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Character Set (character + set)
Selected AbstractsMolecular systematics of Scaphirhynchinae: an assessment of North American and Central Asian Freshwater Sturgeon SpeciesJOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2007C. B. Dillman Summary The sturgeon subfamily Scaphirhynchinae contains two genera of obligate freshwater sturgeon: Scaphirhynchus and Pseudoscaphirhynchus, from North America and Central Asia, respectively. Both genera contain morphologically variable species. A novel data set containing multiple individuals representing four diagnosable morphological variants for two species of Pseudoscaphirhynchus, P. hermanni and P. kaufmanni, was generated. These data were used to test taxonomic hypotheses of monophyly for the subfamily Scaphirhynchinae, monophyly of both Scaphirhynchus and Pseudoscaphirhynchus, monophyly of P. hermanni and P. kaufmanni, and monophyly of the recognized morphological variants. Monophyly of the subfamily Scaphirhynchinae is consistently rejected by all phylogenetic reconstruction methodologies with the molecular character set while monophyly of both river sturgeon genera is robustly supported. The molecular data set also rejects hypotheses of monophyly for sampled species of Pseudoscaphirhynchus as well as monophyly for the recognized intraspecific morphological variants. Interestingly both Scaphirhynchus and Pseudoscaphirhynchus demonstrate the same general pattern in reconstructed topologies; a lack of phylogenetic structure in the clade with respect to recognized diversity. Despite rejection of monophyly for the subfamily Scaphirhynchinae with molecular data, reconstructed hypotheses from morphological character sets consistently support monophyly for this subfamily. Disparities among the data sets, as well as reasons for rejection of monophyly for Scaphirhynchinae and species of Scaphirhynchus and Pseudoscaphirhynchus with molecular characters are examined and a decreased rate of molecular evolution is found to be most consistent with the data. [source] Differentiation of morphology, genetics and electric signals in a region of sympatry between sister species of African electric fish (Mormyridae)JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2008S. LAVOUÉ Abstract Mormyrid fishes produce and sense weak electric organ discharges (EODs) for object detection and communication, and they have been increasingly recognized as useful model organisms for studying signal evolution and speciation. EOD waveform variation can provide important clues to sympatric species boundaries between otherwise similar or morphologically cryptic forms. Endemic to the watersheds of Gabon (Central Africa), Ivindomyrus marchei and Ivindomyrus opdenboschi are morphologically similar to one another. Using morphometric, electrophysiological and molecular characters [cytochrome b sequences and amplified fragment length polymorphism (AFLP) genotypes], we investigated to what extent these nominal mormyrid species have diverged into biological species. Our sampling covered the known distribution of each species with a focus on the Ivindo River, where the two taxa co-occur. An overall pattern of congruence among datasets suggests that I. opdenboschi and I. marchei are mostly distinct. Electric signal analysis showed that EODs of I. opdenboschi tend to have a smaller initial head-positive peak than those of I. marchei, and they often possess a small third waveform peak that is typically absent in EODs of I. marchei. Analysis of sympatric I. opdenboschi and I. marchei populations revealed slight, but significant, genetic partitioning between populations based on AFLP data (FST , 0.04). Taken separately, however, none of the characters we evaluated allowed us to discriminate two completely distinct or monophyletic groups. Lack of robust separation on the basis of any single character set may be a consequence of incomplete lineage sorting due to recent ancestry and/or introgressive hybridization. Incongruence between genetic datasets in one individual, which exhibited a mitochondrial haplotype characteristic of I. marchei but nevertheless fell within a genetic cluster of I. opdenboschi based on AFLP genotypes, suggests that a low level of recent hybridization may also be contributing to patterns of character variation in sympatry. Nevertheless, despite less than perfect separability based on any one dataset and inconclusive evidence for complete reproductive isolation between them in the Ivindo River, we find sufficient evidence to support the existence of two distinctive species, I. opdenboschi and I. marchei, even if not ,biological species' in the Mayrian sense. [source] Taxon combinations, parsimony analysis (PAUP*), and the taxonomy of the yellow-tailed woolly monkey, Lagothrix flavicaudaAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2008Luke J. Matthews Abstract The classifications of primates, in general, and platyrrhine primates, in particular, have been greatly revised subsequent to the rationale for taxonomic decisions shifting from one rooted in the biological species concept to one rooted solely in phylogenetic affiliations. Given the phylogenetic justification provided for revised taxonomies, the scientific validity of taxonomic distinctions can be rightly judged by the robusticity of the phylogenetic results supporting them. In this study, we empirically investigated taxonomic-sampling effects on a cladogram previously inferred from craniodental data for the woolly monkeys (Lagothrix). We conducted the study primarily through much greater sampling of species-level taxa (OTUs) after improving some character