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Molecular Phylogeny (molecular + phylogeny)
Selected AbstractsRAPID SPECIATION AND ECOLOGICAL DIVERGENCE IN THE AMERICAN SEVEN-SPINED GOBIES (GOBIIDAE, GOBIOSOMATINI) INFERRED FROM A MOLECULAR PHYLOGENYEVOLUTION, Issue 7 2003Lukas Rüber Abstract., The American seven-spined gobies (Gobiidae, Gobiosomatini) are highly diverse both in morphology and ecology with many endemics in the Caribbean region. We have reconstructed a molecular phylogeny of 54 Gobio-somatini taxa (65 individuals) based on a 1646-bp region that includes the mitochondrial 12S rRNA, tRNA-Val, and 16S rRNA genes. Our results support the monophyly of the seven-spined gobies and are in agreement with the existence of two major groups within the tribe, the Gobiosoma group and the Microgobius group. However, they reject the monophyly of some of the Gobiosomatini genera. We use the molecular phylogeny to study the dynamics of speciation in the Gobiosomatini by testing for departures from the constant speciation rate model. We observe a burst of speciation in the early evolutionary history of the group and a subsequent slowdown. Our results show a split among clades into coastal-estuarian, deep ocean, and tropical reef habitats. Major habitat shifts account for the early significant acceleration in lineage splitting and speciation rate and the initial divergence of the main Gobiosomatini clades. We found that subsequent diversification is triggered by behavior and niche specializations at least in the reef-associated clades. Overall, our results confirm that the diversity of Gobiosomatini has arisen during episodes of adaptive radiation, and emphasize the importance of ecology in marine speciation. [source] MOLECULAR PHYLOGENY OF DISCOSPORANGIUM MESARTHROCARPUM (PHAEOPHYCEAE) WITH A REINSTATEMENT OF THE ORDER DISCOSPORANGIALES,JOURNAL OF PHYCOLOGY, Issue 1 2007Hiroshi Kawai A molecular phylogenetic analysis of the little-studied filamentous brown alga Discosporangium mesarthrocarpum (Meneghini) Hauck using rbcL and partial 18S rDNA sequences revealed that the species forms a monophyletic clade with Choristocarpus tenellus (Kütz.) Zanardini that is sister to all other brown algae. Although D. mesarthrocarpum has unique disk-shaped plurilocular reproductive organs, D. mesarthrocarpum and C. tenellus share the following basic morphological features, which are considered to be plesiomorphic characters in the brown algae: (1) apical (and diffuse) growth; (2) uniseriate, subdichotomously branched filaments; (3) multiple chloroplasts per cell without pyrenoids; and (4) lack of heterotrichy and of phaeophycean hairs. The rbcL DNA sequence of an Australian D. mesarthrocarpum specimen showed considerable deviation from Mediterranean and Macaronesian specimens. Therefore, the presence of a second species in the genus is suggested; however, the taxonomic treatment of this putative species is not pursued in the present report. Regarding the higher-ranking systematic position of D. mesarthrocarpum, reinstatement of Discosporangiaceae and Discosporangiales is proposed, and the inclusion of Choristocarpaceae in the order is also suggested. Under short-day and long-day culture conditions at 15°C,25°C, Mediterranean D. mesarthrocarpum exhibited a direct type of life history, with a succession of uniseriate filamentous thalli bearing characteristic disk-shaped plurilocular zoidangia, but thalli did not survive at 10°C and below. [source] BIOCHEMICAL PHENOTYPES CORRESPONDING TO MOLECULAR PHYLOGENY OF THE RED ALGAE PLOCAMIUM (PLOCAMIALES, RHODOPHYTA): IMPLICATIONS OF INCONGRUENCE WITH THE CONVENTIONAL TAXONOMY,JOURNAL OF PHYCOLOGY, Issue 1 2006Tomomi Yano Among five species of the genus Plocamium Lamouroux distributed around Japan, P. cartilagineum (Linnaeus) Dixon, P. recurvatum Okamura and P. telfairiae (Hooker and Harvey) Harvey are often difficult to distinguish morphologically from each other. Our previous study demonstrated that P. recurvatum and P. telfairiae were divided into two groups, A and C, based on RUBISCO spacer sequence and that the specimens belonging to group C had acidic cell saps. In this study, we inferred evolutionary relationships of these Plocamium species from internal transcribed spacer sequence of the ribosomal RNA genes and obtained a similar topology to the RUBISCO spacer tree. Color of the dried specimens in the acidic group C was darker red than that in the non-acidic group A, although there was no difference in color in living thalli. The Br, concentration in the cell sap of the acidic group C was 20 times higher than that of the non-acidic group. We could not find any morphological differences to distinguish clearly between groups A and C despite exhaustive investigation of field-collected and cultured thalli in both P. recurvatum and P. telfairiae. These results suggest that the color of dried specimens and the composition of intracellular inorganic ions are significant criteria for interpreting phylogenetic relationships in Japanese Plocamium spp. [source] MORPHOLOGY, LIFE HISTORY, AND MOLECULAR PHYLOGENY OF STSCHAPOVIA FLAGELLARIS (TILOPTERIDALES, PHAEOPHYCEAE) AND THE ERECTION OF THE STSCHAPOVIACEAE FAM.JOURNAL OF PHYCOLOGY, Issue 6 2004The phenology, life history, ultrastructure of reproductive structures, and molecular phylogeny using rbcL and rDNA (5.8S, internal transcribed spacer 2, and partial 26S) gene sequences of Stschapovia flagellaris, endemic to the northwestern Pacific Ocean, were studied. This species was first classified in the order Delamareales together with Delamarea, Coelocladia, and Cladothele. Those three genera, however, were later transferred to Dictyosiphonales, whereas the systematic position of Stschapovia remained unclear. At Abashiri, Hokkaido, Japan, the species regenerated by forming a new erect thallus from a perennial crustose holdfast or by presumably parthenogenetic development of eggs released from the erect thallus. There was no alternation of generations. In winter, the monoecious erect thallus formed reproductive structures (i.e. plurilocular antheridia and oogonia) in the thickened part of the thallus. Sperm had a chloroplast with an eyespot and a long anterior and short posterior flagellum. Eggs contained numerous disc-shaped chloroplasts, physodes, and vacuoles. Neither sexual attraction of the presumptive sperm by eggs nor their sexual fusion was observed. Molecular phylogenetic analyses revealed the closest phylogenetic relationship between Stschapovia and Halosiphonaceae, and they grouped with Phyllariaceae and Tilopteridaceae (Tilopteridales s. s.). Stschapovia and Tilopteridaceae have several important morphological similarities: chloroplasts lacking pyrenoids, lack of sexual reproduction despite the release of obvious sperm, occurrence of monoecious gametophytes, and similarity in the early developmental pattern of the erect thallus. In conclusion, we propose the establishment of the new family Stschapoviaceae to accommodate Stschapovia and the placement of the family in the order Tilopteridales together with Tilopteridaceae, Halosiphonaceae, and Phyllariaceae. [source] TAXONOMY AND MOLECULAR PHYLOGENY OF THE RED ALGAL GENUS LENORMANDIA (RHODOMELACEAE, CERAMIALES),JOURNAL OF PHYCOLOGY, Issue 1 2002Louise E. Phillips The genus Lenormandia Sonder is currently composed of nine species from Australia and New Zealand. Some