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Molecular Phylogenetic Analysis (molecular + phylogenetic_analysis)

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Life Sciences	90%
3 Other Domains	10%

Distribution within Life Sciences

Evolution	27%
Plant Science	10%
Entomology	6%
6 Other Subdomains	30%

Selected Abstracts

COMPARATIVE MORPHOLOGY AND MOLECULAR PHYLOGENETIC ANALYSIS OF THREE NEW SPECIES OF THE GENUS KARENIA (DINOPHYCEAE) FROM NEW ZEALAND,

JOURNAL OF PHYCOLOGY, Issue 1 2004
Allison J. Haywood
Three new dinoflagellate species, Karenia papilionacea sp. nov., Karenia selliformis sp. nov., and Karenia bidigitata sp. nov., were compared with the toxic species Karenia mikimotoi (Miyake & Kominami ex Oda) G. Hansen & Moestrup, Karenia brevis (Davis) G. Hansen & Moestrup, and Karenia brevisulcata (Chang) G. Hansen & Moestrup using the same fixative. Distinguishing morphological characters for the genus Karenia included a smooth theca and a linear apical groove. The new species can be distinguished on the basis of morphological characters of vegetative cells that include the location and shape of the nucleus; the relative excavation of the hypotheca; the characteristics of apical and sulcal groove extensions on the epitheca; the cellular shape, size, and symmetry; the degree of dorsoventral compression; and the presence of an apical protrusion or carina. Species with pronounced dorsoventral compression swim in a distinctive fluttering motion. An intercingular tubular structure traversing the proximal and distal ends of the cingulum is common to the species of Karenia, Karlodinium micrum (Leadbeater & Dodge) J. Larsen, Gymnodinium pulchellum J. Larsen, and Gyrodinium corsicum Paulmier. Molecular phylogenetic analyses of rDNA sequence alignments show that the new species are phylogenetically distinct but closely related to K. mikimotoi and K. brevis. [source]

Phylogenetic diversity of non-nodulating Rhizobium associated with pine ectomycorrhizae

FEMS MICROBIOLOGY ECOLOGY, Issue 3 2009
Megumi Tanaka
Abstract Most Rhizobium species described are symbionts that form nodules on legume roots; however, non-nodulating strains of Rhizobium are also widespread in nature. Unfortunately, knowledge of non-nodulating Rhizobium is quite limited compared with nodulating Rhizobium. Here, we studied the phylogenetic diversity of Rhizobium species that inhabit Japanese red pine roots (Pinus densiflora). Because fine roots of pine trees are usually colonized by ectomycorrhizal fungi in nature, we mainly used ectomycorrhizal root tips for bacterial isolation. Out of 1195 bacteria isolated from 75 independent root samples from the field and greenhouse experiments, 102 isolates were confirmed to be Rhizobium following partial 16S rRNA gene analysis. Rhizobium species were occasionally dominant in culturable bacterial communities, whereas no Rhizobium species were isolated from the soil itself. Molecular phylogenetic analyses using 16S rRNA, atpD, and recA gene sequences revealed that isolated Rhizobium strains were phylogenetically diverse and that several were distantly related to known Rhizobium species. Considering that a single species of pine is associated with unique and phylogenetically diverse Rhizobium populations, we should pay more attention to non-nodulating strains to better understand the diversity, ecology, and evolution of the genus Rhizobium and plant,Rhizobium associations. [source]

MORPHOLOGY, LIFE HISTORY, AND MOLECULAR PHYLOGENY OF STSCHAPOVIA FLAGELLARIS (TILOPTERIDALES, PHAEOPHYCEAE) AND THE ERECTION OF THE STSCHAPOVIACEAE FAM.

JOURNAL OF PHYCOLOGY, Issue 6 2004

The 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]

COMPARATIVE MORPHOLOGY AND MOLECULAR PHYLOGENETIC ANALYSIS OF THREE NEW SPECIES OF THE GENUS KARENIA (DINOPHYCEAE) FROM NEW ZEALAND,

Molecular phylogenetic analyses of the Japanese Ulva and Enteromorpha (Ulvales, Ulvophyceae), with special reference to the free-floating Ulva

PHYCOLOGICAL RESEARCH, Issue 2 2003
Satoshi 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 novel Takeout-like protein expressed in the taste and olfactory organs of the blowfly, Phormia regina

FEBS JOURNAL, Issue 18 2006
Kazuyo Fujikawa
In insects, the functional molecules responsible for the taste system are still obscure. The gene for a 28.5 kDa protein purified from taste sensilla of the blowfly Phormia regina belongs to a gene family that includes takeout of Drosophila melanogaster. Molecular phylogenetic analysis revealed that the Phormia Takeout-like protein is most similar to the protein encoded by a member of the Drosophila takeout gene family, CG14661, whose expression and function have not been identified yet. Western blot analyses revealed that Phormia Takeout-like protein was exclusively expressed in antennae and labellum of the adult blowfly in both sexes. Immunohistochemical experiments demonstrated that Takeout-like protein was localized around the lamella structure of the auxiliary cells and in the sensillar lymph of the labellar taste sensillum. In antennae, Takeout-like protein was distributed at the base of the olfactory sensilla as well. No significant differences in Takeout-like protein expression were found between the sexes. Our results suggest that Phormia Takeout-like protein is involved in some early events concerned with chemoreception in both the taste and olfactory systems. [source]

