Decorospora, a new genus for the marine ascomycete Pleospora gaudefroyi

In this paper, we investigate the phylogenetic placement of Pleospora gaudefroyi using partial SSU as well as ITS ribosomal DNA sequences. Both SSU and ITS data sets agreed in the placement of P. gaudefroyi. Parsimony and neighbor-joining analyses of each data set placed P. gaudefroyi within the Pleosporaceae with 100% bootstrap support. Pleospora gaudefroyi was sister taxon in the Pleosporaceae represented by Alternaria alternata, Cochliobolus sativus, Pleospora herbarum, Pyrenophora tritici-repentis and Setosphaeria rostrata. Pleospora gaudefroyi was separated from other genera in the Pleosporaceae in 94% of the bootstrap replicates in parsimony and neighbor-joining analyses. When P. gaudefroyi was constrained to monophyly with P. herbarum, all resulting trees were significantly worse than the optimal tree in both Kishino-Hasegawa and Shimodaira-Hasegawa tests. Pleospora gaudefroyi was therefore excluded from Pleospora, and transferred to the new genus Decorospora placed in the Pleosporaceae. Decorospora (Dothideomycetes) has characteristic ascospores enclosed in a sheath with 4-5 apical extensions. The distribution and substrate types for D. gaudefroyi are summarized and updated based on additional collections.     

Phylogenetic Relationships in the Macrobiotidae (Tardigrada: Eutardigrada: Parachela)

Characters of the claws, buccal-pharyngeal apparatus and ultrastructure of the cuticle have been examined to identify phyletic relationships within the Macrobiotidae. Several apomorphies have been identified. The resulting cladogram shows two main phyletic lines within the family, corresponding to the subfamilies Macrobiotinae and Murrayinae. The relationships among the genera of the Murrayinae are resolved, whereas in the Macrobiotinae five main phyletic lines are identified, whose relationships are still unknown. Pseudodiphascon and Macrobiotus appear to be polyphyletic genera.     

Monophyly of Endosymbiont Containing Trypanosomatids: Phylogeny versus Taxonomy

To obtain additional information on the phylogenetic relationships within the family Trypanosomatidae (order Kinetoplastida), we have sequenced the small subunit ribosomal RNA genes from the endosymbiont containing species Herpetomonas roitmani TCC080, Herpetomonas sp. TCC263, Crithidia oncopelti ATCC 12982 and a partial large subunit rRNA gene from H. roitmani. The small subunit sequences in the two isolates of Herpetomonas are very similar but not identical, and so are their restriction digest profiles of kinetoplast DNA. The size of minicircles in both isolates is 4.2 kilobases. The inferred ribosomal RNA phylogenetic trees shows the genera Herpetomonas and Crithidia as polyphyletic. Endosymbiont-bearing herpetomonads cluster with the endosymbiont-bearing crithidias and a blastocrithidia to form a monophyletic clade, whereas the endosymbiont-free members of these genera are found elsewhere in the tree. These data support the hypothesis of a monophyletic origin of endosymbiosis in trypanosomatid evolution and also suggest that a taxonomic revision is needed in order to better describe the natural affinities in this family.     

Phylogenetic relationships of Moxostoma and Scartomyzon (Catostomidae) based on mitochondrial cytochrome b sequence data

