Phylogenetic origins of two cleistothecial fungi, Orbicula parietina and Lasiobolidium orbiculoides, within the operculate discomycetes

Parsimony, maximum-likelihood and Bayesian analyses of SSU rDNA sequences of representative taxa of Pezizomycetes, Eurotiomycetes, Dothideomycetes, Leotiomycetes and Sordariomycetes, all strongly support the cleistothecial fungi Orbicula parietina and Lasiobolidium orbiculoides to be of pezizalean origin. Previous hypotheses of close affinities with cleistothecial or highly reduced fungi now placed in the Thelebolales, Eurotiales or Onygenales are rejected. Orbicula parietina and L. orbiculoides are deeply nested within Pyronemataceae (which subsumes the families Ascodesmidaceae, Glaziellaceae and Otideaceae). LSU rDNA sequences suggest that Orbicula is nested within the apothecia-forming genus Pseudombrophila (including Nannfeldtiella and Fimaria) and that L. orbiculoides is closely related. Ascodesmis and Lasiobolus, which have been suggested as closely related to Orbicula and Lasiobolidium, are identified as a sister lineage to the Pseudombrophila lineage. Cleistothecial forms that have lost the ascus operculum and ability to discharge spores actively have evolved at least once in the Pseudombrophila lineage. Some species of Pseudombrophila produce subglobular ascomata initials that are closed early in development and open only in the mid-mesohymenial phase. We hypothesize that, in the Pseudombrophila lineage, ascomata forms that never open are derived from ascomata that open late in development. The placement of O. parietina and L. orbiculoides within Pseudombrophila is supported by morphological characters, ecology and temperature optima for fruiting.     

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。     

Towards a subordinal classification of the Pezizales (Ascomycota): phylogenetic analyses of SSU rDNA sequences.

Phylogenetic analyses of partial SSU rDNA sequences from representatives of 36 pezizales associated genera are presented, including new sequences from 28 species: Aleuria aurantiaca, Ascodesmis sphaerospora, Boudiera acanthospora, Caloscypha fulgens, Cheilymenia stercorea, Cookeina sulcipes, Desmazierella acicola, Geopyxis carbonaria, Hydnotrya tulasnei, Iodophanus carneus, Microstoma protracta, Otidea leporina, Paurocotylis pila, Peziza succosa and P vesiculosa (the type species of the family Pezizaceae and the order Pezizales), Pyronema domesticum, Pulvinula archeri, Saccobolus sp., Sarcoscypha austriaca, Sarcosoma globosum, Sarcosphaera coronaria, Scutellinia scutellata and S. torrentis, Sphaerosporella brunnea, Tarzetta catinus, Thelebolus crustaceus, Trichophaea hybrida, Trichophaeopsis bicuspis, and Wilcoxina mikolae. Two taxon and character matrices were subjected to maximum parsimony, maximum likelihood, and neighbor-joining analyses. The first matrix included 28 taxa and a full character set of 1600 bp, and the second matrix 37 taxa and a restricted set of 1053 characters. The analyses using the restricted character set generally yielded the same topology as the full character set but the resolution was reduced. Three main evolutionary lineages were detected within the order: (1) Pezizaceae and Ascobolaceae, (2) Helvellaceae, Morchellaceae, Tuberaceae, and Caloscypha (Otideaceae), and (3) Sarcoscyphaceae, Sarcosomataceae, Ascodes-midaceae, Glaziellaceae, Otideaceae and Pyronemataceae. The inferred subordinal grouping is compared to extant classification schemes of the Pezizales. Sarcosomataceae and Sarcoscyphaceae are recognized as separate monophyletic groups. The analyses did not support recognition of Pyronemataceae, Ascodesmida-ceae, and Glaziellaceae as separate from the Otideaceae. Thelebolus (Thelebolaceae) clusters with extra-pezizalean genera and does not belong to the order.     

