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6 results for “Eulaemus”
Figure 2 in Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)
Figure 2. Description of hypothesis-testing procedures. Models were constructed in MESQUITE v. 2.74 and simulations of 1000 gene trees were generated for each of the 13 loci for each of the eight models (step 1). We then compared the simulated trees for each locus against the corresponding model in order to obtain an approximation of a probability distribution of expected deep coalescence events (step 2). Finally, we counted the number of deep coalescences of the real gene tree within the model and obtained the probability of observing that value given the model (step 3). If the empirical data fell outside the 95% confidence interval, then the hypothesized number of deep coalescence events for that gene tree (real data) is not expected under the specified model, thus rejecting that hypothesis.
Figure 4 in Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)
Figure 4. Simulation results. Total number of loci supporting each model after comparisons of the data against 1000 simulated data sets for each locus for each model, and compared with data. We compared the 1000 simulated trees against the model and obtained an approximation of a probability distribution of the deep coalescences expected, and then compared the number of deep coalescences on the observed tree (real data) against the probability distribution. Here, we the show number of loci that fell within the 95% confidence intervals of those probability distributions.
Figure 3 in Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)
Figure 3. Empirical Eulaemus phylogenetic hypotheses. Phylogenetic results using the full matrix of 188 taxa (A, B) and a reduced set of 40 taxa chosen to subsample the largest clades (C to F). A, topology recovered from the concatenated matrix; B, species tree recovered by the minimizing deep coalescence (MDC) approach; C, *BEAST results of partial matrix with representatives of largest clades; values on branches are estimated divergences times (upper) and posterior probability values estimated (lower) or separated by a slash; bold branches represent nodal support> 0.90; D, BEST result; E, MDC result of partial matrix; and F, partial concatenated matrix. In (A), (D), and (F) nodes with support <0.90 were collapsed. The calibration point for estimation of divergence times is shown with a white circle in the node corresponding to the divergence of the Eulaemus and Liolaemus clades.
Figure 3 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 3. Posterior probability distributions for mean rates of evolution estimated from the combined data under a partitioned analysis for the mitochondrial (A) and nuclear genes (B). The middle line of each box plot represents mean rates and the top and bottom lines indicate the 95% credibility intervals. CMOS; MXRA-5.
Figure 2 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 2. Age posterior probability distributions for each of the Eulaemus crown groups. Vertical black line represents the Miocene-Pliocene boundary (5.33 Mya).
Figure 1 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 1. Fifty per cent majority rule phylogram from the partitioned BEAST analyses of the combined data set (cytochrome b, 12S, CMOS, and MXRA5). Numbers above and below the nodes represent posterior probability values and mean estimates of divergence dates (in millions of years), respectively.
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