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Evolutionary Relationships (evolutionary + relationships)
Selected AbstractsEvolutionary Relationships of the Dutch Elm Disease Fungus Ophiostoma novo-ulmi to Other Ophiostoma Species Investigated by Restriction Fragment Length Polymorphism Analysis of the rDNA RegionJOURNAL OF PHYTOPATHOLOGY, Issue 9-10 2000N. D. Pipe Restriction fragment length polymorphisms (RFLPs) in the ribosomal RNA gene (rDNA) region were used to assess relationships between the Dutch elm disease fungi Ophiostoma novo-ulmi and Ophiostoma ulmi, the recently described Himalayan Dutch elm disease pathogen, Ophiostoma himal-ulmi, the morphologically similar sapstain fungi, Ophiostoma piceae and Ophiostoma quercus, and several Ophiostoma species from hardwood trees, including Ophiostoma stenoceras and Ophiostoma proliferum. A distance matrix and cluster analysis indicated that the rDNA region of O. himal-ulmi is more closely related to those of O. novo-ulmi and O. ulmi than to those of O. piceae and O. quercus and is more distantly related to O. stenoceras and the other Ophiostoma species, which formed a separate clade. The rDNA region of O. quercus was found to be at least as closely related to that of O. novo-ulmi and O. ulmi as it is to that of O. piceae. The implications of these results for the evolution of the Dutch elm disease fungi are discussed. [source] Homology versus analogy: possible evolutionary relationship of immunoglobulins, cupredoxins, and Cu,Zn-superoxide dismutaseJOURNAL OF MOLECULAR RECOGNITION, Issue 1 2008Fred J. Stevens Abstract The ,immunoglobulin-like' fold is one of most common structural motifs observed in proteins. This topology is found in more than 80 superfamilies of proteins, including Cu,Zn-superoxide dismutase (SOD) and cupredoxin. Evolutionary relationships have not been identified, but may exist. The challenge remains, therefore, of resolving the issue of whether the diverse distribution of the fold is accounted for by divergent evolution of function or convergent evolution of structure following multiple independent origins of function. Since the early studies that revealed conformational similarity of immunoglobulins and other proteins, the number of primary structures available for comparison has dramatically increased and new computational approaches for analysis of sequences have been developed. It now appears that a hypothesis of a common evolutionary origin for cupredoxins, Cu,Zn-SOD, and immunoglobulins may be credible. The distinction between protein homology and protein analogy is fundamental. The immunoglobulin-like fold may represent a robust system within which to examine again the issue of protein homology versus analogy. Copyright © 2007 John Wiley & Sons, Ltd. [source] Evolutionary relationships of sprint speed in Australian varanid lizardsJOURNAL OF ZOOLOGY, Issue 4 2009C. J. Clemente Abstract Ecomorphological studies often seek to link morphology and performance to relevant ecological characteristics. Varanid lizards are unique in that species can vary in body size by almost four orders of magnitude within a single genus, and a question of considerable interest is whether similar ecomorphological relationships exist when constraints on body size are reduced. We studied sprint speed in relation to size, shape and ecology for 18 species of varanid lizards. Maximal speed scaled positively with mass0.166 using least squares regression, and mass0.21 using reduced major-axis regression. However, a curvilinear trend better described this relationship, suggesting an optimal mass of 2.83 kg with respect to speed. Including data for the komodo dragon Varanus komodoensis moves the optimum mass to 2.23 kg. We use this relationship to predict the sprint speed of the Komodo's giant extinct relative Varanus (Megalania) prisca to be 2.6,3 m s,1 similar to that of extant freshwater crocodiles Crocodylus johnstoni. When differences in speed were compared to ecological characteristics, species from open habitats were significantly faster than species from semi-open or closed habitat types, and remained so after correction for size and phylogeny. Thus, despite large variation in body size, varanids appear to share similar associations between performance and ecology as seen in other lizard groups. Varanids did, however, differ in morphological relationships with sprint speed. Differences in relative speed were not related to relative hindlimb length, as is commonly reported for other lizard groups. Instead, size-free forefoot length was negatively related to speed as was the size-free thorax,abdomen length. While shorter forefeet were thought to be an adaptation to burrowing, and thus open habitats, rather than speed per se, the reduction in the thorax,abdomen length may have significant advantages to increasing speed. Biomechanical models predicting this advantage are discussed in relation to a trade-off between speed and manoeuvrability. [source] Female Attraction to Conspecific Chemical Cues in the Palmate Newt Triturus helveticusETHOLOGY, Issue 8 2005Jean Secondi Although chemosignals are largely used in sexual communication in urodeles, olfactometer studies in newts provided contrasting results about the sex specificity of female behavioural responses. Because long-range sexual advertisement is believed to be costly, some species might restrain this activity to close interactions with conspecifics. We tested chemical-mediated sexual attraction in female palmate newt (Triturus helveticus) by measuring the attraction to male and female odours in a linear water olfactometer. Unexpectedly, females were attracted towards conspecifics regardless of sex. They did not show attraction towards Limnaea stagnalis, a common sympatric aquatic gastropod. These results do not support the use of long-range male sexual signalling in the palmate newt. Instead, conspecific attraction is likely to promote aggregation of males and females in breeding ponds. Observations in the field and in the laboratory tend to support the aggregative behaviour of this species. We discuss the possible function of conspecific attraction in this context. Heading towards any conspecific would