Home About us Contact
|
Home About us Contact | ||
|
|
||
Different Clades (different + clade)
Selected AbstractsMorphological evolution of the lizard skull: A geometric morphometrics surveyJOURNAL OF MORPHOLOGY, Issue 1 2005C. Tristan Stayton Abstract Patterns of diversity among lizard skulls were studied from a morphological, phylogenetic, and functional perspective. A sample of 1,030 lizard skulls from 441 species in 17 families was used to create a lizard skull morphospace. This morphospace was combined with a phylogeny of lizard families to summarize general trends in the evolution of the lizard skull. A basal morphological split between the Iguania and Scleroglossa was observed. Iguanians are characterized by a short, high skull, with large areas of attachment for the external adductor musculature, relative to their sister group. The families of the Iguania appear to possess more intrafamilial morphological diversity than families of the Scleroglossa, but rarefaction of the data reveals this to be an artifact caused by the greater number of species represented in Iguanian families. Iguanian families also appear more dissimilar to one another than families of the Scleroglossa. Permutation tests indicate that this pattern is real and not due to the smaller number of families in the Iguanidae. Parallel and convergent evolution is observed among lizards with similar diets: ant and termite specialists, carnivores, and herbivores. However, these patterns are superimposed over the more general phylogenetic pattern of lizard skull diversity. This study has three central conclusions. Different clades of lizards show different patterns of disparity and divergence in patterns of morphospace occupation. Phylogeny imposes a primary signal upon which a secondary ecological signal is imprinted. Evolutionary patterns in skull metrics, taken with functional landmarks, allow testing of trends and the development of new hypotheses concerning both shape and biomechanics. J. Morphol. 263:47,59, 2005. © 2004 Wiley-Liss, Inc. [source] Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical GyreENVIRONMENTAL MICROBIOLOGY, Issue 9 2008Vinh D. Pham Summary High-throughput identification of rRNA gene-containing clones in large insert metagenomic libraries is difficult, because of the high background of host ribosomal RNA (rRNA) and rRNA genes. To address this challenge, a membrane hybridization method was developed to identify all bacterial small subunit rRNA-containing fosmid clones of microbial community DNA from seven different depths in the North Pacific Subtropical Gyre. Out of 101,376 clones screened, 751 rDNA-containing clones were identified that grouped in ,60 different clades. Several rare sequences only remotely related to known groups were detected, including a Wolbachia -related sequence containing a putative intron or intervening sequence, as well as seven sequences from Order Myxococcales not previously detected in pelagic habitats. Stratified, depth-specific population structure was evident within both cultured and uncultured lineages. Conversely, some eurybathyal members of the genera Alcanivorax and Rhizobium shared identical small subunit ribosomal DNA sequences that were distributed from surface waters to the 4000 m depth. Comparison with similar analyses in Monterey Bay microbial communities revealed previously recognized, as well as some distinctive, depth-stratified partitioning that distinguished coastal from open ocean bacterioplankton populations. While some bias was evident in fosmid clone recovery in a few particular lineages, the overall phylogenetic group recovery and distributions were consistent with previous studies, as well as with direct shotgun sequence data from the same source DNA. [source] Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environmentsENVIRONMENTAL MICROBIOLOGY, Issue 4 2008Adrian K. Sharma Summary Proteorhodopsins are light-energy-harvesting transmembrane proteins encoded by genes recently discovered in the surface waters of the world's oceans. Metagenomic data from the Global Ocean Sampling expedition (GOS) recovered 2674 proteorhodopsin-related sequences from 51 aquatic samples. Four of these samples were from non-marine environments, specifically, Lake Gatun within the Panama Canal, Delaware Bay and Chesapeake Bay and the Punta Cormorant Lagoon in Ecuador. Rhodopsins related to but phylogenetically distinct from most sequences designated proteorhodopsins were present at all four of these non-marine sites and comprised three different clades that were almost completely absent from marine samples. Phylogenomic analyses of genes adjacent to those encoding these novel rhodopsins suggest affiliation to the