Evolution of Filamentous Ascomycetes Inferred from LSU rDNA Sequence Data

Abstract: The nuclear LSU rRNA gene was examined in order to evaluate the current phylogeny of ascomycetes, which is mainly based on nuclear SSU rRNA data. Partial LSU rRNA gene sequences of 19 ascomycetes were determined and aligned with the corresponding sequences of 13 other ascomycetes retrieved from Genbank, including all classes traditionally distinguished and most of the recently accepted classes. The classification based on SSU rDNA data and morphological characters is supported, while the traditional classification and classifications based on the ascus type are rejected. Ascomycetes with perithecia and cleistothecia form monophyletic groups, while the discomycetes are a paraphyletic assemblage. The Pezizales are basal to all other filamentous ascomycetes. The monophyly of Loculoascomycetes is uncertain. The results of the LSU rDNA analysis agree with those of the SSU rDNA and RPB2 gene analyses, suggesting that most classes circumscribed in the filamentous ascomycetes are monophyletic. The branching order and relationships among these classes, however, cannot be elucidated with any of these data sets.     

Independent terrestrial origins of the Halosphaeriales (marine Ascomycota)

A phylogenetic study of marine ascomycetes was initiated to test and refine evolutionary hypotheses of marine-terrestrial transitions among ascomycetes. Taxon sampling focused on the Halosphaeriales, the largest order of marine ascomycetes. Approximately 1050 base pairs (bp) of the gene that codes for the nuclear small subunit (SSU) and 600 bp of the gene that codes for the nuclear large subunit (LSU) ribosomal RNAs (rDNA) were sequenced for 15 halosphaerialean taxa and integrated into a data set of homologous sequences from terrestrial ascomycetes. An initial set of phylogenetic analyses of the SSU rDNA from 38 taxa representing 15 major orders of the phylum Ascomycota confirmed a close phylogenetic relationship of the halosphaerialean species with several other orders of perithecial ascomycetes. A second set of analyses, which involved more intensive taxon sampling of perithecial ascomycetes, was performed using the SSU and LSU rDNA data in combined analyses. These second analyses included 15 halosphaerialean taxa, 26 terrestrial perithecial fungi from eight orders, and five outgroup taxa from the Pezizales. In these analyses the Halosphaeriales were polyphyletic and comprised two distinct lineages. One clade of Halosphaeriales comprised 12 taxa from 11 genera and was most closely related to terrestrial fungi of the Microascales. The second clade of halosphaerialean fungi comprised taxa from the genera Lulworthia and Lindra and was an isolated lineage among the perithecial fungi. Both the main clade of Halosphaeriales and the Lulworthia/Lindra clade are supported by the data as being independently derived from terrestrial ancestors.     

A five-gene phylogeny of Pezizomycotina

Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results from weighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-lalpha) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support.     

Molecular Phylogeny of Conjugating Green Algae (Zygnemophyceae,Streptophyta) Inferred from SSU rDNA Sequence Comparisons

Nuclear-encoded SSU rDNA sequences have been obtained from 64 strains of conjugating green algae (Zygnemophyceae, Streptophyta, Viridiplantae). Molecular phylogenetic analyses of 90 SSU rDNA sequences of Viridiplantae (inciuding 78 from the Zygnemophyceae) were performed using complex evolutionary models and maximum likelihood, distance, and maximum parsimony methods. The significance of the results was tested by bootstrap analyses, deletion of long-branch taxa, relative rate tests, and Kishino-Hasegawa tests with user-defined trees. All results support the monophyly of the class Zygnemophyceae and of the order Desmidiales. The second order, Zygnematales, forms a series of early-branching clades in paraphyletic succession, with the two traditional families Mesotaeniaceae and Zygnemataceae not recovered as lineages. Instead, a long-branch Spirogyra/Sirogonium clade and the later-diverging Netrium and Roya clades represent independent clades. Within the order Desmidiales, the families Gonatozygaceae and Closteriaceae are monophyletic, whereas the Peniaceae (represented only by Penium margaritaceum) and the Desmidiaceae represent a single weakly supported lineage. Within the Desmidiaceae short internal branches and varying rates of sequence evolution among taxa reduce the phylogenetic resolution significantly. The SSU rDNA-based phylogeny is largely congruent with a published analysis of the rbcL phylogeny of the Zygnemophyceae (McCourt et al. 2000) and is also in general agreement with classification schemes based on cell wall ultrastructure. The extended taxon sampling at the subgenus level provides solid evidence that many genera in the Zygnemophyceae are not monophyletic and that the genus concept in the group needs to be revised.     