A recent phylogenetic study based on morphological, biochemical and early life history characters resurrected the genus Scartomyzon (jumprock suckers, c . eight−10 species) from Moxostoma (redhorse suckers, c . 10–11 species) and advanced the understanding of relationships among species in these two genera, and the genealogical affinities of these genera with other evolutionary lineages within the tribe Moxostomatini in the subfamily Catostominae. To further examine phylogenetic relationships among moxostomatin suckers, the complete mitochondrial (mt) cytochrome b gene was sequenced from all species within this tribe and representative outgroup taxa from the Catostomini and other catostomid subfamilies. Phylogenetic analysis of gene sequences yielded two monophyletic clades within Catostominae: Catostomus + Deltistes + Xyrauchen + Erimyzon + Minytrema and Moxostoma + Scartomyzon + Hypentelium + Thoburnia . Within the Moxostomatini, Thoburnia was either unresolved or polyphyletic; Thoburnia atripinnis was sister to a monophyletic Hypentelium . In turn, this clade was sister to a monophyletic clade containing Scartomyzon and Moxostoma . Scartomyzon was never resolved as monophyletic, but was always recovered as a polyphyletic group embedded within Moxostoma , rendering the latter genus paraphyletic if ' Scartomyzon ' continues to be recognized. Relationships among lineages within the Moxostoma and' Scartomyzon 'clade were resolved as a polytomy. To better reflect phylogenetic relationships resolved in this analysis, the following changes to the classification of the tribe Moxostomatini are proposed: subsumption of' Scartomyzon 'into Moxostoma ; restriction of the tribe Moxostomatini to Moxostoma ; resurrect the tribe Erimyzonini, containing Erimyzon and Minytrema , classified as incertae sedis within Catostominae; retain the tribe Thoburniini.     

Phylogeny of Gardenieae (Rubiaceae) based on chloroplast DNA sequences from the rps16 intron and trnL(UAA)-F(GAA) intergenic spacer

Chloroplast DNA (cpDNA) sequences of the rps 16 intron and the trn L (UAA)-F(GAA) intergenic spacer were obtained from 59 species, to evaluate phylogenetic relationships among members of the Gardenieae, Rubiaceae. The results indicate that Gardenieae is polyphyletic and that genera included in the subtribe Diplosporinae should be transferred to the Coffeeae and Octotropideae. The Octotropideae tribe may also be polyphyletic. It is also demonstrated that the tribe Pavetteae is polyphyletic. In addition, the present data support a basal position for the disputed genus Bertiera within the Coffeeae clade. Of the informal groups proposed by Robbrecht & Puff within the Gardenieae, the Alibertia group is strongly supported, and is estimated to also include Ibetralia, Genipa aff. williamsii , and one undescribed taxon. However, Genipa americana was not part of this clade suggesting that Genipa is polyphyletic. The Tetrad group is not supported, and character optimisations suggest that pollen released in tetrads may have arisen three times. Most of these genera appear in the same clade as the three neotropical genera Sphinctanthus, Rosenbergiodendron , and Tocoyena , all of which bear pollen in monads. Atractogyne, Mitriostigma , and Oxyanthus form the second group with pollen in tetrads, whereas Gardenia is embedded in a third group. Massularia , with polyads, occurs either singly on a large polytomy or at the base of the Atractocarpus-Porterandia-Trukia clade.     

A molecular systematic revision of two historically problematic songbird clades: Aimophila and Pipilo

The emberizid genera Aimophila and Pipilo represent longstanding taxonomic conundrums. Each is comprised of sub-clades whose members appear to share diagnostic morphological and behavioral characters; however, relationships among sub-clades within each of these genera remain unclear, and numerous authors have suggested that either one or both of these genera may be polyphyletic. We addressed this taxonomic problem by sequencing and analyzing complete mitochondrial cytochrome- b and NADH dehydrogenase subunit 2 genes for all members of Aimophila and Pipilo along with 33 species representing 17 additional emberizid genera. Our maximum likelihood and Bayesian analyses indicate that both Aimophila and Pipilo are polyphyletic. Aimophila is divided into a minimum of three distinct groups. The forms notosticta, ruficeps , and rufescens are part of a well-supported clade that includes all members of Melozone and some members of Pipilo . Aimophila quinquestriata is placed within Amphispiza , and the remaining members of Aimophila are placed within a clade that includes all members of Arremonops and some members of Ammodramus . Within Pipilo , the "rufous-sided" and "brown" towhee groups do not form sister groups. Rather, the former are most closely related to the tropical genus Atlapetes whereas the latter are placed nearest Melozone and some Aimophila . Our analyses reject traditional taxonomic arrangements for both genera, and we present suggestions for a revised taxonomy for all members of Aimophila and Pipilo . These results provide further evidence of discordance among phylogenetic hypotheses based on morphological and molecular characters for groups of birds with generally conserved morphology.     

