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Monophyletic Clade (monophyletic + clade)
Selected AbstractsMorpho-anatomy of the lobopod Magadictyon cf. haikouensis from the Early Cambrian Chengjiang Lagerstätte, South ChinaACTA ZOOLOGICA, Issue 4 2007Jianni Liu Abstract Magadictyon haikouensis (Luo and Hu, 1999) from the Early Cambrian Chengjiang Lagerstätte, an incomplete specimen of a large lobopod with strong appendages, has been regarded as related to the lobopods Microdictyon and Onychodictyon. Newly discovered complete specimens of Magadictyon cf. haikouensis (found by the Early Life Institute field team) show that the taxon, in addition to its strong appendages with appendicules, also had a head bearing similar caecum-like structures to those of the arthropod Naraoia and Chelicerate, ,Peytoia'-like mouthparts and frontal appendages. Because of their similarity, the caecum-like structures of Magadictyon cf. haikouensis are considered to be homologous with those of stem-group arthropods. The ,Peytoia'-like mouthparts and the frontal appendages are similar to those of the AOPK (Anomalocaris,Opabinia,Pambdelurion,Kerygmachela) group. In addition, the appendages with appendicules show that Magadictyon cf. haikouensis is closely related to Onychodictyon. Therefore, Magadictyon cf. haikouensis is regarded here as a rare transitional form between lobopods and arthropods. Besides, together with other lobopods, the morphology of Magadictyon cf. haikouensis demonstrates that the Cambrian lobopods appear to have been diverse and not particularly closely related to one another, and do not seem to represent a monophyletic clade. [source] Widespread occurrence of an intranuclear bacterial parasite in vent and seep bathymodiolin musselsENVIRONMENTAL MICROBIOLOGY, Issue 5 2009Frank U. Zielinski Summary Many parasitic bacteria live in the cytoplasm of multicellular animals, but only a few are known to regularly invade their nuclei. In this study, we describe the novel bacterial parasite "Candidatus Endonucleobacter bathymodioli" that invades the nuclei of deep-sea bathymodiolin mussels from hydrothermal vents and cold seeps. Bathymodiolin mussels are well known for their symbiotic associations with sulfur- and methane-oxidizing bacteria. In contrast, the parasitic bacteria of vent and seep animals have received little attention despite their potential importance for deep-sea ecosystems. We first discovered the intranuclear parasite "Ca. E. bathymodioli" in Bathymodiolus puteoserpentis from the Logatchev hydrothermal vent field on the Mid-Atlantic Ridge. Using primers and probes specific to "Ca. E. bathymodioli" we found this intranuclear parasite in at least six other bathymodiolin species from vents and seeps around the world. Fluorescence in situ hybridization and transmission electron microscopy analyses of the developmental cycle of "Ca. E. bathymodioli" showed that the infection of a nucleus begins with a single rod-shaped bacterium which grows to an unseptated filament of up to 20 ,m length and then divides repeatedly until the nucleus is filled with up to 80 000 bacteria. The greatly swollen nucleus destroys its host cell and the bacteria are released after the nuclear membrane bursts. Intriguingly, the only nuclei that were never infected by "Ca. E. bathymodioli" were those of the gill bacteriocytes. These cells contain the symbiotic sulfur- and methane-oxidizing bacteria, suggesting that the mussel symbionts can protect their host nuclei against the parasite. Phylogenetic analyses showed that the "Ca. E. bathymodioli" belongs to a monophyletic clade of Gammaproteobacteria associated with marine metazoans as diverse as sponges, corals, bivalves, gastropods, echinoderms, ascidians and fish. We hypothesize that many of the sequences from this clade originated from intranuclear bacteria, and that these are widespread in marine invertebrates. [source] DIVERGENCE WITH GENE FLOW IN THE ROCK-DWELLING CICHLIDS OF LAKE MALAWIEVOLUTION, Issue 5 2000Patrick D. Danley Abstract Within the past two million years, more than 450 species of haplochromine cichlids have diverged from a single common ancestor in Lake Malawi. Several factors have been implicated in the diversification of this monophyletic clade, including changes in lake level and low levels of gene flow across limited geographic scales. The objectives of this study were to determine the effect of recent lake-level fluctuations on patterns of allelic diversity in the genus Metriaclima, to describe the patterns of population structure within this genus, and to identify barriers to migration. This was accomplished through an analysis of allele frequencies at four microsatellite loci. Twelve populations spanning four species within Metriaclima were surveyed. The effect of lake-level fluctuations can be seen in the reduced genetic diversity of the most recently colonized sites; however, genetic diversity is not depressed at the species level. Low levels of population structure exist among populations, yet some gene flow persists across long stretches of inhospitable habitat. No general barrier to migration was identified. The results of this study are interpreted with respect to several speciation models. Divergence via population bottlenecks is unlikely due to the large allelic diversity observed within each species. Genetic drift and microallopatric divergence are also rejected because some gene flow does occur between adjacent populations. However, the reduced levels of gene flow between populations does suggest that minor changes in the selective environment could cause the divergence of populations. [source] Phylogeny of major lineages of suboscines (Passeriformes) analysed by nuclear DNA sequence dataJOURNAL OF AVIAN BIOLOGY, Issue 1 2001Martin Irestedt Phylogenetic relationships among major groups of passeriform birds were studied by analyses of nucleotide sequence data from two nuclear genes, c- myc and RAG-1. The results corroborated both the monophyly of the order Passeriformes, and the major dichotomy into oscine and suboscine passerines previously suggested based on syringeal morphology and DNA-DNA hybridizations. The representatives of the Old World suboscines (families Eurylaimidae, Philepittidae and Pittidae) formed a monophyletic clade. The New World suboscines clustered into two clades. The first contained Conopophaga (Conopophagidae), Furnarius (Furnariidae), Lepidocolaptes (Dendrocolaptidae), Thamnophilus (Formicariidae), and Rhinocrypta (Rhinocryptidae). Previously, the monophyly of this group has been inferred from their possession of a unique, "tracheophone" syrinx, and