Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept

Based on embryological and morphological evidence, Lophophorata was long considered to be the sister or paraphyletic stem group of Deuterostomia. By contrast, molecular data have consistently indicated that the three lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida, are more closely related to trochozoans (annelids, molluscs and related groups) than to deuterostomes. For this reason, the lophophorate groups and Trochozoa were united to Lophotrochozoa. However, the relationships of the lophophorate lineages within Lophotrochozoa are still largely unresolved. Maximum-likelihood and Bayesian analyses were performed based on a dataset comprising 11,445 amino acid positions derived from 79 ribosomal proteins of 39 metazoan taxa including new sequences obtained from a brachiopod and a phoronid. These analyses show that the three lophophorate lineages are affiliated with trochozoan rather than deuterostome phyla. All hypotheses claiming that they are more closely related to Deuterostomia than to Protostomia can be rejected by topology testing. Monophyly of lophophorates was not recovered but that of Bryozoa including Ectoprocta and Entoprocta and monophyly of Brachiozoa including Brachiopoda and Phoronida were strongly supported. Alternative hypotheses that are refuted include (i) Brachiozoa as the sister group of Mollusca, (ii) ectoprocts as sister to all other Lophotrochozoa including Platyzoa, and (iii) ectoprocts as sister or to all other protostomes except chaetognaths.     

Phylogenetic evidence for the classification of Acidothermus cellulolyticus into the subphylum of actinomycetes

Abstract The primary structure of the 16S rDNA of Acidothermus cellulolyticus , a cellulolytic, asporogenous rod isolated from a hot spring, was determined by automated sequence analysis. This Gram-variable organism is not related to members of other aerobic thermophilic genera found in similar environments, such as Thermus and Thermomicrobium , but clusters within the phylogenetically defined radiation of the actinomycetes where it represents an individual subline of descent.     

Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian

Concatenated SSU (18S) and partial LSU (28S) sequences (2 kb) from 12 ingroup taxa, comprising 2 phoronids, 2 members of each of the craniid, discinid, and lingulid inarticulate brachiopod lineages, and 4 rhynchonellate, articulate brachiopods (2 rhynchonellides, 1 terebratulide and 1 terebratellide) were aligned with homologous sequences from 6 protostome, deuterostome and sponge outgroups (3964 sites). Regions of potentially ambiguous alignment were removed, and the resulting data (3275 sites, of which 377 were parsimony-informative and 635 variable) were analysed by parsimony, and by maximum and Bayesian likelihood using objectively selected models. There was no base composition heterogeneity. Relative rate tests led to the exclusion (from most analyses) of the more distant outgroups, with retention of the closer pectinid and polyplacophoran (chiton). Parsimony and likelihood bootstrap and Bayesian clade support values were generally high, but only likelihood analyses recovered all brachiopod indicator clades designated a priori. All analyses confirmed the monophyly of (brachiopods+phoronids) and identified phoronids as the sister-group of the three inarticulate brachiopod lineages. Consequently, a revised Linnean classification is proposed in which the subphylum Linguliformea comprises three classes: Lingulata, ‘Phoronata’ (the phoronids), and ‘Craniata’ (the current subphylum Craniiformea). Divergence times of all nodes were estimated by regression from node depths in non-parametrically rate-smoothed and other chronograms, calibrated against palaeontological data, with probable errors not less than 50 My. Only three predicted brachiopod divergence times disagree with palaeontological ages by more than the probable error, and a reasonable explanation exists for at least two. Pruning long-branched ingroups made scant difference to predicted divergence time estimates. The palaeontological age calibration and the existence of Lower Cambrian fossils of both main brachiopod clades together indicate that initial genetic divergence between brachiopod and molluscan (chiton) lineages occurred well before the Lower Cambrian, suggesting that much divergence between metazoan phyla took place in the Proterozoic.