codings and under a variety of outgroup choices. The results indicate that alternative selections of species subsets from within genera produce various tree topologies. These results stand even after adjusting the character set and considering the potential role of interobserver disagreement. We conclude that specific taxon combinations, in this case, generic or species pairings, of the primary study group has a biasing effect in parsimony analysis, and that the cladistic rationale for resurrecting the Oreonax generic distinction for the yellow-tailed woolly monkey (Lagothrix flavicauda) is based on an artifact of idiosyncratic sampling within the study group below the genus level. Some recommendations to minimize the problem, which is prevalent in all cladistic analyses, are proposed. Am J Phys Anthropol, 2008. © 2008 Wiley-Liss, Inc. [source] Comparative analysis of mt LSU rRNA secondary structures of Odonates: structural variability and phylogenetic signalINSECT MOLECULAR BIOLOGY, Issue 6 2003B. Misof Abstract Secondary structures of the most conserved part of the mt 16S rRNA gene, domains IV and V, have been recently analysed in a comparative study. However, full secondary structures of the mt LSU rRNA molecule are published for only a few insect species. The present study presents full secondary structures of domains I, II, IV and V of Odonates and one representative of mayflies, Ephemera sp. The reconstructions are based on a comparative approach and minimal consensus structures derived from sequence alignments. The inferred structures exhibit remarkable similarities to the published Drosophila melanogaster model, which increases confidence in these structures. Structural variance within Odonates is homoplastic, and neighbour-joining trees based on tree edit distances do not correspond to any of the phylogenetically expected patterns. However, despite homoplastic quantitative structural variation, many similarities between Odonates and Ephemera sp. suggest promising character sets for higher order insect systematics that merit further investigations. [source] Phylogeography and morphological variability in land snails: the Sicilian Marmorana (Pulmonata, Helicidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2008VIVIANA FIORENTINO Land snails have long been recognized as suitable organisms for studying phenotypic differentiation and phylogeny in relation to geographical distribution. Morphological data (shell and anatomy biometry on different geographical scales) and partial sequences from mitochondrial genes (cytochrome oxidase subunit I, 16S rDNA) were used to test whether morphological patterns match phylogeny in a diversified group of Sicilian rock-dwelling land snails belonging to the genus Marmorana. The taxonomic implications of the three character sets (shell and anatomical biometry and molecular data) were also considered. The inferred phylogenetic relationships do not match morphological (shell and genitalia) patterns. This result may significantly modify the current taxonomy. Mitochondrial based reconstructions define several supported clades well correlated with geographic distribution and populations were found to be distributed parapatrically. The progressive decline in mitochondrial DNA sequence similarity over a distance of 250 km is consistent with a model of isolation by distance, a pattern previously recognized for other groups of land snails. For one clade of Marmorana, colonization along Mediterranean trade routes appears to be a possibility. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 809,823. [source] Ribosomal DNA pseudogenes are widespread in the eucalypt group (Myrtaceae): implications for phylogenetic analysisCLADISTICS, Issue 2 2008Michael J. Bayly Pseudogenes from the 18S,5.8S,26S cistron of nuclear ribosomal DNA are reported in the eucalypt group (Myrtaceae), which includes seven genera. Putative pseudogenes are identified by a range of sequence comparisons including: the number of CpG and CpNpG methylation sites, GC content, estimated secondary structure stability of internal transcribed spacer transcripts, the presence of conserved motifs, patterns of sequence relationships and inferred substitution patterns. These comparisons indicate that pseudogenes are widespread, being evident in Eucalyptus (subgenera Eucalyptus and Eudesmia), Corymbia (extracodical sections Rufaria, Ochraria and Blakearia), Angophora, Stockwellia quadrifida and Arillastrum gummiferum. At least six sequences used in previous phylogenetic studies are identified as pseudogenes, and a further 10 pseudogenes are newly sequenced here. Gene trees place pseudogenes in a number of distinct lineages: pseudogenes from Eucalyptus group with other Eucalyptus sequences, those from Corymbia and Angophora group with other Corymbia/Angophora sequences, that from Stockwellia groups with other sequences from the Eucalyptopsis group, and that from Arillastrum is placed as sister to the other included sequence of Arillastrum. Some pseudogenes in Eucalyptus, Corymbia and Angophora represent "deep" ribosomal DNA paralogues that pre-date species differentiation in these groups, and a recombination analysis shows no evidence of recombination between putative pseudogenes and their functional counterparts. The presence of divergent paralogues presents both challenges and opportunities for the reconstruction of eucalypt phylogenies using ribosomal DNA sequences. Phylogenetic data sets should include only orthologous sequences, but different paralogues potentially provide additional, independent, character sets for phylogenetic analyses. © The Willi Hennig Society 2007. [source] | ||||||||||