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Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. using the relative complexity measure.

ABSTRACT: BACKGROUND:Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees. Different parameter combinations chosen for the multiple alignment may result in different phylogenies. A new non-alignment based approach, Relative Complexity Measure (RCM), has been introduced to tackle this problem and proven to work in fungi and mitochondrial DNA. RESULT:In this work, we present an application of the RCM method to reconstruct robust phylogenetic trees using sequence data for genus Galanthus obtained from different regions in Turkey. Phylogenies have been analyzed using nuclear and chloroplast DNA sequences. Results showed that, the tree obtained from nuclear ribosomal RNA gene sequences was more robust, while the tree obtained from the chloroplast DNA showed a higher degree of variation. CONCLUSIONS:Phylogenies generated by Relative Complexity Measure were found to be robust and results of RCM were more reliable than the compared techniques. Particularly, to overcome MSA-based problems, RCM seems to be a reasonable way and a good alternative to MSA-based phylogenetic analysis. We believe our method will become a mainstream phylogeny construction method especially for the highly variable sequence families where the accuracy of the MSA heavily depends on the alignment parameters.

SUBMITTER: Bak?s Y

PROVIDER: S-EPMC3564700 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

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Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. using the relative complexity measure.

Bakış Yasin Y Otu Hasan H HH Taşçı Nivart N Meydan Cem C Bilgin Neş'e N Yüzbaşıoğlu Sırrı S Sezerman O Uğur OU

BMC bioinformatics 20130117

<h4>Background</h4>Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees. Different parameter combinations chosen for the multiple alignment may result in different phylogenies. A new non-alignment based approach, Relative Complexity Measure (RCM), has been introduced to tackle this problem and proven to work in fungi and mitochondrial D ...[more]

PMID: 23323678

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Project description:A universally acknowledged, core property of language is its complexity, at each level of structure - sounds, words, phrases, clauses, utterances, and higher levels of discourse. How does this complexity originate and develop in a language? We cannot fully answer this question from spoken languages, since they are all thousands of years old or descended from old languages. However, sign languages of deaf communities can arise at any time and provide empirical data for testing hypotheses related to the emergence of language complexity. An added advantage of the signed modality is a correspondence between visible physical articulations and linguistic structures, providing a more transparent view of linguistic complexity and its emergence (Sandler, 2012). These essential characteristics of sign languages allow us to address the issue of emerging complexity by documenting the use of the body for linguistic purposes. We look at three types of discourse relations of increasing complexity motivated by research on spoken languages - additive, symmetric, and asymmetric (Mann and Thompson, 1988; Sanders et al., 1992). Each relation type can connect units at two different levels: within propositions (simpler) and across propositions (more complex). We hypothesized that these relations provide a measure for charting the time course of emergence of complexity, from simplest to most complex, in a new sign language. We test this hypothesis on Israeli Sign Language (ISL), a young language, some of whose earliest users are still available for recording. Taking advantage of the unique relation in sign languages between bodily articulations and linguistic form, we study fifteen ISL signers from three generations, and demonstrate that the predictions indeed hold. We also find that younger signers tend to converge on more systematic marking of relations, that they use fewer articulators for a given linguistic function than older signers, and that the form of articulations becomes reduced, as the language matures. Mapping discourse relations to the bodily expression of linguistic components across age groups reveals how simpler, less constrained, and more gesture-like expressions, become language.

Dataset Information

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. using the relative complexity measure.

Publications

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. using the relative complexity measure.

Similar Datasets

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