Distribution by Scientific Domains
Distribution within Life Sciences

Kinds of Clades

  • african clade
  • american clade
  • basal clade
  • derived clade
  • different clade
  • distinct clade
  • divergent clade
  • diverse clade
  • dna clade
  • eudicot clade
  • european clade
  • genetic clade
  • haplotype clade
  • large clade
  • main clade
  • major clade
  • mitochondrial clade
  • mitochondrial dna clade
  • monophyletic clade
  • mtdna clade
  • nested clade
  • novel clade
  • one clade
  • other clade
  • phylogenetic clade
  • second clade
  • several clade
  • sister clade
  • south american clade
  • southern clade
  • terminal clade
  • third clade
  • well-supported clade

  • Terms modified by Clades

  • clade analysis
  • clade b

  • Selected Abstracts


    EVOLUTION, Issue 4 2007
    C. Galley
    We construct a species-level phylogeny for the Pentaschistis clade based on chloroplast DNA, from the following regions: trnL-F, trnT-L, atpB-rbcL, rpL16, and trnD-psbA. The clade comprises 82 species in three genera, Pentaschistis, Pentameris, and Prionanthium. We demonstrate that Prionanthium is nested in Pentaschistis and that this clade is sister to a clade of Pentameris plus Pentaschistis tysonii. Forty-three of the species in the Pentaschistis clade have multicellular glands and we use ancestral character state reconstruction to show that they have been gained twice or possibly once, and lost several times. We suggest that the maintenance, absence, loss, and gain of glands are correlated with leaf anatomy type, and additionally that there is a difference in the degree of diversification of lineages that have these different character combinations. We propose that both glands and sclerophyllous leaves act as defense systems against herbivory, and build a cost/benefit model in which multicellular glands or sclerophyllous leaves are lost when the alternative defense system evolves. We also investigate the association between leaf anatomy type and soil nutrient type on which species grow. There is little phylogenetic constraint in soil nutrient type on members of the Pentaschistis clade, with numerous transitions between oligotrophic and eutrophic soils. However, only orthophyllous-leaved species diversify on eutrophic soils. We suggest that the presence of these glands enables the persistence of orthophyllous lineages and therefore diversification of the Pentaschistis clade on eutrophic as well as oligotrophic soils. [source]


    EVOLUTION, Issue 7 2006
    Rainer R. Schoch
    Abstract The Branchiosauridae was a clade of small amphibians from the Permo-Carboniferous with an overall salamander-like appearance. The clade is distinguished by an extraordinary fossil record that comprises hundreds of well-preserved specimens, representing a wide range of ontogenetic stages. Branchiosaurids had external gills and weakly ossified skeletons, and due to this larval appearance their status as neotenic (perennibranchiate) froms has long been accepted. Despite their extensive fossil record large specimens with an adult morphology appeared to be lacking altogether, but recently two adult specimens were identified in a rich sample of Apateon gracilis collected in the 19th century from a locality near Dresden, Saxony. These specimens are unique among branchiosaurids in showing a high level of ossification, including bones that have never been reported in a branchiosaur. These highlight the successive formation of features believed to indicate terrestrial locomotion, as well as feeding on larger prey items. Moreover, these transformations occurred in a small time window (whereas the degree of size increase is used as a proxy of time) and the degree of concentration of developmental events in branchiosaurids is unique among tetrapods outside the lissamphibians. These specimens are compared with large adults of the neotenic branchiosaurid Apateon caducus from the Saar-Nahe Basin, which despite their largetr body size lack the features found in the adult. A. gracilis specimens. These specimens give new insight into patterns of metamorphosis (morphological transformation) in branchiosaurids that are believed to be correlated to a change of habitat, and clearly show that different life-history pathways comparable to those of modern salamanders were already estabilshed in this Paleozoic clade. [source]


    EVOLUTION, Issue 1 2006
    Abstract Why does a trait evolve repeatedly within a clade? When examining the evolution of a trait, evolutionary biologists typically focus on the selective advantages it may confer and the genetic and developmental mechanisms that allow it to vary. Although these factors may be necessary to explain why a trait evolves in a particular instance, they may not be sufficient to explain phylogenetic patterns of repeated evolution or conservatism. Instead, other factors may also be important, such as biogeography and competitive interactions. In squamate reptiles (lizards and snakes) a dramatic transition in body form has occurred repeatedly, from a fully limbed, lizardlike body form to a limbreduced, elongate, snakelike body form. We analyze this trait in a phylogenetic and biogeographic context to address why this transition occurred so frequently. We included 261 species for which morphometric data and molecular phylogenetic information were available. Among the included species, snakelike body form has evolved about 25 times. Most lineages of snakelike squamates belong to one of two ecomorphs, either short-tailed burrowers or long-tailed surface dwellers. The repeated origins of snakelike squamates appear to be associated with the in situ evolution of these two ecomorphs on different continental regions (including multiple origins of the burrowing morph within most continents), with very little dispersal of most limb-reduced lineages between continental regions. Overall, the number of repeated origins of snakelike morphology seems to depend on large-scale biogeographic patterns and community ecology, in addition to more traditional explanations (e.g., selection, development). [source]


