Phylogeny and Systematic Position of Zosterodasys (Ciliophora, Synhymeniida): A Combined Analysis of Ciliate Relationships Using Morphological and Molecular Data

ABSTRACT. The Synhymeniida is characterized both by a band of somatic dikinetids, the synhymenium, extending across the surface of the cell and by a ventral cell mouth lacking specialized feeding cilia but subtended by a well-developed cyrtos. The synhymeniids have been hypothesized to be members of the class Nassophorea but our previous ultrastructural study of the synhymeniid genus Zosterodasys did not show any clear synapomorphies that would permit definitive placement in the Nassophorea or as a sister taxon to any of the other ciliate groups possessing a cyrtos. In the present study, simultaneous analysis of morphological and small subunit rDNA molecular data indicates that the Synhymeniida are sister to the class Phyllopharyngea and that this clade is, in turn, sister to the remaining Nassophorea, although this result is sensitive to dataset inclusion and alignment parameters. While this suggests that taxa with a ventral cyrtos might be united into a named taxon (e.g. resurrecting the Hypostomata), additional data are needed to reach a definitive conclusion.     

Phylogenetic position of Sorogena stoianovitchae and relationships within the class Colpodea (Ciliophora) based on SSU rDNA sequences

The ciliate Sorogena stoianovitchae, which can form a multicellular fruiting body, has been classified based upon its ultrastructure and morphology: the oral and somatic infraciliature of S. stoianovitchae most closely resemble those of members of the order Cyrtolophosidida in the class Colpodea. We characterized the small subunit ribosomal DNA (SSU rDNA) gene sequence from S. stoianovitchae and compared this sequence with those from representatives of all ciliate classes. These analyses placed S. stoianovitchae as either sister to members of the class Nassophorea or Colpodea. In an in-group analysis, including all SSU rDNA sequences from members of the classes Nassophorea and Colpodea and representatives of appropriate outgroups, S. stoianovitchae was always sister to Platyophrya vorax (class Colpodea, order Cyrtolophosidida). However, our analyses failed to support the monophyly of the class Colpodea. Instead, our data suggest that there are essentially three unresolved clades: (1) the class Nassophorea; (2) Bresslaua vorax, Colpoda inflata, Pseudoplatyophrya nana, and Bursaria truncatella (class Colpodea); and (3) P. vorax and S. stoianovitchae (class Colpodea).     

Description of a new epibiotic relationship (Suctorian–Copepoda) in NE Atlantic waters: from morphological to phylogenetic analyses

Paraeuchaeta hebes is one of the most important carnivorous copepods in the coastal upwelling system off Galician waters (Ría de Vigo, NE Atlantic). A suctorian epibiont of the genus Pelagacineta was found attached to the surface of these copepods. The abundance and distribution on the copepod surface were analysed, taking into account the sex of the crustacean, revealing some preference for females and also a different attachment point in both sexes. The morphological study allowed us to identify a new species of this Suctoria epibiont as Pelagacineta hebensis. Moreover, the 18S rRNA gene was partially sequenced to inspect the phylogenetic position of Pelagacineta hebensis within the subclass Phyllopharyngea. The maximum‐likelihood (ML) tree obtained was consistent with the morphological and with previous molecular studies and showed that P. hebensis belongs to the order Endogenina, as a sister clade of the few taxa sequenced within this order. Including new genetic data to the Endogenina will allow building new hypothesis about the evolution of the most derived clade of suctorians.     

Molecular phylogeny of phyllopharyngean ciliates and their group I introns

We analyzed small subunit ribosomal DNA (ssu-rDNA) sequences to evaluate both the monophyly of the ciliate class Phyllopharyngea de Puytorac et al. (1974), and relationships among subclasses. Classifications based on morphology and ultrastructure divide the Phyllopharyngea into four subclasses, the Phyllopharyngia, Chonotrichia, Rhynchodia, and Suctoria. Our analyses of ssu-rDNA genealogies derived from sequence data collected from diverse members representing three of the four subclasses of Phyllopharyngea (Suctoria: Ephelota spp., Prodiscophyra collini, Acineta sp.; Phyllopharyngia: Chlamydodon exocellatus, Chlamydodon triquetrus, Dysteria sp.; and Chonotrichia: Isochona sp.) provide strong support for the monophyly of the Phyllopharyngea, and show that the Chonotrichia emerge from within the Phyllopharyngia. Based on this initial sampling, suctorian budding types are monophyletic, and exogenous budding appears to be basal to evaginative and endogenous budding. Further, we report the discovery of a group I intron at position 891 in the Suctoria Acineta sp. and Tokophrya lemnarum, and a second group I intron at position 1506 in T. lemnarum. These introns represent only the second examples of group I introns in a ciliate ribosomal gene, since the discovery of ribozymes in the LSU rRNA gene of Tetrahymena thermophila. Phylogenetic analyses of Group I introns suggest a complex evolutionary history involving either multiple loses or gains of introns within endogenously budding Suctoria.     

Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae

The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that contains most of the fungi previously recognized as Plectomycetes because of their mostly enclosed ascomata and prototunicate asci; and (ii) the subclass Chaetothyriomycetidae, a group of fungi that produce ascomata with an opening reminiscent of those produced by Dothideomycetes or Sordariomycetes. In this paper we use phylogenetic analyses based on data available from the Assembling the Fungal Tree of Life project (AFTOL), in addition to sequences in GenBank, to outline this important group of fungi. The Eurotiomycetidae include producers of toxic and useful secondary metabolites, fermentation agents used to make food products and enzymes, xerophiles and psychrophiles, and the important genetics model Aspergillus nidulans. The Chaetothyriomycetidae include the common black yeast fungi, some of which are pathogens of humans and animals, as well as some primarily lichenized groups newly found to be phylogenetically associated with this group. The recently proposed order Mycocaliciales shows a sister relationship with Eurotiomycetes. The great majority of human pathogenic Pezizomycotina are Eurotiomycetes, particularly in Eurotiales, Onygenales and Chaetothyriales. Due to their broad importance in basic research, industry and public health, several genome projects have focused on species in Onygenales and Eurotiales.     

A phylogenetic reconsideration of suctorian ciliates (Protista,Ciliophora, Phyllopharyngea) based on small subunit rRNA gene sequences

Compared with other ciliated protozoa, molecular studies of phylogenetic relationships within the subclass Suctoria are rare. In this work, phylogenetic analyses focusing on this group were performed based on all data available. In addition, the small subunit ribosomal RNA (SSU rRNA) genes of three suctorian ciliates (Acineta compressa, Acineta tuberosa and Paracineta limbata) were newly sequenced. Furthermore, the putative secondary structures of the variable region 2 of the SSU rRNA gene were predicted and compared within the Suctoria. Our results show that (i) there is support for the monophyly of the subclass Suctoria, which is a sister clade to the cyrtophorids; (ii) based on combined morphologic and molecular features, we propose the following evolutionary routine within the Suctoria: Exogenina – Evaginogenina – Endogenina; (iii) the similarities of the secondary structures of the V2 region and the SSU rRNA gene sequences within the subclass Suctoria are consistent with the branching of the phylogenetic lineages.     

Phylogenetic analysis of 1.5 Mbp and platypus EST data refute the Marsupionta hypothesis and unequivocally support Monotremata as sister group to Marsupialia/Placentalia

The extant mammalian groups Monotremata, Marsupialia and Placentalia are, according to the 'Theria' hypothesis, traditionally classified into two subclasses. The subclass Prototheria includes the monotremes and subclass Theria marsupials and placental mammals. Based on some morphological and molecular data, an alternative proposition, the Marsupionta hypothesis, favours a sister group relationship between monotremes and marsupials to the exclusion of placental mammals. Phylogenetic analyses of single genes and even multiple gene alignments have not yet been able to conclusively resolve this basal mammalian divergence. We have examined this problem using one data set composed of expressed sequence tags (EST) and another containing 1 510 509 nucleotide (nt) sites from 1358 inferred cDNA genomic sequences. All analyses of the concatenated sequences unambiguously supported the Theria hypothesis. The Marsupionta hypothesis was rejected with high statistical confidence from both data sets. In spite of the strong support for Theria, a non-negligible number of single genes supported either of the two alternative hypotheses. The divergence between monotremes and therian mammals was estimated to have taken place 168–178 Mya, a dating compatible with the fossil record. Considering the long common evolutionary branch of therians, it is surprising that sequence data from many thousand amino acid sites were needed to conclusively resolve their relationship to monotremes. This finding draws attention to other mammalian divergences that have been taken as unequivocally settled based on much smaller alignments. EST data provide a comprehensive random sample of protein coding sequences and an economic way to produce large amounts of data for phylogenetic analysis of species for which genomic sequences are not yet available.     