from DNA-DNA hybridisation data. The second clade of New World suboscines includes Gubernetes and Muscivora (Tyrannidae), Phytotoma (Phytotomidae), Tityra (Cotingidae) and Pipra (Pipridae). This group of families have been considered monophyletic based on morphology (although ambiguously) and DNA-DNA hybridisation. The sister group relationship of Tityra and Phytotoma supports the previously supposed cotingid affinity of Phytotoma. Nuclear DNA data also unambiguously group the lyrebirds Menura with the oscines. The presented results from the analysis of nuclear DNA agree well with morphology and DNA-DNA hybridisation data. The precise age of the divergences studied herein are unknown but based on interpretations of the fossil record of passerine birds many of them might date back to the early Tertiary. The agreement between data from the nuclear DNA and other sources, along with the fact that neither of the studied genes showed sign of saturation, indicate the great potential of these two nuclear genes to resolve very old divergences in birds. [source] Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeetsJOURNAL OF BIOGEOGRAPHY, Issue 9 2009Camila C. Ribas Abstract Aim, We present a molecular phylogenetic analysis of Brotogeris (Psittacidae) using several distinct and complementary approaches: we test the monophyly of the genus, delineate the basal taxa within it, uncover their phylogenetic relationships, and finally, based on these results, we perform temporal and spatial comparative analyses to help elucidate the historical biogeography of the Neotropical region. Location, Neotropical lowlands, including dry and humid forests. Methods, Phylogenetic relationships within Brotogeris were investigated using the complete sequences of the mitochondrial genes cyt b and ND2, and partial sequences of the nuclear intron 7 of the gene for Beta Fibrinogen for all eight species and 12 of the 17 taxa recognized within the genus (total of 63 individuals). In order to delinetae the basal taxa within the genus we used both molecular and plumage variation, the latter being based on the examination of 597 skin specimens. Dates of divergence and confidence intervals were estimated using penalized likelihood. Spatial and temporal comparative analyses were performed including several closely related parrot genera. Results,Brotogeris was found to be a monophyletic genus, sister to Myiopsitta. The phylogenetic analyses recovered eight well-supported clades representing the recognized biological species. Although some described subspecies are diagnosably distinct based on morphology, there was generally little intraspecific mtDNA variation. The Amazonian species had different phylogenetic affinities and did not group in a monophyletic clade. Brotogeris diversification took place during the last 6 Myr, the same time-frame as previously found for Pionus and Pyrilia. Main conclusions, The biogeographical history of Brotogeris implies a dynamic history for South American biomes since the Pliocene. It corroborates the idea that the geological evolution of Amazonia has been important in shaping its biodiversity, argues against the idea that the region has been environmentally stable during the Quaternary, and suggests dynamic interactions between wet and dry forest habitats in South America, with representatives of the Amazonian biota having several independent close relationships with taxa endemic to other biomes. [source] Nocardiosis in large yellow croaker, Larimichthys crocea (Richardson)JOURNAL OF FISH DISEASES, Issue 6 2005G-L Wang Abstract An epizootic in seawater-cage reared large yellow croaker, Larimichthys crocea, in China was caused by a Nocardia sp. from August to October 2003. The cumulative mortality rate was 15% and the diseased fish were 16 months old with individual length varying from 25 to 30 cm. Multiple, white nodules, 0.1,0.2 cm in diameter, were scattered on the heart, spleen and kidney. The morphology of isolated bacteria from Lowenstein,Jensen medium and tryptic soy agar was bead-like or long, slender, filamentous rods. Experimental infection indicated that the isolated bacterium was the pathogen responsible for the mortalities. A partial sequence of the 16S rRNA gene of the organism and the type strain of Nocardia seriolae JCM 3360T (Z36925) formed a monophyletic clade with a high sequence similarity of 99.9%. Based on the morphological, physiological, biological properties and the phylogenetic analysis, the pathogenic organism was identified as N. seriolae. This is the first report on N. seriolae -infected large yellow croaker in aquaculture. [source] Bone vascular supply in monitor lizards (Squamata: Varanidae): Influence of size, growth, and phylogenyJOURNAL OF MORPHOLOGY, Issue 5 2008Vivian de Buffrénil Abstract Bone vascular canals occur irregularly in tetrapods; however, the reason why a species has or lacks bone canals remains poorly understood. Basically, this feature could depend on phylogenetic history, or result from diverse causes, especially cortical accretion rate. The Varanidae, a monophyletic clade that includes species with impressive size differences but similar morphologies, is an excellent model for this question. Cortical vascularization was studied in 20 monitor species, on three bones (femur, fibula, and tibia) that differ in their shaft diameters, and in the absolute growth speed of their diaphyseal cortices. In all species smaller than 398 mm SVL (133,397 mm in sample), bone cortices lack vascular canals, whereas all larger species (460,1,170 mm in sample) display canals. The size 398,460 mm SVL is thus a threshold for the appearance of the canals. The distribution of vascular and avascular bone tissues among species does not precisely reflect phylogenetic relationships. When present, vascular canals always occur in the femur and tibia, but are less frequent, sparser, and thinner in the fibula. Vascular density increases linearly with specific size but decreases exponentially during individual growth. In most species, canal orientation varies between individuals and is diverse in a single section. No clear relationship exists between canal orientation and vascular density. These results suggest that: a) the occurrence and density of bone vascular canals are basically dependant on specific size, not phylogenetic relationships; b) vascular density reflects the absolute growth rates of bone cortices; c) the orientation of vascular canals is a variable feature independent of phylogeny or growth rate. J. Morphol., 2008. © 2007 Wiley-Liss, Inc. [source] PHYLOGEOGRAPHY OF THE GENUS SPONGITES (CORALLINALES, RHODOPHYTA) FROM CHILE,JOURNAL OF PHYCOLOGY, Issue 1 2008Rodrigo Vidal Both the records and the descriptions of the crustose species of coralline algae on the southeastern coast of South America are from the early 1900s. Unlike other algae species on the coast of Chile, the biogeography and distribution of crustose corallines have not been studied despite their abundance. Through recent studies, it has been determined that the genus Spongites is the most conspicuous genus along the rocky intertidal of the Chilean coasts. It is also common to the entire coast of the Southern Hemisphere; however, the relationship between species and the possible reasons for their distribution is unknown. We used nuclear and mitochondrial genetic markers and SEM observations of morphological characters to examine Spongites samples from the Southern Hemisphere and to establish the phylogeographic relationships of Chilean Spongites with specimens from other southern coasts. The combination of these analyses revealed the following: (i) a monophyletic clade that represents the Chilean Spongites and (ii) a paraphyletic clade for South African, New Zealand, and Argentine samples. Consequently, we postulate two nonexclusive hypotheses regarding the relationship of Spongites species in the Southern Hemisphere: (i) a complex history of extinction, speciation, and recolonization that might have erased original Gondwanan split patterns, and (ii) an Antarctic Peninsula origin for the Chilean Spongites species. [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] 120 Exploration of Morphological Variation Within the Genus Pediastrum Meyen 1829 (Chlorophyceae, Chlorophyta)JOURNAL OF PHYCOLOGY, Issue 2003H. A. McManus Monographic works on the green algal genus, Pediastrum Meyen 1829 (Chlorophyceae, Chlorophyta), have described species, varieties and forms based on such characteristics as the size and shape of the marginal cells, pattern of cell wall sculpturing and extent of cell wall sculpturing. Depending on the author, the number of taxa assigned to the genus Pediastrum varies. Due to the lack of quantitative value to these characteristics, it has been difficult for other researchers to assign appropriate taxonomy to wild isolates. A molecular phylogeny including multiple strains from both culture collections and wild samples confirms relationships found by previous molecular studies on fewer taxa, in which the family Hydrodictyaceae forms a monophyletic group within the Sphaeropleales, and that the genera Hydrodictyon and Sorastrum are derived from Pediastrum. Hydrodicyton forms a monophyletic clade and consists of three species, H. reticulatum, H. africanum, and H. patenaeforme. Multiple isolates of H. reticulatum reveal little genetic variation between different geographic localities. Inclusion of wild isolates permits a more thorough exploration of morphological variation within the genus Pediastrum, and what characters may be taxonomically informative, particularly in the species P. boryanum and P. duplex. Wild isolates sampled from different areas also offers information regarding geographic variation and potential morphological convergence. [source] SOME PHYLOGENETIC RELATIONSHIPS WITHIN THE OSCILLATORIALES (CYANOBACTERIA) CLADE USING 16S RDNA GENE SEQUENCE DATAJOURNAL OF PHYCOLOGY, Issue 2000D.A. Casamatta An approximately 1400 base pair region of the 16S rDNA gene was sequenced from taxa within the Oscillatoriales in order to assess phylogenetic relationships. Ten previously unsequenced strains were obtained from the University of Toronto Culture Collection. New sequence data were combined with previously published sequences from a wide representation of cyanobacteria including all currently available, complete Oscillatorialian taxa. Trees constructed using parsimony, distance, and maximum likelihood methods were similar in topology, although a few taxa were variable in their placement depending on the phylogenetic method employed. Newly sequenced taxa of the genera Phormidium, Oscillatoria, and Lyngbya did not form monophyletic clades based on traditional generic designations. Two Lyngbya strains (UTCC296 and 313) and Phormidium subfuscum (UTCC474) formed a well supported monophyletic clade, but the affinity of this clade with other groups was uncertain due to lack of bootstrap support. Oscillatoria sp. (UTCC393) was closely related to the previously sequenced Oscillatoria limnetica and likewise, Phormidium molle (UTCC77) and Phormidium tenue (UTCC473) were placed in a well supported clade with other Oscillatoriales. The other four taxa were variously placed in the trees and their phylogenetic positions could not be determined with certainty. [source] Karyotype and mitochondrial 16S gene characterizations in seven South American Cichlasomatini species (Perciformes, Cichlidae)JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1 2005O. Marescalchi Abstract The family Cichlidae constitutes most of the freshwater fish fauna of South America; its taxonomy is at present mainly based on morphological characters. Here, relationships among seven Cichlasomatini species have been investigated by studying their karyotype structure and by sequencing a 520 bp fragment of the mitochondrial 16S gene. Molecular data sets point to a high affinity of Cichlasoma amazonarum with Aequidens sensu stricto group, in particular with Aequidens tetramerus. Aequidens never form a single monophyletic clade: molecular trees group together ,Aequidens pulcher' and ,Aequidens rivulatus' and suggest their close relationship with Bujurquina and Laetacara, rather than with the A. sensu stricto group. Both molecular and karyotypic data confirm that Cleithracara maronii belongs to a distinct clade, thus supporting its generic differentiation based on morphological characters. Chromosome number, karyotype structure and molecular data suggest that Laetacara dorsigera is related to Bujurquina vittata and confirm their generic level of differentiation. From a cytotaxonomic point of view, a karyotype of 2n = 48 with most acrocentric or subacrocentric chromosomes could be the ancestral one from which the others might have derived. Zusammenfassung Ein großer Teil der südamerikanischen Süßwasserfische gehört zur Familie der Cichliden, deren Taxonomie bisher aber nur auf morphologischen Eigenschaften beruhte. In dieser Arbeit wurden die Verwandtschaftbeziehungen zwischen sieben Arten durch die Untersuchung des Karyotyps und eines 520 bp Teilstücks der mitochondrialen 16S rDNA-Sequenz studiert. Die molekularen Daten weisen auf eine höhere Verwandtschaft zwischen Cichlosoma amazonarum