of these are well known, but others are rare and ill defined. Material of all nine species has been examined and found to fall into three discrete morphological groups forming highly supported clades on analysis of 18S rDNA sequences. The first group contains four Australian-endemic species and includes the type species L. spectabilis Sonder. Plants have a cleft apex that is not inrolled, a distinctive rhombic surface areolation pattern caused by a one- to two-layered medulla of interlocking cells, lack pseudopericentral cells, and produce their reproductive structures on the blade surfaces. The type species of the genus Lenormandiopsis, L. latifolia (Harvey et Greville) Papenfuss, was found to belong to this group and is thus returned to Lenormandia where it was originally placed. Species falling into the other two groups are removed to new genera that are being described separately. One extremely rare species of Lenormandia from southwestern Australia is transferred to the delesseriacean genus Phitymophora. [source] Molecular Phylogeny of Caryophyllidae s.l. Based on MatK Sequences with Special Emphasis on Carnivorous TaxaPLANT BIOLOGY, Issue 2 2000H. Meimberg Abstract: Despite intensive morphological, chemical and cladistic studies on Caryophyllidae, the circumscription of this subclass and the interfamilial relationships are still under discussion. Using comparative sequencing of the chloroplast matK gene, hypotheses of relationships between the carnivorous Droseraceae, Nepenthaceae and Dioncophyllaceae and ten other families of the Caryophyllidae s.l. were tested and compared with previously published cladograms based on rbcL, 18S rDNA and ORF2280 sequences. Parsimony analyses indicate two well-differentiated clades. One strongly supported clade comprises the carnivorous families Droseraceae and Nepenthaceae, along with its close relatives Dioncophyllaceae and Ancistrocladaceae. The second clade is restricted to the Polygonaceae, Plumbaginaceae, Tamaricaceae and Frankeniaceae. The Simmondsiaceae are more closely related to Caryophyllales and are at the base of the remaining taxa. Results of this analysis suggest that carnivory within Caryophyllidae s.l. has a monophyletic origin and, with the exception of Triphyophyllum, this syndrome was lost in the taxa of Dioncophyllaceae and Ancistrocladaceae. The exclusion of Drosophyllum from Droseraceae suggests no close relationship with this family. Finally, the data support a sister group relationship between the Plumbaginaceae and Polygonaceae and the Frankeniaceae and Tamaricaceae. An extensive survey of the rpl2 intron via PCR amplification indicates that the intron is absent from chloroplast genomes of Droseraceae and all taxa of Caryophyllales, but is present in Drosophyllum. Consequently, there is evidence for a multiple loss of the intron and strong support that Drosophyllum has affinities outside the Droseraceae. Our sequence data corroborate many aspects of recent cladistic analyses based predominantly on rbcL sequences. This study shows that matK sequences are useful for'phylogenetic inference among closely related members of Caryophyllidae. [source] Morphology, Ultrastructure, Molecular Phylogeny, and Autecology of Euplotes elegans Kahl, 1932 (Hypotrichida; Euplotidae) Isolated from the Anoxic Mariager Fjord, DenmarkTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2007M. V. JULIAN SCHWARZ ABSTRACT. The morphology, autecology, and molecular phylogeny of an euryhaline Euplotes isolate collected from the anoxic water column of the Mariager Fjord in Denmark were investigated. The isolate matches the original description of Euplotes elegans Kahl, 1932 very well. However, its dorsal silverline system is clearly distinct from the redescription of this species by Tuffrau. Thus, a neotypification is proposed for E. elegans Kahl, 1932. The oval-shaped cell has a mean size of 107 × 51 ,m and is characterized by 9.4 dorsolateral kineties, seven prominent dorsal ridges, large elongated ampullae, which encircle the dorsal kinetids, 18 kinetids in the middorsal row, nine frontoventral cirri, five transversal cirri, and three caudal cirri (two right caudal cirri and one left marginal cirrus). The dorsal silverline system is of the double type with the narrow polygons located on the right side of the dorsal kinetids. The ecological tolerances of this species to pH, salinity, temperature, and oxygen match the ambient environmental conditions of the sampling site. Molecular phylogeny was studied using small subunit rRNA (SSU rRNA) gene sequences. The molecular data cluster E. elegans with Euplotes raikovi, a member of the Euplotopsis group. The data suggest that the E. elegans,E. raikovi clade represents an isolated and deep branch at the base of the Euplotes tree. [source] Molecular Phylogeny of Stentor (Ciliophora: Heterotrichea) Based on Small Subunit Ribosomal RNA SequencesTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 1 2007YING-CHUN GONG ABSTRACT. To determine the phylogenetic position of Stentor within the Class Heterotrichea, the complete small subunit rRNA genes of three Stentor species, namely Stentor polymorphus, Stentor coeruleus, and Stentor roeseli, were sequenced and used to construct phylogenetic trees using the maximum parsimony, neighbor joining, and Bayesian analysis. With all phylogenetic methods, the genus Stentor was monophyletic, with S. roeseli branching basally. [source] Molecular Phylogeny and Surface Morphology of Colpodella edax (Alveolata): Insights into the Phagotrophic Ancestry of ApicomplexansTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 5 2003BRIAN S. LEANDER ABSTRACT. The molecular phylogeny of colpodellids provides a framework for inferences about the earliest stages in apicomplexan evolution and the characteristics of the last common ancestor of apicomplexans and dinoflagellates. We extended this research by presenting phylogenetic analyses of small subunit rRNA gene sequences from Colpodella edax and three unidentified eukaryotes published from molecular phylogenetic surveys of anoxic environments. Phylogenetic analyses consistently showed C. edax and the environmental sequences nested within a colpodellid clade, which formed the sister group to (eu)apicomplexans. We also presented surface details of C. edax using scanning electron microscopy in order to supplement previous ultrastructural investigations of this species using transmission electron microscopy and to provide morphological context for interpreting environmental sequences. The microscopical data confirmed a sparse distribution of micropores, an amphiesma consisting of small polygonal alveoli, flagellar hairs on the anterior flagellum, and a rostrum molded by the underlying (open-sided) conoid. Three flagella were present in some individuals, a peculiar feature also found in the microgametes of some apicomplexans. [source] Tracking island colonization history and phenotypic shifts in Indian Ocean bulbuls (Hypsipetes: Pycnonotidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2005BEN H. WARREN Molecular phylogenies of island organisms provide useful systems for testing hypotheses of convergent or parallel evolution, since selectively neutral molecular characters are likely to be independent of phenotype, and the existence of similar environments on multiple isolated islands provides numerous opportunities for populations to