Systematic position and relationships of Paracreptotrematina limi, based on partial sequences of 28S rRNA and cytochrome c oxidase subunit 1 genes

Paracreptotrematina limi Amin and Myer, 1982 (Trematoda), an intestinal fluke specific to the mudminnow, Umbra limi, is conventionally classified within the papillose Allocreadiidae. Its unusual morphology (lack of identifiable vitellaria, large fully embryonated terminal eggs), assumptions of homology of its 2 atypical muscular oral 'papillae' (lobes) with those of the Bunoderinae, and its unknown life cycle make this classification tenuous. Previous phylogenetic analyses of the papillose allocreadiids, based on morphology, placed P. limi as a basal papillose allocreadiid. We tested this hypothesis with a phylogenetic analysis by using partial sequences of the 28S ribosomal RNA gene and the cytochrome c oxidase subunit I gene from several plagiorchiiform taxa, including reportedly related allocreadiids as well as selected species of Plagiorchiidae, Haematoloechidae, and Macroderoididae. Results of phylogenetic analyses of the 28S rRNA gene fragments by using parsimony criteria support the classification of P. limi as an allocreadiid and place it as a sister taxon to a clade with Allocreadium lobatum Wallin, 1909, Bunodera luciopercae (Müller, 1876) and Crepidostomum cooperi Hopkins, 1931, with Polylekithum ictaluri (Pearse, 1924) basal to all of them. Analysis of the cytochrome c oxidase subunit I gene sequence data from fewer taxa supports the placement of P. limi relative to 3 (A. lobatum, C. cooperi, and P. ictaluri) of the 4 allocreadiid taxa. These results also suggest that the previous conception of the papillose allocreadiids as a monophyletic assemblage that includes P. limi may require a reappraisal.     

Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences

The phylogenetic relationships of nine species of freshwater sponges, representing the families Spongillidae, Lubomirskiidae, and Metaniidae, were inferred from analyses of 18S rDNA, cytochrome oxidase subunit I (COI) mtDNA, and internal transcribed spacer 2 (ITS2) rDNA sequences. These species form a strongly supported monophyletic group within the Demospongiae, with the lithistid Vetulina stalactites as the sister taxon. Within the freshwater sponge clade, the basal taxon is not resolved. Depending upon the method of analysis and sequence, the metaniid species, Corvomeyenia sp., or the spongillid species, Trochospongilla pennsylvanica , emerges as the basal species. Among the remaining freshwater sponge species, the spongillids, Spongilla lacustris and Eunapius fragilis , form a sister group to a clade comprised of the spongillid species, Clypeatula cooperensis , Ephydatia fluviatilis , and Ephydatia muelleri , and the lubomirskiid species, Baikalospongia bacillifera and Lubomisrkia baicalensis . C. cooperensis is the sister taxon of E. fluvialitis , and E. muelleri is the sister taxon of ( B. bacillifera + L. baicalensis ). The family Spongillidae and the genus Ephydatia are thus paraphyletic with respect to the lubomirskiid species; Ephydatia is also paraphyletic to C. cooperensis . We suggest that C. cooperensis be transferred to the genus Ephydatia and that the family Lubomirskiidae be subsumed into the Spongillidae.     

Ultrastructure and chaetotaxy of sensory receptors in the cercariae of a species of Crepidostomum Braun, 1900 and Bunodera Railliet, 1896 (Digenea: Allocreadiidae)

Previous investigations of cercarial sensory systems have focused on chaetotaxy and ultrastructure of sensory receptors and have revealed chaetotaxic patterns within families, genera, and species as well as different types of sensory receptors. However, chaetotaxic and ultrastructural observations have rarely been combined. We investigated the ultrastructure of cercarial sensory receptors in conjunction with the chaetotaxy and neuromorphology in 2 allocreadiid species belonging to the genera Crepidostomum and Bunodera. Cercariae were treated with acetylthiocholine iodide and silver nitrate, and for scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Similar cholinergic nerve networks were revealed. Chaetotaxy was consistent with that of other allocreadiids. Seven and 6 types of receptors were distinguished with SEM in Crepidostomum sp. and Bunodera sp., respectively. Types differed in number of cilia (1 or 2), cilium length (short, moderately long, or long), presence or absence of a tegumentary collar and a domelike base, and tegumentary collar length (low, moderately low, or high), TEM of some types revealed unsheathed cilia, basal body, and thickened nerve collars. Some receptor types were site specific. Thus, long uniciliated receptors were concentrated on the dorsal surface. Other types, such as short uniciliated receptors, were widespread throughout most regions. Ultrastructure and site-specificity observations suggest that most receptors are mechanoreceptors.     

