maximum parsimony yielded four trees, with the strict consensus providing no resolution of relationships among species. Maximum likelihood and minimum evolution methods yielded identical tree topologies, which differed from previous hypotheses of relationships for these species. If this topology is correct, it implies independent evolution of morphological characters, possibly associated with convergent trophic specialization.     

火丝菌科(盘菌目)部分属的系统学研究

本文以核糖体小亚基(SSUrDNA)为分子标记,对28个属60个种的71个序列片段进行序列分析,探讨火丝菌科的属间亲缘关系。研究结果支持广义的火丝菌科概念,表明该科是单起源的,显示5个主要分支。腐生或与植物共生形成菌根、囊盘被表面具有毛状物的15个属构成A分支,该分支中仅部分属之间的关系比较明确;与苔藓植物生长在一起的4个属构成B分支;C分支包括Otidea和Otideopsis两属,后者与Otidea的成员混杂在一起;D分支仅包括Acervus的成员;E分支由Geopyxis,Tarzetta,Paurocotylis等5个属组成。分子系统学的研究结果与形态学分类系统之间存在一定差异,依据形态特征和超微结构建立的亚科和族均未获得支持。     

SYSTEMATIC EVALUATION OF THE GENUS HILDENBRANDIA (RHODOPHYTA): A SYNTHESIS OF TECHNIQUES

The evolutionary relationships among members of the red algal genus Hildenbrandia have not been well understood for several reasons. For example, the genus contains both marine and freshwater representatives, all of which are non-calcified and crustose, and few have definitive morphological characters for classification. Hildenbrandia is also assumed to be completely asexual (reproduction by tetrasporangia in marine forms and by gemmae in freshwater populations), and characters of the female gametangial system and post-fertilization structures are not available for comparative studies. Currently there are 14 marine and five freshwater species and infraspecific taxa recognized within the genus. We used phylogenetic analyses (parsimony, distance and maximum likelihood) of DNA sequences of commonly employed genes ( rbc L and 18S rRNA) to examine the evolutionary relationships among representatives of many of these taxa. In addition, we employed morphometrics (principal co-ordinates and cluster analyses) of several measured characters of these same representatives, as well as all available type specimens, to determine the number of morphologically-delimited entities within the genus. Thus far our results indicate that some characters traditionally used to distinguish species of Hildenbrandia , such as tetrasporangial division pattern, may not be useful in some cases, and a revision of the taxonomy of the genus will be necessary. Although the marine and freshwater species of Hildenbrandia appear to be well separated in our molecular analyses of European specimens, this trend was not observed for North American specimens. High sequence divergence values were calculated for both the rbc L and 18S rRNA genes of Hildenbrandia , compared to other red algal genera.     

A phylogenetic study of Echidnopsis Hook. f. (Apocynaceae-Asclepiadoideae) - taxonomic implications and the colonization of the Socotran archipelago

We investigated the phylogeny, taxonomy and biogeography of the Eritreo-Arabian genus Echidnopsis Hook. f. (Apocynaceae-Asclepiadoideae). Phylogenetic reconstructions based on nrITS sequence data were obtained using maximum likelihood and parsimony analyses. The results reveal two weakly supported clades, each with a mix of African and Arabian taxa, including the genus Rhytidocaulon, and with four Socotran species forming a subclade of their own. Rather than a vicariance origin of these island elements, our data suggest a single dispersal event from eastern Africa. Echidnopsis thus parallels biogeographic patterns found for other Socotran endemic plants. Our revised taxonomy recognizes 28 species and 4 subspecies in the genus. Two new combinations, E. planiflora subsp. chrysantha and E. sharpei subsp. bavazzani are proposed.     

Phylogeny of the genus Lophozia (Dumort.) Dumort. s. str. inferred from nuclear and chloroplast sequences ITS1-2 and TRNL-F

Maximum parsimony and maximum likelihood phylogenetic trees were constructed for 21 taxa of Lophozia s. str. and the related genera, Schistochilopsis (5 species), Protolophozia elongate, and Obtusifolium obtusum based on pooled nuclear ITS 1-2 and chloroplast trnL-F DNA sequences. The trees were characterized by similar topology. It was demonstrated that the genus Lophozia s. str. was monophyletic, excluding L. sudetica, which deserved isolation into a distinct cryptic genus. The species distribution among the clades disagreed with the sections distinguished based on anatomical and morphological data. The relationships within the genus Schistochilopsis were consistent with the sectioning of the genus, based on morphological characters. Analysis of molecular data provided more precise definition of the systematic position of a number of taxa. Small genetic divergence of geographically distant forms was demonstrated.     