See also Electronic Supplement at: http://www.senckenberg.de/odes/05-11.htm     

Monophyly of elapid snakes (Serpentes: Elapidae). An assessment of the evidence

The defining morphological characters of the family Elapidae are analysed in an attempt to evaluate whether the front-fanged, proteroglyphous, snakes constitute a natural (monophyletic) group or whether proteroglyphy is more likely to be a condition achieved independently by a number of higher snake lineages. The evidence relating to presumed elapids whose affinities have been questioned, namely a South African genus Homoroselaps and New World proteroglyphs (Micrurus and Micruroides) , is examined. It concluded that Homoroselaps is a genuinely equivocal case, the evidence for its inclusion in the Elapidae is balanced by features which suggest that it is more closely related to the Aparallactinae. However, Micrurus and Micruroides seem clearly to be more closely related to undisputed elapids than to any other caenophidians. It is suggested that, at least for the present, the family Elapidae be retained in its broad sense to include all proteroglyphous snakes.     

The phylogeny and a new classification of the gingers (Zingiberaceae): evidence from molecular data

The pantropical Zingiberaceae is the largest family in the order Zingiberales with 53 genera and over 1200 species. Classifications of the family first proposed in 1889 and refined by others since that time recognize four tribes (Globbeae, Hedychieae, Alpinieae, and Zingibereae) based on morphological features, such as number of locules and placentation in the ovary, development of staminodia, modifications of the fertile anther, and rhizome-shoot-leaf orientation. New phylogenetic analyses based on DNA sequences of the nuclear internal transcribed spacer (ITS) and plastid matK regions suggest that at least some of these morphological traits are homoplasious and three of the tribes are paraphyletic. The African genus Siphonochilus and Bornean genus Tamijia are basal clades. The former Alpinieae and Hedychieae for the most part are monophyletic taxa with the Globbeae and Zingibereae included within the latter. The results of these phylogenetic investigations are used to propose a new classification of the Zingiberaceae that recognizes four subfamilies and four tribes: Siphonochiloideae (Siphonochileae), Tamijioideae (Tamijieae), Alpinioideae (Alpinieae, Riedelieae), and Zingiberoideae (Zingibereae, Globbeae). Morphological features congruent with this classification and the taxonomic status of various monotypic genera are discussed.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Monophyly or polyphyly of the order Rodentia: Possible conflict between morphological and molecular interpretations

Recent analyses of amino acid sequence data from selected proteins inCavia, Rattus, Homo, Bos, Sus, and a few additional rodents and other eutherians suggested that Rodentia is not a monophyletic taxon and thatCavia and other hystricognaths may have branched off earlier than the separation between Muroidea and Primates during mammalian evolution. Because this hypothesis of polyphyly is contrary to the otherwise unanimous recognition of rodent monophyly, we have reevaluated the morphological and developmental evidence from the cranium, dentition, postcranial skeleton, and fetal membranes for the taxa Hystricognathi, Muroidea, other Rodentia, Primates, Artiodactyla, and Lagomorpha, as well as for the eutherian morphotype. Our character analyses provide strong corroboration for the traditional hypothesis of rodent monophyly and lend additional support to the suggestion that Lagomorpha is the sister taxon of Rodentia. Our survey of published molecular data furnishes little or no support for the proposed hypothesis of rodent polyphyly. We conclude that this hypothesis is the result of poor sampling of sequence data from rodents and other eutherians, rather than any inherent difficulties in the use of molecular evidence for the assessment of mammalian evolution. The available molecular data suggest thatCavia differs considerably from other hystricognaths in many proteins, but the reasons for this remain to be investigated.     

Phylogeny of earwigs (Insecta: Dermaptera) based on molecular and morphological evidence: reconsidering the classification of Dermaptera

Abstract. Dermaptera (earwigs) is a cosmopolitan order of insects, the phylogenetic relationships of which are poorly understood. The phylogeny of Dermaptera was inferred from large subunit ribosomal (28S), small subunit ribosomal (18S), histone-3 (H3) nuclear DNA sequences, and forty-three morphological characters. Sequence data were collected for thirty-two earwig exemplar taxa representing eight families in two suborders: Hemimeridae (suborder Hemimerina); Pygidicranidae, Anisolabididae, Labiduridae, Apachyidae, Spongiphoridae, Chelisochidae and Forficulidae (suborder Forficulina). Eighteen taxa from ten additional orders were also included, representing Ephemeroptera, Odonata, Orthoptera, Phasmida, Embiidina, Mantodea, Isoptera, Blattaria, Grylloblattodea and Zoraptera. These data were analysed via direct optimization in poy under a range of gap and substitution values to test the sensitivity of the data to variations in parameter values. These results indicate that the epizoic Hemimerus is not sister to the remaining Dermaptera, but rather nested as sister to Forficulidae + Chelisochidae. These analyses support the paraphyly of Pygidicranidae and Spongiphoridae and the monophyly of Chelisochidae, Forficulidae, Anisolabididae and Labiduridae.     