PHYLOGENY OF THE DUMONTIACEAE (GIGARTINALES, RHODOPHYTA) AND ASSOCIATED FAMILIES BASED ON SSU rDNA AND INTERNAL TRANSCRIBED SPACER SEQUENCE DATA

Small subunit (SSU) rDNA was sequenced for 25 species in 19 genera of the Gigartinales (Rhodophyta). As well, the internal transcribed spacer (ITS) region was sequenced, and a data matrix of 36 morphological characters was constructed for 16 species of Dumontiaceae. Phylogenetic trees were calculated from a multiple alignment of the SSU sequence data to infer relationships between species of Dumontiaceae and other gigartinalean taxa. The SSU analysis produced a polyphyletic Dumontiaceae. Notably, Acrosymphyton failed to associate with the included Gigartinales, let alone the Dumontiaceae, supporting an earlier proposal to remove it to a new family. The analyses were equivocal about the phylogenetic affinities of Dudresnaya , which clustered with the Kallymeniaceae, and the affinities of the Indo-West Pacific Gibsmithia , Kraftia , and Dasyphloea , the last-mentioned clustering with the Antarctic Gainiaceae, and these four taxa with Portieria (Rhizophyllidaceae). Further investigations are necessary to resolve relationships among these taxa. Rhodopeltis , a genus recently moved to the Dumontiaceae from the Polyideaceae, showed a weak association with the remaining northern Dumontiaceae. The final group consisted of cold-temperate Northern Hemisphere species. Phylogenetic analyses using a combination of SSU, ITS, and morphological data within this clade produced two strongly supported clades, a Dilsea / Neodilsea clade and a Cryptosiphonia / Dumontia clade. Dilsea is derived from a paraphyletic Neodilsea and may itself be polyphyletic. Atlantic and Pacific isolates of Dumontia contorta clearly showed sufficient divergence to warrant recognition as distinct species, and Dumontia alaskana , sp. nov. is proposed for the Pacific species.     

A molecular phylogeny of the fern family Pteridaceae: assessing overall relationships and the affinities of previously unsampled genera

The monophyletic Pteridaceae accounts for roughly 10% of extant fern diversity and occupies an unusually broad range of ecological niches, including terrestrial, epiphytic, xeric-adapted rupestral, and even aquatic species. In this study, we present the results of the first broad-scale and multi-gene phylogenetic analyses of these ferns, and determine the affinities of several previously unsampled genera. Our analyses of two newly assembled data sets (including 169 newly obtained sequences) resolve five major clades within the Pteridaceae: cryptogrammoids, ceratopteridoids, pteridoids, adiantoids, and cheilanthoids. Although the composition of these clades is in general agreement with earlier phylogenetic studies, it is very much at odds with the most recent subfamilial classification. Of the previously unsampled genera, two (Neurocallis and Ochropteris) are nested within the genus Pteris; two others (Monogramma and Rheopteris) are early diverging vittarioid ferns, with Monogramma resolved as polyphyletic; the last previously unsampled genus (Adiantopsis) occupies a rather derived position among cheilanthoids. Interestingly, some clades resolved within the Pteridaceae can be characterized by their ecological preferences, suggesting that the initial diversification in this family was tied to ecological innovation and specialization. These processes may well be the basis for the diversity and success of the Pteridaceae today.     

