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Phylogenetic Information (phylogenetic + information)
Selected AbstractsUsing Phylogenetic Diversity Measures to Set Priorities in Conservation: an Example from Southern South AmericaCONSERVATION BIOLOGY, Issue 5 2001Paula Posadas The goal of these ranks for conservation is to consider as many factors as possible that provide additional taxic information, such as taxa richness, taxa distributional patterns, area endemicity, and complementarity between areas. At present there are many measures that consider phylogenetic information, including node-based, genetic-distance, and feature-based measures. We devised a modified phylogenetic node-based index that we call "taxonomic endemicity standardized weight," which considers not only the taxonomic distinctness of the taxa that inhabit a given area but their endemicity as well. Once the standardized weight of the taxonomic endemicity identifies the area of highest priority, complementarity can be used to identify the second area and so on. We used this node-based index to rank priority areas for conservation in southern South America, and we compared the results of our rankings to results based on other node-based indexes. Our index identified Santiago district, in Central Chile province, as the highest priority area for conservation, followed by Maule, Malvinas, and districts of Subantarctic province. Malvinas exhibits greater complementarity relative to Santiago than Maule does, however, so Malvinas is ranked second in priority. Indexes based on phylogenetic information measure the evolutionary component of biodiversity and allow one to identify areas that will ensure the preservation of evolutionary potential and phylogenetically rare taxa. The modified index we propose is sensitive to taxic distinctness and endemicity as well and allows information from diverse taxa to be combined (i.e., different cladograms). The use of complementarity allows for preservation of the maximum quantity of taxa in a minimal number of protected areas. Resumen: Las medidas de diversidad filogenética jerarquiza a las áreas para prioridades de conservación de biodiversidad con base en información codificada en filogenias (cladogramas), La meta de estas categorías de conservación requiere tomar en consideración tantos factores que proporcionan información adicional (riqueza de taxones, patrones de distribución de los taxones, endemicidad del área y complementariedad entre áreas) como sea posible. Actualmente hay muchas medidas que consideran información filogenética (basadas en nodos, distancia genética y basadas en características). Diseñamos un índice filogenético modificado basado en nodos que denominamos "peso estandarizado de endemicidad taxonómica", el cual considera no solo la peculiaridad genética de los taxa que habitan una región determinada sino también su endemicidad. Una vez que el peso estandarizado de endemicidad identifica el área de mayor prioridad, la complementariedad se puede usar para identificar la segunda área y así sucesivamente. Utilizamos este índice basado en nodos para jerarquizar áreas prioritarias para conservación en el sur de América del Sur, y comparamos los resultados de nuestras jerarquizaciones con resultados obtenidos con otros índices basados en nodos. Nuestro índice identificó al distrito de Santiago, en la provincia de Chile Central, como el área de mayor prioridad para conservación, seguido por Maule, Malvinas y distritos de la provincia Subantártica. Sin embargo, Malvinas presenta mayor complementariedad en relación con Santiago que el Maule y, por tanto, Malvinas ocupa la segunda prioridad. Los índices basados en información filogenética miden el componente evolutivo de la biodiversidad y permiten la identificación de áreas que aseguran la preservación de taxones con potencial evolutivo y filogenéticamente peculiares. El índice modificado que proponemos es sensible tanto a la peculiaridad de los taxones como a la endemicidad y permite combinar información de diversos taxones (i.e. cladogramas diferentes). El uso de la complementariedad permite la preservación de la mayor cantidad de taxones en un número mínimo de áreas protegidas. [source] Evolution of invertebrate nervous systems: the Chaetognatha as a case studyACTA ZOOLOGICA, Issue 1 2010Steffen Harzsch Abstract Harzsch, S. and Wanninger, A. 2010. Evolution of invertebrate nervous systems: the Chaetognatha as a case study. ,Acta Zoologica (Stockholm) 91: 35,43 Although recent molecular studies indicate that Chaetognatha may be one of the earliest Bilaterian offshoots, the phylogenetic position of this taxon still is a matter of ongoing debate. In this contribution, we review recent attempts to contribute phylogenetic information on the Chaetognatha by analysing structure and development of their nervous system (neurophylogeny). Analysing this group of organisms also has a major impact on our understanding of nervous system evolution in Bilateria. We review recent evidence from this