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Phylogenetic Relationships (phylogenetic + relationships)
Selected AbstractsPHYLOGENETIC RELATIONSHIPS AND MORPHOLOGICAL DIVERSITY IN DARWIN'S FINCHES AND THEIR RELATIVESEVOLUTION, Issue 6 2002Kevin J. Burns Abstract Despite the importance of Darwin's finches to the development of evolutionary theory, the origin of the group has only recently been examined using a rigorous, phylogenetic methodology that includes many potential outgroups. Knowing the evolutionary relationships of Darwin's finches to other birds is important for understanding the context from which this adaptive radiation arose. Here we show that analysis of mitochondrial DNA sequence data from the cytochrome b gene confirm that Darwin's finches are monophyletic. In addition, many taxa previously proposed as the sister taxon to Darwin's finches can be excluded as their closest living relative. Darwin's finches are part of a well-supported monophyletic group of species, all of which build a domed nest. All but two of the non-Darwin's finches included in this clade occur on Caribbean islands and most are Caribbean endemics. These close relatives of Darwin's finches show a diversity of bill types and feeding behaviors similar to that observed among Darwin's finches themselves. Recent studies have shown that adaptive evolution in Darwin's finches occurred relatively quickly. Our data show that among the relatives of Darwin's finches, the evolution of bill diversity was also rapid and extensive. [source] SEXUAL PROCESSES AND PHYLOGENETIC RELATIONSHIPS OF A HOMOTHALLIC STRAIN IN THE CLOSTERIUM PERACEROSUM,STRIGOSUM,LITTORALE COMPLEX (ZYGNEMATALES, CHAROPHYCEAE),JOURNAL OF PHYCOLOGY, Issue 2 2010Yuki Tsuchikane Members of the Closterium peracerosum,strigosum,littorale (C. psl.) complex are unicellular charophycean algae in which there are two modes of zygospore formation, heterothallic and homothallic. A homothallic strain of Closterium (designation, kodama20) was isolated from a Japanese rice paddy field. Based on alignment of the 1506 group-I introns, which interrupt nuclear SSU rDNAs, homothallic kodama20 is most closely related to the heterothallic mating group II-B, which is partially sexually isolated from group II-A. Time-lapse photography of the conjugation process in kodama20 revealed that most of the observed zygospores originated from one vegetative cell. The sexual conjugation process consisted of five stages: (1) cell division resulting in the formation of two sister gametangial cells from one vegetative cell, (2) formation of a sexual pair between the two sister gametangial cells (or between gametangial cells of another adjoined individual), (3) formation of conjugation papillae, (4) release of gametic protoplasts from both members of a pair, and (5) formation of the zygospore by protoplast fusion. For conjugation to progress, the cell density and light condition in the culture was critical. We suggested the presence of a conjugation promotion factor. [source] PHYLOGENETIC RELATIONSHIPS WITHIN THE GENUS HYPNEA (GIGARTINALES, RHODOPHYTA), WITH A DESCRIPTION OF H. CAESPITOSA SP.JOURNAL OF PHYCOLOGY, Issue 2 2010Species discrimination within the gigartinalean red algal genus Hypnea has been controversial. To help resolve the controversy and explore phylogeny within the genus, we determined rbcL sequences from 30 specimens of 23 species within the genus, cox1 from 22 specimens of 10 species, and psaA from 16 species. We describe H. caespitosa as a new species characterized by a relatively slender main axis; a pulvinate growth habit with entangled, anastomosing, and subulate uppermost branches; and unilaterally borne tetrasporangial sori. The new species occurs in the warm waters of Malaysia, the Philippines, and Singapore. The phylogenetic trees of rbcL, psaA, and cox1 sequences showed a distant relationship of H. caespitosa to H. pannosa J. Agardh from Baja California and the marked differentiation from other similar species. The rbcL + psaA tree supported monophyly of the genus with high bootstrap values and posterior probabilities. The analysis revealed three clades within the genus, corresponding to three sections, namely, Virgatae, Spinuligerae, and Pulvinatae first recognized by J. G. Agardh. Exceptions were H. japonica T. Tanaka in Pulvinatae and H. spinella (C. Agardh) Kütz. in Spinuligerae. [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] Description and Phylogenetic Relationships of Spumochlamys perforata n. sp. and Spumochlamys bryora n. sp. (Amoebozoa, Arcellinida)THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2009ALEXANDER 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] A "Total Evidence" Analysis of the Phylogenetic Relationships among the Photosynthetic StramenopilesCLADISTICS, Issue 3 2001Ulf SorhannusArticle first published online: 19 JUL 200 Phylogenetic relationships among the nine major autotrophic stramenopile taxa were inferred in a combined analysis of the rbcL, SSU rDNA, partial LSU rRNA, carotenoid, and ultrastructural data sets. The structure of the shortest combined tree is: (Outgroup, ((((Bacillariophyceae, (Pelagophyceae, Dictyochophyceae)),((Phaeophyceae, Xanthophyceae), Raphidophyceae)), Eustigmatophyceae),(Chrysophyceae, Synurophyceae))). The