Phylogenetic relationships of major clades of Catostomidae (Teleostei: Cypriniformes) as inferred from mitochondrial SSU and LSU rDNA sequences

Suckers (Family Catostomidae) are holarctic in distribution and include 76 recent species in 14 genera, with 13 genera and 75 species occurring in North and Central America and Siberia. Although this group constitutes a significant component of many aquatic ecosystems, most historic systematic effort has been either alpha- or limited beta-level studies focusing on the two largest tribes within the family, the Catostomini and the Moxostomatini. A recent phylogenetic study based on morphological, biochemical, and early life history characters has advanced current understanding of relationships among catostomid fishes. To further examine phylogenetic relationships among basal lineages of catostomids, we sequenced the entire mitochondrial (mt) SSU and LSU rRNA genes from genera representing all subfamilies and tribes within Catostomidae. Phylogenetic analysis of gene sequences yielded monophyletic Catostomidae, Ictiobinae, and Catostominae and para- or polyphyletic Cycleptinae, with Myxocyprinus as the basal-most taxon and Cycleptus as either the next most-basal taxon or the taxon basal to the Catostominae. Relationships within the Catostominae were generally consistent with those proposed in the above-noted recent phylogenetic study although Thoburnia and Hypentelium were either a clade sister to or a grade group relative to Moxostoma and Scartomyzon. In all trees, Scartomyzon was paraphyletic and embedded within Moxostoma. Phylogenetic affinities of Erimyzon and Minytrema varied depending on data set and character weighting scheme employed. To better reflect phylogenetic relationships resolved in this extensive analysis, we propose the following changes to the classification of catostomids: formation of the new subfamily Myxocyprininae, containing Myxocyprinus from China; restriction of the Cycleptinae to the two species of Cycleptus from North America; restriction of the tribe Moxostomatini to Moxostoma and Scartomyzon; Erimyzon and Minytrema are incertae sedis within Catostominae; and resurrection of the tribe Thoburniini, containing Thoburnia and expanded to include Hypentelium.     

A global phylogeny of apple snails: Gondwanan origin, generic relationships, and the influence of outgroup choice (Caenogastropoda: Ampullariidae)

Apple snails (Ampullariidae) are a diverse family of pantropical freshwater snails and an important evolutionary link to the common ancestor of the largest group of living gastropods, the Caenogastropoda. A clear understanding of relationships within the Ampullariidae, and identification of their sister taxon, is therefore important for interpreting gastropod evolution in general. Unfortunately, the overall pattern has been clouded by confused systematics within the family and equivocal results regarding the family's sister group relationships. To clarify the relationships among ampullariid genera and to evaluate the influence of including or excluding possible sister taxa, we used data from five genes, three nuclear and two mitochondrial, from representatives of all nine extant ampullariid genera, and species of Viviparidae, Cyclophoridae, and Campanilidae, to reconstruct the phylogeny of apple snails, and determine their affinities to these possible sister groups. The results obtained indicate that the Old and New World ampullariids are reciprocally monophyletic with probable Gondwanan origins. All four Old World genera, Afropomus, Saulea, Pila, and Lanistes, were recovered as monophyletic, but only Asolene, Felipponea, and Pomella were monophyletic among the five New World genera, with Marisa paraphyletic and Pomacea polyphyletic. Estimates of divergence times among New World taxa suggest that diversification began shortly after the separation of Africa and South America and has probably been influenced by hydrogeological events over the last 90 Myr. The sister group of the Ampullariidae remains unresolved, but analyses omitting certain outgroup taxa suggest the need for dense taxonomic sampling to increase phylogenetic accuracy within the ingroup. The results obtained also indicate that defining the sister group of the Ampullariidae and clarifying relationships among basal caenogastropods will require increased taxon sampling within these four families, and synthesis of both morphological and molecular data. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 61–76.     

Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 5′ End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic

The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.     

