Therefore, background selection is unlikely to be the major factor affecting the disparate ratios of variant to invariant repeats across chromosomes: mutation rate variation, divergent levels of different repeat types across chromosomes and locus-specific effects, such as selection, are more likely.
To take into account the role of this mutation rate variation in nucleotide polymorphism levels, we divided our diversity estimates by divergence with D. simulans.
Because of the above-mentioned limitations, it is impractical to study the mutation rate variation at the genome level using such a direct approach.
Thus, our study puts forward a novel determinant of evolutionary rates for yeast proteins - the complex forming ability of proteins emerged as a significant contributor of evolutionary rate variation followed by expression level and protein connectivity.
Moreover, Hodgkinson et al. (2009) recently found that independently derived single-nucleotide polymorphisms at orthologous sites of human and chimpanzee coincide more often than expected by chance, scaling down conservation of mutation rate variation to the nucleotide level.
Levels of rate variation observed for datasets simulated with realistic parameters were even greater than those for simple 8-taxon simulations, suggesting that the level of error in simple simulations provides a minimum for potential error in empirical datasets.
However, correlated rates may be preferable to a strict clock at intermediate levels of rate variation.
Estimates of natural levels of rate variation ranged from 0.05-3.38 for different partitions.
Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation.
Why it might have greater influence at higher levels of rate variation will be explored in future work.
Hence, a secondary aim of this work was to consider its performance across different levels of rate variation.