Synurophyceae/Chrysophyceae is the best supported group followed by the Phaeophyceae/Xanthophyceae and the Pelagophyceae/Dictyochophyceae clades. The monophyletic groups composed of Bacillariophyceae/Pelagophyceae/Dictyochophyceae and Phaeophyceae/Xanthophyceae/Raphidophyceae received the lowest Bremer support values. The optimal combined tree suggests that the diatom frustule is derived from the siliceous "skeleton" in Dictyochophyceae, that the reduced flagellar apparatus arose once in the Bacillariophyceae/Dictyochophyceae/Pelagophyceae clade, and that the specific photoreceptor-eyespot apparatus in Chrysophyceae and the Phaeophyceae/Xantophyceae clade originated independently within the autotrophic stramenopiles. Despite conflicts in tree structure between the most-parsimonious combined phylogeny and the optimal tree(s) of each data partition, it cannot be concluded that extensive incongruence exists between the data sets. [source] Phylogenetic Relationships of the Suborders of Coleoptera (Insecta)CLADISTICS, Issue 1 2000Rolf G. Beutel One hundred seven external and internal characters of larval and adult representatives of 28 genera of the coleopteran suborders were analyzed cladistically. Four groups of Neuropterida were introduced as outgroup. The analysis yielded 18 trees with a minimum of 194 steps (CI 0.691). All trees support the monophyly of all four suborders and a branching pattern (Archostemata + (Adephaga + (Myxophaga + Polyphaga))). The presence of elytra with meso- and metathoracic locking devices, the specific hind-wing folding, the close connection of exposed sclerites, the absence of the mera, the absence of eight thoracic muscles, the reduced abdominal sternite I, and the invagination of terminal segments are autapomorphies of Coleoptera. The monophyly of Coleoptera excl. Archostemata is supported by further transformations of the thoracic sclerites such as absence of the mesothoracic discriminal line and katepisternal joint, by an internalized or absent metathoracic trochantin, by the presence of a bending zone in the hind-wing, and by eight further muscle losses. Fusion of tibia and tarsus and presence of a single claw are larval synapomorphies of Myxophaga and Polyphaga. Adults are characterized by fusion of protrochantin and propleura and by the rigid connection of the meso- and metathoracic ventrites. The eucinetoid lineage of Polyphaga is characterized by the secondary absence of the bending zone of the alae. This results in a distinctly simplified wing folding mechanism. The monophyly of Cucujiformia (+ Bostrichoidea) is supported by the presence of cryptonephric Malpighian tubules. Transformations of fore-and hind-wings, reinforcement and simplification of the thoracic exoskeleton, and an efficient use of a distinctly reduced set of thoracic muscles play an important role in the early evolution of Coleoptera. Many different larval character transformations take place in the earlier Mesozoic within the suborders. [source] Discovery of the genus Skidmorella Johnson (Coleoptera: Ptiliidae) in Japan, with descriptions of two new speciesENTOMOLOGICAL SCIENCE, Issue 4 2003Yoshihiro SAWADA Abstract The genus Skidmorella Johnson, previously known only from the South Pacific islands, is discovered in Japan. The type species, Skidmorella magnifica Johnson, is confirmed from Japan as the first record of the species other than the type locality. In addition, two new species, Skidmorella amamiana sp. nov. and Skidmorella quadrisulucia sp. nov., are described from the Ryukyus, Japan. Phylogenetic relationships of the genus Skidmorella and its allies are discussed on the basis of their morphological characters. [source] Application of nr-DNA ITS sequence for identification of Fusarium culmorum isolates,EPPO BULLETIN, Issue 3-4 2000P. K. Mishra Variation within the internal transcribed spacers (ITS1 and ITS2) and 5.8S ribosomal DNA region of 60 Fusarium culmorum isolates (section Discolor), representing different hosts and diverse geographical origins was examined by polymerase chain reaction (PCR), coupled with sequencing. Phylogenetic relationships of these F. culmorum isolates were estimated in relation to Fusarium spp. from this and other sections of the form-genus, using sequences available from Genbank. The amplified ITS region was approximately 570 bp long in 56 isolates and approximately 585 bp in four other isolates. The inferred phylogeny distinguished clearly four isolates supplied as F. culmorum. These isolates differed in both morphology and sequence from the remaining F. culmorum material. Sequence analysis revealed that the remaining 56 isolates were divided into three ITS types, within which the divergence was extremely low. ITS sequence comparison among the Fusarium isolates showed two major clades, one comprising sections Discolor, Sporotrichiella and Gibbosum and the other comprising Elegans, Liseola, Martiella and Roseum. These results demonstrate the use of the ITS region to resolve the identification and taxonomic problems of Fusarium spp. especially at sectional level but demonstrate the need to develop some other molecular markers for identification at the level of species or race. [source] Phylogenetic diversity of Synechococcus strains isolated from the East China Sea and