increase the probability of finding potential mates. Chemical cues do not need to be sex-specific at that stage so that long-range sexual advertisement might be unnecessary. This work emphasizes the need for studies investigating the evolutionary relationships between sexual signalling systems and population-distribution patterns. [source] PHYLOGENETIC RELATIONSHIPS AND MORPHOLOGICAL DIVERSITY IN DARWIN'S FINCHES AND THEIR RELATIVESEVOLUTION, Issue 6 2002Kevin J. Burns Abstract Despite the importance of Darwin's finches to the development of evolutionary theory, the origin of the group has only recently been examined using a rigorous, phylogenetic methodology that includes many potential outgroups. Knowing the evolutionary relationships of Darwin's finches to other birds is important for understanding the context from which this adaptive radiation arose. Here we show that analysis of mitochondrial DNA sequence data from the cytochrome b gene confirm that Darwin's finches are monophyletic. In addition, many taxa previously proposed as the sister taxon to Darwin's finches can be excluded as their closest living relative. Darwin's finches are part of a well-supported monophyletic group of species, all of which build a domed nest. All but two of the non-Darwin's finches included in this clade occur on Caribbean islands and most are Caribbean endemics. These close relatives of Darwin's finches show a diversity of bill types and feeding behaviors similar to that observed among Darwin's finches themselves. Recent studies have shown that adaptive evolution in Darwin's finches occurred relatively quickly. Our data show that among the relatives of Darwin's finches, the evolution of bill diversity was also rapid and extensive. [source] 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] Comparative metal binding and genomic analysis of the avian (chicken) and mammalian metallothioneinFEBS JOURNAL, Issue 3 2006Laura Villarreal Chicken metallothionein (ckMT) is the paradigm for the study of metallothioneins (MTs) in the Aves class of vertebrates. Available literature data depict ckMT as a one-copy gene, encoding an MT protein highly similar to mammalian MT1. In contrast, the MT system in mammals consists of a four-member family exhibiting functional differentiation. This scenario prompted us to analyse the apparently distinct evolutionary patterns followed by MTs in birds and mammals, at both the functional and structural levels. Thus, in this work, the ckMT metal binding abilities towards Zn(II), Cd(II) and Cu(I) have been thoroughly revisited and then compared with those of the mammalian MT1 and MT4 isoforms, identified as zinc- and copper-thioneins, respectively. Interestingly, a new mechanism of MT dimerization is reported, on the basis of the coordinating capacity of the ckMT C-terminal histidine. Furthermore, an evolutionary study has been performed by means of in silico analyses of avian MT genes and proteins. The joint consideration of the functional and genomic data obtained questions the two features until now defining the avian MT system. Overall, in vivo and in vitro metal-binding results reveal that the Zn(II), Cd(II) and Cu(I) binding abilities of ckMT lay between those of mammalian MT1 and MT4, being closer to those of MT1 for the divalent metal ions but more similar to those of MT4 for Cu(I). This is consistent with a strong functional constraint operating on low-copy number genes that must cope with differentiating functional limitation. Finally, a second MT gene has been identified in silico in the chicken genome, ckMT2, exhibiting all the features to be considered an active coding region. The results presented here allow a new insight into the metal binding abilities of warm blooded vertebrate MTs and their evolutionary relationships. [source] A 49 kDa microtubule cross-linking protein from Artemia franciscana is a coenzyme A-transferaseFEBS JOURNAL, Issue 24 2003Mindy M. Oulton Embryos and larvae of the brine shrimp, Artemia franciscana, were shown previously to possess a protein, now termed p49, which cross-links microtubules in vitro. Molecular characteristics of p49 were described, but the protein's identity and its role in the cell were not determined. Degenerate oligonucleotide primers designed on the basis of peptide sequence obtained by Edman degradation during this study were used to generate p49 cDNAs by RT-PCR and these were cloned and sequenced. Comparison with archived sequences revealed that the deduced amino acid sequence of p49 resembled the Drosophila gene product CG7920, as well as related proteins encoded in the genomes of Anopheles and Caenorhabditis. Similar proteins exist in several bacteria but no evident homologues were found in vertebrates and plants, and only very distant homologues resided in yeast. When evolutionary relationships were compared, p49 and the homologues from Drosophila, Anopheles and Caenorhabditis formed a distinct subcluster within phylogenetic trees. Additionally, the predicted secondary structures of p49, 4-hydroxybutyrate CoA-transferase from Clostridium aminobutyricum and glutaconate CoA-transferase from Acidaminococcus fermentans were similar and the enzymes may possess related catalytic mechanisms. The purified Artemia protein exhibited 4-hydroxybutyrate CoA-transferase activity, thereby establishing p49 as the first crustacean CoA-transferase to be characterized. Probing of Western blots with an antibody against p49 revealed a cross-reactive protein in Drosophila that associated with microtubules, but to a lesser extent than did p49 from Artemia. [source] Genomic BLAST: custom-defined virtual databases for complete and unfinished genomesFEMS MICROBIOLOGY LETTERS, Issue 2 2002Leda Cummings Abstract BLAST (Basic Local Alignment Search Tool) searches against DNA and protein sequence databases have become an indispensable tool for biomedical research. The proliferation of the genome sequencing projects is steadily increasing the fraction of genome-derived sequences in the public databases and their importance as a public resource. We report here the availability of Genomic BLAST, a novel graphical tool for simplifying BLAST searches against complete and