Concatenation Model Research Articles

Phylogeny of the Centrohelida Inferred from SSU rRNA, Tubulins, and Actin Genes

Amoeboid protists are major targets of recent molecular phylogeny in connection with reconstruction of global phylogeny of eukaryotes as well as the search for the root of eukaryotes. The Centrohelida are one of the major groups of Heliozoa, classified in the Actinopodida, whose evolutionary position is not well understood. To clarify the relationships between the Centrohelida and other eukaryotes, we sequenced SSU rRNA, alpha-tubulin, and beta-tubulin genes from a centroheliozoan protist, Raphidiophrys contractilis. The SSU rRNA phylogeny showed that the Centrohelida are not closely related to other heliozoan groups, Actinophryida, Desmothoracida, or Taxopodida. Maximum likelihood analyses of the combined phylogeny using a concatenate model for an alpha- + beta-tubulin + actin data set, and a separate model for SSU rRNA, alpha- and beta-tubulin, and actin gene data sets revealed the best tree, in which the Centrohelida have a closer relationship to Rhodophyta than to other major eukaryotic groups. However, both weighted Shimodaira-Hasegawa and approximately unbiased tests for the concatenate protein phylogeny did not reject alternative trees in which Centrohelida were constrained to be sisters to the Amoebozoa. Moreover, alternative trees in which Centrohelida were placed at the node branching before and after Amoebozoa or Viridiplantae were not rejected by the WSH tests. These results narrowed the possibilities for the position of Centrohelida to a sister to the Rhodophyta, to the Amoebozoa, or to an independent branch between the branchings of Amoebozoa and Rhodophyta (or possibly Plantae) at the basal position within the bikonts clade in the eukaryotic tree.

Combining multiple data sets in a likelihood analysis: which models are the best?

Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecular data sets. Here, we compare several models for combining different genes for the purpose of evaluating the likelihood of tree topologies. Three methods of branch length estimation were studied: assuming all genes have the same branch lengths (concatenate model), assuming that branch lengths are proportional among genes (proportional model), or assuming that each gene has a separate set of branch lengths (separate model). We also compared three models of among-site rate variation: the homogenous model, a model that assumes one gamma parameter for all genes, and a model that assumes one gamma parameter for each gene. On the basis of two nuclear and one mitochondrial amino acid data sets, our results suggest that, depending on the data set chosen, either the separate model or the proportional model represents the most appropriate method for branch length analysis. For all the data sets examined, one gamma parameter for each gene represents the best model for among-site rate variation. Using these models we analyzed alternative mammalian tree topologies, and we describe the effect of the assumed model on the maximum likelihood tree. We show that the choice of the model has an impact on the best phylogeny obtained.

The acoustics of coughing

Coughing is a reflex-generated perturbation of the respiratory function and an important clinical symptom in many respiratory diseases. The information contained in the cough-sound is limited due to the lack of an understanding of the origin of the cough sound. This thesis focuses on (1) automated interpretation, (2) quantification, and (3) sound-production. “In vivo” coughing was registered from individual animal (domestic pig Sus Scrofa) and human subjects in normal and pathological respiratory health conditions. The cough-sound is mathematically presented in the frequency domain. Clustering of the mean spectral features results in automated subject-independent cough-sound-recognition. In addition normal and pathological cough-sounds are distinct for both species. Therefore the simple and noninvasive nature of acquiring information using free field cough-sound-registration makes soundanalysis attractive for on-line follow-up and clinical diagnosis. The vibratory activity of the vocal folds is known to be an important issue in sound production. A three-phase pattern is shown to be a generic cough-feature. A global fundamental frequency was determined. Modeling the acoustic cough waveform aims to parametrize the cough-sound-signal for analysis and physical interpretation. Cough formant frequencies are estimated from the model parameters. A first physical interpretation in terms of a concatenate tube model of the vocal tract is presented. All investigated issues, either parametric or nonparametric, show evidence that the cough-sound character is related to the state of both the supra- and subglottal respiratory system. This finding physically and objectively motivates the statement the “cough-sound is a lung-sound.”

Analysis of gene evolution: the software AGE.

The software AGE (Analysis of Gene Evolution) has been developed both to study a genetic reality, i.e. the identification of statistical properties in genes (e.g. periodicities), and to simulate this observed genetic reality, by models of molecular evolution. AGE has two types of models: (i) models of sequence creation from oligonucleotides: concatenation model in series of an oligonucleotide, independent (or Markov) mixing model of oligonucleotides according to given probabilities (or a Markov matrix); (ii) models of sequence evolution from created sequences: insertion/deletion process of (mono,di,tri)nucleotides, base mutation process. The study of a reality and the development of simulation models are based on several new algorithms: approximated simulation and exact calculus to compute various autocorrelation functions, Fourier transformation of autocorrelation curves, recognition of a curve form, etc. AGE is implemented on IBM or compatible microcomputers and can be used by biologists without any computer knowledge to identify statistical properties in their newly determined DNA sequence and to explain them by models of molecular evolution.

Temporally overlapping segment quantization for speech coding

A method for the efficient segment quantization of LPC spectral parameters is presented for very low-bit-rate speech coding. Recent methods of segment quantization for speech coding have used a concatenation segment model, in which spectral parameters are represented as a concatenation of variable-length code spectral segments. The present method uses a temporally overlapping segment model to capture more efficiently the variance in the spectral parameters due to coarticulation effect in speech. Spectral parameters are represented as a sequence of temporally overlapping segments, in which each code segment is decomposed into fixed-length temporal patterns and their weighted patterns. A dynamic programming procedure is used to determine the optimum code segments and the segment positions of the overlapping model so as to minimize the spectral distance between the input and the model spectral parameters in the analysis window. An iterative algorithm for code segment design in this model is also presented. Comparison of the overlapping model with the concatenation model for speech coding [Shiraki and Honda, to appear in IEEE Trans. ASSP] is described in terms of spectral distortion and computational complexity.

Multimode concatenation modal group analysis

A multimode concatenation model is derived using the link mode power distribution and fiber mode group delay times. The model is used deterministically to predict the bandwidth length exponent γ for seven concatenations. γ depends directly on the amount of correlation existing among the fibers' mode group delays. Under the assumption that the fiber ensemble is stationary and satisfies ergodicity conditions, we are able to evaluate an ensemble-γ. It can be used statistically to estimate the concatenation-γ.