the East SeaFEMS MICROBIOLOGY ECOLOGY, Issue 3 2009Dong Han Choi Abstract Phylogenetic relationships among 33 Synechococcus strains isolated from the East China Sea (ECS) and the East Sea (ES) were studied based on 16S rRNA gene sequences and 16S,23S rRNA gene internal transcribed spacer (ITS) sequences. Pigment patterns of the culture strains were also examined. Based on 16S rRNA gene and ITS sequence phylogenies, the Synechococcus isolates were clustered into 10 clades, among which eight were previously identified and two were novel. Half of the culture strains belonged to clade V or VI. All strains that clustered into novel clades exhibited both phycoerythrobilin and phycourobilin. Interestingly, the pigment compositions of isolates belonging to clades V and VI differed from those reported for other oceanic regions. None of the isolates in clade V showed phycourobilin, whereas strains in clade VI exhibited both phycourobilin and phycoerythrobilin, which is in contrast to previous studies. The presence of novel lineages and the different pigment patterns in the ECS and the ES suggests the possibility that some Synechococcus lineages are distributed only in geographically restricted areas and have evolved in these regions. Therefore, further elucidation of the physiological, ecological, and genetic characteristics of the diverse Synechococcus strains is required to understand their spatial and geographical distribution. [source] Multigene phylogenetic analysis of the Lipomycetaceae and the proposed transfer of Zygozyma species to Lipomyces and Babjevia anomala to DipodascopsisFEMS YEAST RESEARCH, Issue 6 2007Cletus P. Kurtzman Abstract Phylogenetic relationships among species assigned to genera of the family Lipomycetaceae were determined from analysis of the nearly entire large, subunit rRNA gene, the small subunit rRNA gene, mitochondrial small subunit rRNA gene and the translation elongation factor-1, gene. Monophyly of the Lipomycetaceae was strongly supported, and currently described species appear genetically unique. The multigene analysis provided no support for maintaining the genera Kawasakia, Smithiozyma, Waltomyces or Zygozyma, and it is proposed that species in these genera be assigned to the genus Lipomyces. The monotypic genus Babjevia is a member of the Dipodascopsis clade and it is proposed to reassign Babjevia anomala to Dipodascopsis. The proposed changes will result in the Lipomycetaceae having two ascosporic genera, Lipomyces and Dipodascopsis, and the anamorphic genus Myxozyma. [source] Phylogenetic relationships within the tropical soft coral genera Sarcophyton and Lobophytum (Anthozoa, Octocorallia)INVERTEBRATE BIOLOGY, Issue 4 2006Catherine S. McFadden Abstract. The alcyonacean soft coral genera Sarcophyton and Lobophytum are conspicuous, ecologically important members of shallow reef communities throughout the Indo-West Pacific. Study of their ecology is, however, hindered by incomplete knowledge of their taxonomy: most species cannot be identified in the field and the two genera cannot always be distinguished reliably. We used a 735-bp fragment of the octocoral-specific mitochondrial protein-coding gene msh1 to construct a phylogeny for 92 specimens identified to 19 species of Lobophytum and 16 species of Sarcophyton. All phylogenetic methods used recovered a tree with three strongly supported clades. One clade included only morphologically typical Sarcophyton species with a stalk distinct from the polypary, poorly formed club-shaped sclerites in the colony surface, and large spindles in the interior of the stalk. A second clade included only morphologically typical Lobophytum colonies with lobes and ridges on the colony surface, poorly formed clubs in the colony surface, and interior sclerites consisting of oval forms with regular girdles of ornamental warts. The third distinct clade included a mix of Sarcophyton and Lobophytum nominal species with intermediate morphologies. Most of the species in this mixed clade had a polypary that was not distinct from the stalk, and the sclerites in the colony surface were clubs with well-defined heads. Within the Sarcophyton clade, specimens identified as Sarcophyton glaucum belonged to six very distinct genetic sub-clades, suggesting that this morphologically heterogeneous species is actually a cryptic species complex. Our results highlight the need for a complete taxonomic revision of these genera, using molecular data to help confirm species boundaries as well as to guide higher taxonomic decisions. [source] Radiation of Atlantic goldcrests Regulus regulus spp.: evidence of a new taxon from the Canary IslandsJOURNAL OF AVIAN BIOLOGY, Issue 4 2006Martin Päckert Phylogenetic relationships between goldcrest populations from the Atlantic Islands (Azores and Canary Islands) were investigated by two molecular markers (mitochondrial control region and cytochrome b sequences), and partly by morphology and territorial song. The Azorean goldcrest populations are closely related to European nominate R. r. regulus. Most probably, the Azores were colonized by goldcrests in a single late-pleistocene invasion, while colonization of the Canary Islands presumably occurred in two steps: An early invasion to Tenerife and La Gomera 1.9,2.3 million years (my) ago and