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Sequence Data Sets (sequence + data_set)
Selected AbstractsUnravelling evolutionary lineages among South African velvet worms (Onychophora: Peripatopsis) provides evidence for widespread cryptic speciationBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009SAVEL R. DANIELS The endemic South African velvet worm genus Peripatopsis currently contains eight recognized species described from variable morphological characters and the current taxonomy is unsatisfactory. In an attempt to investigate evolutionary relationships within Peripatopsis, we collected 137 individuals from 34 sample localities for six of the eight species. Sequence data derived from two partial mitochondrial (mt)DNA gene loci (COI and 12S rRNA), as well as partial sequence data from the ribosomal nuclear 18S rDNA locus in combination with gross morphological characters and scanning electron microscopy (SEM), was used to examine evolutionary relationships. Phylogenetic relationships were investigated using minimum evolution (ME) and Bayesian inferences (BI). Additionally, we also undertook a maximum likelihood (ML) analyses on the combined DNA sequence data set. The combined DNA evidence topologies derived from the ME, BI, and ML was highly congruent and was characterized by the presence of multiple lineages within recognized taxa. Peripatopsis clavigera, Peripatopsis moseleyi, and Peripatopsis sedgwicki each comprised two evolutionary lineages; Peripatopsis capensis comprised three; and Peripatopsis balfouri comprised six operational taxonomic units respectively. Genealogical exclusivity at both mtDNA and nuclear DNA among the geographically coherent groups coupled with pronounced sequence divergence suggested a two-fold increase in the number of species within Peripatopsis. Previously used gross morphological characters (such as the number of leg pairs and colour) were either highly variable within operational taxonomic units, or were invariant, suggesting that alternative morphological characters are necessary for species discrimination. SEM results revealed potentially useful diagnostic characters that can discriminate between at least discriminate some of the newly-identified lineages. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society 2009, 97, 200,216. [source] Phylogenetic analysis of bovine pestiviruses: testing the evolution of clinical symptomsCLADISTICS, Issue 5 2004L. R. Jones This study presents a phylogenetic analysis of 115 bovine pestiviruses. A sequence data set from the 5, untranslated genomic region was analyzed with maximum parsimony, bootstrapping and parsimony jackknifing. We tested for the proposed classifications of the group and analyzed the evolution of the symptoms associated with Pestivirus infections in bovines. Based on the historical framework provided by our phylogenetic trees, we also characterized the extent and importance of contamination caused in biologicals by the virus. Our phylogenetic analyses showed that the previously defined genotypes are monophyletic, except for genotype 1a. Based on our cladograms, we propose the existence of more than 12 monophyletic groups within the species BVDV 1. The mapping of clinical symptoms suggests that the emergence of some genotypes could have been driven by a change in the pathogenic process. Enteric Problems appear to be ancestral, while Reproductive and Respiratory Problems arise with the emergence of genotypes 1b, 1d and the herein-proposed genotype Arg 1. The distribution of contaminant strains on the cladograms shows that pestiviral contamination is a common process, and also suggests that a contaminated product might be a vehicle for virus dispersion. Implications for virus evolution, virus taxonomy, veterinary medicine and biotechnology are discussed. [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] Mitochondrial DNA differentiation between two forms of trout Salmo letnica, endemic to the Balkan Lake Ohrid, reflects their reproductive isolationMOLECULAR ECOLOGY, Issue 12 2004J. SELL Abstract Mitochondrial haplotype diversity in sympatric populations of Ohrid trout, Salmo letnica was investigated by polymerase chain reaction,restriction fragment length polymorphism (PCR-RFLP) analysis of the mtDNA control region and ND1, ND3/4, ND5/6 segments. A 310 bp fragment at the 5, end, and a 340,572 bp fragment at the 3, end of the control region were sequenced from representatives of the populations studied. Based on pairwise comparison of the sequences, five new haplotypes were identified plus one identical with the brown trout Andalusian haplotype from the southern Iberian Peninsula. The combination of both RFLP and sequence data sets yielded a total of 10 composite haplotypes. A high degree of genetic subdivision between S. letnica typicus and S. letnica aestivalis populations was observed. The notion of a sympatric origin for the two morphs is discussed. Length variation of the mtDNA control region due to the presence of an 82 bp unit, tandemly repeated one to four times, in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA is reported. Further, we demonstrate that a single duplication of the approximately 82 bp repeat unit is a common element of the salmonid mitochondrial control region. The unique genetic structure of Ohrid trout represents a highly valuable genetic resource that deserves appropriate management and conservation. [source] Molecular systematics in the genus Clintonia and related taxa based on rbcL and matK gene sequence dataPLANT SPECIES BIOLOGY, Issue 2 2001Kazuhiko Hayashi Abstract In an attempt to elucidate the affinity and phylogeny of the disjunct North American,eastern Asian genus Clintonia, two chloroplast genes, rbcL and matK, were sequenced for all five species (Clintonia andrewsiana, Clintonia borealis, Clintonia umbellulata, Clintonia uniflora and Clintonia udensis). Similar sequence data sets for both genes supported the idea that a monophyly of Clintonia consists of two clades, one in eastern Asia and one in North America. The North American lineage resolves into an eastern group and a western group. There are surprisingly few site substitutions within these two genes, notwithstanding the wide morphological diversity of the genus. To root the Clintonia trees, Cardiocrinum (=Lilium) cordatum, Medeola virginiana, Scoliopus bigelovii and Scoliopus hallii were used as outgroup taxa. Similar topologies for Clintonia resulted when both the rbcL and matK gene sequences were combined. However, when an amino acid tree was generated for the matK sequence, all differences between the North American species were reduced to similarities due to synonymous codon sequences. Differentiation patterns of some selected morphological, karyological and embryological characters in Clintonia were also reviewed in comparison to the resulting molecular topologies. The unique, Clintonia -type megasporogenesis that produced identical, maternally derived, diploid zygotes and endosperm coupled to polyploid buffering provides a considerable constraint on variability. A search of possible sister genera to Clintonia was also attempted based on the molecular analyses and outgroup analysis, and Medeola virginiana from eastern North America turned out to be the closest relative found. [source] | ||||||||||