Coexistence of two mitochondrial DNA haplotypes in Japanese populations of Hypera postica (Col., Curculionidae)

JOURNAL OF APPLIED ENTOMOLOGY, Issue 4 2005
R. Kuwata
Abstract:, In Japan, the alfalfa weevil, Hypera postica, was first recorded in 1982 from Fukuoka and Okinawa Prefectures and has been spreading to many other prefectures. The weevil seriously infests the Chinese milk vetch, Astragalus sinicus, one of the most important honey resources for honeybees in Japan. Direct sequencing of partial mitochondrial DNA and PCR-RFLP data for alfalfa weevil individuals indicated the coexistence of two haplotypes at various localities in Japan. Molecular phylogenetic analysis for H. postica haplotypes and strains indicated that the two Japanese haplotypes had not derived from a single genetic origin. Based on the results, special comments are made on biological control measures using introduced parasitic waSPS. [source]

Molecular phylogenetic analysis of the white-crowned forktail Enicurus leschenaulti in Borneo

JOURNAL OF AVIAN BIOLOGY, Issue 2 2005
Robert G. Moyle
Comparison of 1017 nucleotides of mitochondrial ND2 and ND3 DNA sequences of 26 individuals of white-crowned forktail Enicurus leschenaulti from SE Asia revealed multiple evolutionary lineages within Borneo. Montane birds were genetically homogeneous across localities, but diverged by more than 4.3% from all other samples. Lowland birds formed two distinct clades, one consisting of individuals from northern Borneo, and the other including individuals from western Borneo, as well as Sumatra and Malaya. Relationships among the subspecies were not well resolved. These findings indicate another example of montane and north Bornean endemicity, support the separation of the montane and lowland species, and define areas of conservation interest. [source]

Molecular phylogenetic analysis of Leibnitzia Cass. (Asteraceae: Mutisieae: Gerbera -complex), an Asian,North American disjunct genus

JOURNAL OF SYSTEMATICS EVOLUTION, Issue 3 2010
Kristen E. BAIRD
Abstract Leibnitzia comprises six species of perennial herbs that are adapted to high elevation conditions and is one of only two Asteraceae genera known to have an exclusively disjunct distribution spanning central to eastern Asia and North America. Molecular phylogenetic analysis of Leibnitzia and other Gerbera -complex members indicates that Leibnitzia is monophyletic, which is in contrast with our expectation that the American Leibnitzia species L. lyrata and L. occimadrensis would be more closely related to another American member of the Gerbera -complex, namely Chaptalia. Ancestral area reconstructions show that the historical biogeography of the Gerbera -complex mirrors that of the entire Asteraceae, with early diverging lineages located in South America that were followed by transfers to Africa and Eurasia and, most recently, to North America. Intercontinental transfer of Leibnitzia appears to have been directed from Asia to North America. Independent calibrations of nuclear (ribosomal DNA internal transcribed spacer region) and chloroplast (trnL,rpl32 intron) DNA sequence data using relaxed clock methods and either mean rate or fossil-based priors unanimously support Miocene and younger divergence times for Gerbera -complex taxa. The ages are not consistent with most Gondwanan vicariance episodes and, thus, the global distribution of Gerbera -complex members must be explained in large part by long-distance dispersal. American species of Leibnitzia are estimated to have diverged from their Asian ancestor during the Quaternary (ca. 2 mya) and either migrated overland to North America via Beringia and retreated southwards along high elevation corridors to their present location in southwestern North America or were dispersed long distance. [source]

Prevailing triple infection with Wolbachia in Callosobruchus chinensis (Coleoptera: Bruchidae)

MOLECULAR ECOLOGY, Issue 2 2002
Natsuko Kondo
Abstract Prevailing triple infection with three distinct Wolbachia strains was identified in Japanese populations of the adzuki bean beetle, Callosobruchus chinensis. When a polymerase chain reaction (PCR) assay was conducted using universal primers for ftsZ and wsp, Wolbachia was detected in all the individuals examined, 288 males and 334 females from nine Japanese populations. PCR,restriction fragment length polymorphism (RFLP) analysis of cloned wsp gene fragments from single insects revealed that three types of wsp sequences coexist in the insects. Molecular phylogenetic analysis of the wsp sequences unequivocally demonstrated that C. chinensis harbours three phylogenetically distinct Wolbachia, tentatively designated as wBruCon, wBruOri and wBruAus, respectively. Diagnostic PCR analysis using specific primers demonstrated that, of 175 males and 235 females from nine local populations, infection frequencies with wBruCon, wBruOri and wBruAus were 100%, 96.3% and 97.0%, respectively. As for the infection status of individuals, triple infection (93.7%) dominated over double infection (6.1%) and single infection (0.2%). The amounts of wBruCon, wBruOri and wBruAus in field-collected adult insects were analysed by using a quantitative PCR technique in terms of wsp gene copies per individual insect. Irrespective of original populations, wBruCon and wBruOri (107,108wsp copies/insect) were consistently greater in amount than wBruAus (106,107wsp copies/insect), suggesting that the population sizes of the three Wolbachia strains are controlled, although the mechanism is unknown. Mating experiments suggested that the three Wolbachia cause cytoplasmic incompatibility at different levels of intensity. [source]