Molecular systematics of Helicoma, Helicomyces and Helicosporium and their teleomorphs inferred from rDNA sequences

Three genera of asexual, helical-spored fungi, Helicoma, Helicomyces and Helicosporium traditionally have been differentiated by the morphology of their conidia and conidiophores. In this paper we assessed their phylogenetic relationships from ribosomal sequences from ITS, 5.8S and partial LSU regions using maximum parsimony, maximum likelihood and Bayesian analysis. Forty-five isolates from the three genera were closely related and were within the teleomorphic genus Tubeufia sensu Barr (Tubeufiaceae, Ascomycota). Most of the species could be placed in one of the seven clades that each received 78% or greater bootstrap support. However none of the anamorphic genera were monophyletic and all but one of the clades contained species from more than one genus. The 15 isolates of Helicoma were scattered through the phylogeny and appeared in five of the clades. None of the four sections within the genus were monophyletic, although species from Helicoma sect. helicoma were concentrated in Clade A. The Helicosporium species also appeared in five clades. The four Helicomyces species were distributed among three clades. Most of the clades supported by sequence data lacked unifying morphological characters. Traditional characters such as the thickness of the conidial filament and whether conidiophores were conspicuous or reduced proved to be poor predictors of phylogenetic relationships. However some combinations of characters including conidium colour and the presence of lateral, tooth-like conidiogenous cells did appear to be predictive of genetic relationships.     

A Molecular Study of Euglenoid Phylogeny using Small Subunit rDNA

The euglenoids are an ancient and extremely diverse lineage of eukaryotic flagellates with unclear relationships among taxa. Synapomorphies for the euglenoids include a surface pellicle and a closed mitosis with a series of separate sub-spindles. The taxonomy currently in use is inconsistent with the available data and needs revision. Most euglenoid phylogenies are largely intuitive reconstructions based on a limited number of morphological characters. Therefore, we have added molecular characters from the Small Subunit (SSU) rDNA to generate an overall phylogenetic framework for the euglenoids. SSU rDNA sequences from photosynthetic, osmotrophic, and phagotrophic euglenoids were aligned based on secondary structure. Phylogenetic analysis using the conserved areas of the sequence was performed using parsimony, maximum likelihood, and distance methods. Trees derived using different criteria are in agreement. The euglenoids form a distinct monophyletic clade with phagotrophic members diverging prior to the phototrophic and osmotrophic members. Among photosynthetic members, the biflagellate form diverged prior to the uniflagellate form. Additionally, the genus Euglena appears to be paraphyletic, with osmotrophic taxa, such as Astasia and Khawkinea, diverging independently within the clade containing the photosynthetic genus Euglena.     

Phylogenetic relationships of the pigeonpea (Cajanus cajan) based on nuclear restriction fragment length polymorphisms.

Nuclear restriction fragment length polymorphisms (RFLPs) were used to determine phylogenetic relationships in the genus Cajanus using 15 random genomic probes and six restriction enzymes. Twenty-four accessions representing 12 species of four genera (Cajanus, Dunbaria, Eriosema, and Rhynchosia) were examined to determine phylogenetic relationships in the genus Cajanus. Eriosema parviflorum was selected as the out-group. Sufficient RFLP polymorphisms were detected among species to resolve in-group taxa into distinct clusters. Topologies of trees from parsimony and similarity matrix analyses were similar but not identical, and clustering patterns agreed broadly with published phylogenies based on seed protein data and, to a lesser extent, data from cytology and breeding experiments. Accessions of cultivated C. cajan shared more DNA fragments with C. scarabaeoides than with C. cajanifolia. Inconsistencies in taxonomic relationships based on data from morphology, cytology, crossability, and RFLPs are discussed.     