PHYLOGENY OF THE EUGLENOID LORICATE GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) INFERRED FROM NUCLEAR SSU AND LSU rDNA1

Previous studies using the nuclear SSU rDNA and partial LSU rDNA have demonstrated that the euglenoid loricate taxa form a monophyletic clade within the photosynthetic euglenoid lineage. It was unclear, however, whether the loricate genera Trachelomonas and Strombomonas were monophyletic. In order to determine the relationships among the loricate taxa, SSU and LSU nuclear rDNA sequences were obtained for eight Strombomonas and 25 Trachelomonas strains and combined in a multigene phylogenetic analysis. Conserved regions of the aligned data set were used to generate maximum‐likelihood (ML) and Bayesian phylogenies. Both methods recovered a strongly supported monophyletic loricate clade with Strombomonas and Trachelomonas species separated into two sister clades. Taxa in the genus Strombomonas sorted into three subclades. Within the genus Trachelomonas, five strongly supported subclades were recovered in all analyses. Key morphological features could be attributed to each of the subclades, with the major separation being that all of the spine‐bearing taxa were located in two sister subclades, while the more rounded, spineless taxa formed the remaining three subclades. The separation of genera and subclades was supported by 42 distinct molecular signatures (33 in Trachelomonas and nine in Strombomonas). The morphological and molecular data supported the retention of Trachelomonas and Strombomonas as separate loricate genera.     

Molecular Phylogeny of Conjugating Green Algae (Zygnemophyceae, Streptophyta) Inferred from SSU rDNA Sequence Comparisons

Abstract Nuclear-encoded SSU rDNA sequences have been obtained from 64 strains of conjugating green algae (Zygnemophyceae, Streptophyta, Viridiplantae). Molecular phylogenetic analyses of 90 SSU rDNA sequences of Viridiplantae (inciuding 78 from the Zygnemophyceae) were performed using complex evolutionary models and maximum likelihood, distance, and maximum parsimony methods. The significance of the results was tested by bootstrap analyses, deletion of long-branch taxa, relative rate tests, and Kishino–Hasegawa tests with user-defined trees. All results support the monophyly of the class Zygnemophyceae and of the order Desmidiales. The second order, Zygnematales, forms a series of early-branching clades in paraphyletic succession, with the two traditional families Mesotaeniaceae and Zygnemataceae not recovered as lineages. Instead, a long-branch Spirogyra/Sirogonium clade and the later-diverging Netrium and Roya clades represent independent clades. Within the order Desmidiales, the families Gonatozygaceae and Closteriaceae are monophyletic, whereas the Peniaceae (represented only by Penium margaritaceum) and the Desmidiaceae represent a single weakly supported lineage. Within the Desmidiaceae short internal branches and varying rates of sequence evolution among taxa reduce the phylogenetic resolution significantly. The SSU rDNA-based phylogeny is largely congruent with a published analysis of the rbcL phylogeny of the Zygnemophyceae (McCourt et al. 2000) and is also in general agreement with classification schemes based on cell wall ultrastructure. The extended taxon sampling at the subgenus level provides solid evidence that many genera in the Zygnemophyceae are not monophyletic and that the genus concept in the group needs to be revised.     

Evolutionary history of the Corallinales (Corallinophycidae, Rhodophyta) inferred from nuclear, plastidial and mitochondrial genomes