Molecular Cloning and Characterization of CD9 cDNA from Sheep and Cashmere Goat

REPRODUCTION IN DOMESTIC ANIMALS, Issue 3 2010
WJ Xing
Contents CD9 is a glycoprotein of the transmembrane 4 superfamily (TM4SF) and is involved in various cellular processes. Some CD9 cDNA have been cloned in mammals and certain fish genera in recent years, but goat and sheep counterparts of cattle, human and mouse have not been identified. To facilitate the studies, we cloned the cDNA encoding for CD9 of cashmere goat (Capra hircus) and sheep (Ovis aries), and expressed sheep CD9 in Escherichia coli cells. Structural analysis indicated for both goat and sheep that a 1123 bp cDNA spanned an open reading frame of 681 bp which predicted a protein of 226 amino acids with a typical TM4SF structure, including four highly conserved transmembrane domains, two extracellular domains and a CCG motif, which is a hallmark of the TM4SF. The predicted amino acid sequences were highly homologous to those of cattle, mouse and human CD9. Molecular phylogenetic analysis based on CD9 cDNA sequences indicated that goat and sheep CD9 were closely related to CD9 of cattle, which is in agreement with their morphological taxonomy. [source]

GENETIC DIVERSITY AND INTROGRESSION IN TWO CULTIVATED SPECIES (PORPHYRA YEZOENSIS AND PORPHYRA TENERA) AND CLOSELY RELATED WILD SPECIES OF PORPHYRA (BANGIALES, RHODOPHYTA),

JOURNAL OF PHYCOLOGY, Issue 2 2009
Kyosuke Niwa
We investigated the genetic variations of the samples that were tentatively identified as two cultivated Porphyra species (Porphyra yezoensis Ueda and Porphyra tenera Kjellm.) from various natural populations in Japan using molecular analyses of plastid and nuclear DNA. From PCR-RFLP analyses using nuclear internal transcribed spacer (ITS) rDNA and plastid RUBISCO spacer regions and phylogenetic analyses using plastid rbcL and nuclear ITS-1 rDNA sequences, our samples from natural populations of P. yezoensis and P. tenera showed remarkably higher genetic variations than found in strains that are currently used for cultivation. In addition, it is inferred that our samples contain four wild Porphyra species, and that three of the four species, containing Porphyra kinositae, are closely related to cultivated Porphyra species. Furthermore, our PCR-RFLP and molecular phylogenetic analyses using both the nuclear and plastid DNA demonstrated the occurrence of plastid introgression from P. yezoensis to P. tenera and suggested the possibility of plastid introgression from cultivated P. yezoensis to wild P. yezoensis. These results imply the importance of collecting and establishing more strains of cultivated Porphyra species and related wild species from natural populations as genetic resources for further improvement of cultivated Porphyra strains. [source]

TAXONOMIC REEXAMINATION OF 17 SPECIES OF NITELLA SUBGENUS TIEFFALLENIA (CHARALES, CHAROPHYCEAE) BASED ON INTERNAL MORPHOLOGY OF THE OOSPORE WALL AND MULTIPLE DNA MARKER SEQUENCES,

JOURNAL OF PHYCOLOGY, Issue 1 2005
Hidetoshi Sakayama
In an attempt to reconstruct the natural taxonomic system for Nitella, 17 species of Nitella subgenus Tieffallenia were reexamined using SEM observations of the internal morphology of the oospore wall (IMOW) and phylogenetic analyses of 4553 base pairs from multiple DNA markers (atpB, rbcL, psaB, and ITS-5.8S rRNA genes). Our SEM observations identified three types of IMOW: homogeneous (HG), weakly spongy (W-SG), and strongly spongy (S-SG) types. Based on differences in the IMOW, species with reticulate or tuberculate oospore wall ornamentation in the external morphology of the oospore wall (EMOW) were subdivided into two distinct groups (characterized by the HG or S-SG types of IMOW, respectively), which were robustly separated from each other in our molecular phylogenetic analyses. In our molecular phylogeny, the subgenus Tieffallenia consisted of four robust monophyletic groups,three clades of the HG type and a spongy (S-SG and W-SG) type clade,that were characterized by differences in the IMOW and EMOW. In addition, our SEM observations and sequence data verified the distinct status of five species (N. japonica Allen, N. oligospira A. Braun, N. vieillardii stat. nov., N. imperialis stat. nov., and N. morongii Allen) that R. D. Wood had assigned as infraspecific taxa. Moreover, our SEM observations of the IMOW also suggested that N. megaspora (J. Groves) Sakayama originally identified by LM includes at least two distinct species, characterized by W-SG and S-SG types of IMOW, respectively. [source]

