Seismic guidelines currently designate constant, time-independent probabilities or mean annual frequencies of exceedance that are assumed to remain invariable for the entire design life.
The models denoted by +I imply that a fraction of data set is assumed to be invariable, where +G is considered to categorize the change of substitution rates among sites in discrete gamma distribution.
The best nucleotide substitution model selected by Modeltest 3.8 for the Seg-3 coding region sequence data set, was the General Time Reversible with gamma distributed rates across sites and a fraction of sites assumed to be invariable (GTR + I + Γ) [52].
We used PAUP [28] to construct a maximum likelihood phylogenetic tree based on parasite cytochrome b sequences (Fig. 2), using a General Time Reversible model of nucleotide substitution with gamma parameter α = 0.623, and assumed proportion of invariable sites = 0.427.
Total sleeping time, working time, and resting time were assumed to be invariable at 8, 10, and 6 h, respectively.
Maximum likelihood analyses were done under the JTT + G + I model, as assigned by ProtTest, and yielded eight trees of equal likelihood (−Ln L = 15631.10; four categories; shape parameter = 1.73358; assumed proportion of invariable sites = 0.0251882).
The GTR model, with some sites assumed to be invariable and with variable sites assumed to follow a discrete gamma distribution (ref. [ 79]; GTR + I + Γ), was selected as the best-fit model of the nucleotide substitution for each partition on the basis of the Akaike Information Criteria (ref. [ 81]; AIC).
The general time-reversible model, with some sites assumed to be invariable and variable sites assumed to follow a discrete gamma distribution (GTR + I + Γ; [ 33]), was selected as the best-fit model of nucleotide substitution by MrModeltest 2.2 http://www.abc.se/~nylander/[ 34].
The general time reversible model with some sites assumed to be invariable and with variable sites assumed to follow a discrete gamma distribution [ref. [ 54]; GTR + I + Γ] was used for model of sequence evolution, as it was selected as best-fitting model with MRMODELTEST (Version 2) [ 55] for each partition except for positions with the RY-coding.
In brief, aligned sequences were analyzed with PAUP* 4.0b10 [ 44] using maximum likelihood (ML) under a general time reversible model of sequence evolution [ 45] with some sites assumed to be invariable, and with rate variation among the remaining sites assumed to follow a gamma distribution [ 46, 47].
Likelihood analysis (including bootstraps) of the GHR data alone also used PAUP [ 36] and the HKY+G model as estimated by the AIC in MrModeltest [ 38], i.e., transition/transversion ratio = 2.2696, nucleotide frequencies A = 0.2805, C = 0.265, G = 0.2218, T = 0.2327, assumed proportion of invariable sites = none, distribution of rates at variable sites = gamma, shape parameter = 0.8383.