unfinished genome sequences. This tool allows the user to compare the query sequence against a virtual database of DNA and/or protein sequences from a selected group of organisms with finished or unfinished genomes. The organisms for such a database can be selected using either a graphic taxonomy-based tree or an alphabetical list of organism-specific sequences. The first option is designed to help explore the evolutionary relationships among organisms within a certain taxonomy group when performing BLAST searches. The use of an alphabetical list allows the user to perform a more elaborate set of selections, assembling any given number of organism-specific databases from unfinished or complete genomes. This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes. [source] The highly compact structure of the mitochondrial DNA polymerase genomic region of Drosophila melanogaster: functional and evolutionary implicationsINSECT MOLECULAR BIOLOGY, Issue 3 2000E. Lefai Abstract The structure of a Drosophila melanogaster genomic region containing five tightly clustered genes has been determined and evaluated with regard to its functional and evolutionary relationships. In addition to the genes encoding the two subunits (, and ,) of the DNA polymerase , holoenzyme, the key enzyme for mitochondrial DNA replication, other genes contained in the cluster may be also involved in the cellular distribution of mitochondria and in the coordination of mitochondrial and nuclear DNA replication. The gene cluster is extremely compact, with very little intergenic space. It contains two bidirectional promoter regions, and particularly notable is the 5, end overlap detected in two of its genes, an exceptional situation in both prokaryotic and eukaryotic genome organization. [source] Phylogenetic analyses of marine sponges within the order Verongida: a comparison of morphological and molecular dataINVERTEBRATE BIOLOGY, Issue 3 2007Patrick M. Erwin Abstract. Because the taxonomy of marine sponges is based primarily on morphological characters that can display a high degree of phenotypic plasticity, current classifications may not always reflect evolutionary relationships. To assess phylogenetic relationships among sponges in the order Verongida, we examined 11 verongid species, representing six genera and four families. We compared the utility of morphological and molecular data in verongid sponge systematics by comparing a phylogeny constructed from a morphological character matrix with a phylogeny based on nuclear ribosomal DNA sequences. The morphological phylogeny was not well resolved below the ordinal level, likely hindered by the paucity of characters available for analysis, and the potential plasticity of these characters. The molecular phylogeny was well resolved and robust from the ordinal to the species level. We also examined the morphology of spongin fibers to assess their reliability in verongid sponge taxonomy. Fiber diameter and pith content were highly variable within and among species. Despite this variability, spongin fiber comparisons were useful at lower taxonomic levels (i.e., among congeneric species); however, these characters are potentially homoplasic at higher taxonomic levels (i.e., between families). Our molecular data provide good support for the current classification of verongid sponges, but suggest a re-examination and potential reclassification of the genera Aiolochroia and Pseudoceratina. The placements of these genera highlight two current issues in morphology-based sponge taxonomy: intermediate character states and undetermined character polarity. [source] The problem of similarity: analysis of repeated patterns of microsculpture on gastropod larval shellsINVERTEBRATE BIOLOGY, Issue 3 2004Carole S. Hickman Abstract. The problem of similarity is one of explaining the causes of striking resemblances between patterns and architectural themes that recur in organisms at various scales of biological organization. Classical explanations that have considered only the alternatives of homology and analogy overlook similarities of form that are primarily a consequence of fabrication, conveying little information about evolutionary relationships or functional role. When viewed at successively higher magnifications and when mapped onto a phylogeny, patterns of delicate cancellate microsculpture and granular microprotuberances on the surfaces of larval shells of marine gastropods fail to meet the predictions of exclusively historical or exclusively functional explanations, but are shown to be rich in fabricational information. Similar patterns suggest that early biomineralization of the initial organic shell is under weaker biological control than the processes that modulate assembly of the multi-layered, hierarchically-organized composite materials of the adult shell. Some patterns suggest remote biomineralization, without direct influence of living tissue. Scanning electron microscopy of larval shell features reveals previously undetected variation on basic themes that may have implications for the traditional disciplines of systematics, functional morphology, and fabricational morphology. The integration of the approaches of the traditional divisions of biology is required for full explanation of similarity and to generate a unified set of principles for the analysis of form in living and fossil organisms. [source] Properties of Human Mitochondrial RibosomesIUBMB LIFE, Issue 9 2003Thomas W. O'Brien Abstract Mammalian mitochondrial ribosomes (55S) differ unexpectedly from bacterial (70S) and cytoplasmic ribosomes (80S), as well as other kinds of mitochondrial ribosomes. Typical of mammalian mitochondrial ribosomes, the bovine mitochondrial ribosome has been developed as a model system for the study of human mitochondrial ribosomes, to address several questions related to the structure, function, biosynthesis and evolution of these interesting ribosomes. Bovine mitochondrial ribosomal proteins (MRPs) from each subunit have been identified and characterized with respect to individuality and electrophoretic properties, amino acid sequence, topographic disposition, RNA binding properties, evolutionary relationships and reaction