GLOBAL SYSTEMATIC AND PHYLOGENETIC ANALYSIS OF SARGASSUM IN THE GULF OF MEXICO, CARIBBEAN AND PACIFIC BASIN

JOURNAL OF PHYCOLOGY, Issue 2000
N. Phillips
Sargassum is one of the most species-rich genera in the brown algae with over 400 described species worldwide. The bulk of these species occurs in Pacific-Indian ocean waters with only a small portion found on the Atlantic side of the Isthmus of Panama. Sargassum also has one of the most subdivided and complex taxonomic systems used within the algae. Systematic distinctions within the genus are further complicated by high rates of phenotypic variability in several key morphological characters. Molecular analyses in such systems should allow testing of systematic concepts while providing insights into speciation and evolutionary patterns. Global molecular phylogenetic analyses using both conserved and variable regions of the Rubisco operon (rbcL and rbcL-IGS-rbcS) were performed with species from the Gulf of Mexico, Caribbean, and Pacific basin. Results confirm earlier analyses based on rbcL-IGS- rbcS from Pacific species at the subgeneric and sectional level while providing additional insights into the systematics and phylogenetics on a global scale. For example, species east of the Isthmus of Panama form a distinct well-resolved clade within the tropical subgenus. This result in sharp contrast to traditional systematic treatments but provides a window into the evolutionary history of this genus in the Pacific and Atlantic Ocean basins and a possible means to time speciation events. [source]

Phylogeny and phylogeography of the Lozekia,Kovacsia species group (Gastropoda: Hygromiidae)

JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2009
Zoltán Fehér
Abstract The Lozekia,Kovacsia species group comprises three species of high conservation concern, Lozekia transsilvanica (Westerlund, 1876), Lozekia deubeli (M. Kimakowicz, 1890) and Kovacsia kovacsi (Varga and L. Pintér, 1972), which occupy relatively small ranges in the Carpathian-Pannonian region. Despite their conservation concern, the phylogeny and biogeographical history of these species have not been studied by molecular methods up to now. This study, based on mitochondrial cytochrome oxidase subunit I gene sequences, has two main objectives: (i) to infer the phylogenetic relationships within the group in order to test the latest morphology-based system, proposed by Nordsieck [1993, Das System der paläarktischen Hygromiidae (Gastropoda: Stylommatophora: Helicoidea). Arch Molluskenkunde 122:1] and (ii) to reconstruct the distribution history of the three species. The monophyly and thus the systematic distinctness of the three species was confirmed, but our findings do not support the monophyly of the Lozekia genus and therefore contradict the current system of the species group. Genetic diversity was found to be much higher within L. deubeli than within the other two species, a possible explanation of this phenomenon is that L. transsilvanica and K. kovacsi are more recently evolved, younger species. Nested clade phylogeographycal analysis showed that the three species evolved by fragmentation events; probably L. deubeli and the ancestor of the other two species split first. At the intraspecific level, fragmentation events, as well as range expansion, played a significant role in the biogeographical history of this species group. As our findings are based on a single mitochondrial gene, we feel premature to propose changes in the generally accepted system and nomenclature. Further molecular phylogenetic analyses, also involving nuclear DNA sequences, should clarify if the evolutionary scenario suggested by our data is valid, and the three species can indeed be placed within the same genus, Lozekia. Zusammenfassung Die Lozekia,Kovacsia Artengruppe umfasst drei endemische Arten, Lozekia transsilvanica (Westerlund, 1876), Lozekia deubeli (M. Kimakowicz, 1890) und Kovacsia kovacsi (Varga and L. Pintér, 1972), die relativ kleine Verbreitungsgebiete in der karpatisch-pannonischen Region besitzen. Trotz ihrer naturschutzfachlichen Bedeutung wurde die Phylogenie ind biogeographische Historie dieser Arten bisher nicht mit molekularen Methoden untersucht. In dieser Studie werden, basierend auf mitochondrialen COI-Sequenzen, zwei Hauptziele verfolgt: (i) Ermittlung der phylogenetischen Beziehungen in der Gruppe um das aktuelle morphologie.basierte System von Nordsieck (1993) zu testen, und (ii) Rekonstruktion der Verbreitungsgeschichte der drei Arten. In Übereinstimmung mit morphologischen Merkmalsausprägungen wurde die Monophylie und somit die systematische Eigenständigkeit der drei Arten bestätigt, im Gegensatz zur Monophylie der Gattung Lozekia. Die genetische Diversität in L. deubeli war viel höher als in den anderen beiden Arten. Eine mögliche Erklärung dieses Befundes ist, dass L. transsilvanica und K. kovacsi rezenter evolvierte, junge Arten sind. Eine Nested clade phylogeographical analysis (NCPA) zeigte, dass die drei Arten durch Fragmentierungsereignisse entstanden, wahrscheinlich teilten sich L. deubeli und der Vorläufer der anderen beiden Arten zuerst. Auf dem intraspezifischen Niveau spielten Fragmentierungsereignisse und ebenso Arealausdehnungen eine signifikante Rolle in der biogeographischen Geschichte der Artengruppe. Da unsere Ergebnisse auf einem einzigen mitochondrialen Gen basieren, ist es zu früh für Veränderungen am generell akzeptierten System und der Nomenklatur. Weitere molekular-phylogenetische Analysen, die auch nukleäre DNA sequenzen involvieren, müssen das auf unseren Daten basierende evolutionäre Szenario bestätigen und die Fragen klären, ob die drei Arten tatsächlich zur gleichen Gattung, Lozekia, gehören. [source]

