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Mitochondrial 16S rDNA (mitochondrial 16s + rdna)
Selected AbstractsExtreme mtDNA divergences in a terrestrial slug (Gastropoda, Pulmonata, Arionidae): accelerated evolution, allopatric divergence and secondary contactJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2005J. PINCEEL Abstract Extremely high levels of intraspecific mtDNA differences in pulmonate gastropods have been reported repeatedly and several hypotheses to explain them have been postulated. We studied the phylogeny and phylogeography of 51 populations (n = 843) of the highly polymorphic terrestrial slug Arion subfuscus (Draparnaud, 1805) across its native distribution range in Western Europe. By combining the analysis of single stranded conformation polymorphisms (SSCP) and nucleotide sequencing, we obtained individual sequence data for a fragment of the mitochondrial 16S rDNA and a fragment of the nuclear ITS1. Additionally, five polymorphic allozyme loci were scored. Based on the 16S rDNA phylogeny, five monophyletic haplotype groups with sequence divergences of 9,21% were found. Despite this deep mitochondrial divergence, the haplotype groups were not monophyletic for the nuclear ITS1 fragment and haplotype group-specific allozyme alleles were not found. Although there is evidence for an accelerated mtDNA clock, the divergence among the haplotype groups is older than the Pleistocene and their current allopatric ranges probably reflect allopatric divergence and glacial survival in separate refugia from which different post-glacial colonization routes were established. A range-overlap of two mtDNA groups (S1 and S2, 21% sequence divergence) stretched from Central France and Belgium up to the North of the British Isles. The nuclear data suggest that this secondary contact resulted in hybridization between the allopatrically diverged groups. Therefore, it seems that, at least for two of the groups, the deep mtDNA divergence was only partially accompanied by the formation of reproductive isolation. [source] Selection of evolutionary models for phylogenetic hypothesis testing using parametric methodsJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2001B. C. Emerson Recent molecular studies have incorporated the parametric bootstrap method to test a priori hypotheses when the results of molecular based phylogenies are in conflict with these hypotheses. The parametric bootstrap requires the specification of a particular substitutional model, the parameters of which will be used to generate simulated, replicate DNA sequence data sets. It has been both suggested that, (a) the method appears robust to changes in the model of evolution, and alternatively that, (b) as realistic model of DNA substitution as possible should be used to avoid false rejection of a null hypothesis. Here we empirically evaluate the effect of suboptimal substitution models when testing hypotheses of monophyly with the parametric bootstrap using data sets of mtDNA cytochrome oxidase I and II (COI and COII) sequences for Macaronesian Calathus beetles, and mitochondrial 16S rDNA and nuclear ITS2 sequences for European Timarcha beetles. Whether a particular hypothesis of monophyly is rejected or accepted appears to be highly dependent on whether the nucleotide substitution model being used is optimal. It appears that a parameter rich model is either equally or less likely to reject a hypothesis of monophyly where the optimal model is unknown. A comparison of the performance of the Kishino,Hasegawa (KH) test shows it is not as severely affected by the use of suboptimal models, and overall it appears to be a less conservative method with a higher rate of failure to reject null hypotheses. [source] Phylogeny of Thalassinidea (Crustacea, Decapoda) inferred from three rDNA sequences: implications for morphological evolution and superfamily classificationJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2008L. M. Tsang Abstract The infraorder Thalassinidea is a group of cryptic marine burrowing decapods of which the higher taxonomy is often contentious. The present analysis attempts to reconstruct phylogenetic relationship among 12 of the 13 currently recognized families using partial nuclear 18S, 28S rDNA and mitochondrial 16S rDNA sequences. The infraorder is divided into two distinct clades, with the first clade consisting of Thalassinidae, Laomediidae, Axianassidae and Upogebiidae, and the second clade including Axiidae, Calocarididae, Eiconaxiidae, Callianassidae, Ctenochelidae, Micheleidae, Strahlaxiidae and Callianideidae. Within the first clade, the Upogebiidae is the basal family. The Axianassidae shows low affinity to other laomediid genera indicating that it is a valid family. The interfamilial relationships are less well resolved in the second clade. The Axiidae is paraphyletic with respect to Calocarididae and Eiconaxiidae. Thus, the status of these two latter families is not supported if the currently defined