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      The hypothesis that coelacanth is the closest living relative of tetrapods 3 was rejected based on three genome-scale approaches

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          Abstract

          Since its discovery of the living fossil in 1938, the coelacanth (Latimeria chalumnae) has generally been considered to be the closest living relative of the land vertebrates, and this is still the prevailing opinion in most general biology textbooks. However, the origin of tetrapods has been the subject of intense debate for decades. The three principal hypothesis (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed. We used the maximum gene-support tree approach to analyze 43 nuclear genes encoding amino acid residues, and compared the results of concatenation and majority-rule tree approaches. The results inferred with three common phylogenetic methods and three genome-scale approaches consistently rejected the hypothesis that the coelacanth is the closest living relative of tetrapods.

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          Comparison of phylogenetic trees

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            Genome-scale phylogeny and the detection of systematic biases.

            Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study of eight yeast species using 106 concatenated genes from complete genomes showed that even small internal edges of a tree received 100% bootstrap support. This effective negation of stochastic error from large data sets is important, but longer sequences exacerbate the potential for biases (systematic error) to be positively misleading. Indeed, when we analyzed the same data set using minimum evolution optimality criteria, an alternative tree received 100% bootstrap support. We identified a compositional bias as responsible for this inconsistency and showed that it is reduced effectively by coding the nucleotides as purines and pyrimidines (RY-coding), reinforcing the original tree. Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error.
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              Combining data in phylogenetic analysis.

              Systematists have access to multiple sources of character information in phylogenetic analysis. For example, it is not unusual to have nucleotide sequences from several different genes, or to have molecular and morphological data. How should diverse data be analyzed in phylogenetic analysis? Several methods have been proposed for the treatment of partitioned data: the total evidence, separate analysis, and conditional combination approaches. Here, we review some of the advantages and disadvantages of the different approaches, with special concentration on which methods help us to discern the evolutionary process and provide the most accurate estimates of phylogeny.
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                Author and article information

                Journal
                10 October 2009
                Article
                0910.1949
                c7345c05-c724-4da8-9fd7-720da7bdd249

                http://arxiv.org/licenses/nonexclusive-distrib/1.0/

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                Custom metadata
                27 Pages, 2 figures and 3 tables
                q-bio.PE q-bio.GN

                Evolutionary Biology,Genetics
                Evolutionary Biology, Genetics

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