with affinity probes of ribosomal functional domains. Several distinctive properties of these ribosomes are being elucidated, including their antibiotic susceptibility and composition. Human mitochondrial ribosomes lack several of the major RNA stem structures of bacterial ribosomes but they contain a correspondingly higher protein content (as many as 80 proteins), suggesting a model where proteins have replaced RNA structural elements during the evolution of these ribosomes. Despite their lower RNA content they are physically larger than bacterial ribosomes, because of the 'extra' proteins they contain. The extra proteins in mitochondrial ribosomes are 'new' in the sense that they are not homologous to proteins in bacterial or cytoplasmic ribosomes. Some of the new proteins appear to be bifunctional. All of the mammalian MRPs are encoded in nuclear genes (a separate set from those encoding cytoplasmic ribosomal proteins) which are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble coordinately with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system. IUBMB Life, 55: 505-513, 2003 [source] Long-standing environmental conditions, geographic isolation and host,symbiont specificity influence the relative ecological dominance and genetic diversification of coral endosymbionts in the genus SymbiodiniumJOURNAL OF BIOGEOGRAPHY, Issue 5 2010Todd C. LaJeunesse Abstract Aim, This study examines the importance of geographic proximity, host life history and regional and local differences in environment (temperature and water clarity) in driving the ecological and evolutionary processes underpinning the global patterns of diversity and distribution of symbiotic dinoflagellates. By comparing and contrasting coral,algal symbioses from isolated regions with differing environmental conditions, we may assess the potential of coral communities to respond to significant changes in climate. Location, Indian Ocean. Methods, Community assemblages of obligate symbiotic invertebrates were sampled at numerous sites from two regions, the north-eastern Indian Ocean (Andaman Sea, western Thailand) and the western Indian Ocean (Zanzibar, Tanzania). Molecular genetic methods, including denaturing gradient gel electrophoresis analysis of the ribosomal internal transcribed spacers, DNA sequencing and microsatellite genotyping, were used to characterize the ,species' diversity and evolutionary relationships of symbiotic dinoflagellates (genus Symbiodinium). Host,symbiont specificity, geographic isolation and local and regional environmental factors were evaluated in terms of their importance in governing the distribution and prevalence of certain symbiont taxa. Results, Host-generalist symbionts (C3u and D1-4, formerly D1a now designated Symbiodinium trenchi) frequently occurred alone and sometimes together in hosts with horizontal modes of symbiont acquisition. However, the majority of Symbiodinium diversity consisted of apparently host-specific ,species'. Clade C Symbiodinium were diverse and dominated host assemblages from sites sampled in the western Indian Ocean, a pattern analogous to symbiont communities on the Great Barrier Reef with similar environmental conditions. Clade D Symbiodinium were diverse and occurred frequently in hosts from the north-eastern Indian Ocean, especially at inshore locations, where temperatures are warmer, water turbidity is high and large tidal exchanges commonly expose coral populations to aerial desiccation. Main conclusions, Regional and local differences in cnidarian,algal combinations indicate that these symbioses are ecologically and evolutionarily responsive and can thrive under various environmental conditions. The high temperatures and turbid conditions of the north-eastern Indian Ocean partly explain the ecological success of Clade D Symbiodinium relative to Clade C. Phylogenetic, ecological and population genetic data further indicate that Clade D has undergone an adaptive radiation, especially in regions around Southeast Asia, during the Pleistocene. [source] Spatial analysis of taxonomic and genetic patterns and their potential for understanding evolutionary historiesJOURNAL OF BIOGEOGRAPHY, Issue 11 2004Sophia A. Bickford Abstract Aim, The aim of this research is to develop and investigate methods for the spatial analysis of diversity based on genetic and taxonomic units of difference. We use monophyletic groups of species to assess the potential for these diversity indices to elucidate the geographical components of macro-scaled evolutionary processes. Location, The range occupied by Pultenaea species in temperate and sub-tropical eastern Australia, extending from western South Australia (133° E,32° S) to Tasmania (146° E,43° S) to coastal central Queensland (148° E,20° S). Methods, We applied a series of both spatially explicit and spatially implicit analyses to explore the nature of diversity patterns in the genus Pultenaea, Fabaceae. We first analysed the eastern species as a whole and then the phylogenetic groups within them. We delineated patterns of endemism and biotic (taxon) regions that have been traditionally circumscribed in biogeographical studies of taxa. Centres of endemism were calculated using corrected weighted endemism at a range of spatial scales. Biotic regions were defined by comparing the similarity of species assemblages of grid cells using the Jaccard index and clustering similar cells using hierarchical clustering. On the basis that genetically coherent areas were likely to be more evolutionary informative than species patterns, genetic indices of similarity and difference were derived. A matrix of similarity distances between taxa was generated based on the number of shared informative characters of two sections of trnL-F and ndhF chloroplast nuclear regions. To identify genetically similar areas, we clustered cells using the mean genetic similarities of the species contained within each pair of cells. Measures of the mean genetic similarity of species in areas were delineated using a geographically local multi-scalar approach. Resultant patterns of genetic diversity are interpreted in relation to theories of the evolutionary relationships between species