Permalink
Browse files

Fix #31

  • Loading branch information...
evogytis committed Oct 31, 2017
1 parent e307848 commit a5bbf12462bd95fc25c0b593d23be547e938a154
Showing with 3 additions and 1 deletion.
  1. +3 −1 mers-structure.tex
View
@@ -589,7 +589,9 @@ \subsection*{Demographic inference of MERS-CoV in the reservoir}
The oldest sequence from each cluster introduced into humans was kept for further analysis.
This procedure removes lineages coalescing rapidly in humans, which would otherwise introduce a strong signal of low effective population size.
These subsampled MERS-CoV sequences from humans were combined with existing sequence data from camels to give us a dataset with minimal demographic signal coming from epidemiological processes in humans.
Sequences belonging to the outgroup clade where most of MERS-CoV sequences from Egypt fall were removed out of concern that MERS epidemics in the Arabian Peninsula and Egypt are distinct epidemics with relatively poor sampling in the latter.
Sequences belonging to the outgroup clade where most of MERS-CoV sequences from Egypt fall were removed out of concern that MERS epidemics in Saudi Arabia and Egypt are distinct epidemics with relatively poor sampling in the latter.
Were more sequences of MERS-CoV available from other parts of Africa we speculate they would fall outside of the diversity that has been sampled in Saudi Arabia and cluster with early MERS-CoV sequences from Jordan and sequences from Egyptian camels.
However, currently there are no indications of what MERS-CoV diversity looks like in camels east of Saudi Arabia.
A flexible skygrid tree prior \citep{gill_2013} was used to recover estimates of relative genetic diversity ($N_{e}\tau$) at 50 evenly spaced grid points across six years, ending at the most recent tip in the tree (2015 August) in BEAST v1.8.4 \citep{drummond_bayesian_2012}, under a relaxed molecular clock with rates drawn from a lognormal distribution \citep{drummond_2006} and codon position partitioned (positions $1+2$ and $3$) HKY$+\Gamma_{4}$ \citep{hky_1985,yang_1994} nucleotide substitution models.
At time of writing advanced flexible coalescent tree priors from the skyline family, such as skygrid \citep{gill_2013} are available in BEAST v1 \citep{drummond_bayesian_2012} but not in BEAST v2 \citep{bouckaert_beast_2014}.
We set up five independent MCMC chains to run for 500 million states, sampling every $50\,000$ states.

0 comments on commit a5bbf12

Please sign in to comment.