Actinobacteria, and hence we propose to name these divergent, non-marine rhodopsins ,actinorhodopsins'. Actinorhodopsins conserve the acidic amino acid residues critical for proton pumping and their genes lack genomic association with those encoding photo-sensory transducer proteins, thus supporting a putative ion pumping function. The ratio of recA and radA to rhodopsin genes in the different environment types sampled within the GOS indicates that rhodopsins of one type or another are abundant in microbial communities in freshwater, estuarine and lagoon ecosystems, supporting an important role for these photosystems in all aquatic environments influenced by sunlight. [source] Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversityJOURNAL OF ECOLOGY, Issue 3 2007OLIVIER J. HARDY Summary 1Analysing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species in ecological communities. 2Unifying previous works, we present a statistical framework to quantify the phylogenetic structure of communities in terms of average divergence time between pairs of individuals or species, sampled from different sites. This framework allows an additive partitioning of the phylogenetic signal into alpha (within-site) and beta (among-site) components, and is closely linked to Simpson diversity. It unifies the treatment of intraspecific (genetic) and interspecific diversity, leading to the definition of differentiation coefficients among community samples (e.g. IST, PST) analogous to classical population genetics coefficients expressing differentiation among populations (e.g. FST, NST). 3Two coefficients which express community differentiation among sites from species identity (IST) or species phylogeny (PST) require abundance data (number of individuals per species per site), and estimators that are unbiased with respect to sample size are given. Another coefficient (,ST) expresses the gain of the mean phylogenetic distance between species found in different sites compared with species found within sites, and requires only incidence data (presence/absence of each species in each site). 4We present tests based on phylogenetic tree randomizations to detect community phylogenetic clustering (PST > IST or ,ST > 0) or phylogenetic overdispersion (PST < IST or ,ST < 0). In addition, we propose a novel approach to detect phylogenetic clustering or overdispersion in different clades or at different evolutionary time depths using partial randomizations. 5IST, PST or ,ST can also be used as distances between community samples and regressed on ecological or geographical distances, allowing us to investigate the factors responsible for the phylogenetic signal and the critical scales at which it appears. 6We illustrate the approach on forest tree communities in Equatorial Guinea, where a phylogenetic clustering signal was probably due to phylogenetically conserved adaptations to the elevation gradient and was mostly contributed to by ancient clade subdivisions. 7The approach presented should find applications for comparing quantitatively phylogenetic patterns of different communities, of similar communities in different regions or continents, or of populations (within species) vs. communities (among species). [source] Species concepts and species reality: salvaging a Linnaean rankJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2003M. S. Y. Lee Abstract The validity of the species category (rank) as a distinct level of biological organization has been questioned. Phenetic, cohesion and monophyletic species concepts do not delimit species-level taxa that are qualitatively distinct from lower or higher taxa: all organisms throughout the tree of life exhibit varying degrees of similarity, cohesion, and monophyly. In contrast, interbreeding concepts delimit species-level taxa characterized by a phenomenon (regular gene flow) not found in higher taxa, making the species category a distinct level of biological organization. Only interbreeding concepts delimit species-level taxa that are all comparable according to a biologically meaningful criterion and qualitatively distinct from entities assigned to other taxonomic categories. Consistent application of interbreeding concepts can result in counterintuitive taxonomies , e.g. many wide polytypic species in plants and narrow cryptic species in animals. However, far from being problematic, such differences are biologically illuminating , reflecting differing barriers to gene flow in different clades. Empirical problems with interbreeding concepts exist, but many of these also apply to other species concepts, whereas others are not as severe as some have argued. A monistic view of species using interbreeding concepts will