1. Rates of Molecular Evolution Suggest Natural History of Life History Traits and a Post-K- Pg Nocturnal Bottleneck of Placentals 
Jiaqi Wu, Takahiro Yonezawa, Hirohisa Kishino 
Current Biology 
Volume 27, Issue 19, Pages e5 (October 2017)
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2. Figure 1 The Bayesian Time Tree of 89 Mammals
We estimated the branch effect by applying the multiplicative ANOVA to the branch lengths of the 1,185 gene trees. A Bayesian relaxed clock method was applied to the branch effect (see STAR Methods). The species tree topology matches that reported previously by others [13, 14]. See also Figure S1 and Tables S1, S2, and S3.
(A) The time tree based on the protein sequences. Numbers at internal nodes are estimated divergence times (mya), with 95% credible intervals indicated by horizontal bars spanning nodes. Nodes with fossil calibrations are indicated by gray bars. Branches in red are associated with accelerated rates of genomic evolution. Scientific names of species are listed in Table S2. Our credible intervals were generally wider than those of the genome-based divergence time estimation study cited above. This discrepancy is possibly due to the fact that our time tree was based on a single set of branch effects, whereas divergence times in the preceding studies were estimated using multiple sets of branch lengths of partitioned data. The authors in the earlier study assumed independent variation of evolutionary rates among partitions, which may have reduced the range of their credible intervals [17].
(B) Comparison of time trees estimated from protein sequences under the Mam+Γ model (protein), codon sequences under the branch model (codon), and DNA sequences under the JC69 model (DNA). The tree topology is same as that of Figure 1A. Horizontal bars spanning nodes indicate 95% credible intervals.
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3. Figure 2 Evolutionary History of Insectivory
(A) Evolutionary history of insectivory reconstructed by rate-based prediction. Examples of the lasso penalized logistic regression input function (gene-branch interaction × coefficients for each gene selected as predictor) are shown at nodes predicted as insectivorous (nodes a and i) or non-insectivorous (node j). The null distributions of predicted probability were obtained by 1,000 replications of training the rate-based predictions on permuted trait values at the terminal nodes and then predicting ancestral states. Here, the null hypothesis assumes independence between trait values and gene-branch interactions (see STAR Methods). The two-sided p value at each node was obtained by comparing the predicted ancestral state probabilities to their null distributions. Examples of null distributions and the setting of two-sided p values are shown in Figures 3E and 3F. The pairs of numbers at the labeled nodes are the predicted probabilities (left) and the two-sided p values (right).
(B) Evolutionary history of insectivory reconstructed by phylogenetic inertia-based prediction.
Nodes are labeled as follows: a, Placentalia; b, Afroinsectiphilia; c, Boreoeutheria; d, Primates; e, Rodents; f, Laurasiatheria; g, Ferungulata; h, Megachiroptera; i, Cetartiodactyla; j, Carnivora + Perissodactyla; k, Carnivora; l, Goats+Chirus. The area of the circle at each node is proportional to the predicted probability that the animal is insectivorous, with the absence of a circle indicating a predicted probability of 0. Animals eating insects occasionally or only as a small part of their diet were not considered to be strict insectivores and were treated as missing data in the analysis. See also Tables S2 and S4.
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4. Figure 3
Evolutionary Histories of Diurnality, Reproductive Seasonality, Sociality, and Diet
(A–C) Evolutionary histories of diurnality (A), reproductive seasonality (B), and sociality (C) reconstructed by rate-based prediction. The pie charts show the predicted probability of each trait state.
(D) Evolutionary history of diet, including reconstructed states of insectivory, carnivory, herbivory, and omnivory. To avoid a misleading picture due to uncertainty, pie charts indicating traits with predicted probabilities larger than 0.8 are shown at nodes.
(E and F) Null distribution of predicted probabilities for selected nodes and two-sided p values by 1,000 replications of analysis with permuted terminal trait states. The pairs of numbers at the labeled nodes are the predicted probabilities (left) and the two-sided p values (right). See also Figures S2 and S3 and Tables S2 and S4. For evolutionary history of arboreality, mating system, and male-biased sexual size dimorphism (labeled as “male larger”), see Figure S4.
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