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The oldest confirmed samples of DNA, a more direct bearer of information of molecular evolution, but more degradable, have come from Neanderthals that lived 30,000 to 50,000 years ago.
The focus was on molecular evolution, but a number of speakers on the topics of experimental and cultural evolution reminded us of the broad scope of the subject.
There have been many claims of adaptive molecular evolution, but what role does positive selection play in functional divergence?
Studies of a number of parasitic plant lineages have suggested faster rates of molecular evolution, but the results of some studies have been mixed.
It may be that domestication can influence mitochondrial molecular evolution, but that it does not do so consistently and uniformly across all domesticated lineages in comparison to their wild relatives.
More sophisticated modelling approaches may more accurately characterize the heterogeneous processes of molecular evolution, but it is also crucial that the parameters of these complex models can be estimated by the data at hand [ 143].
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An immediate consequence of this differing parameterization is that two nucleotide misincorporations per codon per "instantaneous mutation step" necessarily have zero probability under the classical molecular evolution model but non-negligible probability under the unigenic evolution model.
In this approach, noncoding sequences are not compared on a nucleotide-by-nucleotide basis following standard molecular evolution methods, but instead, the density of TFBSs in a specific genomic region are compared across taxa.
We emphasize that we do not use the term neutrality in its meaning of unchanged fitness in the field of molecular evolution [ 15], but merely for brevity, in the sense of preserving viability on a specific set of sulfur sources.
These differences should affect differences in patterns and rates of molecular evolution between species, but the expected differences are not readily apparent [ 17], perhaps because A. thaliana only recently shifted to a selfing mating system [ 25].
Hypotheses for extrinsic causes suggest that aspects of a clade's ecology (its habitat or traits adapted to habitat) affect rates of both molecular evolution and diversification, but these rates do not directly affect each other (Hypothesis 1, Table 1).
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