and species groups. Results, Centres of Pultenaea endemism were defined, those of clades 1 congruent with the spatially separated centres of clades 2 and 3. The taxonomic classification analysis defined cells with shared groups of species, which in some cases clustered when plotted in geographic space, defining biotic regions. In some instances the distribution of biotic regions was congruent with centres of endemism, however larger scale groupings were also apparent. In clade 1 one set of species was replaced by another along the extent of the range, with some connectivity between some geographically disjunct regions due to the presence of widespread species. In the combined analysis of clade 2 and 3 species the major biotic (taxonomic) groups with geographic coherence were defined by species in the respective clades, representing the geographic separation of these clades. However distinctive biotic regions within these main groupings of clades 2 and 3 were also apparent. Clustering cells using the mean genetic similarities of the species contained within each pair of cells indicated that some of the taxonomically defined biotic boundaries were the result of changes in composition of closely related species. This was most apparent in clades 1 and 2 where most cells were highly genetically similar. In clade 3 genetically distinct groups remained and were in part defined by sister taxa with disjunct distributions. Gradients in mean genetic similarity became more apparent from small to larger scales of analysis. At larger scales of analysis, regions of different levels of genetic diversity were delineated. Regions with highest diversity levels (lowest level of similarity) often represented regions where the ranges of phylogenetically distinctive species intergraded. Main conclusions, The combined analysis of diversity, phylogeny and geography has potential to reveal macro-scaled evolutionary patterns from which evolutionary processes may be inferred. The spatial genetic diversity indices developed in this study contribute new methods for identifying coherent evolutionary units in the landscape, which overcome some of the limitations of using taxonomic data, and from which the role of geography in evolutionary processes can be tested. We also conclude that a multiple-index approach to diversity pattern analysis is useful, especially where patterns may be the result of a long history of different environmental changes and related evolutionary events. The analysis contributes to the knowledge of large-scale diversity patterns of Pultenaea which has relevance for the assessment of the conservation status of the genus. [source] Evolution and biogeography of the austral genus Phyllocladus (Podocarpaceae)JOURNAL OF BIOGEOGRAPHY, Issue 10 2004Steven J. Wagstaff Abstract Aim, To infer evolutionary relationships within the genus Phyllocladus and among its close relatives by phylogenetic analysis of DNA sequences. Interpret the inferred relationships in association with the fossil record to examine the origin and diversification of the genus. Location, Australasia. Methods, Phylogenetic analyses of rbcL, matK and internal transcribed spacer (ITS) sequences representing all of the extant species of Phyllocladus and a selection of outgroups from Podocarpaceae and Araucariaceae. Results, The rbcL and matK sequences exhibit little variation within Phyllocladus, but ally its members to Podocarpaceae although its immediate sister remains unclear. The ITS sequences resolve all five species of Phyllocladus and two intraspecific ecotypes of P. alpinus. Main conclusions,Phyllocladus forms a distinct lineage that diverged early in the evolutionary history of Podocarpaceae. The fossil record indicates that the genus was more widely distributed and morphologically diverse during the early Tertiary than at present. Although of Mesozoic origin, the level of sequence variation within Phyllocladus suggests that the extant species radiated during the late Tertiary c. 6.3 ± 0.9 Ma. New Zealand is the present centre of species diversity. [source] Comparative rates of lower jaw diversification in cichlid adaptive radiationsJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 7 2010C. D. HULSEY Abstract The lower jaw (LJ) provides an ideal trophic phenotype to compare rates and patterns of macroevolution among cichlid radiations. Using a novel phylogeny of four genes (ND2, dlx2, mitfb, and s7), we examined the evolutionary relationships among two of the most phylogenetically disparate cichlid radiations: (i) the Central America Heroines; and (ii) the East African Lake Malawi flock. To quantify jaw morphology, we measured two LJ lever systems in approximately 40 species from each lineage. Using geologic calibrations, we generated a chronogram for both groups and examined the rates of jaw evolution in the two radiations. The most rapidly evolving components of the LJ differed between the two radiations. However, the Lake Malawi flock exhibited a much faster rate of evolution in several components of the LJ. This rapid rate of divergence is consistent with natural selection, promoting unparalleled trophic diversification in Lake Malawi cichlids. [source] Phylogenetic evidence for a single, ancestral origin of a ,true' worker caste in termitesJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2000G. J. Thompson Phylogenetic analysis based on sequence variation in mitochondrial large-subunit rRNA and cytochrome oxidase II genes was used to investigate the evolutionary relationships among termite families. Maximum likelihood and parsimony analyses of a combined nucleotide data set yield a single well-supported topology, which is: (((((Termitidae, Rhinotermitidae), Serritermitidae), Kalotermitidae), (Hodotermitidae, Termopsidae)), Mastotermitidae). Although some aspects of this topology are consistent with previous schemes, overall it differs from any published. Optimization of ,true' workers onto the tree suggests that this caste originated once, early in the history of the lineage and has been lost secondarily twice. This scenario differs from the more widely accepted notion that workers are derived and of polyphyletic origin and that extant