    EVOLUTION, Issue 1 2005
    Jeremy M. Brown
    Abstract A recent study of environmental effects on rates of molecular evolution in the plant subgenus Mearnsia shows that species occurring in more equatorial latitudes have higher rates of substitution in rDNa sequences as compared to their more southerly congeners (Wright et al. 2003). However, we believe that the statistical approach employed by Wright et al. (2003) insufficiently accounts for the phylogenetic nonindependence of the species examined, given that all six equatorial species of Mearnsia form a clade. To distinguish between the effect of latitude and that of phylogenetic nonindependence, we have employed a variety of comparative approaches that use independent contrasts to test for an effect of environment across this entire subgenus. We find very little evidence for an effect of latitude on rate of molecular evolution using these approaches and believe that the shared evolutionary history of the clade is a plausible explanation of the apparent rate difference between equatorial and subequatorial Mearnsia species. [source]


    EVOLUTION, Issue 4 2002
    Madalena Branco
    Abstract Nested clade analysis was applied to cytochrome b restriction site data previously obtained on 20 natural populations of the European rabbit across the Iberian Peninsula to test the hypothesis of postglacial dispersal from two main refugia, one in the northeast and the other in the southwest. Apart from historical fragmentation that resulted in geographic discontinuity of two distinct mitochondrial DNA (mtDNA) clades A and B, patterns of haplotype genetic variability have been shaped mostly by restricted gene flow via isolation by distance. The distribution of tip versus interior haplotypes suggests that dispersal occurred from both the southwestern and northeastern groups. Dispersal from the southwest had a north and northwest direction, whereas from the northeast it had mostly a western and southern orientation, with subsequent overlap in a southeastern-northwestern axis across the Iberian Peninsula. The analysis of the pairwise mismatch distribution of a 179,181-bp fragment of the mtDNA control region, for seven of those populations, further supports the idea that major patterns of dispersal were in the direction of central Iberia. Additionally, rabbit populations do not show signs of any significant loss of genetic diversity in the recent past, implying that they maintained large population sizes and structure throughout the ice ages. This is congruent with the fact that the Iberian Peninsula was itself a glacial refugium during Quaternary ice ages. Nonetheless, climatic oscillations of this period, although certainly milder than in northern Europe, were sufficient to affect the range distributions of Iberian organisms. [source]


    JOURNAL OF PHYCOLOGY, Issue 4 2008
    Philip M. Novis
    The quadriflagellate snow alga Chlainomonas Christen, distributed in New Zealand and North America, has several unusual structural attributes. A process assumed to be cytokinesis involves extrusion of protoplasm from the parent through a narrow canal, C. kolii (J. T. Hardy et Curl) Hoham produces a net-like outer envelope rather than a cell wall, and the flagellar basal apparatus of Chlainomonas consists of two semi-independent pairs of basal bodies. Structural connections between basal body pairs appear minimal, but a connecting system different from that observed in other genera exists within each pair. Phylogenetic analysis using rbcL sequences places Chlainomonas in the Chloromonas clade, other known members of which are all biflagellate. Chlainomonas is split into two robust lineages, with New Zealand collections sharing an origin with northern North American collections. Although the quadriflagellate condition is regarded as ancestral in the Chlorophyceae, we speculate,based on ultrastructural and molecular data presented here,that Chlainomonas represents a derived form that has arisen from fusion of two ancestral biflagellate cells. Other explanations (for example, that Chlainomonas represents a diploid form of a biflagellate species) are remotely possible but are presently at odds with extensive observations of field material. Improvements in techniques for experimental manipulation of these sensitive cryophiles will be required to fully characterize their structure and progress our understanding of their biology. [source]


    D.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]

    Genetic structure of Japanese populations of an ambrosia beetle, Xylosandrus germanus (Curculionidae: Scolytinae)

    Masaaki ITO
    Abstract We examined the genetic structures of 13 Japanese populations of an ambrosia beetle, Xylosandrus germanus (Curculionidae: Scolytinae), to understand the effects of geographical barriers on the colonization dynamics of this species. The genetic structure was studied using portions of the mitochondrial cytochrome oxidase I (COI) gene. A phylogenetic analysis revealed three distinct lineages (clades A, B and C) within X. germanus. Clade A contained 21 haplotypes from all 13 populations; whereas clade B contained eight haplotypes from Hokkaido (Sapporo and Furano), Iwate and Nagano populations; and clade C contained only a single a haplotype from the Hokkaido (Furano) population. In the analysis of molecular variance (amova), the greatest amount of genetic variation was detected between populations in Hokkaido and those in Honshu and other southern islands. Between these two groups of populations, all the values of the coefficient of gene differentiation were significantly larger than zero, except for the Hokkaido (Sapporo) versus Nagano comparison. Our results confirm that for X. germanus, gene flow has been interrupted between Hokkaido and Honshu since the last glacial maximum. [source]

    Soils of a Mediterranean hot spot of biodiversity and endemism (Sardinia, Tyrrhenian Islands) are inhabited by pan-European, invasive species of Hypocrea/Trichoderma