The role of character loss in phylogenetic reconstruction as exemplified for the Annelida

JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2007
C. Bleidorn
Abstract Annelid relationships are controversial, and molecular and morphological analyses provide incongruent estimates. Character loss is identified as a major confounding factor for phylogenetic analyses based on morphological data. A direct approach and an indirect approach for the identification of character loss are discussed. Character loss can frequently be found within annelids and examples of the loss of typical annelid characters, like chaetae, nuchal organs, coelomic cavities and other features, are given. A loss of segmentation is suggested for Sipuncula and Echiura; both are supported as annelid ingroups in molecular phylogenetic analyses. Moreover, character loss can be caused by some modes of heterochronic evolution (paedomorphosis) and, as shown for orbiniid and arenicolid polychaetes, paedomorphic taxa might be misplaced in phylogenies derived from morphology. Different approaches for dealing with character loss in cladistic analyses are discussed. Application of asymmetrical character state transformation costs or usage of a dynamic homology framework represents promising approaches. Identifying character loss prior to a phylogenetic analysis will help to refine morphological data matrices and improve phylogenetic analyses of annelid relationships. Zusammenfassung Die Phylogenie der Annelida wird nach wie vor kontrovers diskutiert und morphologische und molekulare Analysen liefern hierbei unterschiedliche Ergebnisse. Merkmalsverluste können phylogenetische Analysen morphologischer Daten in die Irre führen. In der vorliegenden Arbeit werden ein direkter und ein indirekter Ansatz zur Erkennung von Merkmalsverlusten vorgestellt. Es wird gezeigt, dass Merkmalsverlust innerhalb der Anneliden häufig auftritt und das hiervon auch typische Annelidenmerkmale, wie z.B Borsten, Nuchalorgane oder Coelomräume betroffen seien können. Molekularphylogenetische Analysen unterstützen eine Stellung der Echiura und Sipuncula innerhalb der Anneliden und somit ist für diese Taxa ein Verlust der Segmentierung anzunehmen. Es wird demonstriert, dass Merkmalsverlust durch herterochrone Evolution verursacht werden kann. Am Beispiel von Orbiniiden und Arenicoliden wird gezeigt, wie paedomorphe Taxa in kladistischen Analysen morphologischer Daten falsch platziert werden. Verschiedene Ansätze zum Umgang mit Merkmalsverlust in morphologischen Datensätzen werden präsentiert und diskutiert. Hierbei stellen die Verwendung asymmetrischer Merkmalstransformationskosten oder die Verwendung dynamischer Homologiehypothesen aussichtsreiche Ansätze dar. Jedoch werden für alle Ansätze Phylogeniehypothesen benötigt, die in einer Analyse unabhängiger Daten (bspw. Moleküle) erstellt wurden, um Merkmalsverluste sicher zu identifizieren. [source]

New Zealand phylogeography: evolution on a small continent

MOLECULAR ECOLOGY, Issue 17 2009
GRAHAM P. WALLIS
Abstract New Zealand has long been a conundrum to biogeographers, possessing as it does geophysical and biotic features characteristic of both an island and a continent. This schism is reflected in provocative debate among dispersalist, vicariance biogeographic and panbiogeographic schools. A strong history in biogeography has spawned many hypotheses, which have begun to be addressed by a flood of molecular analyses. The time is now ripe to synthesize these findings on a background of geological and ecological knowledge. It has become increasingly apparent that most of the biota of New Zealand has links with other southern lands (particularly Australia) that are much more recent than the breakup of Gondwana. A compilation of molecular phylogenetic analyses of ca 100 plant and animal groups reveals that only 10% of these are even plausibly of archaic origin dating to the vicariant splitting of Zealandia from Gondwana. Effects of lineage extinction and lack of good calibrations in many cases strongly suggest that the actual proportion is even lower, in keeping with extensive Oligocene inundation of Zealandia. A wide compilation of papers covering phylogeographic structuring of terrestrial, freshwater and marine species shows some patterns emerging. These include: east,west splits across the Southern Alps, east,west splits across North Island, north,south splits across South Island, star phylogenies of southern mountain isolates, spread from northern, central and southern areas of high endemism, and recent recolonization (postvolcanic and anthropogenic). Excepting the last of these, most of these patterns seem to date to late Pliocene, coinciding with the rapid uplift of the Southern Alps. The diversity of New Zealand geological processes (sinking, uplift, tilting, sea level change, erosion, volcanism, glaciation) has produced numerous patterns, making generalizations difficult. Many species maintain pre-Pleistocene lineages, with phylogeographic structuring more similar to the Mediterranean region than northern Europe. This structure reflects the fact that glaciation was far from ubiquitous, despite the topography. Intriguingly, then, origins of the flora and fauna are island-like, whereas phylogeographic structure often reflects continental geological processes. [source]