Phylogenetic affinities of Auriculostoma (Digenea: Allocreadiidae), with descriptions of two new species from Peru

Two new allocreadiid trematodes are described from the intestine of characid fishes from Rio Itaya, a tributary of the Amazon River near Iquitos, Peru. Auriculostoma foliaceum n. sp. is described from Bryconops cf. caudomaculatus (Günther, 1864) Backup, 2003, and Auriculostoma diagonale n. sp. from Stethaprion cf. erythrops Cope, 1870. Auriculostoma foliaceum n. sp. differs from its congeners by having a foliated lateral margin and lacking vitelline follicles in the forebody. Auriculostoma diagonale n. sp. differs from all of its congeners except Auriculostoma platense (Szidat, 1954) Scholz, Aguirre-Macedo, and Choudhury, 2004, by having oblique rather than tandem testes and differs from A. platense by having a much more elongated cirrus sac. Phylogenetic hypotheses based on analyses of 3 alignments of partial sequences of the 28S rDNA gene conducted in this study provide a framework for revaluating the classification of Allocreadiidae Looss, 1902. The present analyses show that (1) Paracreptotrematina limi Amin and Myer, 1982, does not belong in the Allocreadiidae; (2) Creptotrematina aguirrepequenoi Jiménez-Guzmán, 1973 (spelled here without diacritic mark), does not belong to Paracreptotrematina Amin and Myer, 1982, but remains in the Allocreadiidae; (3) Auriculostoma astyanace Scholz, Aguirre-Macedo, and Choudhury, 2004, is closely related to C. aguirrepequenoi and Wallinia chavarriae Choudhury, Hartvigsen-Daverdin, and Brooks, 2002; (4) Megalogonia Surber, 1928, is retained as an accepted genus in the Allocreadiidae; and (5) Margotrema Lamothe-Argumedo, 1970, is found to be nested among 3 species of Crepidostomum Braun, 1900.     

Parasites of juvenile brook trout (Salvelinus fontinalis) from Hunt Creek, Michigan

Four parasite species (Crepidostomum cooperi, Cystidicoloides ephemeridarum, Acanthocephalus dirus, Salmincola edwardsii) infected 215 juvenile brook trout (105 young-of-year; 110, 1-yr-old) from Hunt Creek, Michigan, in 2003, 2004, and 2005. Prevalences of these species in 2004 (main study year) varied from 29 to 37%. Crepidostomnum cooperi had the highest mean intensity and mean abundance, followed by C. ephemeridarum. The number of fish infected with each parasite species was significantly higher in 1-yr-old fish than in young-of-year fish. Also, the mean intensities and mean abundances of C. cooperi and C. ephemeridarum and the mean abundance of A. dirus were significantly higher in older fish. The mean intensity of C. cooperi and prevalence of A. dirus were significantly higher in fish between creek sections. Fish length had a significant positive effect on the abundances of C. cooperi and C. ephemeridarum; parasite species richness, on the abundances of A. dirus and S. edwardsii; and parasite species richness in the 2003 and 2004 trout cohorts, respectively. Crepidostomum cooperi, C. ephemeridarum, A. dirus, and S. edwardsii commonly infect Michigan brook trout. The small number of parasite species infecting Hunt Creek brook trout is similar to the number of parasite species of brook trout from other Michigan creeks.     

Enteric helminths of perch (Perca fluviatilis L.) and yellow perch (Perca flavescens Mitchill): stochastic or predictable assemblages?