    Quirico Migheli
    Summary We have used a Mediterranean hot spot of biodiversity (the Island of Sardinia) to investigate the impact of abiotic factors on the distribution of species of the common soil fungus Trichoderma. To this end, we isolated 482 strains of Hypocrea/Trichoderma from 15 soils comprising undisturbed and disturbed environments (forest, shrub lands and undisturbed or extensively grazed grass steppes respectively). Isolates were identified at the species level by the oligonucleotide BarCode for Hypocrea/Trichoderma (TrichOKEY), sequence similarity analysis (Trichoblast) and phylogenetic inferences. The majority of the isolates were positively identified as pan-European and/or pan-global Hypocrea/Trichoderma species from sections Trichoderma and Pachybasium, comprising H. lixii/T. harzianum, T. gamsii, T. spirale, T. velutinum, T. hamatum, H. koningii/T. koningii, H. virens/T. virens, T. tomentosum, H. semiorbis, H. viridescens/T. viridescens, H. atroviridis/T. atroviride, T. asperellum, H. koningiopsis/T. koningiopsis and Trichoderma sp. Vd2. Only one isolate represented a new, undescribed species belonging to the Harzianum,Catoptron Clade. Internal transcribed spacer sequence analysis revealed only one potentially endemic internal transcribed spacer 1 allele of T. hamatum. All other species exhibited genotypes that were already found in Eurasia or in other continents. Only few cases of correlation of species occurrence with abiotic factors were recorded. The data suggest a strong reduction of native Hypocrea/Trichoderma diversity, which was replaced by extensive invasion of species from Eurasia, Africa and the Pacific Basin. [source]

    Karyotype and mitochondrial 16S gene characterizations in seven South American Cichlasomatini species (Perciformes, Cichlidae)

    O. Marescalchi
    Abstract The family Cichlidae constitutes most of the freshwater fish fauna of South America; its taxonomy is at present mainly based on morphological characters. Here, relationships among seven Cichlasomatini species have been investigated by studying their karyotype structure and by sequencing a 520 bp fragment of the mitochondrial 16S gene. Molecular data sets point to a high affinity of Cichlasoma amazonarum with Aequidens sensu stricto group, in particular with Aequidens tetramerus. Aequidens never form a single monophyletic clade: molecular trees group together ,Aequidens pulcher' and ,Aequidens rivulatus' and suggest their close relationship with Bujurquina and Laetacara, rather than with the A. sensu stricto group. Both molecular and karyotypic data confirm that Cleithracara maronii belongs to a distinct clade, thus supporting its generic differentiation based on morphological characters. Chromosome number, karyotype structure and molecular data suggest that Laetacara dorsigera is related to Bujurquina vittata and confirm their generic level of differentiation. From a cytotaxonomic point of view, a karyotype of 2n = 48 with most acrocentric or subacrocentric chromosomes could be the ancestral one from which the others might have derived. Zusammenfassung Ein großer Teil der südamerikanischen Süßwasserfische gehört zur Familie der Cichliden, deren Taxonomie bisher aber nur auf morphologischen Eigenschaften beruhte. In dieser Arbeit wurden die Verwandtschaftbeziehungen zwischen sieben Arten durch die Untersuchung des Karyotyps und eines 520 bp Teilstücks der mitochondrialen 16S rDNA-Sequenz studiert. Die molekularen Daten weisen auf eine höhere Verwandtschaft zwischen Cichlosoma amazonarum und Aequidens sensu strictu, besonders mit A. tetramerus, hin. Die Arten der Gattung Aequidens bilden niemals eine monophyletische Clade; die molekularen Bäume gruppieren immer A. pulcher und A. rivulatus zusammen und machen deren nähere Verwandtschaft zu den Gattungen Bujurquina und Laetacara wahrscheinlicher als zu der als Aequidens sensu strictu bezeichneten Gruppe. Die molekularen und die karyologischen Daten bestärken, daß die Art Cleithracara maroni einer klar getrennten Clade angehört, was auch die morphologischen Ergebnisses unterstützt. Die Chromosomenzahl, die Zusammensetzung des Karyotyps und die molekularen Vergleiche lassen erkennen, daßLaetacara dorsigera mit Bujurquina vittata verwandt ist, aber die Differenzierung den Gattungsstatus rechtfertigt. Vom cytotaxonomischen Standpunkt könnte ein Karyotyp mit 2n = 48 mit vorwiegend akrozentrischen oder subakrozentischen Chromosomen der ursprüngliche sein, von dem die anderen ableitbar sind. [source]

    Phylogeography of the mountain chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change

    MOLECULAR ECOLOGY, Issue 5 2007
    Abstract Since the late 1990s, molecular techniques have fuelled debate about the role of Pleistocene glacial cycles in structuring contemporary avian diversity in North America. The debate is still heated; however, there is widespread agreement that the Pleistocene glacial cycles forced the repeated contraction, fragmentation, and expansion of the North American biota. These demographic processes should leave genetic ,footprints' in modern descendants, suggesting that detailed population genetic studies of contemporary species provide the key to elucidating the impact of the late Quaternary (late Pleistocene,Holocene). We present an analysis of mitochondrial DNA (mtDNA) variation in the mountain chickadee (Poecile gambeli) in an attempt to examine the genetic evidence of the impact of the late Quaternary glacial cycles. Phylogenetic analyses reveal two strongly supported clades of P. gambeli: an Eastern Clade (Rocky Mountains and Great Basin) and a Western Clade (Sierra Nevada and Cascades). Post-glacial introgression is apparent between these two clades in the Mono Lake region of Central California. Within the Eastern Clade there is evidence of isolation-by-distance in the Rocky Mountain populations, and of limited gene flow into and around the Great Basin. Coalescent analysis of genetic variation in the Western Clade indicates that northern (Sierra Nevada/Cascades) and southern (Transverse/Peninsular Ranges) populations have been isolated and evolving independently for nearly 60 000 years. [source]

    Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs

    THE PLANT JOURNAL, Issue 4 2009
    Julia Santiago
    Summary Abscisic acid (ABA) is a key phytohormone involved in adaption to environmental stress and regulation of plant development. Clade A protein phosphatases type 2C (PP2Cs), such as HAB1, are key negative regulators of ABA signaling in Arabidopsis. To obtain further insight into regulation of HAB1 function by ABA, we have screened for HAB1-interacting partners using a yeast two-hybrid approach. Three proteins were identified, PYL5, PYL6 and PYL8, which belong to a 14-member subfamily of the Bet v1-like superfamily. HAB1,PYL5 interaction was confirmed using BiFC and co-immunoprecipitation assays. PYL5 over-expression led to a globally enhanced response to ABA, in contrast to the opposite phenotype reported for HAB1 -over-expressing plants. F2 plants that over-expressed both HAB1 and PYL5 showed an enhanced response to ABA, indicating that PYL5 antagonizes HAB1 function. PYL5 and other members of its protein family inhibited HAB1, ABI1 and ABI2 phosphatase activity in an ABA-dependent manner. Isothermal titration calorimetry revealed saturable binding of (+)ABA to PYL5, with Kd values of 1.1 ,m or 38 nm in the absence or presence of the PP2C catalytic core of HAB1, respectively. Our work indicates that PYL5 is a cytosolic and nuclear ABA receptor that activates ABA signaling through direct inhibition of clade A PP2Cs. Moreover, we show that enhanced resistance to drought can be obtained through PYL5-mediated inhibition of clade A PP2Cs. [source]

    Pathways and Substrate Specificity of DMSP Catabolism in Marine Bacteria of the Roseobacter Clade

    CHEMBIOCHEM, Issue 3 2010
    Jeroen S. Dickschat Dr.
    Abstract The volatiles released by Phaeobacter gallaeciensis, Oceanibulbus indolifex and Dinoroseobacter shibae have been investigated by GC-MS, and several MeSH-derived sulfur volatiles have been identified. An important sulfur source in the oceans is the algal metabolite dimethylsulfoniopropionate (DMSP). Labelled [2H6]DMSP was fed to the bacteria to investigate the production of volatiles from this compound through the lysis pathway to [2H6]dimethylsulfide or the demethylation pathway to [2H3]-3-(methylmercapto)propionic acid and lysis to [2H3]MeSH. [2H6]DMSP was efficiently converted to [2H3]MeSH by all three species. Several DMSP derivatives were synthesised and used in feeding experiments. Strong dealkylation activity was observed for the methylated ethyl methyl sulfoniopropionate and dimethylseleniopropionate, as indicated by the formation of EtSH- and MeSeH-derived volatiles, whereas no volatiles were formed from dimethyltelluriopropionate. In contrast, the dealkylation activity for diethylsulfoniopropionate was strongly reduced, resulting in only small amounts of EtSH-derived volatiles accompanied by diethyl sulfide in P. gallaeciensis and O. indolifex, while D. shibae produced the related oxidation product diethyl sulfone. The formation of diethyl sulfide and diethyl sulfone requires the lysis pathway, which is not active for [2H6]DMSP. These observations can be explained by a shifted distribution between the two competing pathways due to a blocked dealkylation of ethylated substrates. [source]

    Myzostomida Are Not Annelids: Molecular and Morphological Support for a Clade of Animals with Anterior Sperm Flagella

    CLADISTICS, Issue 2 2001
    Jan Zrzavý
    The myzostomes are animals with five pairs of parapodia, living as commensals or (endo)parasites mostly on crinoid and ophiuroid echinoderms. They are generally considered aberrant annelids, possibly phyllodocidan polychaetes. A phylogenetic analysis of 18S and 28S ribosomal DNA sequence data of Myzostoma glabrum, together with 60 morphological, developmental, ultrastructural, and life-history characters, is presented to show that myzostomes are a sister group of the Cycliophora, closely related to the rotifer-acanthocephalan clade (=Syndermata). Myzostomes and syndermates share predominantly the highly derived spermatozoa with anteriorly directed flagella (cycliophoran sperm is insufficiently known). The myzostome-cycliophoran-syndermate clade, accommodated within the Platyzoa (including Platyhelminthes s. str., Gastrotricha, Gnathostomulida, Syndermata, Cycliophora, and Myzostomida), is strongly supported by most analyses, regardless of alignment parameters, character combinations and weighting, species sampling, and tree-building methods. The new name Prosomastigozoa ("forward-flagellar animals") is proposed for the group including three phyla (Cycliophora, Myzostomida, and Syndermata). [source]