evolve independently under the same constraints. Here we construct a phylogenetic hypothesis for Hypsipetes bulbuls of the western Indian Ocean, and use this to test hypotheses of colonization pattern and phenotypic change among islands of the region. Mitochondrial sequence data were collected from all extant taxa of the region, combined with sequence data from relevant lineages in Asia. Data are consistent with a single Hypsipetes colonization of the western Indian Ocean from Asia within the last 2.6 Myr. The expansion of Hypsipetes appears to have occurred rapidly, with descendants found across the breadth of its western Indian Ocean range. The data suggest that a more recent expansion of Hypsipetes madagascariensis from Madagascar led to the colonization of Aldabra and a secondary colonization of the Comoros. Groupings of western Indian Ocean Hypsipetes according to phenotypic similarities do not correspond to mtDNA lineages, suggesting that these similarities have evolved by convergence or parallelism. The direction of phenotypic change cannot be inferred with confidence, since the primary expansion occurred rapidly relative to the rate of mtDNA substitution, and the colonization sequence remains uncertain. However, evidence from biogeography and comparison of independent colonization events are consistent with the persistence of a small grey continental bulbul in India and Madagascar, and multiple independent origins of large size and green plumage in insular island populations of the Comoros, Mascarenes and Seychelles. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85, 271,287. [source] Molecular phylogeny and phylogeography of flightless beetles Parechthistatus gibber and Hayashiechthistatus inexpectus (Coleoptera: Cerambycidae) inferred from mitochondrial COI gene sequencesENTOMOLOGICAL SCIENCE, Issue 2 2008Hiroshi NAKAMINE Abstract To elucidate the speciation patterns of two endemic flightless cerambycid beetles, Parechthistatus gibber and Hayashiechthistatus inexpectus, molecular phylogenetic analysis was carried out. A 1144 bp region of the cytochrome oxidase subunit I gene was sequenced for individuals from 51 local populations of these species. There were nine haplotype lineages of P. gibber, and H. inexpectus was included within a P. gibber lineage. These lineages were highly divergent and occurred in different regions. Based on previously published molecular change rates for the COI gene (1.5,2.3% per million years), the time of divergence of P. gibber COI haplotypes was inferred to be 3.0,4.6 million years ago, in the Pliocene. [source] Molecular phylogeny of Calyptratae (Diptera: Brachycera): the evolution of 18S and 16S ribosomal rDNAs in higher dipterans and their use in phylogenetic inferenceINSECT MOLECULAR BIOLOGY, Issue 5 2001X. Nirmala Abstract Sequences for nearly complete 18S rRNA and partial 16S rRNA genes were determined for sixteen species representing twelve calyptrate families. Two unique insertions are present in expansion regions of the 18S rDNA in nycteribiids. Alignments containing other dipteran rRNA genes provided good resolution at higher taxonomic level: monophyly of Calyptratae is well supported. While both 16S and 18S rDNA matrices produce unstable topologies within Calyptratae when analysed separately, their combination results in a tree with several robust and well supported nodes. Of three superfamilies recognized in recent classifications, the Hippoboscoidea is well supported by 16S rDNA and by combined matrices. The representatives of Muscoidea, Musca sp. and Antipoda sp., display a tendency to cluster within Oestroidea. The comparison of secondary structures of two variable regions indicates that Sarcophagidae are related to Calliphoridae rather than to Tachinidae. [source] Molecular phylogeny of Diabrotica beetles (Coleoptera: Chrysomelidae) inferred from analysis of combined mitochondrial and nuclear DNA sequencesINSECT MOLECULAR BIOLOGY, Issue 4 2001T. L. Clark Abstract The phylogenetic relationships of thirteen Diabrotica (representing virgifera and fucata species groups) and two outgroup Acalymma beetle species (Coleoptera: Chrysomelidae) were inferred from the phylogenetic analysis of a combined data set of 1323 bp of mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) and the entire second internal transcribed spacer region (ITS-2) of nuclear ribosomal DNA of 362 characters. Species investigated were D. adelpha, D. balteata, D. barberi, D. cristata, D. lemniscata, D. longicornis, D. porracea, D. speciosa, D. undecimpunctata howardi, D. u. undecimpunctata, D. virgifera virgifera, D. v. zeae, D. viridula, and outgroup A. blandulum and A. vittatum. Maximum parsimony (MP), minimum evolution (ME), and maximum likelihood (ML) analyses of combined COI and ITS-2 sequences clearly place species into their traditional morphological species groups with MP and ME analyses resulting in identical topologies. Results generally confer with a prior work based on allozyme data, but within the virgifera species group, D. barberi and D. longicornis strongly resolve as sister taxa as well as monophyletic with the neotropical species, D. viridula, D. cristata and D. lemniscata also resolve as sister taxa. Both relationships are not in congruence with the prior allozyme-based hypothesis. Within the fucata species group, D. speciosa and D. balteata resolve as sister taxa. Results also strongly supported the D. virgifera and D. undecimpunctata subspecies complexes. Our proposed phylogeny provides some insight into current hypotheses regarding distribution status and evolution of various life history traits for Diabrotica. [source] Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genesJOURNAL OF FISH BIOLOGY, Issue 9 2009W.-J. Chen Molecular variation in six nuclear genes provides substantive phylogenetic evidence for the recognition of a new cypriniform family, the Ellopostomatidae, to include the enigmatic Southern Asia loach genus Ellopostoma. The current six loach families form a monophyletic group, with the Nemacheilidae as the sister group to Ellopostomatidae; Vaillantellidae forms the sister group to all families exclusive of Botiidae. While the superfamily Cobitoidea includes eight families, the monophyly of this large clade within the Cypriniformes remains a vexing problem despite extensive molecular analyses and is in need of further investigation. [source] Molecular phylogeny of Turkish Trachurus species (Perciformes: Carangidae) inferred from mitochondrial DNA analysesJOURNAL OF FISH BIOLOGY, Issue 5 2008Y. Bektas Genetic variation among three species of Trachurus (T. trachurus, T. mediterraneus and T. picturatus) from Turkey was investigated by phylogenetic analysis of the entire mtDNA control region (CR) (862 bp, n = 182) and partial cytochrome (cyt) b (239 bp, n = 174) sequences. Individuals were collected at nine stations in four geographic locations: North-eastern Mediterranean Sea, Aegean Sea, Sea of Marmara and Black Sea. Polymerase chain reaction-direct sequencing of the CR and the partial cyt b genes produced 28 and 131 distinct haplotypes, respectively. Maximum likelihood, neighbour-joining and maximum parsimony methods produced similar tree topologies. The results of both CR and cyt b sequence analyses revealed the existence of several species-specific nucleotide sites that can be used to discriminate between the three species. Genetic