POLYPHYLY OF TETRASPORALEAN GREEN ALGAE INFERRED FROM NUCLEAR SMALL-SUBUNIT RIBOSOMAL DNA

Ultrastructural studies of tetrasporalean green algae have suggested the order is polyphyletic. These features, including the absolute orientation of the flagellar apparatus and the bi- versus quadriflagellated motile cell morphology, suggest that Chaetopeltis as well as a number of others, may be ancestral to a group that includes Tetraspora. In this study, we examine the phylogenetic relationships of selected tetrasporalean taxa based on analysis of 18S ribosomal RNA gene sequences. Results show that the tetrasporalean taxa are polyphyletic. Biflagellated genera group with biflagellated volvocalean taxa, whereas the quadriflagellated species compose a distinct monophyletic clade not closely related to the biflagellated taxa. In addition, tetrasporalean taxa group with other chlorophycean algal species with similar flagellar apparatus absolute orientation, but the quadriflagellated Tetrasporales do not appear to be ancestral to the entire Chlorophyceae. These results are concordant with previous conclusions drawn from ultrastructural data and further confirm the utility of (small-subunit) ribosomal RNA gene sequences to discern green algal evolutionary relationships.     

Phylogenetic patterns in the fleshy-fruited Myrtaceae – preliminary molecular evidence

A phylogenetic study of selected fleshy-fruited genera of the Myrtaceae was conducted using sequences from the ITS region of nuclear DNA and the psbA-trnH region of plastid DNA. Studies to date have suggested that the fleshy-fruited state has arisen on several occasions in the Myrtaceae. The previously accepted and predominantly Neotropical tribe Myrteae has traditionally been divided into three groups, the subtribes Myrtinae, Eugeniinae and Myrciinae. This subtribal arrangement is analysed in detail here for the first time. The monophyly of the tribe and subtribes are tested and relationships of the genera within them, in particular those of the Myrciinae and anomalous genera sometimes associated with it, are discussed. Combined analyses of these two DNA regions revealed 40 shortest trees, all of which resolve Myrteae (excluding the Acmena group) as monophyletic. Myrciinae appears to be monophyletic whereas Myrtinae and Eugeniinae appear polyphyletic. The phylogenetic positions and relationships of the anomalous genera Myrceugenia, Luma and Blepharocalyx are unclear, but Myrceugenia is never included within the Myrciinae s.str. A Myrciinae s.str. clade emerges within which Myrcia, Calyptranthes and Marlierea appear polyphyletic. Clades emerge, however, that may reflect some natural groupings within the subtribe.We thank David Simpson, Lazlo Csiba, Edith Kapinos and many others from Kew for invaluable advice and support. It would not have been possible to collect the Brazilian samples without the patience and careful guidance of Dr. Vinicius C. Souza, Fiorella F. Mazine (Universidade de São Paulo, ESALQ), Professor Gert Hatschbach, Joel M. de Silva (Museu Botânico Municipal, Curitiba) and many others from the ESA and MBM herbaria. Thanks also to Les Landrum, Andrew Salywon, Marcos Sobral and an anonymous reviewer for helpful comments at different stages of this work. British Airways are gratefully acknowledged for providing a flight to Brazil under their Community and Conservation programme.     

Phylogenetic relationships among genera of the Tetrabothriidae (Eucestoda)

Cladistic analysis of the generic-level relationships within the family Tetrabothriidae was conducted. A single cladogram resulted from evaluation of 28 homologous transformation series representing 41 character states. The genus Tetrabothrius was recognized as plesiomorphic followed by Chaetophallus and Trigonocotyle. The latter was considered as the sister group for the remaining tetrabothriid genera of marine mammals. Anophryocephalus, Strobilocephalus, and Priapocephalus are among the most highly derived genera and are postulated as having close evolutionary affinities. Comparisons to previous explicit hypotheses for relationships among the genera indicated the present analysis was the most efficient phylogenetic statement (consistency index = 85.4%) for the 28 attributes evaluated. The recognition of Tetrabothrius as primitive and a natural grouping of Anophryocephalus, Strobilocephalus, and Priapocephalus in part confirmed results of previous studies of the Tetrabothriidae.     

Polyphyly of the fern family Tectariaceae sensu Ching: Insights from cpDNA sequence data

Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL and atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria and Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with and should be included within the newly-defined Dryopteridaceae, and Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix, and Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae and to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolu- tionary history of this group.