    Some aspects of spiralian development

    ACTA ZOOLOGICA, Issue 1 2010
    Claus Nielsen
    Abstract Nielsen, C. 2010. Some aspects of spiralian development. ,Acta Zoologica (Stockholm) 91: 20,28 Spiralian development is not only a characteristic early cleavage pattern, with shifting orientations of the cleavage planes, but also highly conserved cell lineages, where the origin of several organs can be traced back to identifiable cells in the lineage. These patterns are well documented in annelids, molluscs, nemertines, and platyhelminths and are considered ancestral of a bilaterian clade including these phyla. Spiral cleavage has not been documented in ecdysozoans, and no trace of the spiral development pattern is seen in phoronids and brachiopods. Origin of the spatial organization in spiralian embryos is puzzling, but much of the information appears to be encoded in the developing oocyte. Fertilization and "pseudofertilization" apparently provides the information defining the secondary, anterior-posterior body axis in many species. The central nervous system consists of three components: an apical organ, derived from the apical blastomeres 1a111 -1d111, which degenerates before or at metamorphosis; the cerebral ganglia derived from other blastomeres of the first micromere quartet and retained in the adult as a preoral part of the brain; and the originally circumblastoporal nerve cord, which has become differentiated into a perioral part of the brain, the paired or secondarily fused ventral nerve cords, and a small perianal nerve ring. [source]

    The anatomy of the palatoquadrate in the Lower Triassic Proterosuchus fergusi (Reptilia, Archosauromorpha) and its morphological transformation within the archosauriform clade

    ACTA ZOOLOGICA, Issue 3 2009
    Jozef Klembara
    Abstract The anatomy of the palatoquadrate ossifications of the Lower Triassic archosauromorph Proterosuchus fergusi from South Africa is described. It consists of two ossifications, the epipterygoid and the quadrate, which were joined by cartilage in life. The margins of the cartilage are clearly indicated by ridges and grooves on the dorsal surface of the pterygoid. The epipterygoid ossification consists of two structures: the anteroposteriorly expanded basal portion and, dorsally from it, an extending, slender, ascending process. From the anterior margin of the basal portion of the epipterygoid, a plate-like structure, herein called the lamina epipterygoidea anteromedialis, extends anteromedially to form the anterolateral wall of the cavum epiptericum. Comparisons with the similarly constructed embryonal and adult epipterygoid components of Sphenodon punctatus show that the anteromedial lamina of the epipterygoid of P. fergusi is an additional component of the epipterygoid of this species and that this lamina is absent in the former species. However, a structure in a topologically similar position to the anteromedial lamina of the epipterygoid of P. fergusi is present in the palatoquadrate of Alligator mississippiensis. In the latter species, the structure is called the lamina palatoquadrati anterior; it ossifies in membrane and forms the dorsolateral cover of the huge trigeminal ganglion. It is hypothesized here that the anteromedial lamina of the epipterygoid of P. fergusi and the anterior lamina of the palatoquadrate of A. mississippiensis are most probably homologous structures and are present in both the basal and one of the crown taxa of the archosauromorph clade, respectively. [source]

    Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa

    Sébastien Calvignac
    Abstract Aim, Middle East brown bears (Ursus arctos syriacus Hemprich and Ehrenberg, 1828) are presently on the edge of extinction. However, little is known of their genetic diversity. This study investigates that question as well as that of Middle East brown bear relationships to surrounding populations of the species. Location, Middle East region of south-western Asia. Methods, We performed DNA analyses on 27 brown bear individuals. Twenty ancient bone samples (Late Pleistocene to 20th century) from natural populations and seven present-day samples obtained from captive individuals were analysed. Results, Phylogenetic analyses of the mitochondrial sequences obtained from seven ancient specimens identify three distinct maternal clades, all unrelated to one recently described from North Africa. Brown bears from Iran exhibit striking diversity (three individuals, three haplotypes) and form a unique clade that cannot be linked to any extant one. Individuals from Syria belong to the Holarctic clade now observed in Eastern Europe, Turkey, Japan and North America. Specimens from Lebanon surprisingly appear as tightly linked to the clade of brown bears now in Western Europe. Moreover, we show that U. a. syriacus in captivity still harbour haplotypes closely linked to those found in ancient individuals. Main conclusion, This study brings important new information on the genetic diversity of brown bear populations at the crossroads of Europe, Asia and Africa. It reveals a high level of diversity in Middle East brown bears and extends the historical distribution of the Western European clade to the East. Our analyses also suggest the value of a specific breeding programme for captive populations. [source]

    A new specimen of Baphetes from Ný,any, Czech Republic and the intrinsic relationships of the Baphetidae