field and suggest that Urbilateria already was equipped with the genetic toolkit required to build a complex, concentrated central nervous system (CNS), although this was not expressed phenotypically so that Urbilateria was equipped with a nerve plexus and not a CNS. This implies that in the deep metazoan nodes, concentration of the ancestral plexus occurred twice independently, namely once after the protostome,deuterostome split on the branch leading to the protostomes (resulting in a ventrally positioned nerve cord) and once along the chordate line (with a dorsal nerve cord). [source] Ultrastructure of spermatozoa of scolecophidian snakes (Lepidosauria, Squamata)ACTA ZOOLOGICA, Issue 3 2007L. Tavares-Bastos Abstract We provide a detailed description of the sperm ultrastructure of three species of scolecophidian snakes, Leptotyphlops koppesi (Leptotyphlopidae), Typhlops reticulatus (Typhlopidae) and Liotyphlops beui (Anomalepididae), and make comparisons with the spermatozoa of Ramphotyphlops waitii (Typhlopidae) (Harding et al. 1995). All the species studied bear synapomorphies of Squamata and Serpentes. Among scolecophidian snakes, we identified eight polymorphic characters. Previous analyses of molecular and somatic morphological data provide equivocal solutions to the relationships among Anomalepididae, Leptotyphlopidae and Typhlopidae. A close relationship between Anomalepididae and Typhlopidae is corroborated by two characters of sperm ultrastructure, presence of an electron-dense structure inside the proximal centriole and rounded mitochondria in transverse sections of T. reticulatus, Li. beui and R. waitii, whereas the absence of the ridge on the acrosome surface of Le. koppesi and T. reticulatus support a closer relationship between Typhlopidae and Leptotyphlopidae. The differences observed in sperm ultrastructure within Typhlopidae suggest the existence of snake intrafamilial polymorphism. The sperm characters of blindsnakes contain significant phylogenetic information and may provide important data for snake phylogenetic reconstructions. [source] The merging of community ecology and phylogenetic biologyECOLOGY LETTERS, Issue 7 2009Jeannine Cavender-Bares Abstract The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change. [source] Phylogenetic beta diversity: linking ecological and evolutionary processes across space in timeECOLOGY LETTERS, Issue 12 2008Catherine H. Graham Abstract A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity. [source] Host range of Asobara japonica (Hymenoptera: Braconidae), a larval parasitoid of drosophilid fliesENTOMOLOGICAL SCIENCE, Issue 1 2008Shinsuke IDEO Abstract We studied the host range of Asobara japonica, a larval-pupal parasitoid of drosophilid flies. Habitat selection was found to be an important determinant of host range in this parasitoid; it attacked drosophilid larvae breeding on banana and mushrooms, but seldom attacked those breeding on decayed leaves. This parasitoid was able to use diverse drosophilid taxa as hosts. Attack by A. japonica sometimes killed hosts at the larval stage, and therefore parasitoid larvae also died. Drosophila elegans and D. busckii suffered particularly high larval mortality due to the attack by A. japonica (in the latter species only when young larvae were attacked). Many individuals of D. subpulchrella also died at the pupal stage without producing parasitoids when they were parasitized at the late larval stage. In contrast, D. bipectinata, D. ficusphila, D. immigrans, D. formosana and D. albomicans were resistant to attack: large proportions of the larvae of these drosophilid species grew to adulthood, even in the presence of parasitoids. On the basis of phylogenetic information, we concluded that phylogenetic position has only limited importance as a factor determining whether a species is suitable as a host for A. japonica, at least within the genus Drosophila. [source] Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samplesENVIRONMENTAL MICROBIOLOGY, Issue 12 2009William Marande Summary The recent introduction of molecular techniques in eukaryotic microbial diversity studies, in particular those based in the amplification and sequencing of small-subunit ribosomal DNA (SSU rDNA), has revealed the existence of an unexpected variety of new phylotypes. The taxonomic ascription of the organisms bearing those sequences is generally deduced from phylogenetic analysis. Unfortunately, the SSU rDNA sequence alone has often not enough phylogenetic information to resolve the phylogeny of fast-evolving or very divergent sequences, leading to their misclassification. To address this problem, we tried to increase the phylogenetic signal by amplifying the complete eukaryotic rDNA cluster [i.e. the SSU rDNA, the internal transcribed spacers, the 5.8S rDNA and the large-subunit (LSU) rDNA] from environmental samples, and sequencing the SSU and LSU rDNA part of the clones. Using marine planktonic samples, we showed that surveys based on either SSU or SSU + LSU rDNA