Description and Phylogenetic Relationships of Spumochlamys perforata n. sp. and Spumochlamys bryora n. sp. (Amoebozoa, Arcellinida)

THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2009
ALEXANDER KUDRYAVTSEV
ABSTRACT. Spumochlamys perforata n. sp. and Spumochlamys bryora n. sp. were isolated and described from dry epiphytic moss. The morphology and ultrastructure of both species clearly demonstrate that they belong to the genus Spumochlamys (family Microchlamyiidae). They differ from its only described member, Spumochlamys iliensis (as well as from species of Microchlamys), in the relief of the dorsal surface of the test, revealed by scanning electron microscopy, which can represent a good characteristic for species identification. They also differ in the structure of the dorsal part of the test wall (especially S. perforata). Small subunit ribosomal DNA-based molecular phylogenetic analyses show that Spumochlamys is a deeply branching lineage of the Arcellinida, without any close affinities. Actin gene sequence analysis places this genus within the Tubulinea, close to two other arcellinid lineages but without forming a monophyletic group with them. These data together strongly suggest that the lack of resolution in the arcellinid molecular phylogenies is due to serious undersampling of taxa, a limited number of sequence data, and high divergence rates in most of the species. [source]

Evolution of epiphytes in Davalliaceae and related ferns

BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2006
CHIE TSUTSUMI
The evolution of epiphytes in Davalliaceae was investigated by field observations and molecular phylogenetic analyses. Field studies revealed that in Davalliaceae and related ferns, epiphytes in a broad sense are classified into climber, secondary hemi-epiphyte, and obligate epiphyte, based on combinations of the places (ground vs. tree) of inferred spore germination and sporophyte growth. Some species of Davalliaceae have multiple life forms, i.e. secondary hemi-epiphyte and obligate epiphyte, whereas others are obligate epiphytes. Phylogenetic trees obtained from rbcL and accD gene sequences supported that secondary hemi-epiphytic Oleandra is sister to the epiphytic Davalliaceae and polygrammoid ferns. Analyses of life form evolution based on the phylogenetic relationships suggested that obligate epiphytes of the Davalliaceae and polygrammoid ferns evolved from secondary hemi-epiphytes, or less likely from climbers. We hypothesized a scenario for the evolution of life forms in Davalliaceae and related groups that involves successive changes in rhizome habit, root function, and germination place. Rhizome dorsiventrality and scale morphology, shared by climbers, secondary hemi-epiphytes, and obligate epiphytes examined, may be other innovations for the ferns to have evolved into epiphytes. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 151, 495,510. [source]

Molecular phylogeny and phylogeography of flightless beetles Parechthistatus gibber and Hayashiechthistatus inexpectus (Coleoptera: Cerambycidae) inferred from mitochondrial COI gene sequences

ENTOMOLOGICAL SCIENCE, Issue 2 2008
Hiroshi 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]

Early evolution of a homeobox gene: the parahox gene Gsx in the Cnidaria and the Bilateria

EVOLUTION AND DEVELOPMENT, Issue 4 2003
John R. Finnerty
Summary Homeobox transcription factors are commonly involved in developmental regulation in diverse eukaryotes, including plants, animals, and fungi. The origin of novel homeobox genes is thought to have contributed to many evolutionary innovations in animals. We perform a molecular phylogenetic analysis of cnox2, the best studied homeobox gene from the phylum Cnidaria, a very ancient lineage of animals. Among three competing hypotheses, our analysis decisively favors the hypothesis that cnox2 is orthologous to the gsx gene of Bilateria, thereby establishing the existence of this specific homeobox gene in the eumetazoan stem lineage, some 650,900 million years ago. We assayed the expression of gsx in the planula larva and polyp of the sea anemone Nematostella vectensis using in situ hybridization and reverse transcriptase polymerase chain reaction. The gsx ortholog of Nematostella, known as anthox2, is expressed at high levels in the posterior planula and the corresponding "head" region of the polyp. It cannot be detected in the anterior planula or the corresponding "foot" region of the polyp. We have attempted to reconstruct the evolution of gsx spatiotemporal expression in cnidarians and bilaterians using a phylogenetic framework. Because of the surprisingly high degree of variability in gsx expression within the Cnidaria, it is currently not possible to infer unambiguously the ancestral cnidarian condition or the ancestral eumetazoan condition for gsx expression. [source]

Rhodotorula pinicola sp. nov., a basidiomycetous yeast species isolated from xylem of pine twigs

FEMS YEAST RESEARCH, Issue 2 2002
Jian-Hua Zhao
Abstract Three pink-colored yeast strains 3-1-3, 10-3-3 and 19-3-3 were isolated from xylem of surface-sterilized twigs of Pinus tabulaeformis collected from Dongling Mountain, Beijing, in different seasons. These strains were identified as Rhodotorula minuta (Saito) F.C. Harrison by conventional taxonomic characterization. However, molecular phylogenetic analysis based on internal transcribed spacer region (including 5.8S rDNA) and large-subunit rDNA D1/D2 domain sequences indicated that they represent a novel basidiomycetous yeast species, for which Rhodotorula pinicola is proposed (type strain: AS 2.2193T=CBS 9130T). The new species was most closely related to Rhodotorula laryngis Reiersöl in the R. minuta complex. [source]

Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets

JOURNAL OF BIOGEOGRAPHY, Issue 9 2009
Camila 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]

MOLECULAR PHYLOGENY OF DISCOSPORANGIUM MESARTHROCARPUM (PHAEOPHYCEAE) WITH A REINSTATEMENT OF THE ORDER DISCOSPORANGIALES,

JOURNAL OF PHYCOLOGY, Issue 1 2007
Hiroshi 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]

The phylogenetic position of the East Asian freshwater crayfish Cambaroides within the Northern Hemisphere Astacoidea (Crustacea, Decapoda, Astacida) based on molecular data

JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1 2006
A. Braband
Abstract The phylogenetic position of the four East Asian freshwater crayfish species of the genus Cambaroides is not settled. Morphological phylogenetic analyses suggest close affinities of Cambaroides with North American Cambaridae. This view is based mainly on characters of the male and female reproductive organs. In contrast, the only molecular phylogenetic analysis so far available leaves the phylogenetic position of Cambaroides unresolved. The question of whether Cambaroides is monophyletic or paraphyletic has so far been neither addressed morphologically nor with molecular data sets. Here we present the first comprehensive phylogenetic analysis of all four currently described species of Cambaroides in the framework of Northern Hemisphere freshwater crayfish (Astacoidea) relationships based on partial sequences of two mitochondrial genes (CO1 and 12S rRNA). Despite some evidence in favour of a monophyletic Cambaroides more data is needed to resolve this question. Our analyses suggest a close relationship of the North American Cambaridae and the European Astacidae, leaving the Asian Cambaroides basal to them. If these results hold true the similar reproductive organs of Cambaroides and American Cambaridae must be either homoplastic or ancestral for Northern Hemisphere Astacoidea. Zusammenfassung Die phylogenetische Beziehung der vier ostasiatischen Flusskrebsarten der Gattung Cambaroides in Relation zu den anderen Taxa der Astacoidea ist weitgehend unbestimmt. Phylogenetische Analysen morphologischer Merkmale der Reproduktionsorgane unterstützen eine nahe Verwandtschaft von Cambaroides und den in Nordamerika lebenden Vertretern der Cambaridae. Bislang existierende molekulare Ergebnisse können dieses Ergebnis nicht stützen, lassen aber die Fragen der Monophylie und der phylogenetischen Position von Cambaroides innerhalb der Astacoidea unbeantwortet. Diese Arbeit zeigt die erste umfassende phylogenetische Analyse aller vier beschriebenen rezenten Spezies der Gattung Cambaroides und ihrer phylogenetischen Beziehung innerhalb der Astacoidea, anhand zweier mitochondrialer Genabschnitte (12S rRNA und CO1). Unsere Analyse zeigt die nahe Verwandtschaft der nordamerikanischen Cambaridae und der europäischen Astacidae, während Cambaroides basal zu dieser Gruppierung steht. Dieses Ergebnis lässt den Schluss zu, dass die ähnlichen Reproduktionsorgane von Cambaroides und den amerikanischen Cambaridae entweder plesiomorph für die Astacoidea oder konvergent sind. [source]

Adaptive radiation in Lesser Antillean lizards: molecular phylogenetics and species recognition in the Lesser Antillean dwarf gecko complex, Sphaerodactylus fantasticus

MOLECULAR ECOLOGY, Issue 6 2008
R. S. THORPE
Abstract The time associated with speciation varies dramatically among lower vertebrates. The nature and timing of divergence is investigated in the fantastic dwarf gecko Sphaerodactylus fantasticus complex, a nominal species that occurs on the central Lesser Antillean island of Guadeloupe and adjacent islands and islets. This is compared to the divergence in the sympatric anole clade from the Anolis bimaculatus group. A molecular phylogenetic analysis of numerous gecko populations from across these islands, based on three mitochondrial DNA genes, reveals several monophyletic groups occupying distinct geographical areas, these being Les Saintes, western Basse Terre plus Dominica, eastern Basse Terre, Grand Terre, and the northern and eastern islands (Montserrat, Marie Galante, Petite Terre, Desirade). Although part of the same nominal species, the molecular divergence within this species complex is extraordinarily high (27% patristic distance between the most divergent lineages) and is compatible with this group occupying the region long before the origin of the younger island arc. Tests show that several quantitative morphological traits are correlated with the phylogeny, but in general the lineages are not uniquely defined by these traits. The dwarf geckos show notably less nominal species-level adaptive radiation than that found in the sympatric southern clade of Anolis bimculatus, although both appear to have occupied the region for a broadly similar period of time. Nevertheless, the dwarf gecko populations on Les Saintes islets are the most morphologically distinct and are recognized as a full species (Sphaerodactylus phyzacinus), as are anoles on Les Saintes (Anolis terraealtae). [source]

Tanacetum joharchii sp. nov. (Asteraceae,Anthemideae) from Iran, and its taxonomic position based on molecular data

