The histone tree is instead calibrated using a mean divergence date between annual and perennial Glycine subgenera of 5.25 mya, an average estimated from the divergence dates of several low copy nuclear genes from G. max and G. tomentella D3 (Egan and Doyle 2010; Innes et al. 2008).
Mean divergence date estimates for the split between the chimpanzee and human head/body lice (Pediculus schaeffi and Pediculus humanus, respectively) averaged 6.39 MYA.
However, the length of short branches was similar in a Bayesian and ML framework; therefore, an increase in the estimated average substitution rate results in younger divergence dates for shallow nodes [ 28].
Trees with unequal-length branches more closely approximate empirical datasets; thus, we simulated datasets on the 27-taxon plethodontid salamander phylogeny of Mueller et al. [35] using parameters for five mitochondrial genes with branch lengths set using the average rate for each gene and estimated divergence dates [21].
As for GARLI-PART and RAxML analyses, the last run was repeated after removal of Serranus atricauda from the dataset ('-ADEF -Serranus atricauda' in Fig. 2 and Tables S1 S2), which had no impact on tree topology and little influence on node support (on average -0.19 BPP, Table S1) and divergence date estimates (average difference 0.57%, Table S2).
A weighted average of branch lengths estimated for each partition was used to re-estimate divergence dates via penalized likelihood [ 17] in r8s [ 63], with the identical fossil calibrations used by Mueller [ 37].
We took divergence dates from a recent review of the fossil evidence [25], taking the average of the maximum and minimum dates.
In the largest barcoding study conducted so far on marine fishes to date [7], the average observed distance between conspecifics was 0.4% while the average divergence reached 9.9% between congeneric species.
The supertree (relDate) divergence dates underestimate the multidivtime dates from all genes and mtDNA genes by 88% and 51% on average, respectively.
The dating of these species coincides very well with the chimpanzee modern human divergence dates predicted by molecular genetic work.