retrieved comparable diversity patterns. In addition, phylogenetic trees based on the concatenated SSU + LSU rDNA sequences showed better resolution, yielding good support for major eukaryotic groups such as the Opisthokonta, Rhizaria and Excavata. Finally, highly divergent SSU rDNA sequences, whose phylogenetic position was impossible to determine with the SSU rDNA data alone, could be placed correctly with the SSU + LSU rDNA approach. These results suggest that this method can be useful, in particular for the analysis of eukaryotic microbial communities rich in phylotypes of difficult phylogenetic ascription. [source] WHY DOES A TRAIT EVOLVE MULTIPLE TIMES WITHIN A CLADE?EVOLUTION, Issue 1 2006REPEATED EVOLUTION OF SNAKELINE BODY FORM IN SQUAMATE REPTILES 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] Conflicting phylogenetic signals at the base of the metazoan treeEVOLUTION AND DEVELOPMENT, Issue 4 2003Antonis Rokas Summary A phylogenetic framework is essential for under-standing the origin and evolution of metazoan development. Despite a number of recent molecular studies and a rich fossil record of sponges and cnidarians, the evolutionary relationships of the early branching metazoan groups to each other and to a putative outgroup, the choanoflagellates, remain uncertain. This situation may be the result of the limited amount of phylogenetic information found in single genes and the small number of relevant taxa surveyed. To alleviate the effect of these analytical factors in the phylogenetic recons-truction of early branching metazoan lineages, we cloned multiple protein-coding genes from two choanoflagellates and diverse sponges, cnidarians, and a ctenophore. Comparisons of sequences for ,-tubulin, ,-tubulin, elongation factor 2, HSP90, and HSP70 robustly support the hypothesis that choanoflagellates are closely affiliated with animals. However, analyses of single and concatenated amino acid sequences fail to resolve the relationships either between early branching metazoan groups or between Metazoa and choano-flagellates. We demonstrate that variable rates of evolution among lineages, sensitivity of the analyses to taxon selection, and conflicts in the phylogenetic signal contained in different amino acid sequences obscure the phylogenetic associations among the early branching Metazoa. These factors raise concerns about the ability to resolve the phylogenetic history of animals with molecular sequences. A consensus view of animal evolution may require investigations of genome-scale characters. [source] Combining spatial and phylogenetic eigenvector filtering in trait analysisGLOBAL ECOLOGY, Issue 6 2009Ingolf Kühn ABSTRACT Aim, To analyse the effects of simultaneously using spatial and phylogenetic information in removing spatial autocorrelation of residuals within a multiple regression framework of trait analysis. Location, Switzerland, Europe. Methods, We used an eigenvector filtering approach to analyse the relationship between spatial distribution of a trait (flowering phenology) and environmental covariates in a multiple regression framework. Eigenvector filters were calculated from ordinations of distance matrices. Distance matrices were either based on pure spatial information, pure phylogenetic information or spatially structured phylogenetic information. In the multiple regression, those filters were selected which best reduced Moran's I coefficient of residual autocorrelation. These were added as covariates to a regression model of environmental variables explaining trait distribution. Results, The simultaneous provision of spatial and phylogenetic information was effectively able to remove residual autocorrelation in the analysis. Adding phylogenetic information was superior to adding purely spatial information. Applying filters showed altered results, i.e. different environmental predictors were seen to be significant. Nevertheless, mean annual temperature and calcareous substrate remained the most important predictors to explain the onset of flowering in Switzerland; namely, the warmer the temperature and the more calcareous the substrate, the earlier the onset of flowering. A sequential approach, i.e. first removing the phylogenetic signal from traits and then applying a spatial analysis, did not provide more information or yield less autocorrelation than simple or purely spatial models. Main conclusions, The combination of spatial and spatio-phylogenetic information is recommended in the analysis of trait distribution data in a multiple regression framework. This approach is an efficient means for reducing residual autocorrelation and for testing the robustness of results, including the indication of incomplete parameterizations, and can facilitate ecological interpretation. [source] Patterns of carpal development among anuran amphibiansJOURNAL OF MORPHOLOGY, Issue 3 2001Marissa Fabrezi Abstract The unity and diversity of developmental processes in the vertebrate limb have singular importance in the interpretation of evolutionary