Component communities of perch (Perca fluviatilis L) in Eurasia and the North American yellow perch (Perca flavescens Mitchill) were examined to determine the nature of their parasite communities. The scale of this investigation is continental and includes data collected across the distribution of each host species. Data were compiled from the literature and from 5 sample sites in North America. Four parasite species were found to occur frequently in the helminth component communities of P. flavescens. The cestodes Bothriocephalus cuspidatus and Proteocephalus pearsei, the digenean Crepidostomum cooperi, and the nematode Dichelyne cotylophora comprised a suite of species of which some or all occurred in most samples. Similarly, a group of 4 predictable parasite species was identified for P. fluviatilis in Eurasia, the digenean Bunodera luciopercae, the nematode Camallanus lacustris, the cestode Proteocephalus percae, and the acanthocephalan Acanthocephalus lucii. Specificity was not a requirement for predictability. Despite geographical isolation for millions of years, and different fish species interactions within and between continents, the predictability of these parasite assemblages indicates they are shaped by a biology, especially feeding patterns, common to both perch species. This is evidence that parasite assemblages comprised of nonhost-specific parasites in freshwater fishes are not merely stochastic assemblages but have key components that are predictable at this broad continental scale.     

Phylogenetic relationships of the Raphidophyceae and Xanthophyceae as inferred from nucleotide sequences of the 18S ribosomal RNA gene

Some earlier studies suggested an evolutionary relationship between the Raphidophyceae (chloromonads) and Xanthophyceae (yellow-green algae), whereas other studies suggested relationships with different algal classes or the öomycete fungi. To evaluate the relationships, we determined the complete nucleotide sequences of the 18S ribosomal RNA gene from the raphidophytes Vacuolaria virescens, Chattonella subsalsa, and Heterosigma carterae, and the xanthophytes Vaucheria bursata, Botrydium stoloniferum, Botrydiopsis intercedens, and Xanthonema debile. The results showed that the Xanthophyceae were most closely related to the Phaeophyceae. A cladistic analysis of combined data sets (nucleotide sequences, ultrastructure, and pigments) suggested the Raphidophyceae are the sister taxon to the Phaeophyceae-Xanthophyceae clade, but the bootstrap value was low (40%). The raphidophyte genera were united with high (100%) bootstrap values, supporting a hypothesis based upon ultrastructural features that marine and freshwater raphidophytes form a monophyletic group. We examined the relationship between Vaucheria, a siphoneous xanthophyte alga, and the öomycetes, and we confirmed that Vaucheria is a member of the class Xanthophyceae. Partial nucleotide sequences of the 18S rRNA gene from eight xanthophytes (including Bumillariopsis filiformis, Heterococcus caespitiosus, and Mischococcus sphaerocephalus) produce a phylogeny that is not congruent with the current morphology-based classification scheme.     

Phylogenetic position of the adeleorinid coccidia (Myzozoa, Apicomplexa, Coccidia, Eucoccidiorida, Adeleorina) inferred using 18S rDNA sequences

Investigating the evolutionary relationships of the major groups of Apicomplexa remains an important area of study. Morphological features and host-parasite relationships continue to be important in the systematics of the adeleorinid coccidia (suborder Adeleorina), but the systematics of these parasites have not been well-supported or have been constrained by data that were lacking or difficult to interpret. Previous phylogenetic studies of the Adeleorina have been based on morphological and developmental characters of several well-described species or based on nuclear 18S ribosomal DNA (rDNA) sequences from taxa of limited taxonomic diversity. Twelve new 18S rDNA sequences from adeleorinid coccidia were combined with published sequences to study the molecular phylogeny of taxa within the Adeleorina and to investigate the evolutionary relationships of adeleorinid parasites within the Apicomplexa. Three phylogenetic methods supported strongly that the suborder Adeleorina formed a monophyletic clade within the Apicomplexa. Most widely recognized families within the Adeleorina were hypothesized to be monophyletic in all analyses, although the single Hemolivia species included in the analyses was the sister taxon to a Hepatozoon sp. within a larger clade that contained all other Hepatozoon spp. making the family Hepatozoidae paraphyletic. There was an apparent relationship between the various clades generated by the analyses and the definitive (invertebrate) host parasitized and, to lesser extent, the type of intermediate (vertebrate) host exploited by the adeleorinid parasites. We conclude that additional taxon sampling and use of other genetic markers apart from 18S rDNA will be required to better resolve relationships among these parasites.     