a more recent one to El Hierro and La Palma 1.3,1.8 my ago. Distribution of haplotypes on the Azores suggests a division of R. r. azoricus on São Miguel into an eastern population with close affinities to R. r. sanctaemariae and a western population belonging to the lineage of R. r. inermis on the central and western island group. The Canarian populations are genetically substructured into a northeastern group embracing Tenerife and La Gomera and a second, southwestern group including El Hierro and La Palma. Genetic distances between members of the two Canarian clades range at 3.1,3.4% (TrN distance, control region and cytochrome b). Differentiation between the two groups is also supported by morphology and by territorial song. Substitution rate estimates for the both genes range at approximately the same values of 0.0031 and 0.0044 substitutions per site and lineage per my which roughly corresponds 0.61,0.83% divergence between Regulus lineages per my. Highest local rates occur in island clades of the Azorean and the Canarian population and in R. r. japonensis from the Russian Far East and Japan. However, a general acceleration of a molecular clock in island populations is not evident from the Regulus data set due to extremely low local rate estimates in the Canarian clade of Tenerife and La Gomera. As a taxonomic consequence of the marked differentiation of the two Canarian goldcrest clades the populations from El Hierro and La Palma are described as a taxon new to science and are named Regulus regulus ellenthalerae n. ssp. [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] Phylogenetic relationships of the newly described species Chondrostoma olisiponensis (Teleostei: Cyprinidae)JOURNAL OF FISH BIOLOGY, Issue 4 2010H. F. Gante Phylogenies were generated using mitochondrial cytochrome b and nuclear ß-actin gene DNA sequences to infer the phylogenetic relationships of the newly described Chondrostoma olisiponensis. Results indicate that the species is monophyletic with species of the lemmingii -group in mtDNA phylogenies, while it is monophyletic with species of the arcasii -group in the nuclear ß-actin trees. This is in agreement with the morphological resemblance of C. olisiponensis to both species groups. Results from nuclear but not mitochondrial DNA indicate that one population could be currently hybridizing with sympatric Chondrostoma lusitanicum. Based on a relaxed clock calibration of cytochrome b, it is estimated that C. olisiponensis split 12·5,7·9 million years ago (middle,upper Miocene) from its most recent ancestor, which coincides with a period of endorrheism in the Iberian Peninsula. [source] Phylogenetic relationships of the European lacertid genera Archaeolacerta and Iberolacerta and their relationships to some other ,Archaeolacertae' (sensu lato) from Near East, derived from mitochondrial DNA sequencesJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2003W. Mayer Abstract Parts of the mitochondrial genes coding for 12SrRNA and 16SrRNA (together about 960 bp) were sequenced for all Mediterranean species of ,Mountain lizards' of the genera Archaeolacerta (sensu lato) and Iberolacerta. All subspecies of the Iberian species Iberolacerta cyreni and I. monticola were included in this study. In addition, samples of Apathya cappadocica and Darevskia rudis were analysed to elucidate the relationships of the European ,Mountain lizards' to their possible relatives in the Near East. Maximum parsimony and neighbour joining analyses lead to the following major conclusions: (i) the monophyly of the genus Iberolacerta is very well supported; (ii) Archaeolacerta bedriagae (the type species of the genus) is most basal with respect to the ingroup taxa. If we accept Iberolacerta as a genus, Archaeolacerta becames paraphyletic. Therefore, we propose to restrict Archaeolacerta to the type species and to treat A. mosorensis and A. oxycephala provisionally as members of the collective genus Lacerta; (iii) within the genus Iberolacerta three groups were found: a Pyrenean group, an Iberian group and I. horvathi. The relationships among these groups remain unresolved; and (iv) the Peña de Francia lizards, described originally as a subspecies of I. cyreni, are in fact more closely related to I. monticola. Zusammenfassung Wir sequenzierten Teilabschnitte der Gene für 12SrRNA und 16SrRNA (zusammen ungefähr 960 Basenpaare) von allen europäischen ,Gebirgseidechsen' der Gattungen Archaeolacerta (sensu lato) und Iberolacerta. Alle Subspezies der iberischen Arten Iberolacerta cyreni und I. monticola wurden in die Studie aufgenommen. Zusätzlich wurden Proben von Apathya cappadocica und Darevskia rudis untersucht, um die phylogenetischen Beziehungen der europäischen ,Gebirgseidechsen' zu ihren möglichen Verwandten im Nahen Osten aufzuklären. Maximum Parsimony und Neighbor Joining Analysen führten zu folgenden wesentlichen Ergebnissen: i) Die Monophylie der Gattung Iberolacerta ist gut abgesichert. ii) Archaeolacerta bedriagae (die species typica der Gattung) hat eine basale Position innerhalb der Gruppe der ,Gebirgseidechsen'. Daher schlagen wir vor, Archaeolacerta auf die species typica zu restringieren und A. mosorensis und A. oxycephala provisorisch in der Sammelgattung Lacerta zu belassen. iii) Die Gattung Iberolacerta