We tested this hypothesis using simulations of molecular evolution under standard models of molecular evolution (see Materials and Methods), but we found that at the range of indel to substitution ratios consistent with the yeast polymorphism data (0.05 0.1), estimates of substitution rate are still accurate to long evolutionary distances (supplementary fig. S3, Supplementary Material online).
Actually, evidences of both neutral and non-neutral evolution have been found in different Mytilus taxa and populations, results that were considered in line with a nearly neutral model of molecular evolution (see discussion).
An interesting result reported here is that rates of molecular evolution are found to be non-autocorrelated across the Neornithes tree (Tables 1 and 2), a result previously noted for virus and marsupial data sets [ 47].
After we calibrated demographic histories for populations of M. herderiana and G. fasciatus by applying available rates of molecular evolution, we found that the start of expansion of populations of these species coincide, and could be estimated to 25-50 Kyr BP.
Finally, a recent molecular evolution study of Cas gene evolution found patterns of relatively fast evolutionary change, consistent with a co-evolutionary arms-race between CRISPRs and phage [ 71].
We were interested if the patterns of molecular evolution that are found in Hox clusters can also be identified in other gene clusters and if it is also possible to identify conserved non-coding regions in them.
To date, molecular evolution studies have found that four of the seven known MCPH genes ASPM, CDK5RAP2, CENPJ and MCPH1 evolved rapidly in primates due to Darwinian positive selection, which is associated with the enlargement of the brain during primate evolution and human origin [ 23, 24].
In particular, rates of adaptive molecular evolution have been found to range from low values in yeast (Elyashiv et al. 2010) or humans (Bustamante et al. 2005; Boyko et al. 2008) to high values in flies (Welch 2006; Elyashiv et al. 2010), bacteria (Charlesworth and Eyre-Walker 2006), or mice (Halligan et al. 2013).
For example, a correlation between rates of molecular evolution and fecundity was found in mammals [ 9], even after accounting for variation in other LH-traits.
The typically cold-water Lithodidae king crab comprises weakly divergent species, suggesting either that the family represents an extreme situation of rapid morphological diversification, and/or slow molecular evolution, reflecting a slow metabolism found in organisms that inhabit cold environments [69], [70], or possessing larger body sizes [71], [72] or both [73] [75].