Phylogenetic position of the Tardigrada based on the 18S ribosomal RNA gene sequences

The phylogenetic position of the Tardigrada remains uncertain. This is due to the limited information available, and the uncertainty of whether some characters are homologous or analogous with other taxa. Based on some morphological characters, current discussion centres on whether the taxon branches from the annelid-arthropod lineage, or lies within the arthropod complex. The molecular data presented here from an analysis of the 18S rRNA gene sequences are used to test the validity of these two hypotheses. Phylogenetic inference by the maximum parsimony and distance (neighbour-joining) methods suggests that the Tardigrada is a sister group of the major protostome eucoelomate assemblage that emerged before the arthropods, annelids, molluscs, and sipunculids evolved. The tardigrade clade also appears as an independent lineage separate from the nematode clade, thus supporting the current idea that tardigrades do not have a close aschelminth relationship. The molecular data also imply that several morphological features, considered significant in determining the phylogenetic relationships of tardigrades, are not synapomorphic characters.     

A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata)

We examine phylogenetic relationships among salamanders of the family Salamandridae using approximately 2700 bases of new mtDNA sequence data (the tRNALeu, ND1, tRNAIle, tRNAGln, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI genes and the origin for light-strand replication) collected from 96 individuals representing 61 of the 66 recognized salamandrid species and outgroups. Phylogenetic analyses using maximum parsimony and Bayesian analysis are performed on the new data alone and combined with previously reported sequences from other parts of the mitochondrial genome. The basal phylogenetic split is a polytomy of lineages ancestral to (1) the Italian newt Salamandrina terdigitata, (2) a strongly supported clade comprising the "true" salamanders (genera Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), and (3) a strongly supported clade comprising all newts except S. terdigitata. Strongly supported clades within the true salamanders include monophyly of each genus and grouping Chioglossa and Mertensiella as the sister taxon to a clade comprising Lyciasalamandra and Salamandra. Among newts, genera Echinotriton, Pleurodeles, and Tylototriton form a strongly supported clade whose sister taxon comprises the genera Calotriton, Cynops, Euproctus, Neurergus, Notophthalmus, Pachytriton, Paramesotriton, Taricha, and Triturus. Our results strongly support monophyly of all polytypic newt genera except Paramesotriton and Triturus, which appear paraphyletic, and Calotriton, for which only one of the two species is sampled. Other well-supported clades within newts include (1) Asian genera Cynops, Pachytriton, and Paramesotriton, (2) North American genera Notophthalmus and Taricha, (3) the Triturus vulgaris species group, and (4) the Triturus cristatus species group; some additional groupings appear strong in Bayesian but not parsimony analyses. Rates of lineage accumulation through time are evaluated using this nearly comprehensive sampling of salamandrid species-level lineages. Rate of lineage accumulation appears constant throughout salamandrid evolutionary history with no obvious fluctuations associated with origins of morphological or ecological novelties.     

Phylogeny of the cave shrimp Troglocaris: Evidence of a young connection between Balkans and Caucasus

The remarkably discontinuous distribution of the cave shrimp genus Troglocaris in South France, West Balkans, and West Caucasus has long been considered a biogeographic enigma. To solve it, its phylogeny was reconstructed by analyzing sequences from two mitochondrial (cytochrome oxidase I and 16S rRNA) and one nuclear gene (28S rRNA) using maximum likelihood, parsimony and Bayesian inference. The genus was found to be polyphyletic because the French taxon T. inermis had no direct common ancestry with other Troglocaris taxa but was sister to the epigean freshwater atyid Dugastella valentina. All other Troglocaris species constituted a well-supported monophylum, the second cave shrimp genus Spelaeocaris nested within. The monophylum had a well-defined structure: (1) a clade restricted to the Dinaric area of the Western Balkans containing the type species T. anophthalmus along with some unnamed species, and (2) a geographically mixed clade split between the Caucasian T. kutaissiana species complex on one, and T. hercegovinensis, S. pretneri, plus an unnamed taxon on the other side. It was surprising to find the dichotomy between the Caucasian and one of the West-Balkan lineages so low in the phylogenetic hierarchy of the genus. Taking into account molecular rates of other decapods, we tentatively dated this split at 6-11 Myr. This time is in agreement with the brackish and freshwater phase of the Paratethys thus allowing for a freshwater common ancestor of Caucasian and Dinaric cave shrimps. This would weaken the marine relicts hypothesis that has often been invoked to explain the distribution of freshwater cave species with close marine relatives.     