und Aequidens sensu strictu, besonders mit A. tetramerus, hin. Die Arten der Gattung Aequidens bilden niemals eine monophyletische Clade; die molekularen Bäume gruppieren immer A. pulcher und A. rivulatus zusammen und machen deren nähere Verwandtschaft zu den Gattungen Bujurquina und Laetacara wahrscheinlicher als zu der als Aequidens sensu strictu bezeichneten Gruppe. Die molekularen und die karyologischen Daten bestärken, daß die Art Cleithracara maroni einer klar getrennten Clade angehört, was auch die morphologischen Ergebnisses unterstützt. Die Chromosomenzahl, die Zusammensetzung des Karyotyps und die molekularen Vergleiche lassen erkennen, daßLaetacara dorsigera mit Bujurquina vittata verwandt ist, aber die Differenzierung den Gattungsstatus rechtfertigt. Vom cytotaxonomischen Standpunkt könnte ein Karyotyp mit 2n = 48 mit vorwiegend akrozentrischen oder subakrozentischen Chromosomen der ursprüngliche sein, von dem die anderen ableitbar sind. [source] Molecular systematics, biogeography and population structure of Neotropical freshwater needlefishes of the genus PotamorrhaphisMOLECULAR ECOLOGY, Issue 3 2000N. R. Lovejoy Abstract Phylogenetic relationships of populations and species within Potamorrhaphis, a genus of freshwater South American needlefishes, were assessed using mitochondrial cytochrome b sequences. Samples were obtained from eight widely distributed localities in the Amazon and Orinoco rivers, and represented all three currently recognized species of Potamorrhaphis. The phylogeny of haplotypes corresponded imperfectly to current morphological species identities: haplotypes from P. guianensis, the most widespread species, did not make up a monophyletic clade. Geography played a strong role in structuring genetic variation: no haplotypes were shared between any localities, indicating restricted gene flow. Possible causes of this pattern include limited dispersal and the effects of current and past geographical barriers. The haplotype phylogeny also showed a complex relationship between fishes from different river basins. Based on the geographical distribution of clades, we hypothesize a connection between the middle Orinoco and Amazon via rivers of the Guianas. More ancient divergence events may have resulted from Miocene alterations of river drainage patterns. We also present limited data for two other Neotropical freshwater needlefish genera: Belonion and Pseudotylosurus. Pseudotylosurus showed evidence of substantial gene flow between distant localities, indicating ecological differences from Potamorrhaphis. [source] THE TAXONOMIC AND PHYLOGENETIC POSITION OF THE PLESIOSAUROIDEA FROM THE LOWER JURASSIC POSIDONIA SHALE OF SOUTH-WEST GERMANYPALAEONTOLOGY, Issue 3 2007FRANZISKA GROßMANNArticle first published online: 17 MAY 200 Abstract:, The two plesiosauroid species from the Posidonia shale of Holzmaden, ,Plesiosaurus'guilelmiimperatoris and ,Plesiosaurus'brachypterygius, do not belong to Plesiosaurus but form new monotypic genera. The new genus Hydrorion is erected for ,P.'brachypterygius, and the genus Seeleyosaurus is re-established for ,P.'guilelmiimperatoris. The recently described species Plesiopterys wildii is regarded as a junior synonym of S. guilelmiimperatoris. A short phylogenetic analysis shows that S. guilelmiimperatoris and Muraenosaurus are basal elasmosaurs. H. brachypterygius, Occitanosaurus tournemirensis from France and Microcleidus homalospondylus from England form a monophyletic clade, which is the sister taxon to the Cretaceous elasmosaurs. A palaeobiogeographical comparison of plesiosaur localities in the Lower Jurassic shows distinct palaeobiogeographical zones for the Toarcian, with different plesiosaur taxa in England, Germany and France. [source] Phylogenetic relationships of Early,Middle Ordovician ostracods of BaltoscandiaPALAEONTOLOGY, Issue 2 2004Oive Tinn Phylogenetic analysis of the Early and early Middle Ordovician (Tremadoc and Arenig) ostracod species of Baltoscandia suggests a polyphyletic origin for the suborder Beyrichiocopa. Binodicopes, leiocopes and eridostracans are excluded from the beyrichiocopide clade. An independent origin from the basal ostracods is suggested for the binodicopes and eridostracans. The palaeocopes form a strongly supported monophyletic clade. Within this suborder, the ctenonotellid and the tetradellid families together form a monophyletic clade. The tetradellids are paraphyletic, being a stem-group for the ctenonotellids. Nanopsis nanella, the earliest known ostracod from the Tremadoc, is a basal palaeocope. The early eridostracans Conchoprimitia and Incisua, with their uncomplicated carapace morphology, might be the most primitive ostracods. [source] Molecular phylogenetic analyses of the Japanese Ulva and Enteromorpha (Ulvales, Ulvophyceae), with special reference to the free-floating UlvaPHYCOLOGICAL RESEARCH, Issue 2 2003Satoshi Shimada SUMMARY In order to elucidate the species composition of free-floating Ulva that cause green tide in several bays in Japan, and to clarify the generic status of Ulva and Enteromorpha (Ulvales, Ulvophyceae), the nuclear encoded internal transcribed spacer (ITS) region including the 5.8S gene and the plastid encoded large subunit of ribulose-1, 5-bisphosphate carboxylase/ oxgenase (rbcL) gene sequences for 15 species were determined. Both ITS and rbcL analyses indicate that free-floating Ulva samples are divided into four different lineages that correspond to Ulva lactuca Linnaeus, U. pertusa Kjellman, U. armoricana Dion etal. and U. fasciata Delile. These four species are distinguished by cell morphology including the arrangement of cells, the shape and size of cells and the position of chloroplasts. Molecular data also indicated that Ulva and Enteromorpha are not separated as respective monophyletic groups within a large monophyletic clade and congeneric as shown by previous molecular studies using the ITS sequences alone. This strongly suggests that these genera are congeneric and Enteromorpha should be reduced to the synonym of Ulva. [source] A Molecular Phylogenetic Investigation of Opisthonecta and Related Genera (Ciliophora, Peritrichia, Sessilida)THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2007DANIEL WILLIAMS ABSTRACT. The gene encoding 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in the sessiline peritrichs Opisthonecta minima and Opisthonecta matiensis, whose free-swimming, paedomorphic trophonts resemble telotrochs. Using these new sequences, phylogenetic trees were constructed with four different methods to test a previously published association between Opisthonecta henneguyi