Systematics of the red algal order Corallinales has a long and convoluted history. In the present study, molecular approaches were used to assess the phylogenetic relationships based on the analyses of two datasets: a large dataset of SSU sequences including mainly sequences from GenBank; and a combined dataset including four molecular markers (two nuclear: SSU, LSU; one plastidial: psbA; and one mitochondrial: COI). Phylogenetic analyses of both datasets re-affirmed the monophyly of the Corallinales as well as the two families (Corallinaceae and Hapalidiaceae) currently recognized within the order. Three of the four subfamilies of the Corallinaceae (Corallinoideae, Lithophylloideae, Metagoniolithoideae) were also resolved as a monophyletic lineage whereas members of the Mastophoroideae were resolved as four distinct lineages. We therefore propose to restrict the Mastophoroideae to the genera Mastophora, Metamastophora, and possibly Lithoporella in the aim of rendering this subfamily monophyletic. In addition, our phylogenies resolved the genus Hydrolithon in two unrelated lineages, one containing the generitype Hydrolithon reinboldii and the second containing Hydrolithon onkodes, which used to be the generitype of the now defunct genus Porolithon. We therefore propose to resurrect the genus Porolithon for the second lineage encompassing those species with primarily monomerous thalli, and trichocyte arrangements in large pustulate horizontal rows. Moreover, our phylogenetic analyses revealed the presence of cryptic diversity in several taxa, shedding light on the need for further studies to better circumscribe species frontiers within the diverse order Corallinales, especially in the genera Mesophyllum and Neogoniolithon.     

A phylogenetic study of the genus Cookeina

Cookeina, with seven recognized species, is one of the commonly encountered genera of the Sarcoscyphaceae (Pezizales) in tropical and subtropical areas around the world. Morphologically the species are distinguished by combinations of several features including ascospore shape and surface relief, presence and origin of apothecial hairs and presence or absence of gelatinous material within the cortical layer of the excipular tissue. Color of the hymenium, attributed to carotenoid pigments, is particularly variable in some collections especially those referred to as C. speciosa. In this study phylogenetic analyses were carried out using rDNA ITS and rDNA LSU sequences. Forty-four collections were studied which included a broad sampling of color variants of C. speciosa from a field site in Venezuela. The genus was shown to be monophyletic with several well-supported lineages. These analyses generally support the established, morphologically distinguished taxa within a monophyletic genus Cookeina. Collections referred to as C. speciosa segregate within a clade in which hymenial color differences are associated with groups within the clade. Cookeina sinensis is sister to C. tricholoma but is distinct from it; C. indica fails to resolve with any of the major clades. The placement of C. insititia is ambiguous but it falls within Cookeina and thus is considered in the genus Cookeina rather than in a separate genus, Boedijnopeziza.     

Phylogenetic relationships of Gomphillaceae and Asterothyriaceae: evidence from a combined Bayesian analysis of nuclear and mitochondrial sequences

The phylogeny and systematic position of Gomphillaceae was reconstructed using a combined Bayesian analysis of nuclear LSU rDNA and mitochondrial SSU rDNA sequences. Twenty-four partial sequences of 12 taxa (11 Gomphillaceae and one Asterothyriaceae) plus two new sequences of Stictis radiata (Ostropales outgroup) were generated and aligned with the corresponding sequences retrieved from GenBank, resulting in an alignment of 82 taxa that was analyzed using a Bayesian approach with Markov chain Monte Carlo (B/MCMC) methods. Our results confirm Gomphillaceae sensu Vezda and Poelt plus Asterothyriaceae to be a monophyletic group, with an unresolved relationship between the two families. Placement of Gomphillaceae and Asterothyriaceae within Ostropales sensu Kauff and Lutzoni, as sister of Thelotremataceae, also is strongly supported. Alternative hypotheses placing Gomphillaceae in Lecanorales (Cladoniaceae), Agyriales (Baeomycetaceae) or within bitunicate Ascomycota (Arthoniomycetes, Chaetothyriomycetes, Dothideomycetes) were rejected with our dataset. After recent synonymization of Dimerella with Coenogonium (Ostropales: Coenogoniaceae), we propose the new combination Coenogonium pineti (one of our Ostropales outgroup taxa in this analysis).     