Axiidae is maintained. All three families appear to be basal in the thalassinidean clade. The Micheleidae is closely related to the Callianideidae and they form a sister group to the Strahlaxiidae. The monophyletic Callianassidae aligns with the Micheleidae + Callianideidae + Strahlaxiidae clade. The relationship among the Axiidae + Calocarididae + Eiconaxiidae clade, Callianassidae + Micheleidae + Callianideidae + Strahlaxiidae clade and the Ctenochelidae cannot be resolved which might be due to a rapid radiation of the three lineages. Our results do not support the generally used classification scheme of Thalassinidea and suggest that the infraorder might be divided into two superfamilies instead of three as suggested based on larval morphology, second pereiopod morphology in adults and gastric mill structure. The two superfamilies are Thalassinoidea (i.e. Thalassinidae, Laomediidae, Upogebiidae and Axianassidae) and Callianassoidea (i.e. Axioidea + Callianassoidea, as defined in Martin and Davis (2001) but excluding Laomediidae and Upogebiidae). It also appears that gill-cleaning adaptations are important in thalassinidean evolution while the presence of linea thalassinica is a result of parallel evolution. Résumé L'infraordre des Thalassinidea est un groupe de décapodes marins fouisseurs cryptiques dont la taxonomie au niveau supérieur est souvent controversée. Cette analyse tente de reconstruire les relations phylogénétiques entre 12 familles sur les 13 actuellement reconnues en utilisant les séquences partielles de rDNA nucléaire 18S, 28S et de rDNA mitochondrial 16S. L'infraordre est divisé en deux clades distincts, le premier comprenant les Thalassinidae, Laomediidae, Axianassidae et Upogebiidae, et le deuxième comprenant les Axiidae, Calocarididae, Eiconaxiidae, Callianassidae, Ctenochelidae, Micheleidae, Strahlaxiidae et Callianideidae. Dans le premier clade, les Upogebiidae est la famille basale. Les Axianassidae montre peu d'affinité avec les autres genres de laomedidés, ce qui indique que la famille est valide. Les relations interfamiliales sont moins bien résolues dans le second clade. La famille des Axiidae est paraphylétique par rapport aux Calocarididae et Eiconaxiidae. Ainsi le statut de ces deux dernières familles n'est pas supporté si la famille des Axiidae est maintenue dans sa définition actuelle. Toutes les trois familles apparaissent basales dans le clade thalassinidéen. La famille des Micheleidae est très proche des Callianideidae et elles forment un groupe frère des Strahlaxiidae. La famille monophylétique des Callianassidae s'aligne avec le clade Micheleidae + Callianideidae + Strahlaxiidae. La relation entre le clade Axiidae + Calocarididae + Eiconaxiidae, le clade des Callianassidae + Micheleidae + Callianideidae + Strahlaxiidae et la famille des Ctenochelidae ne peut être résolue, ce qui pourrait être dûà une radiation rapide des trois lignées Nos résultats ne supportent pas le schéma de classification généralement utilisé pour les Thalassinidea et suggèrent que l'infraordre pourrait être divisé en deux superfamilles au lieu de trois comme suggéré sur la base de la morphologie larvaire, de la morphologie du deuxième péréiopode de l'adulte et de la structure du moulin gastrique. Les deux superfamilles sont: les Thalassinoidea (c'est-à-dire Thalassinidae, Laomediidae, Upogebiidae et Axianassidae) et Callianassoidea (c'est-à-dire Axioidea + Callianassoidea, comme définis dans Martin et Davis 2001 mais excluant les Laomediidae et les Upogebiidae). Il apparaît aussi que les adaptations pour le nettoyage des branchies sont importantes dans l'évolution thalassinidéenne alors que la présence de la linea thalassinica est le résultat d'une évolution parallèle. [source] Phylogeny of Syllidae (Polychaeta) based on combined molecular analysis of nuclear and mitochondrial genesCLADISTICS, Issue 6 2007M. Teresa Aguado The phylogeny of Syllidae is assessed in a combined analysis of molecular data from nuclear 18S rDNA and mitochondrial 16S rDNA and cytochrome c oxidase subunit I. In total, 103 terminal taxa are examined: 88 syllids in the four classical subfamilies Eusyllinae, Exogoninae, Syllinae and Autolytinae, as well as 15 outgroup taxa from Phyllodocida and Eunicida. Maximum parsimony analysis of the combined data set indicates that Syllidae, as currently delineated, is monophyletic, though not with very high support values. Astreptosyllis Kudenov & Dorsey, 1982, Streptosyllis Webster & Benedict, 1884 and SyllidesÖrsted, 1845 comprise a monophyletic group well differentiated from the rest of the Syllidae. The subfamilies Autolytinae and Syllinae are monophyletic. Exogoninae is monophyletic, although not well supported, and Eusyllinae is clearly paraphyletic. Results corroborate previous studies about the evolution of reproductive modes in that epigamy is the plesiomorphic condition and schizogamy appeared independently in Autolytinae and Syllinae. © The Willi Hennig Society 2007. [source] | ||||||||||