and members of the families Vorticellidae and Astylozoidae. All trees had similar topologies, with O. minima, O. henneguyi, Vorticella microstoma, and Astylozoon enriquesi forming a well-supported, certainly monophyletic clade. On the basis of genetic evidence, genera of the families Opisthonectidae and Astylozoidae are assigned to the family Vorticellidae, which already includes some species with free-swimming morphotypes. The ssu rRNA sequence of O. matiensis places it in the family Epistylididae; its taxonomic revision will be left to another group of authors. A close association of Ophrydium versatile with members of the family Vorticellidae was confirmed, casting doubt on the validity of the family Ophrydiidae. Epistylis galea, Campanella umbellaria, and Opercularia microdiscum are confirmed as comprising an extremely distinct, monophyletic, but morphologically heterogeneous clade that is basal to other clades of sessiline peritrichs. [source] Combining genetic and ecological data to assess the conservation status of the endangered Ethiopian walia ibexANIMAL CONSERVATION, Issue 2 2009B. Gebremedhin Abstract Knowledge about the phylogenetic history, genetic variation and ecological requirements of a species is important for its conservation and management. Unfortunately, for many species this information is lacking. Here we use multiple approaches (phylogenetics, population genetics and ecological modelling) to evaluate the evolutionary history and conservation status of Capra walie, an endangered flagship species of wild goat endemic to Ethiopia. The analysis of mitochondrial cytochrome b and Y-chromosome DNA sequences suggests that C. walie forms a monophyletic clade with Capra nubiana, but potentially has been isolated for up to 0.8 million years from this closely related species. Microsatellite DNA analyses show that C. walie has very low genetic variation (mean heterozygosity=0.35) compared with other endangered mammals. This reduced variation likely derives from a prolonged demographic decline and small effective population size. Ecological niche modelling using the bioclimatic features of habitats occupied by C. walie, suggests ecological differences between C. walie and C. nubiana, and identifies the areas most suitable for future reintroductions of C. walie. The genetic and bioclimatic data suggest that C. walie is distinct and requires immediate conservation actions including genetic monitoring and reintroductions to establish independent populations. This study illustrates how combining noninvasive sampling along with genetic and ecological (bioclimatic) approaches can help assess conservation status of poorly known species. [source] Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence dataBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2002NINA RØNSTED A molecular phylogenetic study of Plantago L. (Plantaginaceae) analysed nucleotide variation in the internal transcribed spacers (ITS) of nuclear ribosomal and plastid trnL-F regions. Included are 57 Plantago species, with two Aragoa species as the ingroup and three Veronica species as the outgroup. Phylogenetic analysis using maximum parsimony identified five major clades, corresponding to the taxonomic groups Plantago subgenera Plantago, Coronopus, Psyllium, Littorella and Bougueria. Aragoa is sister to genus Plantago. Plantago subgenus Littorella is sister to the other subgenera of Plantago. The results are in general correlated with a morphological phylogenetic study and iridoid glucoside patterns, but Plantago subgenus Albicans is paraphyletic and should be included in Plantago subgenus Psyllium sensu lato to obtain a monophyletic clade with six sections. Plantago section Hymenopsyllium is more closely related to section Gnaphaloides than to section Albicans. Plantago subgenus Bougueria is sister to subgenus Psyllium s.l. section Coronopus in Plantago subgenus Coronopus is subdivided in two series. Only some of the sections can be resolved into series. DNA variation within genus Plantago is high, a result that would not have been predicted on the basis of morphology, which is relatively stereotyped. If we calibrate a molecular clock based on the divergence of P. stauntoni, endemic to New Amsterdam in the southern Indian Ocean, we calculate the time of the split between Plantago and Aragoa to be 7.1 million years ago, which is congruent with the fossil record. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society, 2002, 139, 323,338. [source] Phylogeny of the Myllaenini and related taxa (Coleoptera: Staphylinidae: Aleocharinae)CLADISTICS, Issue 2 2004Kee-Jeong Ahn A cladistic analysis of the tribe Myllaenini Ganglbauer and related genera is presented. Monophyly of the Myllaenini is tested, and the tribe is hypothesized to be a monophyletic group consisting of nine genera (Myllaena Erichson, Amazonopora Pace, Dimonomera Cameron, Bryothinusa Casey, Philomina Blackwelder, Polypea Fauvel, Brachypronomaea Sawada, Rothium Moore and Legner, and Lautaea Sawada), based on the synapomorphy of antero-lateral angles of mentum prolonged into spinose processes. A history of the classification of the Myllaenini is discussed. The data set for phylogenetic analysis comprised 99 characters representing 297 character states derived from adult morphology. The analysis agrees on the monophyly of the Myllaenini and the monophyly of the Pronomaeini Ganglbauer (Pronomaea Erichson, Pseudomniophila Pace, Nopromaea Cameron and Tomoxelia Bernhauer). The tribe Dimonomerini (Dimonomera Cameron) is confirmed to be a member of the Myllaenini. Masuriini is a possible sister group of the Myllaenini. Stylopalpus Cameron shows a sister group relationship to the Pronomaeini. Several other clades are also consistently recovered. However, the phylogenetic relationships of the genus Dysacrita are ambiguous. The rogue genus Diglotta Champion is not recovered as a member of the Myllaenini or Pronomaeini. On the contrary, it forms a monophyletic clade with the liparocephaline genera Halorhadinus Sawada and Amblopusa Casey. Evolution of the defensive gland on abdominal tergite VII among aleocharine lineages is reconsidered, and the origin of an intertidal habitat in the Myllaenini is discussed. [source] Cladogenesis and reticulation in the Hawaiian endemic mints (Lamiaceae)CLADISTICS, Issue 6 2003Charlotte Lindqvist The Hawaiian endemic mints, which comprise 58 species of dry-fruited Haplostachys and fleshy-fruited Phyllostegia and Stenogyne, represent a major island radiation that likely originated from polyploid hybrid ancestors in the temperate North American Stachys lineage. In