encounter strong historical inertia, but can save the species category from redundancy with other categories, and thus justify continued recognition of the species category. [source] The tick Ixodes ricinus: distribution and climate preferences in the western PalaearcticMEDICAL AND VETERINARY ENTOMOLOGY, Issue 2 2006A. ESTRADA-PEÑA Abstract In this study, multivariate spatial clustering on monthly normalized difference vegetation index (NDVI) maps is used to classify ecological regions over the western Palaearctic. This classification is then used to delineate the distribution and climate preferences of populations (clades) of the tick Ixodes ricinus L. (Acari: Ixodidae) from a geographically extensive dataset of tick records and a gridded 2.5-km resolution climate dataset. Using monthly layers of the NDVI, regions of similar ecological attributes were defined and nine populations with significant differences in critical climate parameters (P < 0.005) were detected. Grouping of tick records according to other categories, such as political divisions, a 4°× 4° grid overlying the study area, or the CORINE) and USGS) vegetation classification schemes did not provided significantly separated populations (P= 0.094,0.304). Factor analysis and hierarchical tree clustering provided an ecological overview of these tick clades: two Mediterranean and one Scandinavian (western) clades are clearly separated from a node that includes clades of different parts of central Europe and the British Isles, with contrasting affinities between the different clades. The capture records of these ecologically separated clades produce a clear bias when bioclimate envelope modelling is applied to the mapping of habitat suitability for the tick in the western Palaearctic. The best-performing methods (Cohen's kappa = 0.834,0.912) use partial models developed with data from each ecoregion, which are then overlapped over the region of study. It is concluded that the use of ecologically derived ecoregions is an objective step in assessing the presence of ecologically different clades, and provides a guide in the development of data partitioning for habitat suitability modelling. [source] The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical watersMOLECULAR ECOLOGY, Issue 11 2010M. EITEL Abstract Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. The genetic data also suggest deep phylogenetic branching patterns between clades. [source] Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysisMOLECULAR ECOLOGY, Issue 18 2008ELENA IVARS-MARTÍNEZ Abstract Twenty-three isolates of the widely distributed marine bacteria Alteromonas macleodii have been analysed by multilocus sequence analysis combined with phylogenetic and multivariate statistical analyses. The strains originated from the Pacific Ocean, Mediterranean Sea, English Channel, Black Sea and Thailand. Using the nucleotide sequences of nine loci for each of the 23 isolates, a robust identification was achieved of different clades within the single species. Strains generally clustered with the depth in the water column from which the isolate originated. Strains also showed more recombination with isolates from the same vicinity, suggesting that genetic exchange plays a role in diversification of planktonic marine prokaryotes. This study thus shows for the first time for a large set of isolates of a species of planktonic marine prokaryotes that multilocus sequence analysis overcomes the problems associated with the analysis of individual marker genes or presence of extensive recombination events. It can thus achieve intraspecific identification to the level of genotypes and, by comparison with relevant environmental data, ecotypes. [source] The evolution of bipedal postures in varanoid lizardsBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2009GORDON W. SCHUETT The bipedal posture (BP) and gait of humans are unique evolutionary hallmarks, but similar stances and forms of locomotion have had enormous influences on a range of phylogenetically diverse tetrapods, particularly dinosaurs and birds, and a range of mammalian lineages, including non-human apes. The complex movements involved in bipedalism appear to have modest evolutionary origins, and it is presumed that a stable and erect posture is a prerequisite for erect strides and other bipedal movements. Facultative bipedalism in several lineages of lizards is achieved by running, but some varanid lizards (genus Varanus) exhibit BPs without running. In these cases, BPs (BPstanding) are not used as a form of locomotion; rather, BPstanding is associated with defensive displays, and such postures also probably permit better inspection of the environment. Yet, in other