pseudergates, or ,false' workers, are their developmentally unspecialized ancestor caste. Worker gains and losses covary directly in number and direction with shifts in ,ecological life type'. A test for correlated evolution which takes phylogenetic structure into account indicates that this pattern is of biological significance and suggests that the variable occurrence of a worker caste in termites has ecological determinants, apparently linked to differences in feeding and nesting habits. [source] Novel ,-conotoxins identified by gene sequencing from cone snails native to Hainan, and their sequence diversityJOURNAL OF PEPTIDE SCIENCE, Issue 11 2006Sulan Luo Abstract Conotoxins (CTX) from the venom of marine cone snails (genus Conus) represent large families of proteins, which show a similar precursor organization with surprisingly conserved signal sequence of the precursor peptides, but highly diverse pharmacological activities. By using the conserved sequences found within the genes that encode the ,-conotoxin precursors, a technique based on RT-PCR was used to identify, respectively, two novel peptides (LiC22, LeD2) from the two worm-hunting Conus species Conus lividus, and Conus litteratus, and one novel peptide (TeA21) from the snail-hunting Conus species Conus textile, all native to Hainan in China. The three peptides share an ,4/7 subfamily ,-conotoxins common cysteine pattern (CCX4CX7C, two disulfide bonds), which are competitive antagonists of nicotinic acetylcholine receptor (nAChRs). The cDNA of LiC22N encodes a precursor of 40 residues, including a propeptide of 19 residues and a mature peptide of 21 residues. The cDNA of LeD2N encodes a precursor of 41 residues, including a propeptide of 21 residues and a mature peptide of 16 residues with three additional Gly residues. The cDNA of TeA21N encodes a precursor of 38 residues, including a propeptide of 20 residues and a mature peptide of 17 residues with an additional residue Gly. The additional residue Gly of LeD2N and TeA21N is a prerequisite for the amidation of the preceding C -terminal Cys. All three sequences are processed at the common signal site -X-Arg- immediately before the mature peptide sequences. The properties of the ,4/7 conotoxins known so far were discussed in detail. Phylogenetic analysis of the new conotoxins in the present study and the published homologue of ,4/7 conotoxins from the other Conus species were performed systematically. Patterns of sequence divergence for the three regions of signal, proregion, and mature peptides, both nucleotide acids and residue substitutions in DNA and peptide levels, as well as Cys codon usage were analyzed, which suggest how these separate branches originated. Percent identities of the DNA and amino acid sequences of the signal region exhibited high conservation, whereas the sequences of the mature peptides ranged from almost identical to highly divergent between inter- and intra-species. Notably, the diversity of the proregion was also high, with an intermediate percentage of divergence between that observed in the signal and in the toxin regions. The data presented are new and are of importance, and should attract the interest of researchers in this field. The elucidated cDNAs of these toxins will facilitate a better understanding of the relationship of their structure and function, as well as the process of their evolutionary relationships. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd. [source] PSEUDULVELLA AMERICANA BELONGS TO THE ORDER CHAETOPELTIDALES (CLASS CHLOROPHYCEAE), EVIDENCE FROM ULTRASTRUCTURE AND SSU RDNA SEQUENCE DATA,JOURNAL OF PHYCOLOGY, Issue 4 2006M. Virginia Sanchez-Puerta The genus Pseudulvella Wille 1909 includes epiphytic, freshwater, or marine disk-shaped green microalgae that form quadriflagellate zoospores. No ultrastructural or molecular studies have been conducted on the genus, and its evolutionary relationships remain unclear. The purpose of the present study is to describe the life history, ultrastructural features, and phylogenetic affiliations of Pseudulvella americana (Snow) Wille, the type species of the genus. Thalli of this microalga were prostrate and composed of radiating branched filaments that coalesced to form a disk. Vegetative cells had a pyrenoid encircled by starch plates and traversed by one or two convoluted cytoplasmic channels. They had well-defined cell walls without plasmodesmata. Asexual reproduction was by means of tetraflagellate zoospores formed in numbers of two to eight from central cells of the thallus. The flagellar apparatus of zoospores was cruciate, with four basal bodies and four microtubular roots. The paired basal bodies lay directly opposite (DO) one another. The microtubular root system had a 5-2-5-2 alternation pattern, where the "s" roots contained five microtubules in a four-over-one configuration. A tetralobate nonstriated distal fiber connected all four basal bodies. A wedge-shaped proximal sheath subtended each of the basal bodies. The ultrastructural features of the zoospores were those of members of the order Chaetopeltidales. Phylogenetic analyses based on SSU rDNA placed P. americana sister to Chaetopeltis orbicularis in a well-supported Chaetopeltidales clade. Such a combination of features confirmed that this alga is a member of the order Chaetopeltidales. [source] BIOCHEMICAL PHENOTYPES CORRESPONDING TO MOLECULAR PHYLOGENY OF THE RED ALGAE PLOCAMIUM (PLOCAMIALES, RHODOPHYTA): IMPLICATIONS OF INCONGRUENCE WITH THE CONVENTIONAL TAXONOMY,JOURNAL OF PHYCOLOGY, Issue 1 2006Tomomi Yano Among five species of the genus Plocamium Lamouroux distributed around Japan, P. cartilagineum (Linnaeus) Dixon, P. recurvatum Okamura and P. telfairiae (Hooker and Harvey) Harvey are often difficult to distinguish morphologically from each other. Our previous study demonstrated that P. recurvatum and P. telfairiae were divided into two groups, A and C, based on RUBISCO spacer sequence and that the specimens belonging to group C had acidic cell saps. In this study, we inferred evolutionary relationships of these Plocamium species from internal transcribed spacer sequence of the ribosomal RNA genes and obtained a similar topology to the