Figure 1.
Density Histogram of Overall Transmembrane Gene Duplication Events
The density trace (blue line) was obtained by using the Gaussian kernel density estimation with the bandwidth selected by Sheather and Jones' method [55]. The red line shows the estimate of the systemic bias in the overall distribution of duplication events, which was obtained by recalculating the mean value in each bin of 10,000 Monte Carlo–simulated histograms and smoothing the mean values with function “lowess” available in the statistics package of R environment [54]. The distinct transitions of the density trace are marked with red arrows.
Figure 2.
Correlation Analysis between the Maximum Number of Cell Types and the Density of the Transmembrane Gene Duplicates throughout the History of Life
The estimates of the number of cell types in eukaryotes at different times in the past was derived from the work of Hedges et al. [23], and the corresponding density of duplicates was calculated by using linear interpolation in the time series inferred from the overall density trace (for details, see Protocol S1).
Figure 3.
Density Trace of Transmembrane Gene Duplicates during the Phanerozoic Phase
The trace was obtained by using the Gaussian kernel density estimation with a smaller “reasonable” bandwidth [33]. Arrows indicate the times of the major extinctions [5], and stars indicate the evolutionary events of plants [26–28].
Figure 4.
Periodogram Analysis of the Density Trace of Transmembrane Gene Duplicates during the Phanerozoic Phase
(A) Fourier spectrum of the detrended density trace of the transmembrane gene duplicates during the Phanerozoic phase. Dot-dashed line (R model) and dashed line (modified W model) are estimates of spectral background [7]. The arrows indicate three potential peaks (Table S3), which are of statistical significance in finding the indicated peak at the specified period in either model, and accounts for at least 5% of the variance (i.e., biological significance cutoff) in the diversity signal.
(B) The detrended density trace of the transmembrane gene duplicates during the Phanerozoic phase with a 62-Myr sine wave inferred from fossil data (solid line) [7] and a superimposed 61-Myr wave from our data (dashed line). The arrows indicate the times of major extinctions [5].