contrast with considerable morphological and ecological diversity among taxa, sequence variation in the nrDNA 5S non-transcribed spacer was found to be remarkably low, which when analyzed using standard parsimony resulted in a lack of phylogenetic resolution among accessions of insect-pollinated Phyllostegia and bird-pollinated Stenogyne. However, many within-individual nucleotide polymorphisms were observed, and under the assumption that they could contain phylogenetic information, these ambiguities were recoded as new character states. Substantially more phylogenetic structure was obtained with these data, including the resolution of most Stenogyne species into a monophyletic group with an apparent recent origin on O'ahu (3.0 My) or the Maui Nui island complex (2.2 My). Subsequent diversification appears to have involved multiple inter-island dispersal events. Intergeneric placements for a few morphotypes, seemingly misplaced within either Phyllostegia or Stenogyne, may indicate reticulation as one polymorphism-generating force. For a finer scale exploration of hybridization, preliminary AFLP fragment data were examined among putative hybrids of Stenogyne microphylla and S. rugosa from Mauna Kea, Hawai'i, that had been identified based on morphology. Cladistic analysis (corroborated by multivariate correspondence analysis) showed the morphologically intermediate individuals to group in a strongly supported monophyletic clade with S. microphylla. Therefore, reticulation could be both historic and active in Stenogyne, and perhaps a force of general importance in the evolution of the Hawaiian mints. The relatively greater extent of lineage-sorted polymorphisms in Stenogyne may indicate selective differentiation from other fleshy-fruited taxa, perhaps through the agency of highly specialized bird pollinators that restricted gene flow with other Hawaiian mint morphotypes. [source] Incipient speciation of Catostylus mosaicus (Scyphozoa, Rhizostomeae, Catostylidae), comparative phylogeography and biogeography in south-east AustraliaJOURNAL OF BIOGEOGRAPHY, Issue 3 2005Michael N Dawson Abstract Aim, Phylogeography provides a framework to explain and integrate patterns of marine biodiversity at infra- and supra-specific levels. As originally expounded, the phylogeographic hypotheses are generalities that have limited discriminatory power; the goal of this study is to generate and test specific instances of the hypotheses, thereby better elucidating both local patterns of evolution and the conditions under which the generalities do or do not apply. Location, Coastal south-east Australia (New South Wales, Tasmania and Victoria), and south-west North America (California and Baja California). Methods, Phylogeographic hypotheses specific to coastal south-east Australia were generated a priori, principally from existing detailed distributional analyses of echinoderms and decapods. The hypotheses are tested using mitochondrial cytochrome c oxidase subunit I (COI) and nuclear internal transcribed spacer 1 (ITS1) DNA sequence data describing population variation in the jellyfish Catostylus mosaicus, integrated with comparable data from the literature. Results, Mitochondrial COI distinguished two reciprocally monophyletic clades of C. mosaicus (mean ± SD: 3.61 ± 0.40% pairwise sequence divergence) that were also differentiated by ITS1 haplotype frequency differences; the boundary between the clades was geographically proximate to a provincial zoogeographic boundary in the vicinity of Bass Strait. There was also limited evidence of another genetic inhomogeneity, of considerably smaller magnitude, in close proximity to a second hypothesized zoogeographic discontinuity near Sydney. Other coastal marine species also show genetic divergences in the vicinity of Bass Strait, although they are not closely concordant with each other or with reported biogeographic discontinuities in the region, being up to several hundreds of kilometres apart. None of the species studied to date show a strong phylogeographic discontinuity across the biogeographic transition zone near Sydney. Main conclusions, Patterns of evolution in the Bass Strait and coastal New South Wales regions differ fundamentally because of long-term differences in extrinsic factors. Since the late Pliocene, periods of cold climate and low sea-level segregated warm temperate organisms east or west of an emergent Bassian Isthmus resulting in population divergence and speciation; during subsequent periods of warmer and higher seas, sister taxa expanded into the Bass Strait region leading to weakly correlated phylogeographic and biogeographic patterns. The Sydney region, by contrast, has been more consistently favourable to shifts in species' ranges and long-distance movement, resulting in a lack of intra-specific and species-level diversification. Comparisons between the Sydney and Bass Strait regions and prior studies in North America suggest that vicariance plays a key role in generating coastal biodiversity and that dispersal explains many of the deviations from the phylogeographic hypotheses. [source] Biogeographical patterns of genetic differentiation in dung beetles of the genus Trypocopris (Coleoptera, Geotrupidae) inferred from mtDNA and AFLP analysesJOURNAL OF BIOGEOGRAPHY, Issue 7 2004Loredana Carisio Abstract Aim, To examine the phylogeography and population structure of three dung beetle species of the genus Trypocopris (Coleoptera, Geotrupidae). We wanted to test whether genetic differences and genealogies among populations were in accordance with morphologically described subspecies and we aimed to establish times of divergence among subspecies to depict the appropriate temporal framework of their phylogeographical differentiation. We also wished to investigate the historical demographic events and the relative influences of gene flow and drift on the distribution of genetic variability of the different populations. Location, Europe (mostly Italy). Methods, We collected adult males from dung pats from 15 Italian localities over the period 2000,2002. For sequence analysis, some dried specimens from Albania, Croatia, Slovakia and Spain were also used. We applied cytochrome oxidase I mitochondrial DNA sequencing and the amplified fragment length polymorphism (AFLP) technique to determine whether phylogeographical patterns within the three species support the proposed hypotheses of subspecies designations, and to detect further structure among populations that might mediate diversification. Results and main conclusions, The results show a high concordance between the distribution of mtDNA