RUBISCO spacer tree. Color of the dried specimens in the acidic group C was darker red than that in the non-acidic group A, although there was no difference in color in living thalli. The Br, concentration in the cell sap of the acidic group C was 20 times higher than that of the non-acidic group. We could not find any morphological differences to distinguish clearly between groups A and C despite exhaustive investigation of field-collected and cultured thalli in both P. recurvatum and P. telfairiae. These results suggest that the color of dried specimens and the composition of intracellular inorganic ions are significant criteria for interpreting phylogenetic relationships in Japanese Plocamium spp. [source] The evolution of beasts and babies: Recapitulation, instinct, and the early discourse on child developmentJOURNAL OF THE HISTORY OF THE BEHAVIORAL SCIENCES, Issue 4 2005David Hoogland Noon The field of "child study" emerged at the end of the nineteenth century with the purpose of disclosing children's "nature" for the benefit of parents, educators, psychologists, and other interested groups. Borrowed from the biological sciences, narratives of biological recapitulation were common in the discourses about child development during this period. Such theories often measured children against "savages," but they also suggested that the study of childhood offered clues into the evolutionary relationships between humans and animals. By emphasizing the relevance of children's "instincts," observers of child development explained child behavior as the tissue that linked humans and animals. © 2005 Wiley Periodicals, Inc. [source] Origin and phylogeny of Guyniidae (Scleractinia) in the light of microstructural dataLETHAIA, Issue 1 2000Jaros, aw Stolarski The set of skeletal characters of the Recent azooxanthellate coral Guynia annulata Duncan, 1872 is unique among extant scleractinians and encompasses: (a) undifferentiated septal calcification centers (in most extant scleractinians calcification centers are clearly separated); (b) completely smooth septal faces (septa of almost all extant scleractinians bear granular ornamentation); (c) deeply recessed septa in respect to the epithecal rim in the adult coralla (in adults of the majority of extant scleractinians the relationships between septa and wall are the reverse); and (d) an aseptal part of the initial ontogenetic stage, just above the basal plate (almost all known scleractinians have a septate initial coralla). Skeletal features of five other extant traditional guyniids are typical of other caryophylliines (and of Scleractinia). However, the wall types present in different species of traditional guyniids exceed limits traditionally attributed to one caryophylliine family: i.e., Stenocyathus and Truncatoguynia have a marginothecal wall like the Flabellidae, whereas Schizocyathus and Temnotrochus usually have an entirely epithecal wall, as in Gardineriidae (Volzeioidea). Moreover, Pourtalocyathus and Schizocyathus show intraspecific variation in distribution of septal calcification centers (separated vs. non-separated) and in wall types (epithecal vs. consisting of large spherulite-like bodies). These major differences in skeletal architecture form the basis for a new, threefold taxonomical subdivision of the traditional guyniids: (1) Guyniidae Hickson, 1910, containing only monospecific Guynia with an epithecal wall, and septa with non-separated calcification centers; (2) Schizocyathidae fam.n., groups Microsmilia Schizocyathus, Pourtalocyathus, Temnotrochus, which have an epithecal wall and septa with usually well-separated calcification centers; and (3) Stenocyathidae fam.n. with Stenocyathus and Truncatoguynia which have a marginothecal wall and septa with well-separated calcification centers. Despite differences in the basic architecture of the skeleton, all taxa attributed to these families have ,thecal pores' formed by selective dissolution of the skeleton. I propose two hypotheses for evolutionary relationships among Guyniidae, Schizocyathidae, and Stenocyathidae: (1) Hypothesis A: the three families are not phylogenetically related and ,pores' originated independently in different scleractinian lineages: e.g., Guyniidae may represent distant zardinophyllid or gigantostyliid descendants, Schizocyathidae may be a volzeioid offshoot, whereas Stenocyathidae may be a flabellid descendant; (2) Hypothesis B: the three families are phylogenetically related and ,thecal pores' are synapomorphic for the clade (superfamily Guynioidea). Additional approaches, such as anatomical observations, molecular studies on guyniid DNA sequences, and in-depth studies on scleractinian biomineralization will be necessary to test these hypotheses. [source] The species delimitation problem in the Simulium damnosum complex, blackfly vectors of onchocerciasisMEDICAL AND VETERINARY ENTOMOLOGY, Issue 3 2009R. MORALES-HOJAS Abstract. The Simulium damnosum Theobald complex (Diptera: Simuliidae) comprises 57 cytoforms grouped into six subcomplexes. Previous phylogenetic studies using gene sequences have not completely resolved the evolutionary relationships of the cytoforms. The present study investigated the systematics of the complex using a phylogeographic approach. The differentiation between eastern and western forms observed in the phylogenetic studies is confirmed in the estimated haplotype networks. However, haplotypes tend to group in geographical clades and not according to cytoforms. Spatial analyses of the molecular variance also resulted in optimal groupings of sequences that did not correspond to cytoform boundaries. Moreover, Mantel tests showed significant correlations, although not strong, between genetic and geographical distances. This suggests an isolation-by-distance model of differentiation. Furthermore, there are instances in which genetic differentiation between cytoforms is low and not significant. These results indicate a lack of clear genetic differentiation between the cytoforms, which may be explained either by a separation of the taxa recent enough to allow the accumulation of few genetic differences or by recombination between the genomes of the cytoforms, which