Warsaw Breakage Syndrome, a Cohesinopathy Associated with Mutations in the XPD Helicase Family Member DDX11/ChlR1

The iron-sulfur-containing DNA helicases XPD, FANCJ, DDX11, and RTEL represent a small subclass of superfamily 2 helicases. XPD and FANCJ have been connected to the genetic instability syndromes xeroderma pigmentosum and Fanconi anemia. Here, we report a human individual with biallelic mutations in DDX11. Defective DDX11 is associated with a unique cellular phenotype in which features of Fanconi anemia (drug-induced chromosomal breakage) and Roberts syndrome (sister chromatid cohesion defects) coexist. The DDX11-deficient patient represents another cohesinopathy, besides Cornelia de Lange syndrome and Roberts syndrome, and shows that DDX11 functions at the interface between DNA repair and sister chromatid cohesion.     

A proposed phylogeny of the flagellated protostelids.

The flagellated members of the group of mycetozoans known as protostelids have been recognized for some time to be members of a monophyletic group which also includes the myxomycetes. This inference was based primarily upon comparisons of the flagellar apparatus of the amoeboflagellate state. However, more detailed comparisons based on the whole life history and comparisons with an outgroup were necessary to have information sufficient to determine the interrelationships within the group. Recent studies of the other states of the life history of protostelids have provided a wealth of additional morphological and developmental characters such that an in depth phylogenetic analysis is possible. The results show that the group can be resolved into two major clades, one of which contains the myxomycetes and the myxomycete-like protostelid genera, Protosporangium, Clastostelium, and Ceratiomyxa, and another which contains the protostelid genera Planoprotostelium, Cavostelium, and Ceratiomyxella. As the myxomycetes appear to be part of the ingroup, and not a sister group to the protostelids, L.S. Olive's subclass Protostelia must be considered paraphyletic.     

Patterns of clade support across the major lineages of moss phylogeny

Relationships among the major branches of moss phylogeny are understudied compared with other major land‐plant groups. We addressed this by surveying 14–17 plastid genes from taxa representing the major lineages, using different phylogenetic methods (parsimony, likelihood) and codon‐ and gene‐based data partitioning schemes (likelihood). Our phylogenetic inferences generally corroborated the best supported clades across multiple recent studies, with comparable or higher levels of clade support here. We resolved persistent ambiguities with strong to moderate support across analyses, including several early nodes in subclass Dicranidae, and relationships among other subclasses of peristomate mosses. In particular, we resolved a sister‐group relationship between Bryidae and Dicranidae, between these subclasses and Timiidae, and between this entire clade and Funariidae. We consistently recovered Tetraphidopsida (a nematodontous class) as the sister group of arthrodontous mosses (Bryopsida), although with only weak support. Strongly conflicting arrangements at the base of moss phylogeny concerning Takakiopsida and Sphagnopsida, two non‐peristomate moss lineages, were inferred in parsimony and likelihood analysis, but this depended on how base‐frequency parameters were estimated and how data were partitioned in likelihood analysis. Relationships inferred for the remaining peristomate and non‐peristomate moss clades, and their associated support values, were otherwise broadly congruent across analyses.     

Phylogeny of the Bangiophycidae (Rhodophyta) and the secondary endosymbiotic origin of algal plastids

The Rhodophyta (red algae) are composed of the subclasses Bangiophycidae and Florideophycidae. Two evolutionarily interesting features of the Bangiophycidae are: (1) they are the ancestral pool from which the more morphologically complex taxa in the Florideophycidae have arisen and (2) they are the sources of the plastids, through secondary endosymbioses, for the Cryptophyta, Haptophyta, and the Heterokonta. To understand Bangiophycidae phylogeny and to gain further insights into red algal secondary endosymbioses, we sequenced the plastid-encoded small subunit ribosomal DNA (rDNA) coding region from nine members of this subclass and from two members of the Florideophycidae. These sequences were included in phylogenetic analyses with all available red algal plus chlorophyll a + c algal plastid rDNA coding regions. Our results are consistent with a monophyletic origin of the Florideophycidae with these taxa forming a sister group of the Bangiales. The Bangiophycidae is of a paraphyletic origin with orders such as the Porphyridiales polyphyletic and distributed over three independent red algal lineages. The plastids of the heterokonts are most closely related to members of the Cyanidium-Galdieria group of Porphyridiales and are not directly related to cryptophyte and haptophyte plastids. The phylogenies provide strong evidence for the independent origins of these "complex" algal plastids from different members of the Bangiophycidae.     