zerfällt in drei Gruppen: eine Pyrenäen-Gruppe, eine iberische Gruppe und I. horvathi. Die Beziehungen zwischen diesen Gruppen konnten nicht aufgeklärt werden. iv) Die Eidechsen von Peña de Francia, ursprünglich als Subspezies von I. cyreni beschrieben, sind tatsächlich näher mit I. monticola verwandt. [source] Phylogeny of the Eurasian freshwater turtles of the genus Mauremys Gray 1869 (Testudines), with special reference to a close affinity of Mauremys japonica with Chinemys reevesiiJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2002M. Honda Phylogenetic relationships of the freshwater turtles of the genus Mauremys and representatives of several other batagurid genera were inferred from variations in 863 base positions of mitochondrial 12S and 16S rRNA genes. Results strongly suggested the non-monophyly of Mauremys by indicating the closest affinity of Mauremys japonica with Chinemys reevesii, the type species of the genus Chinemys. Recent morphological analyses of the batagurid genera suggested that Mauremys is a basal stock of the subfamily Geoemydinae, whereas Chinemys is a member of the subfamily Batagurinae as supported by several putative synapomorphs with other batagurine genera. It is thus probable that the morphological character states used to define Mauremys actually represent symplesiomorphy, and that morphological character states shared between Chinemys and other batagurine genera have resulted from convergence. Also, our results did not support a sister-group relationship between Mauremys annamensis and Mauremys mutica, which has been implicitly or explicitly assumed by a number of previous authors on the basis of morphological data. Instead, M. annamensis was indicated to be closest to Mauremys iversoni, a species assumed to be most divergent among the East Asian Mauremys by previous authors. Phylogenie der eurasischen Su¨ßwasserschildkro¨ten der Gattung Mauremys Gray 1869 (Testudines), mit besonderem Hinweis auf eine enge A¨hnlichkeit von Mauremys japonica mit Chinemys reevesii. Die phylogenetischen Beziehungen zwischen den Süßwasserschildkröten der Gattung Mauremys und Vertretern einiger anderer bataguriner Gattungen wurde aus den Unterschieden an 863 Positionen der 12S-und der 16S-rRNA-Gene des Mitochondriengenoms ermittelt. Die Ergebnisse weisen sehr stark darauf hin, daß die Gattung Mauremys wegen der starken Ähnlichkeit zwischen M. japonica und Chinemys reevesii nicht monophyletisch sein kann. Neue morphologische Analysen der batagiurinen Gattungen ließen vermuten, daß Mauremys einen basalen Ast der Unterfamilie Geomydinae darstellt, während Chinemys zur Unterfamile Batagurinae gehört, was aus den anzunehmenden Synapomorphien mit anderen batagurinen Gattungen gestützt wird. Es ist daher auch wahrscheinlich, daß die zur Beschreibung von Mauremys verwendeten morphologischen Merkmalszustände eher Plesiomorphien darstellen und daß die morphologischen Merkmalsausprägungen, die Chinemys und anderen batagurinen Gattungen gemeinsam sind, auf Konvergenz beruhen. Unsere Ergebnisse unterstützen auch nicht eine Schwestergruppen-Beziehung zwischen M. anamensis und M. mutica, was direkt oder indirekt von einer Zahl von früheren Untersuchern auf Grund morphologischer Daten angenommen wurde. Statt dessen erwies sich M. anamensis am engsten verwandt mit M. iversoni, einer Art, die von früheren Autoren als am stärksten divergent zu den ostasiatischen Mauremys-Arten angesehen wurde. [source] Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): insight into deep and shallow history in northwestern North AmericaMOLECULAR ECOLOGY, Issue 5 2001John R. Demboski Abstract Phylogenetic relationships among the dusky shrew (Sorexmonticolus) and eight related species (S. bairdi, S. bendirii, S. neomexicanus, S.ornatus, S. pacificus, S. palustris, S. sonomae and S.vagrans) were assessed using sequences from the mitochondrial cytochrome b gene (801 bp). Analyses using parsimony and maximum likelihood revealed significant molecular variation not reflected in previous morphological studies of these species. Conversely, three morphologically defined species (S.bairdi, S.neomexicanusandS.pacificus) were poorly differentiated. SorexornatusandS.vagrans represented basal taxa for a more inclusive group that included: (i) a widespread Continental clade containing S.monticolus (Arizona to Alaska, including S. neomexicanus); (ii) a Coastal clade containing S.monticolus (Oregon to south-east Alaska, including S. bairdiandS. pacificus); (iii) the semiaquatic species (S. bendiriiandS. palustris); and (iv) S.sonomae. Additional subdivision was observed within the Continental clade corresponding to populations from the northern and southern Rocky Mountains. Average uncorrected sequence divergence between the Coastal and Continental clades was 5.3% (range 4.5,6.2%), which exceeds many interspecific comparisons within this species complex and within the genus Sorex. Lack of resolution of internal nodes within topologies suggests a deep history of rapid diversification within this group. Late Pleistocene/Holocene glacial perturbations are reflected in the shallow phylogeographic structure within these clades in western North America. Our results suggest also that S. monticolus is not monophyletic under current taxonomic