may be the result of hybridization with introgression or of non-independent evolutionary lineages. The results also emphasize the need for further sampling and for the use of more variable markers in order to clarify the evolutionary history of the group. [source] Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversityMOLECULAR ECOLOGY, Issue 8 2009ROSS BARNETT Abstract Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions. [source] Cospeciation in the triplex symbiosis of termite gut protists (Pseudotrichonympha spp.), their hosts, and their bacterial endosymbiontsMOLECULAR ECOLOGY, Issue 6 2007S. NODA Abstract A number of cophylogenetic relationships between two organisms namely a host and a symbiont or parasite have been studied to date; however, organismal interactions in nature usually involve multiple members. Here, we investigated the cospeciation of a triplex symbiotic system comprising a hierarchy of three organisms , termites of the family Rhinotermitidae, cellulolytic protists of the genus Pseudotrichonympha in the guts of these termites, and intracellular bacterial symbionts of the protists. The molecular phylogeny was inferred based on two mitochondrial genes for the termites and nuclear small-subunit rRNA genes for the protists and their endosymbionts, and these were compared. Although intestinal microorganisms are generally considered to have looser associations with the host than intracellular symbionts, the Pseudotrichonympha protists showed almost complete codivergence with the host termites, probably due to strict transmissions by proctodeal trophallaxis or coprophagy based on the social behaviour of the termites. Except for one case, the endosymbiotic bacteria of the protists formed a monophyletic lineage in the order Bacteroidales, and the branching pattern was almost identical to those of the protists and the termites. However, some non-codivergent evolutionary events were evident. The members of this triplex symbiotic system appear to have cospeciated during their evolution with minor exceptions; the evolutionary relationships were probably established by termite sociality and the complex microbial community in the gut. [source] Combining paternally and maternally inherited mitochondrial DNA for analysis of population structure in musselsMOLECULAR ECOLOGY, Issue 6 2004Robert A. Krebs Abstract Sequence divergence for a fragment of the 16S rRNA gene was compared to identify the advantages in using mitochondrial genes that descend separately through the female and male lineages to examine population structure. The test compared divergence among four local species of freshwater mussels (Unionidae) and was extended to multiple populations of one species, Pyganodon grandis. For the same gene, the male-inherited sequences diverged at a faster rate, producing longer branch lengths in the phylogenies. Of particular use were sequences extracted from P. grandis populations from the southern region of the Lake Erie watershed (Ohio, USA); five male-inherited haplotypes were found. Only one change was observed in the female-inherited form in this region. Therefore, more rapid evolution has occurred in the male form of the gene, and this form provided stronger evidence of geographical isolation among populations. A combination of analyses on haplotypes derived through males and females creates complementary opportunities to identify evolutionary relationships caused by drift and migration in mussels. [source] A set of 16 consensus primer pairs amplifying the complete mitochondrial genomes of orange-spotted grouper (Epinephelus coioides) and Hong Kong grouper (Epinephelus akaara)MOLECULAR ECOLOGY RESOURCES, Issue 6 2009XUAN ZHUANG Abstract Groupers are of considerable economic value; however, their classification and evolutionary relationships have long been hindered by the overwhelming number of species and lack of morphological specializations. Mitochondrial genome is a source of original markers that are potentially useful in the study of phylogeny and population genetics of groupers. We describe a set of 16 new primer pairs that allow PCR amplification of the entire mitochondrial genomes of orange-spotted grouper and Hong Kong grouper. This primer set has been defined for consensus over eight other grouper species, facilitating further studies on the molecular evolution and population genetics of groupers. [source] A set of polymorphic microsatellite loci for Vriesea gigantea and Alcantarea imperialis (Bromeliaceae) and cross-amplification in other bromeliad speciesMOLECULAR ECOLOGY RESOURCES, Issue 4 2007C. PALMA-SILVA Abstract Fifteen polymorphic microsatellite markers were isolated and characterized in two species of Bromeliaceae: Vriesea gigantea and Alcantarea imperialis. The number of alleles observed for each locus ranged from three to 16. The loci will be used for studies of the genetic structure of natural populations, reproductive biology, and evolutionary relationships among and within these genera. A cross-amplification test in 22 taxa suggests that the markers will be useful for similar applications in numerous other bromeliad species. [source] PRIMER NOTE: Primers for amplifying the hypervariable, male-transmitted COII-COI junction region in amblemine freshwater mussels (Bivalvia: Unionoidea: Ambleminae)MOLECULAR ECOLOGY RESOURCES, Issue 3 2007JENNIFER M. WALKER Abstract Freshwater bivalves in the superfamily Unionoidea possess distinct male (M)- and female (F)-transmitted mitochondrial DNA (mtDNA). The former evolves independently of and at a significantly faster rate than the latter. Thus, population genetic and phylogenetic analyses of M sequences facilitate the generation of independent estimates of genetic variation and evolutionary relationships which are often more robust than those provided by analyses of F sequences alone. However, M mtDNA's rapid substitution rate often renders polymerase chain reaction (PCR) amplification difficult with ,universal' primers. Herein, we report on three pairs of PCR primers that consistently amplify the hypervariable M COII-COI gene junction region in 25 bivalve genera (Unionoidea: Ambleminae). [source] | |||||||||||||||||||||||||||||||||||||