    ACTA ZOOLOGICA, Issue 2009
    Angela C. Milner
    Abstract ,Loxomma'bohemicum from the Upper Carboniferous assemblage from Ný,any, Czech Republic, is a nomen dubium restricted to the type and only specimen. The new binomen Baphetes orientalis is created for a skull referred to Baphetes bohemicus by later authors. A previously undescribed baphetid specimen from Ný,any is referred to B. orientalis despite differences in skull proportions. It comprises a skull in dorsal aspect, mandibles and some associated postcranial elements. The skull possesses sclerotic ring elements within the orbital region of the dorsal fenestration of the skull, confirming the eye location. The elongate gastralia are arranged perpendicular to the interclavicle edge in contrast to the condition in temnospondyls and colosteids. Cladistic analysis of 24 characters of 11 baphetoids was carried out using Acanthostega and Crassigyrinus as outgroups. Eucritta was the most primitive baphetoid, with Spathicephalus being the sister-taxon to the remaining taxa, justifying a monotypic Spathicephalidae as a sister-taxon to the Baphetidae. The Baphetidae are divided into a subfamily Baphetinae nom.nov. containing two Baphetes species; and a subfamily Loxommatinae with Loxomma as a paraphyletic grade leading to a Megalocephalus +Kyrinion clade. The Linton taxon ,Baphetes' lintonensis is transferred to the genus Loxomma to give the new combination Loxomma lintonensis. [source]

    Anatomy and systematics of the minute syrnolopsine gastropods from Lake Tanganyika (Caenogastropoda, Cerithioidea, Paludomidae)

    ACTA ZOOLOGICA, Issue 4 2008
    Ellen E. Strong
    Abstract The minute syrnolopsine gastropods endemic to Lake Tanganyika have been allied to a number of freshwater, marine and terrestrial groups as a consequence of superficial conchological similarity. Although early anatomical studies confirmed the cerithioid organization of this clade, their close relationship to other lake species was not consistently recognized. In several recent cladistic analyses based on molecular data, the higher taxonomic placement and sister group relationships of syrnolopsines have been unstable. The present analysis confirms that syrnolopsines possess a spermatophore-forming organ , a synapomorphy of the Paludomidae , corroborating their placement in this family. Consistent with the molecular data, syrnolopsine monophyly is supported by two characters that occur exclusively in this group (salivary gland ducts that bypass the nerve ring and a linear albumen gland). Several characters in Martelia tanganyicensis, the most diminutive syrnolopsine , are only evident in the smallest lake species thus far investigated (Bridouxia, Stormsia) namely reduction of ctenidial leaflets, sorting area, intestine length and number of statoconia. These features are interpreted as being correlated with reduction in size. Nevertheless, close examination reveals differences in detail that allow more refined hypotheses of homology and are consistent with their independent origin. [source]

    Morpho-anatomy of the lobopod Magadictyon cf. haikouensis from the Early Cambrian Chengjiang Lagerstätte, South China

    ACTA ZOOLOGICA, Issue 4 2007
    Jianni Liu
    Abstract Magadictyon haikouensis (Luo and Hu, 1999) from the Early Cambrian Chengjiang Lagerstätte, an incomplete specimen of a large lobopod with strong appendages, has been regarded as related to the lobopods Microdictyon and Onychodictyon. Newly discovered complete specimens of Magadictyon cf. haikouensis (found by the Early Life Institute field team) show that the taxon, in addition to its strong appendages with appendicules, also had a head bearing similar caecum-like structures to those of the arthropod Naraoia and Chelicerate, ,Peytoia'-like mouthparts and frontal appendages. Because of their similarity, the caecum-like structures of Magadictyon cf. haikouensis are considered to be homologous with those of stem-group arthropods. The ,Peytoia'-like mouthparts and the frontal appendages are similar to those of the AOPK (Anomalocaris,Opabinia,Pambdelurion,Kerygmachela) group. In addition, the appendages with appendicules show that Magadictyon cf. haikouensis is closely related to Onychodictyon. Therefore, Magadictyon cf. haikouensis is regarded here as a rare transitional form between lobopods and arthropods. Besides, together with other lobopods, the morphology of Magadictyon cf. haikouensis demonstrates that the Cambrian lobopods appear to have been diverse and not particularly closely related to one another, and do not seem to represent a monophyletic clade. [source]

    Forage collection, substrate preparation, and diet composition in fungus-growing ants

    1. Variation and control of nutritional input is an important selective force in the evolution of mutualistic interactions and may significantly affect coevolutionary modifications in partner species. 2. The attine fungus-growing ants are a tribe of more than 230 described species (12 genera) that use a variety of different substrates to manure the symbiotic fungus they cultivate inside the nest. Common ,wisdom' is that the conspicuous leaf-cutting ants primarily use freshly cut plant material, whereas most of the other attine species use dry and partly degraded plant material such as leaf litter and caterpillar frass, but systematic comparative studies of actual resource acquisition across the attine ants have not been done. 3. Here we review 179 literature records of diet composition across the extant genera of fungus-growing ants. The records confirm the dependence of leaf-cutting ants on fresh vegetation but find that flowers, dry plant debris, seeds (husks), and insect frass are used by all genera, whereas other substrates such as nectar and insect carcasses are only used by some. 4. Diet composition was significantly correlated with ant substrate preparation behaviours before adding forage to the fungus garden, indicating that diet composition and farming practices have co-evolved. Neither diet nor preparation behaviours changed when a clade within the paleoattine genus Apterostigma shifted from rearing leucocoprinous fungi to cultivating pterulaceous fungi, but the evolutionary derived transition to yeast growing in the Cyphomyrmex rimosus group, which relies almost exclusively on nectar and insect frass, was associated with specific changes in diet composition. 5. The co-evolutionary transitions in diet composition across the genera of attine ants indicate that fungus-farming insect societies have the possibility to obtain more optimal fungal crops via artificial selection, analogous to documented practice in human subsistence farming. [source]