nomenclature. This perspective on phylogeographic history was developed within a growing comparative framework for other organisms in western North America. [source] The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR)MOLECULAR ECOLOGY, Issue 7 2000J. Hess Abstract Phylogenetic relationships in the Olea europaea complex and the phylogeography of 24 populations of the Macaronesian olive (O. europaea ssp. cerasiformis) were assessed by using three molecular markers: nuclear ribosomal internal transcribed spacer 1 (ITS-1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR). Parsimony analysis of the ITS-1 sequences and Neighbour-joining (NJ) analyses of RAPD and ISSR banding variation revealed four major lineages in the O. europaea complex: (1) ssp. cuspidata; (2) ssp. cerasiformis from Madeira; (3) ssp. laperrinei; and (4) ssp. cerasiformis from the Canary Islands plus ssp. europaea. These results provide unequivocal support for two independent dispersal events of Olea to the Madeira and Canary Islands. Molecular and morphological evidence led to recognition of two separate olive taxa in Macaronesia, to date included in ssp. cerasiformis. NJ analyses of the combined RAPD and ISSR data suggest that the colonization of the Canaries by O. europaea may have followed an east to west stepping-stone model. An interisland dispersal sequence can be recognized, starting from the continent to Fuerteventura, Gran Canaria, Tenerife, La Gomera, and finally La Palma. High dispersal activity of the lipid-rich Olea fruits by birds in the Mediterranean region is congruent with multiple dispersal of olives to Macaronesia and successive colonization of the archipelagos. The observation of strong genetic isolation between populations of different islands of the Canary Islands suggests, however, that subsequent interisland dispersal and establishment has been very rare or may not have occurred at all. [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] 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] Chloroplast DNA Variation and Biogeography in the Genus Rorippa Scop. (Brassicaceae)PLANT BIOLOGY, Issue 1 2002W. Bleeker Abstract: Phylogenetic relationships and biogeography of 25 Rorippa species were studied using sequences of two non-coding regions of chloroplast DNA (trnL intron, trnL/F spacer). Our results indicate a close relationship between European (R. islandica ssp. islandica, R. pyrenaica) and North American (R. curvipes, R. sinuata) mountain species. The polyploid European lowland species R. amphibia, R. palustris and R. sylvestris are much younger than the mountain species and have their closest relatives in western Asia and Siberia. Different colonization routes of the southern hemisphere are discussed for Rorippa. Australasia was colonized at least twice, most likely via the Malayan route. A molecular clock approach dates the first colonization to the end of Pliocene or early Pleistocene. R. gigantea reached Australia later in the Pleistocene. Our data provide evidence for an amphitropical disjunction between the South American (R. philippiana) and North American (R. curvisiliqua) species. Long-distance dispersal via migrating birds is the most likely explanation for this intercontinental disjunction. Two of the analysed African species (R. nudiuscula, R. madagascariensis) have their closest relative (R. austriaca) in eastern Europe and western Asia. The lack of sequence divergence among these species indicates a colonization event probably not earlier than 100 000 years ago. [source] Phylogenetic relationships and pathogenicity of Colletotrichum acutatum isolates from grape in subtropical AustraliaPLANT PATHOLOGY, Issue 3 2007M. A. Whitelaw-Weckert The identity of Colletotrichum acutatum as the causal pathogen of grape ripe-rot, which causes yield loss and a bitter taint that lowers wine quality in Australian subtropical wine-grape regions, was confirmed using species-specific primers. Cultural, morphological and molecular methods (RAPD-PCR and sequencing of parts of the 5·8S-ITS regions and the ,-tubulin-2 gene) were used to determine the phylogenetic relationships of Australian C. acutatum isolates from wine grapes and other horticultural crops. A combination of RAPD-PCR and ,-tubulin-2 gene data showed that all wine-grape ripe-rot isolates from northern regions of New South Wales (NSW) and Queensland belong to a proposed new C. acutatum group (A9), together with isolates from Australian strawberry, mango, blueberry and olive. The 5·8S-ITS sequences for these grape pathogens were identical to published sequences for an isolate from Cyclamen (the Netherlands) and differed by 1 bp from isolates from Capsicum (Taiwan) and orange (Costa Rica). The grape ripe-rot isolates from the Shoalhaven Valley (southern NSW) were clustered within two other C. acutatum groups: A2 and A5. In vitro infection studies showed that Australian C. acutatum isolates from almond, blueberry, chilli, grape, mango, olive, strawberry and tomato were able to infect grape and could also infect blueberry and strawberry, indicating a lack of host specificity. This lack of host specificity, the genetic similarity with non-grape isolates, and the fact that many of the non-grape hosts were isolated from wine-growing regions, suggest the potential for