![]() More than 130 studies (>98%) used models that have more free parameters than the K80 model. All studies assumed stationarity and time-reversiblity of evolutionary processes, with the GTR + Γ and GTR + Γ+I being the most preferred models. Model + Γ(+I) means that either a gamma distribution for incorporating rate variation across sites is used, or a proportion of sites are assumed to be invariant across sequences, or both are used along with the corresponding substitution model K80, HKY, TrN and GTR represent Kimura-2-parameter ( Kimura, 1980), Hasegawa–Kishino–Yano ( Hasegawa et al., 1985), Tamura–Nei ( Tamura and Nei, 1993) and GTR model ( Tavaré, 1986), respectively. The GTR model provides for different rates for all the transitions and transversional substitutions as well as the unequal frequency of bases. In addition to time-reversibility, the use of a GTR model in phylogenetic methods, as implemented in most of the software packages, automatically assumes that the substitution process does not change over time i.e. This translates into assuming that the rates of different types of base substitutions are the same across evolutionary lineages and over time. Violation of this stationarity assumption is evident from differences in base composition across sequences (e.g. Galtier and Gouy, 1998 Kumar and Gadagkar, 2001 Rosenberg and Kumar, 2003 Tamura and Kumar, 2002).
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