Halosarpheia unicellularis sp. nov. (Halosphaeriales, Ascomycota) based on morphological and molecular evidence

Halosarpheia unicellularis sp. nov. is described from decayed attached wood ofAvicennia marina collected from two mangrove sites in the Red Sea, Egypt. The ascomycete is compared with other marine taxa having ascospores with polar unfurling appendages. It is also compared with other marine genera with oval, round or ellipsoid hyaline, unicellular ascospores, but for which appendages have not been reported. Molecular data confirms the assignment of the fungus toHalosarpheia which forms a clade with the type speciesHalosarpheia fibrosa.     

Phylogeny of the tribe Abrotrichini (Cricetidae,Sigmodontinae): integrating morphological and molecular evidence into a new classification

The tribe Abrotrichini (five genera and 14 living species) is a small clade within the speciose subfamily Sigmodontinae (Rodentia, Cricetidae), representing one of the extant successful radiations of mammals at southern high latitudes of the Neotropics. Its distribution is mostly Andean, reaching its greatest diversity in southern Argentina and Chile. We evaluate the phylogenetic relationships within this tribe through parsimony and Bayesian approaches based on 99 morphological characters (including 19 integumental characters, 38 skull characters, 31 dental characters, three postcranial skeletal characters, seven from the male accessory glands and phallus and one from the digestive system) and six molecular markers (one mitochondrial and five nuclear). We include representatives of all, except one, of the currently recognized species of living Abrotrichini plus one fossil form. Based on total evidence, we recovered a primary division between the genus Abrothrix and a group including the long‐clawed Abrotrichini, Chelemys, Geoxus, Notiomys and Pearsonomys. Both clades are recognized and named here as subtribes. The large degree of morphological variation observed within Abrothrix suggests that species in the genus fall into four groups, which we recognize as subgenera. In addition, the two known species of Chelemys do not form a monophyletic group, and Geoxus was recovered as paraphyletic with respect to Pearsonomys. To reconcile classification and phylogenetics, we describe a new genus for Chelemys macronyx and include Pearsonomys as a junior synonym of Geoxus. Our results highlight the importance of both morphology and molecules in resolving the phylogenetic relationships within this tribe. Based on biogeographical analyses, we hypothesize that Abrotrichini originated in south‐western South America by vicariance and then diversified mostly by successive dispersal events.     

On the organization of the lophophore in phoronids (Lophophorata: Phoronida)

The organization of the lophophore is the main feature used for the identification of phoronid species. The structure of the lophophore and tentacles in seven phoronid species (Phoronis ovalis, P. ijimai, P. hippocrepia, P. svetlanae, P. australis, Phoronopsis harmeri, and Ph. malakhovi) collected in different areas of the World Ocean was studied. Two new patterns of the phoronid lophophore structure were found: “transition to horseshoe-shaped” (as in P. ovalis from Aniva Bay and in P. ijimai from the coast of Iturup Island, Sea of Okhotsk) and “transition to spiral” (in burrowing specimens P. hippocrepia from Aniva Bay, P. svetlanae and Ph. harmeri from Vostok Bay, Sea of Japan). For the first time it was shown that phoronid species with different types of the lophophore structure possess different kinds of tentacles. Thus, five types of phoronid tentacles were identified that vary in the shape of their cross section: rounded, oval, ellipsoid, rectangular, and skittle-shaped. A correlation was found between lophophore organization and the type of tentacles in phoronids. A table of the correlation between body size, lophophore organization, tentacle structure, and mode of life in different phoronid species is proposed.     

