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Evolution of a RNA Polymerase Gene Family in Silene - Systematic ...

Evolution of a RNA Polymerase Gene Family in Silene - Systematic ...

2004 POPP AND

2004 POPP AND OXELMAN—EVOLUTION OF A RNA POLYMERASE GENE FAMILY IN SILENE 919 TABLE 3. Matrix and tree statistics. rps16 ITS RPA2 RPB2 RPD2 Combined Terminals 29 29 29 33 60 29 Included characters 933 533 883 728 1070 5033 Number/% PIC a 119/13 157/29 220/25 229/31 366/34 962/19 Number/lengths of MP trees 691/378 6/625 528/620 3836/624 1296/1118 2/3240 CI/RI 0.722/0.738 0.536/0.638 0.823/0.836 0.768/0.765 0.719/0.886 0.739/0.718 a Percentage parsimony informative characters. Another limitation with PLATO (and many other model-based congruence tests) is that it is not possible to distinguish between the topology parameter and other parameters such as the shape of the gamma distribution, base frequencies, or the substitution rates. In other words, it is not possible to discern whether data have evolved under a different topology or if other parameters are causing the potential anomalies detected. We used a nonparametric bootstrap approach to isolate the topology parameter from the rest of the parameters in the model and test if all the data sets evolved under the same topology. Let Xcomb be the combined data set excluding a deviating data set, and Xdev be the deviating data set. Further, let Tcomb be the ML topology for the combined data set excluding the deviating data set, and Tdev be the ML topology for the deviating data set. Xi dev denotes the ith pseudoreplicate of Xdev obtained by nonparametric bootstrapping. The free parameters (all but topology) in the model are denoted and the −log likelihood −ln L. We generated 100 pseudoreplicates of Xdev and −ln L (Xi dev | Tdev) was calculated reestimating for each pseudoreplicate, thus generating a null distribution. Then −ln L(Xdev | Tcomb) was calculated reestimating , and subsequently ranked in the null distribution. The null hypothesis was rejected if −ln L (Xdev | Tcomb) was extreme at some level of significance. As noted by Goldman et al. (2000), the selection of a ML topology a posteriori (in our case, the deviating data ML topology) obscures the statistical interpretation of the obtained probability value. First, the test must obviously be one-sided, because the ML topology has higher likelihood than any other tree. Secondly, the probability must be corrected for all other possible tree topologies, as is done by some implementations of the Shimodaira- Hasegawa test (Goldman et al., 2000). This, however, severely reduces the power of the test. Parametric tests, such as those devised by Goldman et al. (2000), are much more sensitive, but also much more dependent on adequate models. Therefore, we refrain from making strict probabilistic conclusions from our tests, but rather use them to evaluate the relative topological incongruence from the data sets identified by PLATO as favoring significantly different models. RESULTS Table 3 summarizes the number of terminals, included characters, parsimony informative characters, percentage parsimony informative characters, number and lengths of MP trees, consistency index (CI), and retention index (RI) for the different DNA regions. The ML estimates of model parameter values for each data set and the combined data set are presented in Table 4. MPB percentages and posterior probabilities for groups in the tree from the combined data set (see Fig. 8) and comparable groups in the individual data sets are presented in Table 5. rps16 and ITS Both the rps16 and ITS data sets support the monophyly of Atocion, Lychnis, and Eudianthe (Figs. 3 and 4). Although Silene was recovered in a strict consensus of the most parsimonious trees from the ITS data (Fig. 4), neither the rps16 nor the ITS data sets have MPB percentages above 50 for a monophyletic Silene. There were TABLE 4. Maximum likelihood estimates of separate and combined data sets under the general time reversible + gamma (GTR+Ɣ) model and maximum parsimony topologies. Data partition rps16 ITS RPA2 RPB2 RPD2 Combined −ln L Base frequencies 3205.6218 3735.0188 4458.4968 4040.7808 7538.5282 23030.0220 A 0.3543 0.1906 0.2585 0.2576 0.2580 0.2728 C 0.1321 0.2855 0.1742 0.1559 0.1799 0.1801 G 0.1631 0.2946 0.1867 0.2171 0.1744 0.1989 T 0.3505 0.2294 0.3807 0.3694 0.3876 0.3482 Relative nucleotide substitution rates AC 1.1098 1.1337 1.1998 0.5638 0.7559 0.8804 AG 1.0683 2.6794 3.3094 1.9755 2.4075 2.0159 AT 0.3726 2.5900 1.0250 0.8088 0.7235 0.8003 CG 0.3289 0.3088 1.1390 0.9604 1.3284 0.7877 CT 1.3763 5.6042 2.4894 2.0557 2.0409 2.3557 Gamma shape (α) 0.4228 0.3581 1.8761 1.3218 3.0581 0.7585 Downloaded from http://sysbio.oxfordjournals.org/ by guest on April 7, 2013

920 SYSTEMATIC BIOLOGY VOL. 53 TABLE 5. Summary of MPB percentages/posterior probabilities for nodes in the combined data tree (Fig. 8), and comparable nodes in the individual data sets. Negative numbers refer to conflicting nodes, numbers in italics indicate groups that are not found in all most parsimonious trees. Incongruencies that are considered “hard” are indicated in bold. Node Combined rps16 ITS RPA2 RPB2 RPD2a RPD2b 1 99/1 75/.77 96 n/a 100 100 100 2 100/1 100/1 87 100 n/a n/a n/a 3 100/1 87/1 98 100 50 n/a 99 4 90/1 54/.92

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