Alignments of mitochondrial genome arrangements: Applications to metazoan phylogeny

Mitochondrial genomes provide a valuable dataset for phylogenetic studies, in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence-based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combine pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements. We, furthermore, demonstrate that our approach is also applicable to the much larger genomes of chloroplasts

Rate variations, phylogenetics, and partial orders

The systematic assessment of rate variations across large datasets requires a systematic approach for summarizing results from individual tests. Often, this is performed by coarse-graining the phylogeny to consider rate variations at the level of sub-claded. In a phylo-geographic setting, however, one is often more interested in other partitions of the data, and in an exploratory mode a pre-specified subdivision of the data is often undesirable. We propose here to arrange rate variation data as the partially ordered set defined by the significant test results

Can Neutrino Mixings Arise from the Charged Lepton Sector?

The neutrino mixing matrix U is in general of the form U=U_e^+ U_nu, where U_e arises from the diagonalization of charged leptons and U_nu is from the neutrino sector. We discuss the possibility that U_nu is nearly diagonal (in the lagrangian basis) and the observed mixing arises with good accuracy from U_e. We find that the fact that, in addition to the nearly maximal atmospheric mixing angle theta_{23}, the solar angle theta_{12} is definitely also large while at the same time the third mixing angle theta_{13} is small, makes the construction of a natural model of this sort considerably more complicated. We present an example of a natural model of this class. We also find that the case that U_nu is exactly of the bimixing type is severely constrained by the bound on theta_{13} but not excluded. We show that planned experimental searches for theta_{13} could have a strong impact on bimixing models.Comment: v1: 16 pages, 3 figures; v2: added references and corrected misprint

The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis

The phylogenetic position of Xenoturbella bocki has been a matter of controversy since its description in 1949. We sequenced a second complete mitochondrial genome of this species and performed phylogenetic analyses based on the amino acid sequences of all 13 mitochondrial protein-coding genes and on its gene order. Our results confirm the deuterostome relationship of Xenoturbella. However, in contrast to a recently published study (Bourlat et al. in Nature 444:85–88, 2006), our data analysis suggests a more basal branching of Xenoturbella within the deuterostomes, rather than a sister-group relationship to the Ambulacraria (Hemichordata and Echinodermata)

Noisy: Identification of problematic columns in multiple sequence alignments

<p>Abstract</p> <p>Motivation</p> <p>Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction.</p> <p>Results</p> <p>We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of "tree quality". In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters.</p> <p>Software</p> <p>The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignment is low, and (2) there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from <url>http://www.bioinf.uni-leipzig.de/Software/noisy/</url>.</p

Tri-Bimaximal Neutrino Mixing from Discrete Symmetry in Extra Dimensions

We discuss a particularly symmetric model of neutrino mixings where, with good accuracy, the atmospheric mixing angle theta_{23} is maximal, theta_{13}=0 and the solar angle satisfies sin^2(theta_{12})=1/3 (Harrison-Perkins-Scott (HPS) matrix). The discrete symmetry A_4 is a suitable symmetry group for the realization of this type of model. We construct a model where the HPS matrix is exactly obtained in a first approximation without imposing ad hoc relations among parameters. The crucial issue of the required VEV alignment in the scalar sector is discussed and we present a natural solution of this problem based on a formulation with extra dimensions. We study the corrections from higher dimensionality operators allowed by the symmetries of the model and discuss the conditions on the cut-off scales and the VEVs in order for these corrections to be completely under control. Finally, the observed hierarchy of charged lepton masses is obtained by assuming a larger flavour symmetry. We also show that, under general conditions, a maximal theta_{23} can never arise from an exact flavour symmetry.Comment: 24 pages, 1 figure, misprints corrected and references adde

A PCR Survey of Xenoturbella bocki Hox Genes

Xenoturbella bocki has recently been identified as one of the most basal deuterostomes, although an even more basal phylogenetic position cannot be ruled out. Here we report on a polymerase chain reaction survey of partial Hox homeobox sequences of X. bocki. Surprisingly, we did not find evidence for more than five Hox genes, one clear labial/PG1 ortholog, one posterior gene most similar to the PG9/10 genes of Ambulacraria, and three central group genes whose precise assignment to a specific paralog group remains open. We furthermore report on a re‐evaluation of the available published evidence of Hox genes in other basal deuterostomes

Ergodicity of the LLR method for the Density of States

The LLR method is a novel algorithm that enables us to evaluate the density of states in lattice gauge theory. We present our study of the ergodicity properties of the LLR algorithm for the model of Yang-Mills SU(3). We show that the use of the replica exchange method alleviates significantly the topological freeze-out that severely affects other algorithms

Noisy: Identification of problematic columns in multiple sequence alignments

Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of 'tree quality'. In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignment is low, and (2) there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/