Revision of the New Caledonian endemic genus Gracilipsodes (Trichoptera: Leptoceridae: Grumichellini)

The taxonomy and systematics of the New Caledonian endemic caddisfly genus Gracilipsodes Sykora, 1967 (Trichoptera: Leptoceridae: Grumichellini) are reviewed. Seven new species represented by males are described and illustrated: Gracilipsodes aoupiniensis sp. nov. , Gracilipsodes aureus sp. nov. , Gracilipsodes aurorus sp. nov. , Gracilipsodes grandis sp. nov. , Gracilipsodes koghiensis sp. nov. , Gracilipsodes lanceolatus sp. nov. , and Gracilipsodes robustus sp. nov. Molecular phylogenetic analyses are applied to discern the relationships among the species of the genus and their closest relatives, based on sequence characters from the nuclear gene translation elongation factor-1α (EF-1α) and the three mitochondrial genes cytochrome oxidase I (COI), COII, and ribosomal large subunit (16S). The data are analyzed using parsimony and Bayesian inference, revealing a monophyletic Gracilipsodes with the eastern Australian monotypic genus Triplexa as its closest relative. Gracilipsodes is in turn divided into two major lineages.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 425–452.     

A phylogenetic study of Chinese Polygonatum (Polygonateae,Asparagaceae)

Polygonatum Mill., which consists of more than 60 species are mainly distributed in eastern Asia, especially China and Japan, has received considerable attention from plant taxonomists. Nevertheless, there are still gaps in our knowledge of this genus, especially concerning those species that are endemic to China and which have often not been included in previous studies. Here, we re‐evaluate the taxonomy of 28 Chinese Polygonatum species with emphasis on molecular evidence. Phylogenetic analyses were carried out on sequence data from four plastid DNA regions: atpB‐rbcL, matK, rbcL and rps16, using maximum parsimony and Bayesian approaches. Analyses of the combined datasets of the four regions revealed that: 1) Chinese Polygonatum are monophyletic at the current level of sampling; 2) three major lineages in Polygonatum are well supported and largely correlated with cytological and morphological characters; 3) our results, along with the results of previous works support that P. simizui is a synonym of P. odoratum, and 4) Polygonatum cirrhifoliodes is shown to be distinct from P. cirrhifolium.     

Phylogeny in Echinocereus (Cactaceae) based on combined morphological and molecular evidence: taxonomic implications

Echinocereus is a morphologically diverse genus that includes 64 species grouped into eight taxonomic sections based on morphological traits. In previous molecular phylogenetic analyses, the relationships amongst Echinocereus species were not entirely revealed and useful characters to recognize clades were not provided. The inclusion of several sources of evidence in a phylogenetic analysis is likely to produce more supported hypotheses. Therefore, we performed a combined phylogenetic analysis with a set of 44 morphological characters and six chloroplast DNA sequences. Topologies from parsimony and Bayesian analyses were mostly congruent. However, the relationships of E. poselgeri were not consistent between analyses. A second Bayesian analysis using a long-branch extraction test resulted in a topology with the morphological position of E. poselgeri congruent with that in parsimony analysis. Parsimony and Bayesian analyses corroborated the monophyly of Echinocereus, which included eight monophyletic groups. The combined phylogeny integrated into different clades those taxa that were not determined in previous analyses and changed the relationships of some recognized clades. The clades did not recover the recent infrageneric classification. In the present study, a new sectional classification for Echinocereus is proposed based on the eight recovered clades, which is supported by a combination of morphological and molecular characters. An identification key for sections in the genus is included.     

New insights on the phylogeny of Tectaria (Tectariaceae), with special reference to Polydictyum as a distinct lineage

