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In both Figures 2 and 3 it can clearly be seen that the context-dependent substitution patterns for the third codon position increase model fit substantially, even without accommodating additional evolutionary effects such as nucleotide frequency bias or assuming among-site rate variation for each codon position (see Tables S1, S2 and S3 in Additional file 1 for numerical results).
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This mechanism provides a potential basis for the evolutionary compensatory effects such as the binding site turnover [ 30- 32].
Therefore, if we want to address the effects of residue interaction on the evolutionary rate, and discern them from other structural effects such as solvent exposure, the noncontact set used as reference should be restricted to avoid buried residues.
One approach to eco-evolutionary effects is to examine how genetic variation among individual plants influences their ecological effects, such as on attendant arthropod or plant communities.
Hypotheses explaining the relative success of invasive species span the entire spectrum of population and community ecology including evolutionary arguments such as local adaptation, i.e. evolution of increased competitive ability, EICA [31], [32] to more stochastically driven processes such as disturbance [33], [34] or pure sampling effects such as propagule pressure [35].
Instead, Gould (1998) asserted that evolution operates in a matrix of random effects, such as chaos and contingency, and its products are simply a result of sorting among locally available genotypes following the evolutionary path of least resistance (Stebbins 1970).
Evolutionary theory predicts that mutations of large phenotypic effect, such as resistance mutations, are likely to be costly to their bearers in environments where they were not selected [ 31, 32].
If they are, a lineage effect, such as generation time, may lead to the best possible answer for the evolutionary stasis of cycad plastomes.
Evolutionary biologists have suggested that religion is either a result of the sophisticated human brain or was selected for due to a beneficial effect, such as promoting cooperation among people.
A relative measure of the evolutionary rates of the orthologous genes between annuals and perennials enabled us to effectively disentangle the genome-wide effect of plant life history trait on the evolutionary rate from locus-specific effects of evolutionary forces such as protein dispensability or selective constraints.
Here, we were mainly interested by the potential effects of evolutionary mechanisms such as balancing selection and gene conversion on the patterns of HLA molecular variability, compared to the influence of demographic factors such as gene flow and genetic drift.
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