    Host specificity of ambrosia and bark beetles (Col., Curculionidae: Scolytinae and Platypodinae) in a New Guinea rainforest

    Abstract 1.,Bark and ambrosia beetles are crucial for woody biomass decomposition in tropical forests worldwide. Despite that, quantitative data on their host specificity are scarce. 2.,Bark and ambrosia beetles (Scolytinae and Platypodinae) were reared from 13 species of tropical trees representing 11 families from all major lineages of dicotyledonous plants. Standardised samples of beetle-infested twigs, branches, trunks, and roots were taken from three individuals of each tree species growing in a lowland tropical rainforest in Papua New Guinea. 3.,A total of 81 742 beetles from 74 species were reared, 67 of them identified. Local species richness of bark and ambrosia beetles was estimated at 80,92 species. 4.,Ambrosia beetles were broad generalists as 95% of species did not show any preference for a particular host species or clade. Similarity of ambrosia beetle communities from different tree species was not correlated with phylogenetic distances between tree species. Similarity of ambrosia beetle communities from individual conspecific trees was not higher than that from heterospecific trees and different parts of the trees hosted similar ambrosia beetle communities, as only a few species preferred particular tree parts. 5.,In contrast, phloeophagous bark beetles showed strict specificity to host plant genus or family. However, this guild was poor in species (12 species) and restricted to only three plant families (Moraceae, Myristicaceae, Sapindaceae). 6.,Local diversity of both bark and ambrosia beetles is not driven by the local diversity of trees in tropical forests, since ambrosia beetles display no host specificity and bark beetles are species poor and restricted to a few plant families. [source]

    Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

    ECOLOGY LETTERS, Issue 8 2009
    Daniel L. Rabosky
    Abstract Diversification rate is one of the most important metrics in macroecological and macroevolutionary studies. Here I demonstrate that diversification analyses can be misleading when researchers assume that diversity increases unbounded through time, as is typical in molecular phylogenetic studies. If clade diversity is regulated by ecological factors, then species richness may be independent of clade age and it may not be possible to infer the rate at which diversity arose. This has substantial consequences for the interpretation of many studies that have contrasted rates of diversification among clades and regions. Often, it is possible to estimate the total diversification experienced by a clade but not diversification rate itself. I show that the evidence for ecological limits on diversity in higher taxa is widespread. Finally, I explore the implications of ecological limits for a variety of ecological and evolutionary questions that involve inferences about speciation and extinction rates from phylogenetic data. [source]

    No evidence that sexual selection is an ,engine of speciation' in birds

    ECOLOGY LETTERS, Issue 3 2003
    Edward H. Morrow
    Abstract Sexual selection has been implicated as having a role in promoting speciation, as it should increase the rate of evolution of reproductive isolation, and there is some comparative evidence that sexual selection may be related to imbalances in clade size seen in resolved phylogenies. By employing a new comparative method we are able to investigate the role of sexual selection in explaining the patterns of species richness across birds. We used data for testes size as an index of post-mating sexual selection, and sexual size dimorphism and sexual dichromatism as indices of pre-mating sexual selection. These measures were obtained for 1031 species representing 467 genera. None of the variables investigated explained the patterns of species richness. As sexual selection may also increase extinction rates, the net effect on species richness in any given clade will depend on the balancing effects of sexual selection upon speciation and extinction rates. We suggest that variance across clades in this balance may have resulted in the lack of a relationship between species richness and sexual selection seen in birds. [source]

    Body size and invasion success in marine bivalves

    ECOLOGY LETTERS, Issue 2 2002
    Kaustuv Roy
    The role of body size in marine bivalve invasions has been the subject of debate. Roy et al. found that large-bodied species of marine bivalves were more likely to be successful invaders, consistent with patterns seen during Pleistocene climatic change, but Miller et al. argued that such selectivity was largely driven by the inclusion of mariculture species in the analysis and that size-selectivity was absent outside of mariculture introductions. Here we use data on non-mariculture species from the north-eastern Pacific coast and from a global species pool to test the original hypothesis of Roy et al. that range limits of larger bivalves are more fluid than those of smaller species. First, we test the hypothesis that larger bivalve species are more successful than small species in expanding their geographical ranges following introduction into new regions. Second, we compare body sizes of indigenous and non-indigenous species for 299 of the 303 known intertidal and shelf species within the marine bivalve clade that contains the greater number of non-mariculture invaders, the Mytilidae. The results from both tests provide additional support for the view that body size plays an important role in mediating invasion success in marine bivalves, in contrast to Miller et al. Thus range expansions in Recent bivalves are consistent with patterns seen in Pleistocene faunas despite the many differences in the mechanisms. [source]

    Liriomyza huidobrensis in Yunnan, China: current distribution and genetic structure of a recently established population