The fern genus Tectaria (Tectariaceae) Cav. is morphologically diverse and difficult in terms of recognizing species and species groups. To infer the systematic positions of some species and identity-unknown collections with special morphological characters, we undertook phylogenetic analyses based on sequences of five plastid regions (atpB, ndhF + ndhF-trnL, rbcL, rps16-matK + matK, and trnL-F). Three analysis methods (maximum parsimony, maximum likelihood, and Bayesian inference) were used to reconstruct the phylogeny of Tectaria. The most surprising result is that T. menyanthidis (C. Presl) Copel., T. ternata (Baker) Copel., and T. variabilis Tardieu & Ching are revealed to represent a distinct lineage from Tectaria, which should be called Polydictyum C. Presl, and is supported as sister to Pteridrys C. Chr. & Ching. Other accessions of Tectaria are well resolved into four major clades, which is consistent with the results of previous studies. Of the four clades, Clade II (T. subtriphylla (Hook. & Arn.) Copel. group) is unpredictable, with morphologically very diverse species clustered there, and is supposed to be a minor evolutionary line within Tectaria in the Old World. In addition, the position of the climbing genus Arthropteris J. Sm. and the utility of molecular data in recognizing species of Tectaria are briefly discussed. As a conclusion, we formally reinstate the genus Polydictyum by providing diagnostic characters, key to species, nomenclature, and information of detailed distribution and habitat for the currently known three species.     

Phylogeny of West AfricanCaryedon(Coleoptera: Bruchidae): Congruence between Molecular and Morphological Data

Seed beetles belonging to the Old World genusCaryedonfeed in the seeds of various Caesalpinioideae, Mimosoideae, and Combretaceae. In an attempt to resolve broad phylogenetic relationships within the genus, we obtained 332 base pair sequences of mitochondrial 12S ribosomal DNA and morphological data for the 16 West AfricanCaryedonspecies. Morphological characters were analyzed under maximum parsimony and sequences were compared under maximum parsimony, maximum likelihood, and neighbor joining. Using a partition homogeneity test, we determined that morphological and molecular data sets were combinable. Combined data were analyzed under maximum parsimony. Morphological and molecular trees were congruent at the species group level and total evidence analyses yielded the same topologies as molecular data with each of the three outgroups used. Four main terminal clades are recognized, each corresponding with a group of species generally feeding on the same host plant family, subfamily, genus, or species. The monophyly of legume feedingCaryedonis supported by both data sets, and Combretaceae feeders split in two monophyletic assemblages.     

Multivariate analysis of the phenotypic relationships of the species of Paragalaxias and Galaxias (Pisces: Galaxiidae) in Tasmania

The 10 species of Galaxias in Tasmania, G. olidus from mainland Australia and the four species of Paragalaxias were studied using principal co-ordinates analysis (PCOA) and cluster analysis of a standardized Euclidean distance matrix based upon variate means, and by canonical variate analysis (CVA) conducted as a stepwise multiple discriminant analysis. Thirty-five variables comprising 30 morphometric and five meristic characters were analysed. The meristic characters were not included in the CVA. Excellent separation of the two genera was achieved in all analyses. The multivariate analyses were repeated on each genus separately to see if relationships suggested by the overall analysis remain stable. When the resultant groupings of species are compared for the different analyses, no consistent, distinct groupings of species within each genus are apparent. Despite the absence of distinct groupings, some trends in the affinities of some species are evident. In particular, species affinities as indicated by the CVA are more consistent with established opinions of species relationships. From the results of the study it is suggested that caution be exercised in the application of multivariate statistical analyses of morphological data to ichthyological systematics and phylogeny.     

Analysis of genetic relationships of Central American and Mexican pines using RAPD markers that distinguish species

Phylogenetic relationships were inferred for six Central American and Mexican pine species by analysing RAPD marker differences among pooled DNA samples. This population level pooling strategy discounts low-frequency allelic variation within taxa, thus obtaining a 'cumulative genotype' to compare among taxa. We used the morphologically based taxonomy of pines as the basis for inference concerning molecular marker divergence. Only RAPD polymorphisms that were repeatable and intensely amplified were used. The resulting data set was found to have strong hierarchical structure. Phylogenetic analyses were carried out using both neighbour-joining and maximum parsimony. The phylogenetic relationships indicated by analysis of the pine RAPD data provide new insights on pine taxonomy. The phylogenetic analyses of the RAPD marker data placed Pinus tecunumanii and P. patula clearly into two different subgroups, strongly supporting the classification of P. tecunumanii as a distinct species, and raise a new set of issues concerning the distinctions between Pinus tecunumanii and P. caribaea . Phylogenetically informative RAPD markers will be useful tools to address ex-situ conservation issues that involve taxonomic identification and species admixture.