cross-infection between grape and other horticultural crops. [source] Phylogenetic relationships among the Lorisoidea as indicated by craniodental morphology and mitochondrial sequence dataAMERICAN JOURNAL OF PRIMATOLOGY, Issue 1 2007Judith C. Masters Abstract The phylogeny of the Afro-Asian Lorisoidea is controversial. While postcranial data attest strongly to the monophyly of the Lorisidae, most molecular analyses portray them as paraphyletic and group the Galagidae alternately with the Asian or African lorisids. One of the problems that has bedevilled phylogenetic analysis of the group in the past is the limited number of taxa sampled for both ingroup families. We present the results of a series of phylogenetic analyses based on 635 base pairs (bp) from two mitochondrial genes (12S and 16S rRNA) with and without 36 craniodental characters, for 11 galagid and five lorisid taxa. The outgroup was the gray mouse lemur (Microcebus murinus). Analyses of the molecular data included maximum parsimony (MP), neighbor joining (NJ), maximum likelihood (ML), and Bayesian methods. The model-based analyses and the combined "molecules+morphology" analyses supported monophyly of the Lorisidae and Galagidae. The lorisids form two geographically defined clades. We find no support for the taxonomy of Galagidae as proposed recently by Groves [Primate Taxonomy, Washington, DC: Smithsonian Institution Press. 350 p, 2001]. The taxonomy of Nash et al. [International Journal of Primatology 10:57,80, 1989] is supported by the combined "molecules+morphology" analysis; however, the model-based analyses suggest that Galagoides may be an assemblage of species united by plesiomorphic craniodental characters. Am. J. Primatol. 69:6,15, 2007. © 2006 Wiley-Liss, Inc. [source] Genetic heterogeneity and selection signature at the KIT gene in pigs showing different coat colours and patternsANIMAL GENETICS, Issue 5 2010L. Fontanesi Summary Mutations in the porcine KIT gene (Dominant white locus) have been shown to affect coat colours and colour distribution in pigs. We analysed this gene in several pig breeds and populations (Sicilian black, completely black or with white patches; Cinta Senese; grey local population; Large White; Duroc; Hampshire; Pietrain; wild boar; Meishan) with different coat colours and patterns, genotyping a few polymorphisms. The 21 exons and parts of the intronic regions were sequenced in these pigs and 69 polymorphisms were identified. The grey-roan coat colour observed in a local grey population was completely associated with a 4-bp deletion of intron 18 in a single copy KIT gene, providing evidence that this mutation characterizes the Id allele described in the early genetic literature. The white patches observed in black Sicilian pigs were not completely associated with the presence of a duplicated KIT allele (Ip), suggesting that genetic heterogeneity is a possible cause of different coat colours in this breed. Selection signature was evident at the KIT gene in two different belted pig breeds, Hampshire and Cinta Senese. The same mutation(s) may cause the belted phenotype in these breeds that originated in the 18th,19th centuries from English pigs (Hampshire) and in Tuscany (Italy) in the 14th century (Cinta Senese). Phylogenetic relationships of 28 inferred KIT haplotypes indicated two clades: one of Asian origin that included Meishan and a few Sicilian black haplotypes and another of European origin. [source] Unravelling evolutionary lineages among South African velvet worms (Onychophora: Peripatopsis) provides evidence for widespread cryptic speciationBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009SAVEL R. DANIELS The endemic South African velvet worm genus Peripatopsis currently contains eight recognized species described from variable morphological characters and the current taxonomy is unsatisfactory. In an attempt to investigate evolutionary relationships within Peripatopsis, we collected 137 individuals from 34 sample localities for six of the eight species. Sequence data derived from two partial mitochondrial (mt)DNA gene loci (COI and 12S rRNA), as well as partial sequence data from the ribosomal nuclear 18S rDNA locus in combination with gross morphological characters and scanning electron microscopy (SEM), was used to examine evolutionary relationships. Phylogenetic relationships were investigated using minimum evolution (ME) and Bayesian inferences (BI). Additionally, we also undertook a maximum likelihood (ML) analyses on the combined DNA sequence data set. The combined DNA evidence topologies derived from the ME, BI, and ML was highly congruent and was characterized by the presence of multiple lineages within recognized taxa. Peripatopsis clavigera, Peripatopsis moseleyi, and Peripatopsis sedgwicki each comprised two evolutionary lineages; Peripatopsis capensis comprised three; and Peripatopsis balfouri comprised six operational taxonomic units respectively. Genealogical exclusivity at both mtDNA and nuclear DNA among the geographically coherent groups coupled with pronounced sequence divergence suggested a two-fold increase in the number of species within Peripatopsis. Previously used gross morphological characters (such as the number of leg pairs and colour) were either highly variable within operational taxonomic units, or were invariant, suggesting that alternative morphological characters are necessary for species discrimination. SEM results revealed potentially useful diagnostic characters that can discriminate between at least discriminate some of the newly-identified lineages. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society 2009, 97, 200,216. [source] Phylogenetic relationships of Atherina hepsetus and Atherina boyeri (Pisces: Atherinidae) populations from Greece, based on mtDNA sequencesBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2007ELENI KLOSSA-KILIA The genetic divergence and the phylogenetic relationships of six Atherina boyeri (freshwater and marine origin) and five Atherina hepsetus populations from Greece were investigated using partial sequence analysis of 12s rRNA, 16s rRNA and control region mtDNA segments. Three different well divergent groups were revealed; the first one includes A. boyeri populations living in the sea, the second includes A. boyeri populations living in the lakes and lagoons whereas the third one includes all A. hepsetus populations. Fifty-seven different haplotypes were detected among the populations studied. In all three mtDNA segments examined, sequence analysis revealed the existence of fixed haplotypic differences discriminating A. boyeri populations inhabiting the lagoon and the lakes from both the coastal A. boyeri and the A. hepsetus populations. The genetic divergence values estimated between coastal (marine) A. boyeri populations and those living in the lagoon and the lakes are of the same order of magnitude as those observed among coastal A. boyeri and A. hepsetus populations. The results obtained by different phylogenetic methods were identical. The deep sequence divergence with the fixed different haplotypes observed suggests the occurrence of a cryptic or sibling species within A. boyeri complex. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92, 151,161. [source] Molecular phylogeny of icefish Salangidae based on complete mtDNA cytochrome b sequences, with comments on estuarine fish evolutionBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2007JIE ZHANG Phylogenetic relationships among 15 species in the family Salangidae were constructed based on the complete cytochrome b sequence (1141 bp). We confirmed the monophyly of the family Salangidae and defined four primitive lineages within this family: (I) Protosalanx, Neosalanx anderssoni, Neosalanx tangkahkeii, and Neosalanx argentea; (II) Neosalanx reganius, Neosalanx jordani, Neosalanx oligodontis, and Neosalanx sp.; (III) Hemisalanx, Salanx, Leucosoma, and Salangichthys ishikawae; and (IV) Salangichthys microdon. A major finding of our study is the key basal placement of Sg. microdon. According to the tentative estimation, the divergence of the four lineages appears to have been initiated in the early Miocene (21 Mya), with most speciation events occurring 1.05,9.90 Mya. Taxonomic revisions on subfamilial, generic, and specific levels were carried out based on phylogenetic relationships and genetic distance, taking into account some key morphological characters. The speciation mechanism in Salangidae is also discussed, and the evidence shows that geographical isolation, water mass, as well as some ecological factors, may not always play important roles in the speciation of temperate estuarine fish. In the most cases, sympatric salangids are not monophyletic, indicating that their coexistence reflects secondary contact rather than sympatric speciation. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 91, 327,342. [source] Molecular evidence suggests an ancient radiation for the fairy shrimp genus Streptocephalus (Branchiopoda: Anostraca)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2004SAVEL R. DANIELS Phylogenetic relationships among assumed Gondwanan aquatic inland invertebrate fauna are generally largely neglected, and biogeographical hypotheses for these organisms are generally inferred from historic (palaeogeographical) and contemporary distribution patterns. The distribution of the monogeneric thermophilic freshwater fairy shrimp family Streptocephalidae (Streptocephalus) provides a particularly useful framework to test the three contrasting biogeographical scenarios proposed for the evolution of this group: (1) the genus evolved in Laurasia and subsequently dispersed into Africa and North America; (2) the genus evolved and dispersed out of Africa and (3) the current distribution of the genus is the result of vicariance following the fragmentation of Gondwana. In the present study, the phylogenetic relationships of species in this genus are examined with the use of two mitochondrial genes (12S rRNA and COI mtDNA), while the phylogenetic relationships among the North American species and selected African taxa was investigated using the nuclear fragment (5.8S-ITS-1-18S). Phylogenetic results indicate that Streptocephalus probably evolved in Gondwana and that the current distribution patterns are a consequence of a combination of vicariance and limited dispersal. The implications for the evolution of continental freshwater crustaceans are discussed. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 313,327. [source] | ||||||||||||||||||||||||||||||||||||||||