Positive selection (lack of) in Zika (Asia/Pacific/Americas)


Continuing the discussion from 2 new SE Asian genomes + updated tree: In the 18 genomes in the Asia clade from Malaysia/1966 forwards, Slr shows no signal for positive selection. Output as zip here: https://dl.dropboxusercontent.com/u/6742199/No%20selection%20signal%20so%20far.zip

Picture is of just the variable sites. Micronesia/2007 has a frameshift that still doesn’t provoke any false positive signal, neither do any substitutions that may have accumulated in passage (eg Malaysia/1966).


Lots of sites with non-synonymous substitutions, but synonymous rate is so high that site-wise omegas are never significant at p<0.05


overall omega across polyprotein is 0.048, kappa is 11.0.