基于Rag1基因序列变异的鲤形目鱼类系统发育重建:采样策略对生命之树的影响

The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future climatic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent molecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential problems. The recent Cypriniformes Tree of Life initiative is an effort to achieve this goal with morphological and molecular (mitochondrial and nuclear) data. In this early synthesis of our understanding of the phylogenetic relationships of these fishes, all types of data have contributed historically to improving our understanding, but not all analyses are complementary in taxon sampling, thus precluding direct understanding of the impact of taxon sampling on achieving accurate phylogenetic inferences. However, recent molecular studies do provide some insight and in some instances taxon sampling can be implicated as a variable that can influence sister group relationships. Other instances may also exist but without inclusion of more taxa for both mitochondrial and nuclear genes, one cannot distinguish between inferences being dictated by taxon sampling or the origins of the molecular data.     

Morphological evidence for sister group relationship between flamingos (Aves: Phoenicopteridae) and grebes (Podicipedidae)

A recent molecular analysis strongly supported sister group relationship between flamingos (Phoenicopteridae) and grebes (Podicipedidae), a hypothesis which has not been suggested before. Flamingos are long-legged filter-feeders whereas grebes are morphologically quite divergent foot-propelled diving birds, and sister group relationship between these two taxa would thus provide an interesting example of evolution of different feeding strategies in birds. To test monophyly of a clade including grebes and flamingos, I performed a cladistic analysis of 70 morphological characters which were scored for 17 taxa. Parsimony analysis of these data supported monophyly of the taxon (Podicipedidae + Phoenicopteridae) and the clade received high bootstrap support. Previously overlooked morphological, oological and parasitological evidence is recorded which supports this hypothesis, and which makes the taxon (Podicipedidae + Phoenicopteridae) one of the best supported higher-level clades within modern birds. The phylogenetic significance of some fossil flamingo-like birds is discussed. The Middle Eocene taxon Juncitarsus is most likely the sister taxon of the clade (Podicipedidae + (Palaelodidae + Phoenicopteridae)) although resolution of its exact systematic position awaits revision of the fossil material. Contrary to previous assumptions, it is more parsimonious to assume that flamingos evolved from a highly aquatic ancestor than from a shorebird-like ancestor.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 157–169.     

Aligned 18S and insect phylogeny

The nuclear small subunit rRNA (18S) has played a dominant role in the estimation of relationships among insect orders from molecular data. In previous studies, 18S sequences have been aligned by unadjusted automated approaches (computer alignments that are not manually readjusted), most recently with direct optimization (simultaneous alignment and tree building using a program called "POY"). Parsimony has been the principal optimality criterion. Given the problems associated with the alignment of rRNA, and the recent availability of the doublet model for the analysis of covarying sites using Bayesian MCMC analysis, a different approach is called for in the analysis of these data. In this paper, nucleotide sequence data from the 18S small subunit rRNA gene of insects are aligned manually with reference to secondary structure, and analyzed under Bayesian phylogenetic methods with both GTR+I+G and doublet models in MrBayes. A credible phylogeny of Insecta is recovered that is independent of the morphological data and (unlike many other analyses of 18S in insects) not contradictory to traditional ideas of insect ordinal relationships based on morphology. Hexapoda, including Collembola, are monophyletic. Paraneoptera are the sister taxon to a monophyletic Holometabola but weakly supported. Ephemeroptera are supported as the sister taxon of Neoptera, and this result is interpreted with respect to the evolution of direct sperm transfer and the evolution of flight. Many other relationships are well-supported but several taxa remain problematic, e.g., there is virtually no support for relationships among orthopteroid orders. A website is made available that provides aligned 18S data in formats that include structural symbols and Nexus formats.     