variation and the main morphological groups recognized as subspecies, which thus may represent independent evolutionary units. The degree of mitochondrial divergence suggests that speciation events occurred during the Pliocene, while diversification of the main subspecific lineages took place in the Pleistocene, from c. 0.3 to 1.5 Ma. Mitochondrial and nuclear data also reveal that there is phylogeographical structuring among populations within each of the main groups and that both contemporary and historical processes determined this pattern of genetic structure. Geographical populations form monophyletic clades in both phylogenetic and network reconstructions. Despite the high levels of intrapopulational diversity, FST values indicate moderate but significant genetic differentiation among populations, and a Bayesian clustering analysis of the AFLP data clearly separates the geographical populations. Nucleotide and gene diversity estimates reveal interspecific differences in the degree of diversification among populations that may be related to the different ecological requirements of the three species. [source] SOME PHYLOGENETIC RELATIONSHIPS WITHIN THE OSCILLATORIALES (CYANOBACTERIA) CLADE USING 16S RDNA GENE SEQUENCE DATAJOURNAL OF PHYCOLOGY, Issue 2000D.A. Casamatta An approximately 1400 base pair region of the 16S rDNA gene was sequenced from taxa within the Oscillatoriales in order to assess phylogenetic relationships. Ten previously unsequenced strains were obtained from the University of Toronto Culture Collection. New sequence data were combined with previously published sequences from a wide representation of cyanobacteria including all currently available, complete Oscillatorialian taxa. Trees constructed using parsimony, distance, and maximum likelihood methods were similar in topology, although a few taxa were variable in their placement depending on the phylogenetic method employed. Newly sequenced taxa of the genera Phormidium, Oscillatoria, and Lyngbya did not form monophyletic clades based on traditional generic designations. Two Lyngbya strains (UTCC296 and 313) and Phormidium subfuscum (UTCC474) formed a well supported monophyletic clade, but the affinity of this clade with other groups was uncertain due to lack of bootstrap support. Oscillatoria sp. (UTCC393) was closely related to the previously sequenced Oscillatoria limnetica and likewise, Phormidium molle (UTCC77) and Phormidium tenue (UTCC473) were placed in a well supported clade with other Oscillatoriales. The other four taxa were variously placed in the trees and their phylogenetic positions could not be determined with certainty. [source] Clades within the ‘higher land birds’, evaluated by nuclear DNA sequencesJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1-2 2001Johansson In this study we investigated the phylogenetic relationships within the ‘higher land birds’ by parsimony analysis of nucleotide DNA sequences obtained from the two nuclear, protein-coding genes, c- myc and RAG-1. Nuclear genes have not previously been used to address this phylogenetic question. The results include high jackknife support for a monophyletic Apodiformes (including the Trochilidae). This arrangement was further supported by the observation of an insertion of four amino acids in the c- myc gene in all apodiform taxa. Monophyly was also inferred for each of the two piciform groups Galbulae and Pici. Within Pici, the Capitonidae was found to be paraphyletic, with the New World barbets more closely related to the Ramphastidae than to the Old World barbets. Another clade with high jackknife support consists of the Upupidae, Phoeniculidae and Bucerotidae. The families Momotidae and Todidae, and Coraciidae and Brachypteraciidae, respectively, also form well supported monophyletic clades. The results are inconclusive regarding the monophyly of the orders Coraciiformes and Piciformes, respectively. Die von nuklearen DNA-Sequenzen abgeleiten Kladen bei den ‘Höheren and vögeln’ Es wurde eine Studie über die phylogenetischen Beziehungen bei den ‘höheren Landvögeln’ mit Hilfe einer Parsimonie-Analyse von DNA-Kernsequenzen zweier proteincodierender Genen, c-myc und RAG-1, durchgeführt. Kerngene wurden bisher noch nicht für die Untersuchung dieser phylogentischen Frage eingesetzt. Die Ergebnisse unterstützen mit hohen Jackknife-Werten eine Monophylie der Apodiformes (einschließlich der Trochilidae). Eine solche Einordnung wird auch durch die Beobachtung einer Einfüngung von vier Aminosäuren im c-myc -Gen bei allen apodiformen Taxa unterstützt. Eine Monophylie konnte ebenso für die beiden picidiformen Gruppen, Glabulae und Pici, bestätigt werden. Bei den Pici erweisen sich die Capitonidae als paraphyletisch, wobei die Bartvögel der NeuenWelt näher mit den Ramphistidae verwandt sind als mit den Bartvögeln der Alten Welt. Eine weitere Klade, die durch hohe Jackknife-Werte unterstützt wird, besteht aus den Upupidae, Phoeniculidae und Bucerotidae. Die Familien Momotidae und Todidae bzw. Coraciidae und Brachypteraciidae bilden ebenfalls gut unterstützte Kladen. Über die Monophylie der Ordnungen Coraciiformes und Piciformes können die Ergebnisse jedoch keine Entscheidung herbeiführen. [source] Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerineMOLECULAR ECOLOGY, Issue 12 2007ALICIA TOON Abstract While many studies have documented the effect that glacial cycles have had on northern hemisphere species, few have attempted to study the associated effect of aridification at low latitudes in the southern hemisphere. We investigated the past effects that cyclic aridification may have had on the population structure and history of a widespread endemic Australian bird species, the Australian magpie (Gymnorhina tibicen). One thousand one hundred and sixty-six samples from across its native range were analysed for mitochondrial control region sequence variation and variation at six microsatellite loci. Analysis of mitochondrial control region sequence data indicated monophyletic clades that were geographically congruent with an eastern and western region. The contemporary distribution of east and west clades is nonoverlapping but in close proximity. Populations were estimated to have diverged in the Pleistocene around 36 000 years ago. The putative Carpentarian and Nullarbor arid barriers appear to be associated with the divergence between east and west mainland populations. Nested clade analysis indicated a signature of range expansion in the eastern region suggesting movement possibly inland and northward subsequent to the last period of aridity. The island population of Tasmania was