Supplementary Material

Supplementary figures and online appendices 1 and 2

Online Appendix 4

R code employed to conduct analyse

Alignment and Tree

Alignment of DNA sequences and tree. Nexus format

The prior probabilities influence the posterior distribution.

<p>Running the sampler with no data so that the posterior probabilities are determined by the prior probabilities only (<b>a</b>), with flat priors (<b>b</b>), or with different values of the shape parameter for the gamma distributions of genome length and number of contigs (<b>c–e</b>) all cause shifts in the posterior distribution of edge frequencies. The baseline for the change in frequency is Chain 1 from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099497#pone-0099497-g003" target="_blank">Figure 3</a> with , and all chains here were initialized with the same random seed as Chain 1.</p

Evidence of good mixing and convergence of three independent MCMC assembly chains.

<p>(<b>a</b>) Early in the sampling, the log(likelihood) reaches a stationary distribution with random noise, indicating good mixing of the chains. (<b>b</b>) Plotting the cumulative node/edge frequencies shows that most of the frequencies have reached a stationary value. (<b>c</b>) The average standard deviation among the three chains of the cumulative frequencies approaches zero. (<b>d</b>) A bivariate plot comparing node/edge frequencies between each pair of chains shows that the frequencies are in agreement across all chains. Both (<b>c</b>) and (<b>d</b>) indicate convergence.</p

Revisiting the Nonadiabatic Process in 1,2-Dioxetane

Determining the ground and excited-state decomposition mechanisms of 1,2-dioxetane is essential to understand the chemiluminescence and bioluminescence phenomena. Several experimental and theoretical studies has been performed in the past without reaching a converged description. The reason is in part associated with the complex nonadiabatic process taking place along the reaction. The present study is an extension of a previous work (De Vico, L.; Liu, Y.-J.; Krogh, J. W.; Lindh, R. <i>J. Phys. Chem. A</i> <b>2007</b>, <i>111</i>, 8013–8019) in which a two-step mechanism was established for the chemiluminescence involving asynchronous O–O′ and C–C′ bond dissociations. New high-level multistate multi configurational reference second-order perturbation theory calculations and <i>ab initio</i> molecular dynamics simulations at constant temperature are performed in the present study, which provide further details on the mechanisms and allow to rationalize further experimental observations. In particular, the new results explain the high ratio of triplet to singlet dissociation products

Chiral Hydrogen Bond Environment Providing Unidirectional Rotation in Photoactive Molecular Motors

Generation of a chiral hydrogen bond environment in efficient molecular photoswitches is proposed as a novel strategy for the design of photoactive molecular motors. Here, the following strategy is used to design a retinal-based motor presenting singular properties: (i) a single excitation wavelength is needed to complete the unidirectional rotation process (360°); (ii) the absence of any thermal step permits the process to take place at low temperatures; and (iii) the ultrafast process permits high rotational frequencies