distances indicated that T. mediterraneus and T. picturatus are more closely related to each other than either is to T. trachurus. Inter-nucleotide and intra-nucleotide diversities of T. picturatus were larger than those of T. mediterraneus and T. trachurus. There was no evidence of a geographical difference in haplotype frequencies of these two mtDNA regions to be clustered. [source] Molecular phylogeny of Enchytraeidae (Oligochaeta) indicates separate invasions of the terrestrial environmentJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2010Bent Christensen Abstract Enchytraeidae is a family of soil inhabiting small- to medium-sized oligochaete worms using degradable plant material as a food source and primarily adapted to terrestrial or semi-terrestrial environments. The molecular phylogeny based upon both mitochondrial and nuclear genes indicates early segregations of the two genera Enchytraeus and Lumbricillus leaving the remaining genera included in this study as a later segregated major monophyletic branch. Extant members of the two former genera dominate in decaying seaweed in the littoral zone along the sea although members of in particular the genus Enchytraeus have also invaded other habitats. Historically the littoral zone of the sea is undoubtedly the first terrestrial or semi-terrestrial habitat where dead plant material accumulates to any greater extent and Enchytraeus and Lumbricillus may represent early successful attempts to exploit this resource. Inland soils probably had to await the emergence of land plants in order to provide a similar food resource and here the major branch of enchytraeid genera diversified into a high number of species in the numerous decomposer networks of this varied environment. A subdivision into the genera Enchytraeus and Lumbricillus on the one hand and a branch of mainly inland genera on the other is supported by differences in two somewhat neglected morphological features. Firstly, in Enchytraeus and Lumbricillus the testes are enclosed in a testis sac within which the male cells mature, by one possible exception a unique feature among Oligochaeta, The other enchytraeid genera studied and Oligochaeta in general lack this sac and the male cells mature directly in the cavity of the testicular segment. Secondly, species of Enchytraeus and Lumbricillus generally have a higher reproductive output than species of the inland terrestrial branch and this may represent an adaptation to the unpredictable littoral zone compared to the more stable nature of inland habitats. In the older literature the genus Mesenchytraeus is considered to have a basic position within the entire family but our molecular data do not support this expectation. In Enchytraeidae the nephridia are elaborate organs of a characteristic and constant shape covering species from different genera in a pattern following the molecular phylogeny. Other much used morphological features such as shape of setae, anteclitellar origin of the dorsal vessel and various modifications of the intestine have arisen more than once. Zusammenfassung Enchytraeidae sind eine Familie kleiner bis mittelgroßer edaphischer Oligochaeten, welche abbaubares Pflanzenmaterial als Nahrungsquelle nutzen und primär an terrestrische oder semiterrestrische Lebensräume angepaßt sind. Die hier vorgestellte, auf mitochondrialen und nukleären Genen beruhende molekulare Phylogenie indiziert eine frühe Abtrennung der beiden Gattungen Enchytraeus und Lumbricillus und beläßt die übrigen der in dieser Studie untersuchten Gattungen als eine später abgezweigte monophyletische Großgruppe. Rezente Glieder der beiden erwähnten Gattungen dominieren in verrottendem Strandanwurf des Meereslitorals, obwohl Arten insbesondere der Gattung Enchytraeus auch andere Lebensräume erobert haben. Historisch gesehen ist das Meereslitoral zweifelsohne das erste terrestrische oder semiterrestrische Habitat, in dem totes Pflanzenmaterial in größerem Ausmaß akkumulierte, und Enchytraeus und Lumbricillus könnten frühe erfolgreiche Versuche der Nutzung dieser Ressource darstellen. Festlandsböden dagegen bedurften wahrscheinlich der Entwicklung von Landpflanzen, um eine vergleichbare Nahrungsquelle zur Verfügung zu stellen, und hier diversifizierte sich der Hauptzweig der Enchytraeidengattungen in viele Arten in den diversen Zersetzernetzen dieses vielgestaltigen Lebensraums. Eine Unterteilung in die Gattungen Enchytraeus und Lumbricillus auf der einen Seite und einen Zweig mit vorwiegend terrestrischen Gattungen auf der anderen wird durch zwei bislang eher vernachlässigte morphologische Merkmale gestützt. Erstens, bei Enchytraeus und Lumbricillus wird der Hoden von einem Testis-Sack, in dem die männlichen Zellen reifen, umschlossen. Dies ist mit einer möglichen Ausnahme einzigartig bei Oligochaeten. Bei den übrigen untersuchten Enchytraeidengattungen und bei Oligochaeten generell fehlt dieser Sack, und die männlichen Zellen reifen unmittelbar in der Körperhöhle des Hodensegmentes. Zweitens, die Reproduktionsrate von Enchytraeus und Lumbricillus ist generell höher als die der Arten des Festlandszweigs. Dies könnte eine Anpassung an die im Vergleich zu Festlandsböden instabileren Bedingungen des Meereslitorals bedeuten. In der älteren Literatur wird der Gattung Mesenchytraeus eine basale Position innerhalb der gesamten Familie zugewiesen, aber unsere molekularen Daten stützen diese Annahme nicht. Die Nephridien der Enchytraeiden sind komplexe Organe mit einer charakteristischen und artübergreifend konstanten Form, deren gattungsmäßige Abwandlungen der molekularen Phylogenie entsprechen. Andere oft verwendete morphologische Merkmale wie Borstenform, anteclitellarer Ursprung des Dorsalgefäßes und verschiedene Darmmodifikationen sind mehr als einmal entstanden. [source] Molecular phylogeny of grapsoid crabs (Decapoda, Brachyura) and allies based on two mitochondrial genes and a proposal for refraining from current superfamily classificationJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2006C. D. Schubart Abstract Grapsoid and ocypodoid crabs receive a lot of attention in the literature due to their predominance and important role as primary and secondary consumers in intertidal as well as supratidal marine habitats. They are especially species-rich in the tropics, where they have been found to repeatedly invade terrestrial and freshwater habitats. However, the systematics of the crabs belonging to these two superfamilies is still not settled, despite recent steps clarifying phylogenetic relationships and introducing new taxa. In this study, a molecular phylogeny of grapsoid crabs primarily based on East African representatives is constructed based on DNA sequences of the mitochondrial small and large ribosomal subunits (12S and 16S rRNA), thus complementing previous molecular taxonomic studies that had been carried out with the American and East Asian fauna. In addition, selected representatives of all ocypodoid families and subfamilies were included. The monophyly of Grapsidae, Ocypodidae (sensu stuctu), Sesarmidae and Varunidae is well confirmed, if the genera Cyclograpsus, Helice are considered Varunidae and Euchirograpsus a Plagusiidae, as previously suggested. The monophyly of the family Gecarcinidae cannot be supported with our data. The family Plagusiidae in its present composition is polyphyletic. Special attention was given to the