varanids, BPs have been observed only during combat episodes (BPcombat), where both contestants rise together and embrace in the so-called clinch phase. Numerous other species, however, show neither type of BP. Past researchers have commented that only large-bodied varanids exhibit BP, a behaviour that appears to show phylogenetic trends. We termed this idea the King,Green,Pianka (KGP) bipedal hypothesis. In this article, we address two main questions derived from the KGP hypothesis. First, what is the phylogenetic distribution of BP in Varanus and close relatives (varanoids)? Second, is BP positively correlated with the phylogenetic distribution of large body size (e.g. snout,vent length, SVL)? In addition, we asked a related question: do the lengths of the femur and tail show body size-independent adaptive trends in association with BP? Because varanid species that show BPstanding also use these postures during combat (BPcombat), both types of BP were analysed collectively and simply termed BP. Using comparative phylogenetic analyses, the reconstruction of BP required three steps, involving a single gain and two losses. Specifically, BP was widespread in the monophyletic Varanus, and the single gain occurred at the most recent common ancestor of the African clade. The two losses of BP occurred in different clades (Indo-Asian B clade and Indo-Australian Odatria clade). BPs are absent in the sister group to Varanus (Lanthanotus borneensis) and the other outgroup species (Heloderma spp.). Our phylogenetic reconstruction supports the KGP prediction that BP is restricted to large-bodied taxa. Using the Hansen model of adaptive evolution on a limited, but highly relevant morphological dataset (i.e. SVL; femur length, FL; tail length, TL), we demonstrated that these characters were not equivalent in their contribution to the evolution of BP in Varanus. SVL was significantly correlated with BP when modelled in a phylogenetic context, but the model identified random processes as dominant over adaptive evolution, suggesting that a body size threshold might be involved in the evolution of BP. A Brownian motion (BM) model outperformed the selection model in our analysis of relative TL, suggesting that TL and BP evolved independently. The selection model for relative FL outperformed the BM model, indicating that FL and BP share an adaptive history. Our non-phylogenetic analyses involving regression residuals of FL and TL vs. SVL showed no significant correlation between these characters and BP. We suggest that BP in Varanus provides a convergent or analogue model from which to investigate various forms of bipedalism in tetrapod vertebrates, especially other reptiles, such as theropod dinosaurs. Because BPstanding in varanids is possibly an incipient stage to some form of upright locomotion, its inclusion as a general model in evolutionary analyses of bipedalism of vertebrates will probably provide novel and important insights. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 652,663. [source] Phylogeny of the Pantomorus,Naupactus complex based on morphological and molecular data (Coleoptera: Curculionidae)CLADISTICS, Issue 2 2005María A. Scataglini The Pantomorus,Naupactus complex is a Neotropical group of broad-nosed weevils (Coleoptera: Curculionidae) including several parthenogenetic species usually assigned to the genera Naupactus Dejean, Pantomorus Schoenherr, Asynonychus Crotch, Aramigus Horn, Eurymetopus Schoenherr and Graphognathus Buchanan. Sixteen species were studied to test hypotheses on the monophyly of these genera, and on the origin of the parthenogenetic lineages. A matrix of 30 morphological characters and 999 positions of the Cytochrome Oxidase I gene, was analyzed with separate partitions and simultaneously, under equal and implied weights, and with different transversion/transitions costs. The ILD test indicates that the incongruence between the molecular and morphological data is not significant. Under equal weights, the molecular data resulted in a single tree and morphology in 34 trees; under implied weights morphology gave a different tree, and under TV:TS ,,4:1 molecular and combined analyses resulted in the same optimal tree. According to the latter, Naupactus includes Graphognathus, and is thus paraphyletic and basal regarding remaining genera, Pantomorus is polyphyletic and includes Aramigus and Asynonychus, and Eurymetopus is monophyletic. The species in which apomictic parthenogenesis has been verified (Aramigus tessellatus, Asynonychus cervinus and Graphognathus lecuoloma), belong to different clades of the Pantomorus-Naupactus complex, with basal sexual relatives. © The Willi Hennig Society 2005. [source] | ||||||||||