Of these novel STs, ST161 and ST162, were single-locus variants (SLV; differing from the ancestor ST in one allele) of ST64 and ST72, respectively.
Results that differ in their ancestor prediction may also indicate a recombinant origin.
We did this for all eight fitness components and then counted how many simulated MA lines differed from the ancestor for 0 8 traits.
We observed that fitness on PP statistically differed from the ancestor in a majority of these comparisons (19 of 31 tests), and most of these outcomes showed fitness significantly lower than the ancestor (18 of 19 tests).
That the rate of virion assembly does not differ between the ancestor and the mutants at either temperature suggests that capsid assembly is not the rate-limiting step once virion assembly begins.
By the end of the study, each of the 16 clones at the tips of the tree differed from the ancestor (clone A1) by 4 to 13 substitutions (mean = 8.2 ± 2.7 s.d)., excluding reversions.
However, the ancestral state of this pair in their last common ancestor was G-C, and thus, A. viridis evolved via CBC (G-C → A-U), whereas its sister species differs from the ancestor by one hCBC (G-C → G-U).
Given our estimate of the mutation rate, the probability of a mutation occurring at any of these sites in any line during the experiment is ∼0.007, indicating that failure to detect a site that differed in the ancestor is almost certainly a false negative.
For example, Wertheim et al. (2012) analysed major subtypes of pandemic HIV-1 group M, which are thought to exemplify closely related lineages with different substitution rates, and found that the times to the most recent common ancestor differed markedly when subtypes were analysed separately compared to jointly.
Indeed, selected breeds do not only differ from their ancestors in only one target trait, but differences affect many correlated traits, all contributing to increase fitness under selection conditions, creating 'domestication syndromes' (Harlan 1971).