large family Sesarmidae, which has many endemic genera in the Indo-West Pacific. According to this study, two of the most speciose genera, Chiromantes and Parasesarma, are not monophyletic and need to be redefined. On the higher taxonomic level, it becomes evident that both superfamilies, Grapsoidea and Ocypodoidea, are not monophyletic in their current composition, as exemplified by a proposed sister group relationship of Varunidae and Macrophthalmidae. These results confirm those from previous molecular studies and we therefore propose to refrain from the traditional use of the Grapsoidea and Ocypodoidea as monophyletic superfamilies and treat the constituent families separately. Riassunto I granchi appartenenti alle superfamiglie Grapsoidea e Ocypodoidea da sempre sono oggetto di notevole interesse scientifico a causa del loro importante ruolo ecologico negli ambienti intertidali o sopratidali. Le due superfamiglie sono particolarmente rappresentate, in termini di numero di specie e d'abbondanza relativa, nelle zone tropicali e subtropicali, dove hanno invaso ripetutamente anche ambienti dulcacquicoli e terrestri. La sistematica delle specie appartenenti a queste due superfamiglie è ancora lontana dall'essere completamente risolta, nonostante studi molecolari recenti abbiano chiarito specifiche relazioni filogenetiche e definito nuovi taxa. Questo studio ha ricostruito la filogenesi di alcune specie di Grapsoidea dell'Africa Orientale sequenziando una porzione delle due subunità ribosomali del DNA mitocondriale (12S e 16S rRNA), confermando e completando precedenti studi molecolari condotti su specie americane e asiatiche. In questo studio sono stati inclusi anche rappresentanti di tutte le famiglie e sottofamiglie di ocipodidi. I nostri risultati confermano la monofilia della famiglia Grapsidae, Ocypodidae (sensu stuctu) Sesarmidae e Varunidae a condizione che, secondo quanto recentemente suggerito, i generi Cyclograpsus e Helice siano rimossi dalla famiglia Sesarmidae ed attribuiti ai Varunidae, ed Euchirograpsus dalla famiglia Varunidae ai Plagusiidae. Invece, i nostri dati supportano solo debolmente o non supportano per niente la monofilia della famiglia Gecarcinidae. La famiglia Plagusiidae è probabilmente polifiletica. Questo studio pone inoltre particolare attenzione alle relazioni interne alla famiglia Sesarmidae che include molti generi endemici nell'area Indo-Pacifica occidentale. Sulla base dei nostri dati, i generi Chiromantes, Parasesarma e Perisesarma sono polifiletici e necessitano di essere ridefiniti. Infine, i risultati di questo studio mostrano chiaramente che la superfamiglia Grapsoidea e Ocypodidea non sono monofiletiche così come attualmente definite, come evidenziato dalla relazione di sister group tra Varunidae e Macropthalmidae. Questo conferma i risultati di precedenti studi molecolari e pertanto proponiamo di non attenersi al tradizionale uso delle superfamiglie Grapsoidea ed Ocypodoidea. [source] Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNAJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2004J. Zhou Abstract The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp ,Cyprinus carpio haematopterus, Yuanjiang River wild common carp ,Cyprinus carpio rubrofuscus and Volga River wild common carp ,Cyprinus carpio carpio) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus, C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus, most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus) to 1.47%(between C. c. carpio and C. c. rubrofuscus). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus. Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus. Zusammenfassung Die gesamte Cytochrom b- und die Kontrollregion der mtDNA (etwa 2070 bp insgesamt) wurde für zehn Stämmen der drei Unterarten des Flußkarpfens sequenziert. Die Stämme umfassen die drei wild lebenden Subspecies (den Jangtsekiang Flußkarpfen -- Cyprinus carpio haematopterus, den Juanjiang Flußkarpfen -- Cyprinus carpio rubrofuscus und den Wolga-Flußkarpfen -- Cyprinus carpio carpio) und sieben domestizierte Stämme (Roter Xingguo-Karpfen, Russischer zerstreutschuppiger Spiegelkarpfen, Qingtian-Karpfen, Japanischer Koi-Karpfen, Roter Spitzmaulkarpfen, Big-Belly-Karpfen, Deutscher Spiegelkarpfen). Die phylogenetische Analyse zeigt drei distinkte Claden, die den Unterarten C. c. haematopterus, C. c. rubrofuscus und C. c. carpio entsprechen. Der rote Spitzmaulkarpfen, eine endemische, domestizierte Form aus der Provinz Jiangxi Chinas, zeigt im Vergleich mit anderen Stämmen der Unterart C. c. haematopterus die höchste Evolutionsrate, vermutlich durch die starke Selektion und die lange Zeit der Domestikation bedingt. Die Basensubstitutionsrate zwischen den drei Unterarten variiert zwischen 0.78% (zwischen C. c. haematopterus und C. c. rubrofuscus) und 1.47% (zwischen C. c. carpio und C. c. rubrofuscus). Die Topographie des phylogenetischen Baums und die geographische Verteilung der drei Subspecies entsprechen einander sehr stark. Die Divergenzzeit zwischen C. c. carpio und den beiden anderen Unterarten wird auf 0.9 Mil. Jahre geschätzt und die zwischen C. c. haematopterus und C. c. rubrofuscus auf 0.5 Mil Jahre. Nach der phylogenetischen Analyse dürfte sich C. c. rubrofuscus von C. c. haematopterus abgespalten haben. [source] Molecular phylogeny and biogeography of Honey-buzzards (genera Pernis and Henicopernis)JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 2 2004A. Gamauf Abstract A partial sequence of the cytb gene (382 bp) was amplified and sequenced from 35 individuals (mainly museum specimens) of the genus Pernis representing all valid taxa (10) and two taxa (P. p. gurneyi, P. p. japonicus) with questionable validity as well as representatives of the Old World Perninae, namely Henicopernis and Aviceda, to assess their relationships to the genus Pernis. Furthermore, Gypaetus barbatus, Neophron percnopterus, and Buteo buteo were included as outgroup taxa. In the trees derived from the sequence data, Aviceda represents the sister group of the genus Pernis. The genus Henicopernis and the Old World vultures Gypaetus andNeophron appear rather distantly related to Pernis. Within the genus Pernis, two of the described species (Pernis apivorus, Pernis ptilorhyncus) form monophyletic groups, whereas the relationships of the two clades representing three subspecies of Pernis celebensis are still uncertain. Although this study is based on comparatively short DNA-sections, the trees deduced from these sequences can be considered as a first approach for inferring the phylogenetic relationships of the genus Pernis and related genera and for addressing questions concerning the evolutionary history, biogeography, and systematics of this group. Zusammenfassung Eine Teilsequenz des Cytochrom b Gens (382 bp) wurde von 35 Individuen (hauptsächlich Museumsmaterial) der Gattung Pernis amplifiziert und sequenziert. Inkludiert wurden alle validen Taxa (10) und zwei weitere (P.p. gurneyi, P. p. japonicus) mit zweifelhaftem taxonomischen Status. Weiters wurden die übrigen Vertreter der altweltlichen Perninae (Henicopernis, Aviceda) untersucht, um deren Verwandtschaft zum Genus Pernis festzustellen. Als Außengruppen-Taxa wurden Bartgeier Gypaetus barbatus, Schmutzgeier Neophron percnopterus und Mäusebussard Buteo buteo verwendet. In den aus den Sequenzen errechneten Bäumen stellt Aviceda die Schwestergruppe der