    Liping He
    Abstract Liriomyza huidobrensis Blanchard (Diptera: Agromyzidae) is a very serious and economically important pest around the world. Liriomyza huidobrensis in China was first reported from Kunming of Yunnan province in 1993. We report here that this pest has recently expanded its distribution, along with a host plant range extension and population explosion. The mitochondrial cytochrome oxidase II gene was sequenced for eight populations from Yunnan. All individuals were identical: no genetic variation was observed between populations either from different geographical localities or from different host plants. The phylogenetic analysis shows that the Yunnan population is grouped into the South American clade, which also includes other recently introduced Asian populations. Together with ecological data and colonization history of this pest, our results suggest that Yunnan population might have an ultimate, albeit not immediate, origin from South American populations. [source]

    Phylogeography of the leaf beetle Chrysolina virgata in wetlands of Japan inferred from the distribution of mitochondrial haplotypes

    Teiji SOTA
    Abstract The genetic differentiation among populations of the leaf beetle Chrysolina virgata living in wetlands of Japan was studied based on the sequence data of the mitochondrial cytochrome oxidase subunit I gene region (750 bp). Two distinct lineages of mitochondrial haplotypes were found: one (clade A) consisted of 26 haplotypes distributed over the distribution range of C. virgata between north-east Honshu and Kyushu, whereas the other (clade B) was monotypic and confined to a small region in north-east Honshu where it coexisted with clade A. Nested clade analysis for these haplotypes suggested that range expansion and following differentiation due to isolation by distance might have resulted in the present distribution pattern of the haplotypes in clade A. We discuss the evolutionary process leading to the occurrence of two distinct haplotype clades in Japan in terms of repeated colonization from the continent and range expansion and contraction during climatic changes. [source]

    Two new species that are likely to represent the most basal clade of the genus Trichadenotecnum (Psocoptera: Psocidae)

    Kazunori YOSHIZAWA
    Abstract Two new Trichadenotecnum species, T. corniculum and T. germinatum, were described from Japan. These species were considered to compose a monophyletic group newly defined here as the corniculum group. Judging from morphology of male terminalia, the corniculum group was considered to represent the basal most clade of the genus Trichadenotecnum. [source]

    A molecular assessment of the iron stress response in the two phylogenetic clades of Trichodesmium

    P. Dreux Chappell
    Summary Trichodesmium spp. play key roles in global carbon and nitrogen budgets and thus defining what controls their productivity is important for understanding climate change. While iron availability has been shown to be an important chemical factor for controlling both growth and nitrogen fixation rates in Trichodesmium, all culture experiments to date have focused solely on representatives from one clade of Trichodesmium. Genomic sequence analysis determined that the Trichodesmium erythraeum (IMS101) genome contains many of the archetypical genes involved in the prokaryotic iron stress response. Focusing on three of these genes, isiB, idiA and feoB, we found that all three showed an iron stress response in axenic T. erythraeum (IMS101), and their sequences were well conserved across four species in our Trichodesmium culture collection [consisting of two T. erythraeum strains (IMS101 and GBRTRLI101), two Trichodesmium tenue strains (Z-1 and H9-4), Trichodesmium thiebautii and Trichodesmium spiralis]. With clade-specific quantitative PCR (qPCR) primers for one of these genes, isiB, we found that high isiB expression at low Fe levels corresponded to specific reductions in N2 fixation rates in both major phylogenetic clades of Trichodesmium (the T. erythraeum clade and T. tenue clade). With regard to the two clades, the most significant difference determined was temperature optima, while more subtle differences in growth, N2 fixation rate and gene expression responses to Fe stress were also observed. However the apparent conservation of the Fe stress response in the Trichodesmium genus suggests that it is an important adaptation for their niche in the oligotrophic ocean. [source]

    Dynamics of the SAR11 bacterioplankton lineage in relation to environmental conditions in the oligotrophic North Pacific subtropical gyre

    Alexander Eiler
    Summary A quantitative PCR assay for the SAR11 clade of marine Alphaproteobacteria was applied to nucleic acids extracted from monthly depth profiles sampled over a 3-year period (2004,2007) at the open-ocean Station ALOHA (A Long-term Oligotrophic Habitat Assessment; 22°45,N, 158°00,W) in the oligotrophic North Pacific Ocean. This analysis revealed a high contribution (averaging 36% of 16S rRNA gene copies) of SAR11 to the total detected 16S rRNA gene copies over depths ranging from the surface layer to 4000 m, and revealed consistent spatial and temporal variation in the relative abundance of SAR11 16S rRNA gene copies. On average, a higher proportion of SAR11 rRNA gene copies were detected in the photic zone (< 175 m depth; mean = 38%) compared with aphotic (> 175 m depth; mean = 30%), and in the winter months compared with the summer (mean = 44% versus 33%, integrated over 175 m depth). Partial least square to latent structure projections identified environmental variables that correlate with variation in the absolute abundance of SAR11, and provided tools for developing a predictive model to explain time and depth-dependent variations in SAR11. Moreover, this information was used to hindcast temporal dynamics of the SAR11 clade between 1997 and 2006 using the existing HOT data set, which suggested that interannual variations in upper ocean SAR11 abundances were related to ocean-climate variability such as the El Niño Southern Oscillation. [source]