NORDIC JOURNAL OF BOTANY, Issue 1 2010
Ali Sonboli
Tanacetum joharchii Sonboli & Kazempour Osaloo sp. nov. (Asteraceae,Anthemideae) is described and illustrated from the Khorasan province, northeast Iran. Tanacetum joharchii is a suffruticulose species from rocky limestone mountains in Hezarmasjed and Binalud (Khorasan province) at altitudes of 1900,2500 m a.s.l. The diagnostic morphological characteristics that distinguish it from the allied species T. kotschyi are presented. In addition, a distribution map of T. joharchii and the related species is given. In order to provide some hypothesis on its phylogenetic position, a molecular phylogenetic analysis based on nrDNA ITS sequence data of 14 representatives of the genus Tanacetum was performed. [source]

Phylogeny, diversification patterns and historical biogeography of euglossine orchid bees (Hymenoptera: Apidae)

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2010
SANTIAGO R. RAMÍREZ
The orchid bees constitute a clade of prominent insect pollinators distributed throughout the Neotropical region. Males of all species collect fragrances from natural sources, including flowers, decaying vegetation and fungi, and store them in specialized leg pockets to later expose during courtship display. In addition, orchid bees provide pollination services to a diverse array of Neotropical angiosperms when foraging for food and nesting materials. However, despite their ecological importance, little is known about the evolutionary history of orchid bees. Here, we present a comprehensive molecular phylogenetic analysis based on ,4.0 kb of DNA from four loci [cytochrome oxidase (CO1), elongation factor 1-, (EF1 -,), arginine kinase (ArgK) and RNA polymerase II (Pol-II)] across the entire tribe Euglossini, including all five genera, eight subgenera and 126 of the approximately 200 known species. We investigated lineage diversification using fossil-calibrated molecular clocks and the evolution of morphological traits using disparity-through-time plots. In addition, we inferred past biogeographical events by implementing model-based likelihood methods. Our dataset supports a new view on generic relationships and indicates that the cleptoparasitic genus Exaerete is sister to the remaining orchid bee genera. Our divergence time estimates indicate that extant orchid bee lineages shared a most recent common ancestor at 27,42 Mya. In addition, our analysis of morphology shows that tongue length and body size experienced rapid disparity bursts that coincide with the origin of diverse genera (Euglossa and Eufriesea). Finally, our analysis of historical biogeography indicates that early diversification episodes shared a history on both sides of Mesoamerica, where orchid bees dispersed across the Caribbean, and through a Panamanian connection, thus reinforcing the hypothesis that recent geological events (e.g. the formation of the isthmus of Panama) contributed to the diversification of the rich Neotropical biota. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 552,572. [source]

Origin of the disjunct distribution of flower colour polymorphism within Limonium wrightii (Plumbaginaceae) in the Ryukyu Archipelago

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009
SHUN'ICHI MATSUMURA
The sea lavender, Limonium wrightii, has six morphs of flower colour variation. The geographical distribution of flower colour morphs is disjunct; the distribution of the pink flower morph is divided into two subregions, and that of the yellow flower morph intervenes between them. The present study aimed to examine the origin of this apparent distribution pattern of flower colour in L. wrightii. Two main hypotheses (i.e. past dispersal events and phenotypic changes by natural selection and/or stochastic processes) have been proposed to account for the origin of leapfrog distribution patterns. To determine which hypothesis was applicable, we conducted a molecular phylogenetic analysis using sequence variation in chloroplast DNA (three regions of intergenic spacers, trnG - trnfM, trnV - trnM, and psbA-trnH). We sequenced 58 accessions of L. wrightii frin 28 islands in the Ryukyu Archipelago and the Izu-Ogasawara Islands, located south of the Japanese mainland, and 12 accessions of four congeneric species. Within L. wrightii, we obtained four lineages of ten haplotypes. These lineages and haplotypes did not correlate with the different flower colours. These results indicate that the formation processes of populations are complex. The haplotypes of the pink flower morph did not show a sister relationship between the two disjunct subregions, indicating that the disjunct populations of the pink flower morphs are unlikely to share the pink flower colour as a result of common ancestry. We conclude that the observed leapfrog distribution pattern is caused by natural selection and/or stochastic processes. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 709,717. [source]

Molecular phylogenetics of Uvaria (Annonaceae): relationships with Balonga, Dasoclema and Australian species of Melodorum

BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2010
LINLIN ZHOU
An extended molecular phylogenetic analysis of Uvaria (Annonaceae) is presented, using maximum parsimony, maximum likelihood and Bayesian methods, based on sequences of four plastid DNA regions (matK, psbA-trnH spacer, rbcL and trnL-F). The additional taxa include the monotypic West African genus Balonga, the monotypic South-East Asian genus Dasoclema and seven Australian representatives of the genus Melodorum. The results indicate that all of these taxa are nested within a well-supported clade otherwise consisting of Uvaria species, indicating that their taxonomic treatment needs to be reassessed. The distinguishing morphological characteristics of the taxa are re-evaluated and interpreted as specialized adaptations of the basic Uvaria structure. The genus Uvaria is accordingly extended following the transfer of these species, necessitating six new nomenclatural combinations and two replacement names. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163, 33,43. [source]