Gattung Pernis dar. Die Gattungen, Henicopernis und die Altweltgeier Gypaetus und Neophron erscheinen mit der Gattung Pernis nur entfernt verwandt. Innerhalb der Gattung Pernis formen zwei der beschriebenen Arten (P. apivorus, P. ptilorhyncus) eine monophyletische Gruppe, die Verwandtschaftsverhältnisse der beiden anderen Clades, welche die drei Unterarten von P. celebensis repräsentieren, können jedoch auf der Basis dieser Sequenz nicht eindeutig geklärt werden. Obwohl diese Analyse auf relativ kurzen DNA-Abschnitten basiert, können die aus den Sequenzen abgeleiteten Stammbäume als erster Versuch angesehen werden, die Phylogenie der Wespenbussard-Gattung Pernis und verwandter Genera mittels molekularer Methoden und unter Berücksichtigung evolutionsbiologischer, biogeographischer und systematischer Aspekte darzustellen. [source] Molecular phylogeny of the freshwater sponges in Lake BaikalJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 2 2003H. C. Schröder Abstract The phylogenetic relationship of the freshwater sponges (Porifera) in Lake Baikal is not well understood. A polyphyletic and/or monophyletic origin have been proposed. The (endemic) Baikalian sponges have been subdivided into two families: endemic Lubomirskiidae and cosmopolitan Spongillidae. In the present study, two new approaches have been made to resolve the phylogenetic relationship of Baikalian sponges; analysis of (1) nucleotide sequences from one mitochondrial gene, the cytochrome oxidase subunit I (COI) and of (2) one selected intron from the tubulin gene. Specimens from the following endemic Baikalian sponge species have been studied; Lubomirskia baicalensis , Baikalospongia intermedia, Baikalospongia recta , Baikalospongia bacillifera and Swartschewskia papyracea . They are all grouped to the family of Lubomirskiidae. Sequence comparisons were performed with the ubiquitously distributed freshwater sponge Spongilla lacustris (family Spongillidae) as well as with one marine sponge, Suberites domuncula . A sequence comparison, of the mitochondrial COI gene revealed a monophyletic grouping of the endemic Baikalian sponges with S. lacustris as the most related species to the common ancestor. The sequences of the COI gene from B. recta , B. intermedia , B. bacillifera and L. baicalensis were found to be identical and separated from those of S. lacustris and S. papyracea . In a second approach, the exon/intron sequences framing the intron-2 of the sponge tubulin gene were chosen for the phylogenetic analysis. The intron sequences were aligned and used for construction of a phylogenetic tree. This analysis revealed again a monophyletic grouping with S. lacustris as the closest related species to the common ancestor. It is concluded that the Baikalian sponges, which have been studied here, are of monophyletic origin. Furthermore, the data suggest that the endemic species S. papyracea is the phylogenetically oldest, extant, endemic Baikalian sponge species. Zusammenfassung Die phylogenetischen Beziehungen der Süßwasserschwämme [Porifera] des Baikalsees sind nur wenig verstanden; sowohl ein polyphyletischer als auch monophyletischer Urspung werden vermutet. Die Baikalschwämme werden in zwei Familien, Lubomirskiidae und Spongillidae, eingeteilt. In der vorliegenden Arbeit wird versucht, die phylogenetischen Beziehungen der Baikalschwämme über zwei Wege aufzuklären: über (i) eine Analyse der Nukleotidsequenzen eines Teils des mitochondrialen Gens der Cytochromoxidase-Untereinheit I (COI) und (ii) eines ausgewählten Introns des Tubulingens. Folgende endemischen Spezies wurden untersucht: Lubomirskia baicalensis , Baikalospongia intermedia , Baikalospongia recta , Baikalospongia bacillifera und Swartschewskia papyracea . Sie werden alle der Familie der Lubomirskiidae zugerechnet. Die Sequenzen wurden mit den entsprechenden Sequenzen des ubiquitär vorkommenden Süßwasserschwammes Spongilla lacustris sowie des Meeresschwammes Suberites domuncula verglichen. Die Sequenzvergleiche der mitochondrialen COI-Gene zeigten, daß die Baikalschwämme monophyletischen Ursprungs sind und zusammen mit S. lacustris von einem gemeinsamen Vorfahren abstammen. Die Sequenzen des COI-Gens von B. recta , B. intermedia , B. bacillifera und L. baicalensis sind identisch und trennen sich phylogenetisch von S. lacustris und S. papyracea ab. Bei dem zweiten von uns gewählten Weg wurden die Sequenzen des zweiten Introns des Schwamm-Tubulingens zur phylogenetischen Analyse herangezogen. Auch dabei konnte gezeigt werden, daß die Baikalschwämme , zusammen mit S. lacustris als dem nächsten verwandten gemeinsamen Vorfahren , einen monophyletischen Ursprung haben. S. papyracea stellt den phylogenetisch ältesten endemischen Baikalschwamm dar. [source] Morphology, Ultrastructure, Molecular Phylogeny, and Autecology of Euplotes elegans Kahl, 1932 (Hypotrichida; Euplotidae) Isolated from the Anoxic Mariager Fjord, DenmarkTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2007M. V. JULIAN SCHWARZ ABSTRACT. The morphology, autecology, and molecular phylogeny of an euryhaline Euplotes isolate collected from the anoxic water column of the Mariager Fjord in Denmark were investigated. The isolate matches the original description of Euplotes elegans Kahl, 1932 very well. However, its dorsal silverline system is clearly distinct from the redescription of this species by Tuffrau. Thus, a neotypification is proposed for E. elegans Kahl, 1932. The oval-shaped cell has a mean size of 107 × 51 ,m and is characterized by 9.4 dorsolateral kineties, seven prominent dorsal ridges, large elongated ampullae, which encircle the dorsal kinetids, 18 kinetids in the middorsal row, nine frontoventral cirri, five transversal cirri, and three caudal cirri (two right caudal cirri and one left marginal cirrus). The dorsal silverline system is of the double type with the narrow polygons located on the right side of the dorsal kinetids. The ecological tolerances of this species to pH, salinity, temperature, and oxygen match the ambient environmental conditions of the sampling site. Molecular phylogeny was studied using small subunit rRNA (SSU rRNA) gene sequences. The molecular data cluster E. elegans with Euplotes raikovi, a member of the Euplotopsis group. The data suggest that the E. elegans,E. raikovi clade represents an isolated and deep branch at the base of the Euplotes tree. [source] Molecular phylogeny and evolution of the Asian lineage of vole genus Microtus (Rodentia: Arvicolinae) inferred from mitochondrial cytochrome b sequenceBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2010ANNA A. BANNIKOVA To examine phylogenetic relationships within the Asian lineage of voles (Microtus) belonging to subgenus Alexandromys, the mitochondrial cytochrome b gene (cytb) was sequenced for its representatives, and the results were compared with the cytogenetic, morphological, and paleontological data. In all the trees inferred from maximum likelihood, parsimony, and Bayesian phylogenetic analyses, the Asian clade is subdivided into highly supported Alexandromys s.s. and moderately supported Pallasiinus lineages. Four subclades are recovered within Alexandromys: (1) Microtus maximowiczii and Microtus sachalinensis; (2) Microtus miiddendorffii s.l., Microtus mongolicus and Microtus gromovi; (3) Microtus fortis; and (4) Microtus limnophilus. Thus, M. limnophilus demonstrates clear affinities to Alexandromys s.s. but not to Microtus oeconomus (subgenus Pallasiinus), which was always regarded as its sibling species. The results obtained indicate M. mongolicus as a member of Alexandromys but not of the Microtus arvalis group, thus being concordant with the cytogenetic data. The mitochondrial data support the species status of M. gromovi; moreover, its placement as a part of a trichotomy with M. miiddendorffii s.l. and M. mongolicus contradicts the traditional affiliation of M. gromovi with M. maximowiczii. The divergence rate of cytb third position transversions in Microtus is estimated at approximately 8% per Myr, which corresponds to approximately 30% per Myr for all substitution types at all codon positions. The maximum likelihood distance based on complete sequence showed a tendency for a progressive underestimation of divergence and time for older splits. According to our molecular clock analysis employing nonlinear estimation methods, the split between Alexandromys and Pallasiinus and basal radiation within Alexandromys date back to approximately 1.2 Mya and 800 Kya, respectively. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 595,613. [source] Molecular phylogeny of icefish Salangidae based on complete mtDNA cytochrome b sequences, with comments on estuarine fish evolutionBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2007JIE ZHANG Phylogenetic relationships among 15 species in the family Salangidae were constructed based on the complete cytochrome b sequence (1141 bp). We confirmed the monophyly of the family Salangidae and defined four primitive lineages within this family: (I) Protosalanx, Neosalanx anderssoni, Neosalanx tangkahkeii, and Neosalanx argentea; (II) Neosalanx reganius, Neosalanx jordani, Neosalanx oligodontis, and Neosalanx sp.; (III) Hemisalanx, Salanx, Leucosoma, and Salangichthys ishikawae; and (IV) Salangichthys microdon. A major finding of our study is the key basal placement of Sg. microdon. According to the tentative estimation, the divergence of the four lineages appears to have been initiated in the early Miocene (21 Mya), with most speciation events occurring 1.05,9.90 Mya. Taxonomic revisions on subfamilial, generic, and specific levels were carried out based on phylogenetic relationships and genetic distance, taking into account some key morphological characters. The speciation mechanism in Salangidae is also discussed, and the evidence shows that geographical isolation, water mass, as well as some ecological factors, may not always play important roles in the speciation of temperate estuarine fish. In the most cases, sympatric salangids are not monophyletic, indicating that their coexistence reflects secondary contact rather than sympatric speciation. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 91, 327,342. [source] Molecular phylogeny of the Sphaerophorus globosus species complexCLADISTICS, Issue 3 2003Filip Högnabba The Sphaerophorus globosus complex (Lecanorales, lichenized Ascomycota) shows a large morphological variation, and three relatively distinct morphotypes can be distinguished in parts of the distribution area. Here, we utilize a multigene-based maximum-parsimony approach (nITS+ LSU rDNA, mtSSU rDNA, ,-tubulin, and actin) to investigate whether these morphotypes constitute distinct species. The results show that there are at least two well-supported monophyletic groups that we interpret as phylogenetic species within the S. globosus complex. These species do not completely correspond to the predefined morphotypes. One group, an apparently undescribed species, contains noncoralloid specimens from the North American Pacific Northwest. The other group, S. globosus, consists of two well-supported monophyletic groups: one contains coralloid epiphytic specimens from the North American Pacific Northwest that are morphologically indistinguishable from epiphytic specimens from Europe and are presently interpreted as belonging to the same species and the other is morphologically variable and contains terrestrial specimens from Europe, North America, and southernmost South America and coralloid epiphytic and epilithic specimens from Europe. The results suggest that the population in southernmost South America originated by long-distance dispersal from arctic populations in the Northern Hemisphere. [source] Horizontal transmission of Wolbachia in a Drosophila communityECOLOGICAL ENTOMOLOGY, Issue 4 2005Eleanor R. Haine Abstract., 1.,Wolbachia bacteria are reproductive parasites of arthropods and infect an estimated 20% of all insect species worldwide. In order to understand patterns of Wolbachia infection, it is necessary to determine how infections are gained or lost. Wolbachia transmission is mainly vertical, but horizontal transmission between different host species can result in new infections, although its ecological context is poorly understood. Horizontal transmission is often inferred from molecular phylogenies, but could be confounded by recombination between different Wolbachia strains. 2.,This study addressed these issues by using three genes: wsp, ftsZ, and groE, to study Wolbachia infections in fruit- and fungus-feeding Drosophila communities in Berkshire, U.K. 3.,Identical sequences were found for all three genes in Drosophila ambigua and Drosophila tristis. This suggests horizontal transmission of Wolbachia between these two previously unstudied Drosophila species, which may be the result of the two host species sharing the same food substrates or parasites. 4.,Wolbachia infections might be lost from species due to curing by naturally occurring antibiotics and the presence of these is likely to vary between larval food substrates. 5.,It was investigated whether Wolbachia incidence was lower in fungus-feeding than in fruit-feeding Drosophila species, but no significant difference based on food substrate was found. [source] Facilitation can increase the phylogenetic diversity of plant communitiesECOLOGY LETTERS, Issue 11 2007Alfonso Valiente-Banuet Abstract With the advent of molecular phylogenies the assessment of community assembly processes has become a central topic in community ecology. These processes have focused almost exclusively on habitat filtering and competitive exclusion. Recent evidence, however, indicates that facilitation has been important in preserving biodiversity over evolutionary time, with recent lineages conserving the regeneration niches of older, distant lineages. Here we test whether, if facilitation among distant-related species has preserved the regeneration niche of plant lineages, this has increased the phylogenetic diversity of communities. By analyzing a large worldwide database of species, we showed that the regeneration niches were strongly conserved across evolutionary history. Likewise, a phylogenetic supertree of all species of three communities driven by facilitation showed that nurse species facilitated distantly related species and increased phylogenetic diversity. [source] Metagenomic signatures of 86 microbial and viral metagenomesENVIRONMENTAL MICROBIOLOGY, Issue 7 2009Dana Willner Summary Previous studies have shown that dinucleotide abundances capture the majority of variation in genome signatures and are useful for quantifying lateral gene transfer and building molecular phylogenies. Metagenomes contain a mixture of individual genomes, and might be expected to lack compositional