Failure of OKT3 monoclonal antibody to induce lymphocyte mitogenesis: a familial defect in monocyte helper function

Monoclonal antibodies to the T3 molecule on human T cells have mitogenic activity. Although anti-T3 antibodies of the IgG1 subclass (e.g., UCHT1) induce mitogenesis in lymphocyte cultures from only 60 to 70% of normal donors, antibodies of Ig2a subclass (e.g., OKT3) invariably have been found to be mitogenic in all subjects tested up to the present. This paper describes a family (a mother, six daughters, and one son) in which five members failed to respond mitogenically to OKT3 although the proportion of OKT3-reactive cells in their peripheral blood was normal. Mitogenic responses to PHA, Con A, and PWM were normal. Five members comprising four OKT3 nonresponders were also unresponsive to UCHT1. Unresponsiveness to OKT3 and unresponsiveness to UCHT1 were not absolutely linked to each other, nor were they linked to an HLA haplotype inherited from the mother. Upon stimulation by OKT3, lymphocyte preparations from OKT3-nonresponders failed to produce interleukin 2 (IL 2) and to display IL 2 receptors. OKT3 unresponsiveness was due to defective monocyte help: thus, responsiveness to OKT3 of T cells from an OKT3-nonresponder was restored by the addition of monocytes from an HLA-identical sister who had a normal response to OKT3. Inversely, T cells from the OKT3 responder had no reactivity to OKT3 when cultured in the presence of monocytes from an HLA-identical, OKT3-nonresponsive sister. Unresponsiveness to OKT3 could not be overcome by the addition of phorbol myristate acetate to the cultures. These data on a familial, non-HLA-linked deficiency of monocytes to exert their auxiliary function provide better insight into the mechanism of anti-T3-induced T cell activation.     

Phylogenetic Relationships of the Nassulida Within the Phylum Ciliophora Inferred from the Complete Small Subunit rRNA Gene Sequences of Furgasonia blochmanni, Obertrumia georgiana, and Pseudomicrothorax dubius

ABSTRACT. Using comparisons of complete small subunit rRNA sequences from the ciliated protozoans Furgasonia blochmanni, Obertrumia georgiana , and Pseudomicrothorax dubius we inferred the phylogenetic position of the Nassulida (Class Nassophorea) within the Ciliophora. In distance matrix analyses the Nassulida share a common ancestry with the colpodean ciliate Colpoda inflata. Distance matrix and parsimony methods convincingly demonstrate that the Nassulida plus Colpodida are members of a complex ciliate assemblage that also includes the oligohymenophorans and phyllopharyngeans. These phylogenetic inferences are largely congruent with recent analyses of 23S-like rRNA gene sequences and morphogenetic features. Groups traditionally thought to represent ancestral lineages now appear as highly derived ciliates. In contrast, heterotrichs which were considered to represent a highly evolved group, diverge at the base of the ciliates.     

Molecular phylogenetics of 'river dolphins' and the baiji mitochondrial genome

It is well known that the classical river dolphins are not a natural group, but up to now the phylogenetic relationships among them are not very clear because different views have been referred from different studies. In the present study, we determined the complete nucleotide sequence of the mitochondrial (mt) genome of the baiji (Lipotes vexillifer), the most endangered cetacean species, and conducted phylogenetic analyses for the classical river dolphins based on data from cetacean mitochondrial genomes available. In our analyses, the classical river dolphins split into two separate lineages, Platanista and Lipotes+(Inia+Pontoporia), having no sister relationship with each other, and the Platanista lineage is always within the odontocete clade instead of having a closer affinity to Mysticeti. The position of the Platanista is more basal, suggesting separate divergence of this lineage well before the other one. The Lipotes has a sister relationship with Inia+pontoporia, and they together formed the sister group to the Delphinoidea. This result strongly supports paraphyly of the classical river dolphins, and the nonplatanistoid river dolphins do represent a monophyletic grouping, with the Lipotidae as the sister taxa to (Iniidae+Pontoporiidae), and is well congruent with the studies based on short interspersed repetitive elements (SINEs).     