Phylogenetic relationships among the Braconidae (Hymenoptera: Ichneumonoidea) inferred from partial 16S rDNA, 28S rDNA D2, 18S rDNA gene sequences and morphological characters

Phylogenetic relationships among the Braconidae were examined using homologous 16S rDNA, 28S rDNA D2 region, and 18S rDNA gene sequences and morphological data using both PAUP* 4.0 and MRBAYES 3.0B4 from 88 in-group taxa representing 35 subfamilies. The monophyletic nature of almost all subfamilies, of which multiple representatives are present in this study, is well-supported except for two subfamilies, Cenocoelinae and Neoneurinae that should probably be treated as tribal rank taxa in the subfamily Euphorinae. The topology of the trees generated in the present study supported the existence of three large generally accepted lineage or groupings of subfamilies: two main entirely endoparasitic lineages of this family, referred to as the "helconoid complex" and the "microgastroid complex," and the third "the cyclostome." The Aphidiinae was recovered as a member of the non-cyclostomes, probably a sister group of Euphorinae or Euphorinae-complex. The basal position of the microgastroid complex among the non-cyclostomes has been found in all our analyses. The cyclostomes were resolved as a monophyletic group in all analyses if two putatively misplaced groups (Mesostoa and Aspilodemon) were excluded from them. Certain well-supported relationships evident in this family from the previous analyses were recovered, such as a sister-group relationships of Alysiinae+Opiinae, of Braconinae+Doryctinae, and a close relationship between Macrocentrinae, Xiphozelinae, Homolobinae, and Charmontinae. The relationships of "Ichneutinae + ((Adeliinae + Cheloninae) + (Miracinae + (Cardiochilinae + Microgastrinae)))" was confirmed within the microgastroid complex. The position of Acampsohelconinae, Blacinae, and Trachypetinae is problematic.     

Phylogenetic relationships in Nuphar (Nymphaeaceae): evidence from morphology,chloroplast DNA,and nuclear ribosomal DNA

The genus Nuphar consists of yellow-flowered waterlilies and is widely distributed in north-temperate bodies of water. Despite regular taxonomic evaluation of these plants, no explicit phylogenetic hypotheses have been proposed for the genus. We investigated phylogenetic relationships in Nuphar using morphology and sequences of the chloroplast gene matK and of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. Two major lineages within Nuphar are consistently resolved with the morphological and molecular data sets. One lineage comprises New World taxa and the other represents a primarily Old World lineage. Relationships within the major lineages were poorly resolved by morphology and ITS, yet certain relationships were elucidated by all analyses. Most notable is the strong support for a monophyletic lineage of dwarf taxa and the alliance of the North American N. microphylla with the Eurasian taxa. Minor discordance between the independent cladograms is accounted for by hybridization. The common taxonomic practice of uniting all North American and Eurasian taxa under one species is not supported phylogenetically.     

MOLECULAR SYSTEMATICS OF THE FLORIDEOPHYCEAE (RHODOPHYTA) USING NUCLEAR LARGE AND SMALL SUBUNIT rDNA SEQUENCE DATA

Sequence data are presented for approximately 85% of the nuclear large subunit (LSU) rDNA gene for one member of the Bangiophyceae and 47 members of the Florideophyceae, the latter representing all but one of the currently recognized florideophyte orders. Distance, parsimony, and maximum likelihood analyses of these data were used to generate phylogenetic trees, and bootstrap resampling was implemented to infer robustness for distance and parsimony results. LSU phylogenies were congruent with published nuclear small subunit (SSU) rDNA results in that four higher level florideophyte lineages were resolved: lineage 1, containing the order Hildenbrandiales; lineage 2, recovered only under distance analysis, composed of the orders Acrochaetiales, Balliales, Batrachospermales, Corallinales, Nemaliales, Palmariales, and Rhodogorgonales; lineage 3, containing the Ahnfeltiales; and lineage 4, composed of the orders Bonnemaisoniales, Ceramiales, Gelidiales, Gigartinales, Gracilariales, Halymeniales, Plocamiales, and Rhodymeniales. Analyses were also performed on a combined LSU–SSU data set and an SSU-only data set to account for differences in taxon sampling relative to published studies using this latter gene. Combined LSU–SSU analyses resulted in phylogenetic trees of similar topology and support to those obtained from LSU-only analyses. Phylogenetic trees produced from SSU-only analyses differed somewhat in particulars of branching within lineages 2 and 4 but overall were congruent with the LSU-only and combined LSU–SSU results. We close with a discussion of the phylogenetic potential that the LSU has displayed thus far for resolving relationships within the Florideophyceae.     