Morphogenetic regulation in the shells of bivalves and brachiopods: evidence from the geometry of the spiral

Ackerly. S. C. 1992 07 15: Morphogenetic regulation in the shells of bivalves and brachiopods: evidence from the geometry of the spiral.
Analyses of the spiral geometry in shells of the mollusc Pecten maximus and the brachiopod Terebratulina retusa indicate a relative reduction in morphological variability within the population during growth. The spiral, as measured by a model of exponential radial expansion, tends to converge on a particular adult form, irrespective of irregularities during early growth phases. The recurrence of this pattern of variability in populations from two separate phyla (molluscs and brachiopods) suggests a common mechanism controlling shell form. Brachiopoda. Mollusca, coiling, spiral. morphogenetic regulation, growth .     

Monophyly of the Citharidae (Pleuronectoidei: Pleuronectiformes: Teleostei) with considerations of pleuronectoid phylogeny

The monophyly of Citharidae, the pleuronectoid family thought to be a transitional group between the Psettodoidei and other typical pleuronectoids, has been in question mainly because of the lack of recognized synapomorphies for the family. In this study, the citharid skeleton is described, and the monophyly of the family and its phylogenetic position within the Pleuronectoidei are reassessed following a phylogenetic analysis based on 45 osteological, myological, and external characters. The Citharidae was found to represent a monophyletic group, supported by six synapomorphies (e.g., first dorsal proximal radials firmly wedged into notch of blind side lateral ethmoid; anterior dorsal proximal radials tightly mutually attached; blind side posterior nostril considerably enlarged). Two previously recognized subfamilies, sinistral Citharinae and dextral Brachypleurinae, are invalid because of their nonmonophylies. Interrelationships of the pleuronectoids shown herein are discussed. Received: February 19, 2001 / Revised: July 10, 2001 / Accepted: July 23, 2001     

Primula jiugongshanensis sp. nov. (Primulaceae) from China,based on morphological and molecular evidence

Primula jiugongshanensis J. W. Shao, a new species from Mt Jiugongshan in Hubei Province, China, is described and illustrated. This species is a biennial glabrous herb with pinnately compound leaves, and affiliated to P. sect. Ranunculoides C. M. Hu. It is distinguished from other species of the section by outer simple leaves ovate, flowers distylous, corolla lobe apex conspicuously emarginate, and lack of bulblets. Molecular phylogenetic analysis of nrDNA internal transcribed spacer sequences (ITS) was conducted and the results also supported the recognition of P. jiugongshanensis as a new species. The species is known from only three separated unprotected populations and is categorized as ‘Endangered’ (EN).     

Uncovering an overlooked radiation: molecular phylogeny and biogeography of Madagascar's endemic river snails (Caenogastropoda: Pachychilidae: Madagasikara gen. nov.)

By analysing key morphological characters (with emphasis on shell, radula and stomach anatomy) and a partial fragment of the mitochondrial 16S rRNA gene (alignment length 860 bp), we examined patterns of diversity and differentiation of a previously overlooked radiation of Madagascan pachychilid freshwater gastropods. These analyses resulted in the discovery of three new species in addition to the two species that were already recognized. The complex nomenclatural and taxonomic implications are discussed and the finding of a viviparous reproductive mode in at least one among otherwise oviparous species is reported. Using a mitochondrial phylogeny that includes all currently accepted pachychilid genera and a strict molecular clock approach, we address the historical biogeography of the Madagascan species with respect to vicariant versus dispersalist biogeographical models. Using two alternative calibrations that were previously suggested for other gastropods, the molecular clock tree suggested that the origin of the Pachychilidae dates back to no more than 50 Mya, whereas the origin of the Madagascan lineage is estimated to date to a period between 15.6–31.5 Mya. These estimates are approximately concurrent with the dating of colonization events in a number of other Madagascan animal taxa. The pachychilid radiation on Madagascar appears not to be older than 3–5 Mya. Thus, although the global patterns of pachychilid distribution have earlier been interpreted to suggest a Gondwanan origin of the family, the present study does not support this postulate. Neither the topology of the molecular phylogeny, nor the timing of events as suggested from a molecular clock were found to be congruent with a vicariance scenario within the framework of Gondwanan fragmentation during the Mesozoic but, instead, imply overseas dispersal during the Cenozoic. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 867–894.     