TRIBAL INTERRELATIONSHIPS OF THE ASTERACEAE

Abstract— A cladistic analysis involving 27 tribes and subtribes of Asteraceae and 81 characters is presented. The terminal taxa are mainly those of present tribal classification, though some apparently poly- and paraphyletic tribes, notably the Mutisieae and the Inuleae, have been represented by sub-tribal taxa. Characters are assembled from all available sources. Corolla types, styles and stamens have provided many characters. The Lobeliaceae are used as an outgroup and are considered as the most probable sister group of the Asteraceae. There is a basal dichotomy in the family, the Mutisieae-Barnadesiinae being the monophyletic sister group of the remaining major, also monophyletic part of the family. The recent family division into two subfamilies about equal in size, the Cichorioideae and the Asteroideae, neither represents a basal dichotomy nor a sister group relationship within the Asteraceae. The Asteroideae are monophyletic and have their sister group within the paraphyletic Cichorioideae. Interrelationships among the cichorioid tribes are still unclear. The Lactuceae, Eremothamneae, Vernonieae and Liabeae may be one monophyletic group, and the Arctoteae, Carlineae, Echinopsideae and Cardueae another. The Mutisieae are a paraphyletic grade at the base of the family. Within the subfamily Asteroideae tribal interrelationships are also rather unclear. The Anthemideae and the Heliantheae sensu lato (including the Helenieae, Tageteae, Coreopsideae and all helenioid/helianthoid representatives sometimes placed in the Senecioneae) may be sister groups. The Heliantheae appear to be monophyletic and there is little support for the hypothesis that other tribes are derived from or have their sister group within the Heliantheae. The Astereae and the Eupatorieae may be sister groups, though a closer relationship between the Eupatorieae and the Heliantheae is possible. The Inuleae are a paraphyletic grade group at the base of the subfamily Asteroideae in the same way as the Mutiseae are a grade group at the base of the family.     

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.     

Phylogeny and biogeography of the Malagasy and Australasian rainbowfishes (Teleostei: Melanotaenioidei): Gondwanan vicariance and evolution in freshwater

Phylogenetic relationships of the Malagasy and Australasian rainbowfishes are investigated using 4394 characters derived from five mitochondrial genes (12S, 16S, tRNA-Valine, ND5, and COI), three nuclear genes (28S, histone H3, and TMO-4c4), and 102 morphological transformations. This study represents the first phylogenetic analysis of the endemic Malagasy family Bedotiidae and includes a nearly complete taxonomic review of all nominal species, as well as numerous undescribed species. Simultaneous analysis of the molecular and morphological datasets results in two equally most parsimonious trees. Results indicate that Bedotiidae (Bedotia+Rheocles) and Bedotia are monophyletic, whereas Rheocles is paraphyletic with the inclusion of two recently described species from northeastern Madagascar, R. vatosoa, and R. derhami. Rheocles vatosoa and R. derhami are sister taxa, and this clade is recovered as the sister group to Bedotia. The remaining species of Rheocles are not sexually dimorphic and comprise a clade that is recovered as the sister group to Bedotia+(R. derhami+R. vatosoa), all of which are sexually dichromatic, and sexually dimorphic for pigmentation and fin development. Three geographically distinct clades are recovered within Bedotia, one comprising species with distributions ranging from mid- to southeastern Madagascar, another including species restricted to eastern drainages north of the Masoala Peninsula, and a third comprising taxa with distributions extending from the Masoala Peninsula south to the Ivoloina River. The Australian/New Guinean melanotaeniids are monophyletic and are recovered as the sister group to Bedotiidae. The Australasian Telmatherinidae and Pseudomugilidae comprise a clade that is recovered as the sister group to the Melanotaeniidae-Bedotiidae clade. This sister-group relationship between Malagasy bedotiids and a clade restricted to Australia-New Guinea, and the absence of a close relationship between bedotiids and African or Mascarene atheriniforms, is congruent with the break-up of Gondwana, not a scenario reliant on Cenozoic trans-oceanic dispersal. Finally, results of the phylogenetic analysis indicate that Atheriniformes is polyphyletic and further corroborate recent morphological hypotheses, which have recovered Bedotiidae in a derived position within Atherinoidei.