signatures. In many metagenomic data sets the majority of sequences have no significant similarities to known sequences and are effectively excluded from subsequent analyses. To circumvent this limitation, di-, tri- and tetranucleotide abundances of 86 microbial and viral metagenomes consisting of short pyrosequencing reads were analysed to provide a method which includes all sequences that can be used in combination with other analysis to increase our knowledge about microbial and viral communities. Both principal component analysis and hierarchical clustering showed definitive groupings of metagenomes drawn from similar environments. Together these analyses showed that dinucleotide composition, as opposed to tri- and tetranucleotides, defines a metagenomic signature which can explain up to 80% of the variance between biomes, which is comparable to that obtained by functional genomics. Metagenomes with anomalous content were also identified using dinucleotide abundances. Subsequent analyses determined that these metagenomes were contaminated with exogenous DNA, suggesting that this approach is a useful metric for quality control. The predictive strength of the dinucleotide composition also opens the possibility of assigning ecological classifications to unknown fragments. Environmental selection may be responsible for this dinucleotide signature through direct selection of specific compositional signals; however, simulations suggest that the environment may select indirectly by promoting the increased abundance of a few dominant taxa. [source] EXTINCTION DURING EVOLUTIONARY RADIATIONS: RECONCILING THE FOSSIL RECORD WITH MOLECULAR PHYLOGENIESEVOLUTION, Issue 12 2009Tiago B. Quental Recent application of time-varying birth,death models to molecular phylogenies suggests that a decreasing diversification rate can only be observed if there was a decreasing speciation rate coupled with extremely low or no extinction. However, from a paleontological perspective, zero extinction rates during evolutionary radiations seem unlikely. Here, with a more comprehensive set of computer simulations, we show that substantial extinction can occur without erasing the signal of decreasing diversification rate in a molecular phylogeny. We also find, in agreement with the previous work, that a decrease in diversification rate cannot be observed in a molecular phylogeny with an increasing extinction rate alone. Further, we find that the ability to observe decreasing diversification rates in molecular phylogenies is controlled (in part) by the ratio of the initial speciation rate (Lambda) to the extinction rate (Mu) at equilibrium (the LiMe ratio), and not by their absolute values. Here we show in principle, how estimates of initial speciation rates may be calculated using both the fossil record and the shape of lineage through time plots derived from molecular phylogenies. This is important because the fossil record provides more reliable estimates of equilibrium extinction rates than initial speciation rates. [source] Tracking the origins of the bilaterian Hox patterning system: insights from the acoel flatworm Symsagittifera roscoffensisEVOLUTION AND DEVELOPMENT, Issue 5 2009Eduardo Moreno SUMMARY Genes of the Hox cluster encode for transcriptional regulators that show collinear expression along the anteroposterior (AP) body axis in all bilateral animals. However, it is still unclear when in the evolutionary history of bilaterians the Hox system first conferred positional identity along the AP-axis. Recent molecular phylogenies have convincingly shown that the acoel flatworms, traditionally classified within the Platyhelminthes, are the sister group of the remaining Bilateria, branching out before the common ancestor of protostomes, and deuterostomes (the so-called PDA). This key phylogenetic position offers the opportunity to search for the presence and early role of Hox cluster genes to pattern the AP axis in acoels. Here, we report on the cloning, genomic arrangement, and expression domains of Hox genes in Symsagittifera roscoffensis. Three Hox genes were detected: one from each of the major groups of Hox genes, which are anterior, central, and posterior. In bacterial artificial chromosome cloning, sequencing, and chromosomal fluorescence in situ hybridization, Hox genes were not observed as being clustered in a unique genomic region. Nevertheless, despite its dispersion within the genome, Hox genes are expressed in nested domains along the AP axis in the juvenile worm. The basic set of Hox genes in acoels and their coarse nested spatial deployment might be the first indicators of the role of Hox genes in the evolution of bilateral symmetry and AP positional identity from a hypothetical radial ancestor. [source] Speciation chronology of rockhopper penguins inferred from molecular, geological and palaeoceanographic dataJOURNAL OF BIOGEOGRAPHY, Issue 4 2009Marc De Dinechin Abstract Aim, The Southern Ocean is split into several biogeographical provinces between convergence zones that separate watermasses of different temperatures. Recent molecular phylogenies have uncovered a strong phylogeographic structure among rockhopper penguin populations, Eudyptes chrysocome sensu lato, from different biogeographical provinces. These studies suggested a reclassification as three species in two major clades, corresponding, respectively, to warm, subtropical and cold sub-Antarctic watermasses rather than to geographic proximity. Such a phylogeographic pattern, also observed in plants, invertebrates and fishes of the Southern Ocean, suggests that past changes in the positions of watermasses may have affected the evolutionary history of penguins. We calculated divergence times among various rockhopper penguin clades and calibrated these data with palaeomagmatic and palaeoceanographic events to generate a speciation chronology in rockhopper penguins. Location, Southern Ocean. Methods, Divergence times between populations were calculated using five distinct mitochondrial DNA loci, and assuming a molecular clock model as implemented in mdiv. The molecular evolution rate of rockhopper penguins was calibrated using the radiochronological age of St Paul Island and Amsterdam Island in the southern Indian Ocean. Separations within other clades were correlated with palaeoceanographic data using this calibrated rate. Results, The split between the Atlantic and Indian populations of rockhopper penguins was dated as 0.25 Ma, using the date of emergence of St Paul and Amsterdam islands, and the divergence between sub-Antarctic and subtropical rockhopper penguins was dated as c. 0.9 Ma (i.e. during the mid-Pleistocene transition, a major change in the Earth's climate cycles). Main conclusions, The mid-Pleistocene transition is known to have caused a major southward shift in watermasses in the Southern Ocean, thus changing the environment around the northernmost rockhopper penguin breeding sites. This ecological isolation of northernmost populations may have caused vicariant speciation, splitting the species into two major clades. After the emergence of St Paul and Amsterdam islands in the subtropical Indian Ocean 0.25 Ma, these islands were colonized by penguins from the subtropical Atlantic, 6000 km away, rather than by penguins from the sub-Antarctic Indian Ocean, 5000 km closer. 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