hypotheses of tetrapod diversification. In anurans, the intraordinal diversity of forelimbs seems to be related to the fusion of distal carpals, whereas proximal carpals are invariable. However, there are different ontogenetic pathways involved in the differentiation of proximal carpals. This study presents a comparative analysis of early developmental features in one archeobatrachian and 23 neobatrachian species representing five families and explores the variability in the differentiation of carpal cartilages. We found new evidence supporting the presence of an embryonic intermedium that incorporates with the ulnare. Difference between the pipid Xenopus and the neobatrachians is interpreted as a change in the rate of differentiation of Distal Carpal 5 that does not affect the developmental pattern of digits. The developmental variability exhibited by the intermedium, radiale, and Element Y is combined in patterns that converge on the same adult carpal morphology among neobatrachians; these patterns appear to contain potentially useful phylogenetic information. J. Morphol. 249:210,220, 2001. © 2001 Wiley-Liss, Inc. [source] DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA),JOURNAL OF PHYCOLOGY, Issue 2 2006Hwan Su Yoon Previous phylogenetic studies of the Rhodophyta have provided a framework for understanding red algal phylogeny, but there still exists the need for a comprehensive analysis using a broad sampling of taxa and sufficient phylogenetic information to clearly define the major lineages. In this study, we determined 48 sequences of the PSI P700 chl a apoprotein A1 (psaA) and rbcL coding regions and established a robust red algal phylogeny to identify the major clades. The tree included most of the lineages of the Bangiophyceae (25 genera, 48 taxa). Seven well-supported lineages were identified with this analysis with the Cyanidiales having the earliest divergence and being distinct from the remaining taxa; i.e. the Porphyridiales 1,3, Bangiales, Florideophyceae, and Compsopogonales. We also analyzed data sets with fewer taxa but using seven proteins or the DNA sequence from nine genes to resolve inter-clade relationships. Based on all of these analyses, we propose that the Rhodophyta contains two new subphyla, the Cyanidiophytina with a single class, the Cyanidiophyceae, and the Rhodophytina with six classes, the Bangiophyceae, Compsopogonophyceae, Florideophyceae, Porphyridiophyceae classis nov. (which contains Porphyridium, Flintiella, and Erythrolobus), Rhodellophyceae, and Stylonematophyceae classis nov. (which contains Stylonema, Bangiopsis, Chroodactylon, Chroothece, Purpureofilum, Rhodosorus, Rhodospora, and Rufusia). We also describe a new order, Rhodellales, and a new family, Rhodellaceae (with Rhodella, Dixoniella, and Glaucosphaera). [source] Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009MARC OREMUS Pilot whales (Globicephala spp.) provide an interesting example of recently diverged oceanic species with a complex evolutionary history. The two species have wide but largely non-overlapping ranges. Globicephala melas (long-finned pilot whale; LFPW) has an antitropical distribution and is found in the cold-temperate waters of the North Atlantic and Southern Hemisphere, whereas Globicephala macrorhynchus (short-finned pilot whale; SFPW) has a circumglobal distribution and is found mainly in the tropics and subtropics. To investigate pilot whale evolution and biogeography, we analysed worldwide population structure using mitochondrial DNA (mtDNA) control region sequences (up to 620 bp) from a variety of sources (LFPW = 643; SFPW = 150), including strandings in New Zealand and Tasmania, and whale-meat products purchased on the markets of Japan and Korea. Phylogenetic reconstructions failed to support a reciprocal monophyly of the two species, despite six diagnostic substitutions, possibly because of incomplete lineage sorting or inadequate phylogenetic information. Both species had low haplotype and nucleotide diversity compared to other abundant widespread cetaceans (LFPW, , = 0.35%; SFPW, , = 0.87%) but showed strong mtDNA differentiation between oceanic basins. Strong levels of structuring were also found at the regional level. In LFPW, phylogeographic patterns were suggestive either of a recent demographic expansion or selective sweep acting on the mtDNA. For SFPW, the waters around Japan appear to represent a centre of diversity, with two genetically-distinct forms, as well as a third population of unknown origin. The presence of multiple unique haplotypes among SFPW from South Japan, together with previously documented morphological and ecological differences, suggests that the southern form represents a distinct subspecies and/or evolutionary significant unit. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 729,744. [source] The role of wood anatomy in phylogeny reconstruction of EricalesCLADISTICS, Issue 3 2007Frederic Lens The systematic significance of wood anatomical characters within Ericales is evaluated using separate and combined parsimony analyses including 23 wood characters and 3945 informative molecular characters. Analyses of wood features alone result in poorly resolved and conflicting topologies. However, when pedomorphic character states are coded as inapplicable, the combined bootstrap topology results in an increase of resolution and support at most deeper nodes compared with the molecular analyses. This suggests that phylogenetic information from the limited number of morphological characters is not completely swamped by an overwhelming amount of molecular data. Based on the morphology of vessels and fibers, and the distribution of axial parenchyma, two major wood types can be distinguished within Ericales: (i) a "primitive" type, nearly identical to the wood structure in the more basal outgroup Cornales, which is likely to have persisted in one major clade, and (ii) a "derived" type that must have evolved in at least two separate evolutionary lines. The occurrence of the first type is strongly correlated with shrubs to small trees growing in cold temperate or tropical montane regions, while the second type is common in tall trees of tropical lowlands. This favors the inclusion of ecologically adaptive features in phylogeny reconstruction. © The Willi Hennig Society 2006. [source] Evolution of advertisement signals in North American hylid frogs: vocalizations as end-products of calling behaviorCLADISTICS, Issue 6 2006Tony Robillard We studied the advertisement signals in two clades of North American hylid frogs in order to characterize the relationships between signal acoustic structure and underlying behavior. A mismatch was found between the acoustic structure and the mechanism of sound production. Two separate sets of phylogenetic characters were coded following acoustic versus mechanistic criteria, and exploratory treatments were made to compare their respective phylogenetic content in comparison with the molecular phylogeny (Faivovich et al., 2005). We discuss the consequences of the acoustic/mechanistic mismatch in terms of significance of acoustic characters for phylogenetic and comparative studies; and the evolution of vocalizations in North American treefrogs. Considering only the acoustic structure of frog vocalizations can lead to misleading results in terms of both phylogenetic signal and evolution of vocalizations. In contrast, interpreting the acoustic signals with regard to the mechanism of sound production results in consistent phylogenetic information. The mechanistic coding also provides strong homologies for use in comparative studies of frog vocalizations, and to derive and test evolutionary hypotheses. © The Willi Hennig Society 2005. [source] Cladogenesis and reticulation in the Hawaiian endemic mints (Lamiaceae)CLADISTICS, Issue 6 2003Charlotte Lindqvist The Hawaiian endemic mints, which comprise 58 species of dry-fruited Haplostachys and fleshy-fruited Phyllostegia and Stenogyne, represent a major island radiation that likely originated from polyploid hybrid ancestors in the temperate North American Stachys lineage. In contrast with considerable morphological and ecological diversity among taxa, sequence variation in the nrDNA 5S non-transcribed spacer was found to be remarkably low, which when analyzed using standard parsimony resulted in a lack of phylogenetic resolution among accessions of insect-pollinated Phyllostegia and bird-pollinated Stenogyne. However, many within-individual nucleotide polymorphisms were observed, and under the assumption that they could contain phylogenetic information, these ambiguities were recoded as new character states. Substantially more phylogenetic structure was obtained with these data, including the resolution of most Stenogyne species into a monophyletic group with an apparent recent origin on O'ahu (3.0 My) or the Maui Nui island complex (2.2 My). Subsequent diversification appears to have involved multiple inter-island dispersal events. Intergeneric placements for a few morphotypes, seemingly misplaced within either Phyllostegia or Stenogyne, may indicate reticulation as one polymorphism-generating force. For a finer scale exploration of hybridization, preliminary AFLP fragment data were examined among putative hybrids of Stenogyne microphylla and S. rugosa from Mauna Kea, Hawai'i, that had been identified based on morphology. Cladistic analysis (corroborated by multivariate correspondence analysis) showed the morphologically intermediate individuals to group in a strongly supported monophyletic clade with S. microphylla. Therefore, reticulation could be both historic and active in Stenogyne, and perhaps a force of general importance in the evolution of the Hawaiian mints. The relatively greater extent of lineage-sorted polymorphisms in Stenogyne may indicate selective differentiation from other fleshy-fruited taxa, perhaps through the agency of highly specialized bird pollinators that restricted gene flow with other Hawaiian mint morphotypes. [source] | ||||||||||||||||||||||