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The case study in which MP outperforms ML under heterogeneous conditions [ 33] is unrealistic in the sense that no evolutionary heterogeneity except a very strong heterotachy (0.36 < τ < 0.75) was considered.
Bryan studied the effect of evolutionary heterogeneity on current phylogenetic methods and developing new mixed-model techniques that are more accurate when the evolutionary process varies among lineages and sites.
A second proposed advantage of BI over ML is that Bayesian MCMC provides a more reliable method for analyzing data using complex models that incorporate evolutionary heterogeneity among sites, such as those that use mixture models or partition sites into independent classes [3], [10], [12], [14].
Also in K. drymeia and K. integrifolia (see above) high variation in RGS can be explained by evolutionary heterogeneity [ 34].
However, we also showed that evolutionary patterns may differ between species and that there is a substantial evolutionary heterogeneity even within enzyme families (e.g. NMNATs, PARPs).
To avoid overparameterisation [ 78] but still allow for evolutionary heterogeneity, the concatenated alignment were analysed using a mix-model approach where each gene partition was lumped in a "substitution model -partition according to their AIC-best chosen model -partition
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Phylogenetic reconstruction is rendered difficult by the occurrence of numerous evolutionary heterogeneities in molecular sequence data.
Indeed, a larger amount of data is necessary to detect heterotachy [ 25, 28] relative to other evolutionary heterogeneities.
Here, we have found that MP can be affected by heterotachy and that it is much less efficient than probabilistic methods in dealing with all other evolutionary heterogeneities.
All other kinds of evolutionary heterogeneities have been successfully and naturally addressed in a probabilistic framework [ 47], whereas various attempts to decrease the sensitivity of MP to these problems are far from being efficient and widely accepted.
Existing rooting methods are hampered by evolutionary rate heterogeneity or the unavailability of auxiliary phylogenetic information.
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