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Science 23 December 2005:
Vol. 310. no. 5756, pp. 1933 - 1938
DOI: 10.1126/science.1116759
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Research Articles
Animal Evolution and the Molecular Signature of Radiations Compressed in Time
Antonis Rokas*,
Dirk Krüger and
Sean B. Carroll
Howard Hughes Medical Institute, Laboratory of Molecular Biology, R. M. Bock Labs, University of Wisconsin–Madison, 1525 Linden Drive, Madison, WI 53706, USA.
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Fig. 1. The lack of resolution in phylogenetic relationships among major metazoan phyla. Values above internodes correspond to support values from ML and MP analyses, respectively. Only internodes with significant support in at least one of the two analyses (ML and MP) or internodes present in majority-rule consensus trees of both analyses are drawn. Analyses were also performed by Bayesian inference (15) (fig. S1). Although certain analyses provided strong support for particular clades, analyses of different subsets of taxa produced significantly different and conflicting results (table S3).
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Fig. 2. The contrast in phylogenetic resolution between the clades of Metazoa and Fungi. Values above internodes are as in Fig. 1. Eleven out of 13 internodes in the fungal clade are significantly supported by both optimality criteria (ML and MP), whereas only 4 out of 14 internodes in the metazoan clade are significant. Analyses were also performed by Bayesian inference (15) (fig. S4 and table S3).
[View Larger Version of this Image (42K GIF file)]
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Fig. 3. Phylogenetic accuracy is inversely correlated with the length of time elapsed since a closely spaced series of cladogenetic events. A simulation analysis of increasing the age of origin of the 42-million-year window of mammalian order diversification is shown. (A) The best estimate of the mammalian phylogenetic tree at present under the molecular clock assumption (36) (time span of 107 million years). (B) The mammalian phylogenetic tree, assuming a 600-million-year time span. Branch lengths are shown in million-year time units. The topology and branch lengths within the 42-million-year window (left of the dashed grey line) of trees in (A) and (B) are identical. There is a compression in the lengths of internodes in the 42-million-year window of the tree in (B), due to the longer time span elapsed. (C) Graph showing the relationship between phylogenetic accuracy of internodes in the 42-million-year window and total time span simulated, after MP analysis of 100 simulated data matrices, each containing 16,000 characters (of which roughly 6000 are variable). (D) The same graph as in (C), but with simulated data matrices, each containing 73,000 characters (of which roughly 28,000 are variable). Similar results were obtained by neighbor-joining (NJ) analyses (fig. S5). Only 10 exemplar internodes are shown (all the internodes are shown in fig. S5). The numbers of internodes in all panels are according to (36).
[View Larger Version of this Image (28K GIF file)]
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Fig. 4. The limit for resolution of cladogenetic events of Cambrian age, under the best of circumstances, may be an order of magnitude higher than previously thought. The phylogenetic accuracy with which internodes are resolved (the ordinate) is plotted against the length of each internode in million years (the abscissa). Data sets of two different lengths (data set in blue, 16,000 characters, of which 6000 are variable; data set in red, 73,000 characters, of which 28,000 are variable) were generated by simulation, assuming a tree with a 600-million-year time span. For many internodes with lengths much higher than 1 million years, resolution accuracy values are low, irrespective of data set size. Not all internodes of a given age exhibit the same resolution accuracy. For example, certain 3-million-year internodes are resolved with 100% accuracy, whereas other internodes of similar (or greater) age exhibit much lower values of resolution accuracy. Results are shown for analyses using MP [similar results are obtained by NJ analyses (fig. S7)].
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