of very recent origin, possibly since sea levels rose 16 000 years ago. Given the east-west structure, there was no congruence between morphology and recent history of this species indicating a lack of support for morphological taxa. Overall mitochondrial DNA and microsatellite variation suggest that increasing aridity and Pleistocene refugia played a role in structuring populations of the Australian magpie; however, the dispersal ability and generalist habitat requirements may have facilitated the movement of magpies into an almost contiguous modern distribution across the continent. This study supports the idea that Pleistocene aridification played an important role in structuring intraspecific variation in low latitudinal southern hemisphere avian species. [source] Comparative phylogeography of sympatric sister species, Clevelandia ios and Eucyclogobius newberryi (Teleostei, Gobiidae), across the California Transition ZoneMOLECULAR ECOLOGY, Issue 6 2002M. N Dawson Abstract It is paradigmatic in marine species that greater dispersal ability often, but not always, results in greater gene flow and less population structure. Some of the exceptions may be attributable to studies confounded by comparison of species with dissimilar evolutionary histories, i.e. co-occurring species that are not closely related or species that are closely related but allopatric. Investigation of sympatric sister species, in contrast, should allow differences in phylogeographic structure to be attributed reliably to recently derived differences in dispersal ability. Here, using mitochondrial DNA control region sequence, we first confirm that Clevelandia ios and Eucyclogobius newberryi are sympatric sister taxa, then demonstrate considerably shallower phylogeographic structure in C. ios than in E. newberryi. This shallower phylogeographic structure is consistent with the higher dispersal ability of C. ios, which most likely results from the interaction of habitat and life-history differences between the species. We suggest that the paradigm will be investigated most rigorously by similar studies of other sympatric sister species, appended by thorough ecological studies, and by extending this sister-taxon approach to comparative phylogeographic studies of monophyletic clades of sympatric species. [source] DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and PlanotortrixMOLECULAR ECOLOGY RESOURCES, Issue 3 2009PIA LANGHOFF Abstract Molecular techniques such as DNA barcoding have become popular in assisting species identification especially for cryptic species complexes. We have analysed data from a 468-bp region of the mitochondrial cytochrome oxidase subunit I (COI) gene from 200 specimens of 12 species of endemic New Zealand leafroller moths (Tortricidae) from the genera Planotortrix and Ctenopseustis to assess whether the DNA barcoding region can distinguish these species. Among the 200 sequences analysed, 72 haplotypes were recovered, with each genus forming a separate major clade. Maximum likelihood phylogenetic methods were used to test whether species fell into reciprocally monophyletic clades. The optimal phylogeny showed that four species within the genus Ctenopseustis (C. obliquana, C. herana, C. filicis and C. fraterna) and three within Planotortrix (P. octo, P. excessana and P. avicenniae) are polyphyletic. Shimodaira,Hasegawa tests rejected a null hypothesis of monophyly for the species C. obliquana, C. herana, P. octo and P. excessana. Comparisons of within and between species levels of sequence divergence for the same set of seven species showed cases where maximum levels of within-species divergence were greater than some levels of between-species divergence. DNA barcoding using this region of the COI gene is able to distinguish the two genera and some species within each genus; however, many species cannot be identified using this method. Finally, we discuss the possible reasons for this polyphyly, including incomplete lineage sorting, introgression, horizontal gene transfer and incorrect taxonomy. [source] Composition, geographical affinities and endemism of the Iberian Peninsula orchid floraNORDIC JOURNAL OF BOTANY, Issue 3-4 2007Sonia Bernardos The orchid flora of the Iberian Peninsula is relatively well known, but its biogeographical and diversity patterns have until now remained unanalysed. This work compares the richness of this flora with that of 27 other territories in different continents and at different latitudes, with the aim of establishing whether it is richer or poorer than might be expected. Latitude was found to be an excellent predictor of regional orchid species richness. With 122 taxa, the orchid flora of the Iberian Peninsula is more or less as diverse as that of other Mediterranean areas of similar latitude (e.g. France, Greece or Italy), but more diverse than other European or indeed North African orchid floras. In this study, the Iberian orchid species were assigned to eight monophyletic clades and the global distribution of these are mapped to establish continental affinities between the floras. A recent floristic account on the Iberian orchids was also used to assign the orchid taxa to habitats, and the relationship between the number of endemisms and their habitats was analysed. The patterns of endemism differed in different habitats. Very high levels of endemism were found in habitats peculiar to the Mediterranean Basin, indicating the relict status of its orchid flora. [source] The complete mitochondrial genome of the domestic red deer (Cervus elaphus) of New Zealand and its phylogenic position within the family CervidaeANIMAL SCIENCE JOURNAL, Issue 5 2010Kenta WADA ABSTRACT We determined the complete nucleotide sequence of the mitochondrial genome of the semidomestic red deer (Cervus elaphus) of New Zealand. The genome was 16 357 bp long and contained 13 protein-coding genes, 12SrRNA, 16SrRNA, 22 tRNAs and a D-loop as found in other mammals. Database homology searches showed that the mitochondrial DNA (mtDNA) sequence from the New Zealand semidomestic deer was similar to partial mtDNA sequences from the European, Norwegian (C. e. atlanticus) and Spanish red deer (C. e. hispanicus). Phylogenetic analysis of the mitochondrial protein-coding regions revealed two well-defined monophyletic clades in subfamilies Cervinae and Muntiacinae. However, red deer and Sika deer were not found to be close relatives. The analysis did identify the red deer as a sister taxon of a Samber/Sika deer clade, although it was more closely related to the Samber than the Sika group. [source] | |||||||||||||||||||||||||||||||||||||