The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters

Consensus is elusive regarding the phylogenetic relationships among neornithine (crown clade) birds. The ongoing debate over their deep divergences is despite recent increases in available molecular sequence data and the publication of several larger morphological data sets. In the present study, the phylogenetic relationships among 43 neornithine higher taxa are addressed using a data set of 148 osteological and soft tissue characters, which is one of the largest to date. The Mesozoic non‐neornithine birds Apsaravis, Hesperornis, and Ichthyornis are used as outgroup taxa for this analysis. Thus, for the first time, a broad array of morphological characters (including both cranial and postcranial characters) are analyzed for an ingroup densely sampling Neornithes, with crown clade outgroups used to polarize these characters. The strict consensus cladogram of two most parsimonious trees resultant from 1000 replicate heuristic searches (random stepwise addition, tree‐bisection‐reconnection) recovered several previously identified clades; the at‐one‐time contentious clades Galloanseres (waterfowl, fowl, and allies) and Palaeognathae were supported. Most notably, our analysis recovered monophyly of Neoaves, i.e., all neognathous birds to the exclusion of the Galloanseres, although this clade was weakly supported. The recently proposed sister taxon relationship between Steatornithidae (oilbird) and Trogonidae (trogons) was recovered. The traditional taxon “Falconiformes” (Cathartidae, Sagittariidae, Accipitridae, and Falconidae) was not found to be monophyletic, as Strigiformes (owls) are placed as the sister taxon of (Falconidae + Accipitridae). Monophyly of the traditional “Gruiformes” (cranes and allies) and ”Ciconiiformes” (storks and allies) was also not recovered. The primary analysis resulted in support for a sister group relationship between Gaviidae (loons) and Podicipedidae (grebes)—foot‐propelled diving birds that share many features of the pelvis and hind limb. Exclusion of Gaviidae and reanalysis of the data set, however, recovered the sister group relationship between Phoenicopteridae (flamingos) and grebes recently proposed from molecular sequence data.     

PHYLOGENY OF THE ULVOPHYCEAE (CHLOROPHYTA): CLADISTIC ANALYSIS OF NUCLEAR-ENCODED rRNA SEQUENCE DATA1

Cladistic analysis of nuclear-encoded rRNA sequence data provided us with the basis for some new hypotheses of relationships within the green algal class Ulvophyceae. The orders Ulotrichales and Ulvales are separated from the clade formed by the remaining orders of siphonous and siphonocladous Ulvophyceae (Caulerpales, Siphonocladales /Cladophorales [S/C] complex, and the Dasycladales), by the Chlorophyceae and Pleurastrophyceae. Our results suggest that the Ulvophyceae is not a monophyletic group. Examination of inter- and intra-ordinal relationships within the siphonous and siphonocladous ulvophycean algae revealed that Cladophora, Chaetomorpha, Anadyomene, Microdictyon, Cladophoropsis and Dictyosphaeria form a clade. Thus the hypothesis, based on ultrastructural features, that the Siphonocladales and Cladophorales are closely related is supported. Also, the Caulerpales is a monophyletic group with two lineages; Caulerpa, Halimeda, and Udotea comprise one, and Bryopsis and Codium comprise the other. The Dasycladales (Cymopolia and Batophora) also forms a clade, but this clade is not inferred to be the sister group to the S/C complex as has been proposed. Instead, it is either the sister taxon to the Caulerpales or basal to the Caulerpales and S/C clade The Trentepohliales is also included at the base of the siphonous and siphonocladous ulvophycean clade. The Pleurastrophyceae, which, like the Ulvophyceae, posses a counter-clockwise arrangement of flagellar basal bodies, are more closely related to the Chlorophyceae than to the Ulvophyceae based on rRNA sequences. Thus, the arrangement of basal bodies does not diagnose a monophyletic group. Previously reported hypotheses of phylogenetic relationships of ulvophycean algae were tested. In each case, additional evolutionary steps were required to obtain the proposed relationships. Relationships of ulvophycean algae to other classes of green algae are discussed.