Searching for natural lineages within the Cerylonid Series (Coleoptera: Cucujoidea)

Phylogenetic relationships within the diverse beetle superfamily Cucujoidea are poorly known. The Cerylonid Series (C.S.) is the largest of all proposed superfamilial cucujoid groups, comprising eight families and representing most of the known cucujoid species diversity. The monophyly of the C.S., however, has never been formally tested and the higher-level relationships among and within the constituent families remain equivocal. Here we present a phylogenetic study based on 18S and 28S rDNA for 16 outgroup taxa and 61 C.S. ingroup taxa, representing seven of the eight C.S. families and 20 of 39 subfamilies. We test the monophyly of the C.S., investigate the relationships among the C.S. families, and test the monophyly of the constituent families and subfamilies. Phylogenetic reconstruction of the combined data was achieved via standard static alignment parsimony analyses, Direct Optimization using parsimony, and partitioned Bayesian analysis. All three analyses support the paraphyly of Cucujoidea with respect to Tenebrionoidea and confirm the monophyly of the C.S. The C.S. families Bothrideridae, Cerylonidae, Discolomatidae, Coccinellidae and Corylophidae are supported as monophyletic in all analyses. Only the Bayesian analysis recovers a monophyletic Latridiidae. Endomychidae is recovered as polyphyletic in all analyses. Of the 14 subfamilies with multiple terminals in this study, 11 were supported as monophyletic. The corylophid subfamily Corylophinae and the coccinellid subfamilies Chilocorinae and Scymninae are recovered as paraphyletic. A sister grouping of Anamorphinae+Corylophidae is supported in all analyses. Other taxonomic implications are discussed in light of our results.     

Phylogenetic analysis of the Metastrongyloidea (Nematoda: Strongylida) inferred from ribosomal RNA gene sequences

Phylogenetic relationships among nematodes of the strongylid superfamily Metastrongyloidea were analyzed using partial sequences from the large-subunit ribosomal RNA (LSU rRNA) and small-subunit ribosomal RNA (SSU rRNA) genes. Regions of nuclear ribosomal DNA (rDNA) were amplified by polymerase chain reaction, directly sequenced, aligned, and phylogenies inferred using maximum parsimony. Phylogenetic hypotheses inferred from the SSU rRNA gene supported the monophyly of representative taxa from each of the 7 currently accepted metastrongyloid families. Metastrongyloid taxa formed the sister group to representative trichostrongyloid sequences based on SSU data. Sequences from either the SSU or LSU RNA regions alone provided poor resolution for relationships within the Metastrongyloidea. However, a combined analysis using sequences from all rDNA regions yielded 3 equally parsimonious trees that represented the abursate Filaroididae as polyphyletic, Parafilaroides decorus as the sister species to the monophyletic Pseudaliidae, and a sister group relationship between Oslerus osleri and Metastrongylus salmi. Relationships among 3 members of the Crenosomatidae, and 1 representative of the Skrjabingylidae (Skrjabingylus chitwoodorum) were not resolved by these combined data. However, members of both these groups were consistently resolved as the sister group to the other metastrongyloid families. These relationships are inconsistent with traditional classifications of the Metastrongyloidea and existing hypotheses for their evolution.     

Nuclear-encoded rDNA group I introns: origin and phylogenetic relationships of insertion site lineages in the green algae

Group I introns are widespread in eukaryotic organelles and nuclear- encoded ribosomal DNAs (rDNAs). The green algae are particularly rich in rDNA group I introns. To better understand the origins and phylogenetic relationships of green algal nuclear-encoded small subunit rDNA group I introns, a secondary structure-based alignment was constructed with available intron sequences and 11 new subgroup ICI and three new subgroup IB3 intron sequences determined from members of the Trebouxiophyceae (common phycobiont components of lichen) and the Ulvophyceae. Phylogenetic analyses using a weighted maximum-parsimony method showed that most group I introns form distinct lineages defined by insertion sites within the SSU rDNA. The comparison of topologies defining the phylogenetic relationships of 12 members of the 1512 group I intron insertion site lineage (position relative to the E. coli SSU rDNA coding region) with that of the host cells (i.e., SSU rDNAs) that contain these introns provided insights into the possible origin, stability, loss, and lateral transfer of ICI group I introns. The phylogenetic data were consistent with a viral origin of the 1512 group I intron in the green algae. This intron appears to have originated, minimally, within the SSU rDNA of the common ancestor of the trebouxiophytes and has subsequently been vertically inherited within this algal lineage with loss of the intron in some taxa. The phylogenetic analyses also suggested that the 1512 intron was laterally transferred among later-diverging trebouxiophytes; these algal taxa may have coexisted in a developing lichen thallus, thus facilitating cell- to-cell contact and the lateral transfer. Comparison of available group I intron sequences from the nuclear-encoded SSU rDNA of phycobiont and mycobiont components of lichens demonstrated that these sequences have independent origins and are not the result of lateral transfer from one component to the other.      