Molecular taxonomy and phylogeny of the Geodiidae (Porifera, Demospongiae, Astrophorida) – combining phylogenetic and Linnaean classification

Cárdenas, P., Rapp, H. T., Schander, C. & Tendal, O. S. (2009). Molecular taxonomy and phylogeny of the Geodiidae (Porifera, Demospongiae, Astrophorida) – combining phylogenetic and Linnaean classification.—Zoologica Scripta, 39, 89–106. According to the fossil records, the Geodiidae represents one of the oldest families of demosponges (Phylum Porifera). There are approximately 220 described extant species, geographically and bathymetrically widely distributed around the world. Species of this family all share a two-layered cortex with ball-shaped spicules called ‘sterrasters’ in the endocortex. However, molecular studies have questioned the monophyly of the group. Moreover, the evolutionary history and the intrafamily relationships of the Geodiidae are not fully resolved. Using a partial sequence of the cytochrome c oxidase subunit 1 (COI) gene and a partial sequence of the 28S rDNA gene (D1–D2 domains), we present the first molecular phylogeny focusing on this group. The congruent results from the two gene fragments suggest that (i) the Geodiidae is monophyletic, (ii) the Erylinae/Geodinae subdivision sensu Sollas, 1888 is valid and that (iii) Isops and Sidonops are junior synonyms of Geodia. The synonymization of Isops and Sidonops implies that the oscule/pore morphology as a diagnostic character should be abandoned. Geodia hentscheli nom. nov. has been given for Geodia mesotriaena ( Hentschel, 1929 ). This study served as the basis for a revised phylogenetic classification of the Geodiidae. Well-supported clades led to the establishment of clade names following the PhyloCode. The Geodinae clade is strongly supported and notably composed of Depressiogeodia, Cydonium and Geodia. A morphological synapomorphy of Geodinae is the presence of euasters in the ectocortex. The Erylinae (Erylus, Penares, Caminus and Pachymatisma) form a strongly supported monophyletic group with three morphological synapomorphies: (i) loss of anatriaenes and protriaenes, (ii) microrhabds (or spherules) in the ectocortex and (iii) short-shafted triaenes. The Erylus monophyly is ambiguous. Erylus species are distributed in three well-supported clades. Finally, spicule homology in the cortex of the Geodiidae is discussed.     

The Linnaean species of the family Tephritidae (Insecta: Diptera)

Linnaeus described nine species of Musca now placed in the Tephritidae. The Linnaean Collection was examined; a syntype of Tephritis hyoscyami and a possible syntype of Urophora solstitialis were identified. Syntypes of Tephritis arnicae, Urophora cardui and Rhagolelis cerasi were not found; specimens illustrated by Aldrovandi and de Reaumur are designated as lectotypes. No syntypic material of Euleia heracleii, Oxyna parietina, Terellia serratulae or Ensina sonchi could be found.     

Corynoplastis japonica gen. et sp. nov. and Dixoniellales ord. nov. (Rhodellophyceae,Rhodophyta) based on morphological and molecular evidence

A new unicellular red alga, Corynoplastis japonica gen. et sp. nov., is described from Tobishima, Japan. Cells are spherical, 18–33 µm in diameter, pale purple to brownish red and surrounded by a mucilaginous sheath. A single chloroplast with many lobes extends from the cell periphery to the cell center. A peripheral thylakoid is present. A pyrenoid occurs at each innermost chloroplast lobe end and one or two thylakoids are present in the pyrenoid matrix. The nucleus is eccentric to peripheral and Golgi bodies are scattered throughout the cell and associated with endoplasmic reticulum. Cells have a slow random gliding motility. The low molecular weight carbohydrate mannitol is present in the cells. Molecular phylogenetic analysis indicates that this alga is closely related to members of the genus Rhodella. A new order, Dixoniellales, is established for Dixoniella, Neorhodella and Glaucosphaera based on molecular and ultrastructural evidence (Golgi bodies associated only with the nucleus). The redefined order Rhodellales in which Rhodella and Corynoplastis are placed is characterized ultrastructurally by Golgi bodies scattered throughout the cytoplasm and associated with endoplasmic reticulum.