A REEXAMINATION OF THE SYSTEMATICS OF THE ACROCHAETIALES (RHODOPHYTA) USING LARGE-SUBUNIT RDNA SEQUENCE DATA

The taxonomic history of the red algal order Acrochaetiales is chaotic. There is no consensus in the literature as to how many genera should be recognized or in the assignment of the over 400 species to these genera. Morphological and anatomical studies have provided a suite of possible characters to delineate genera within this order, but there have been major discrepancies in the assessment and use of these features. The phylogenetic placement of the Acrochaetiales has also been the focus of debate. Once thought to be the most ancestral florideophyte lineage, recent molecular systematic studies have illustrated that this order is a derived lineage closely related to the Nemaliales and Palmariales. Phylogenies using sequences of the small-subunit (SSU) rDNA have strongly supported two very divergent lineages within a possibly polyphyletic Acrochaetiales. The relationships between these two groups and among other closely related rhodophyte orders were not resolved. We have generated large-subunit (LSU) rDNA sequence data for representatives of the Acrochaetiales and related taxa. Distance and parsimony phylogenies based on LSU and combined SSU and LSU data will be presented. The increased phylogenetic signal afforded by this approach will shed light on previous conundrums in the systematics of this group.     

Interrelationships of the Gastrotricha and their place among the Metazoa inferred from 18S rRNA genes

The phylum Gastrotricha includes about 700 species. They are small worm‐like organisms abundant among marine and freshwater meiobenthos. In spite of their ubiquity, diversity and relative abundance, phylogenetic relationships of these animals remain enigmatic due to the conflicting results of morphological and molecular cladistic analyses. Also unclear are the alliances within the phylum. In order to best estimate the position of Gastrotricha among the Metazoa and to shed some light on the ingroup phylogenetic relationships, small subunit (SSU) ribosomal DNA (rDNA) from 15 species of Chaetonotida (eight genera) and 28 species of Macrodasyida (26 genera) were included in an alignment of 50 metazoan taxa representing 26 phyla. Of the gastrotrich SSU rDNA sequences, eight are new and, along with published sequences represent eight families, including the five marine most speciose. Gastrotricha were resolved within a monophyletic Lophotrochozoa as part of a clade including Micrognathozoa, Rotifera and Cycliophora. The Gnathostomulida were sister to this clade. Nodal support was low for all of these relationships except the grouping of the Micrognathozoa, Rotifera and Cycliophora. Bayesian inference resolved the Gastrotricha as monophyletic with weak nodal support; the Macrodasyida were resolved as paraphyletic with many basal nodes poorly supported. Within the Chaetonotida, the monotypic Multitubulatina Neodasys was found in alliance with the macrodasyidan Urodasys while all the Paucitubulatina were found to form a single, well‐supported clade, with Musellifer as the most basal member. Among the more densely sampled Macrodasyida the Lepidodasyidae and Macrodasyidae were each found to be polyphyletic while monophyly was well supported for the Turbanellidae and Thaumastodermatidae. The congruence of our results with those of the cladistic analysis based on morphological traits provides confidence about the value of each dataset, and calls for widening of the research to include additional taxa of particular phylogenetic significance such as the Dactylopodolidae, Diuronotus, Heteroxenotrichula and Draculiciteria. The study highlights the problems in working with small species, the need for voucher specimens and the confused taxonomic status and membership of various gastrotrich families.