PCA of good patient in suppl
authorFabio Zanini <fabio.zanini@tuebingen.mpg.de>
Mon, 4 Feb 2013 11:05:06 +0000 (12:05 +0100)
committerFabio Zanini <fabio.zanini@tuebingen.mpg.de>
Mon, 4 Feb 2013 11:05:06 +0000 (12:05 +0100)
figures/Shankarappa_PCA_p1.pdf [new file with mode: 0644]
figures/Shankarappa_PCA_p1.svg [new file with mode: 0644]
figures/Shankarappa_PCA_p7.pdf
figures/Shankarappa_PCA_p7.svg
figures/Shankarappa_allele_freqs_trajectories_nonsyn_p7.pdf
figures/Shankarappa_allele_freqs_trajectories_nonsyn_p7.svg
supplementary.tex
synmut.tex

diff --git a/figures/Shankarappa_PCA_p1.pdf b/figures/Shankarappa_PCA_p1.pdf
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diff --git a/figures/Shankarappa_PCA_p1.svg b/figures/Shankarappa_PCA_p1.svg
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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \begin{figure}[h]
 \begin{center}
-\includegraphics[width=0.48\linewidth]{Shankarappa_PCA_p7}
-\includegraphics[width=0.48\linewidth]{Shankarappa_allele_freqs_trajectories_nonsyn_p7}
-\caption{Left: PCA of all sequences from patient p7 (colors indicate time from seroconversion,
-from blue to red). Right: Allele frequency trajectories for nonsynonymous
-changes in the same patient.}
-\label{fig:aftp7}
+\includegraphics[width=0.4\linewidth]{Shankarappa_PCA_p1}
+\includegraphics[width=0.4\linewidth]{Shankarappa_allele_freqs_trajectories_nonsyn_p1}
+\includegraphics[width=0.4\linewidth]{Shankarappa_PCA_p7}
+\includegraphics[width=0.4\linewidth]{Shankarappa_allele_freqs_trajectories_nonsyn_p7}
+\caption{Panel A) PCA of all sequences from patient p1 (colors indicate time from seroconversion,
+from blue to red). Panel B) Allele frequency trajectories for nonsynonymous
+changes in the same patient. Panels C and D) the same plots from patient p7, whose
+sequences show signs of compartimentalization.}
+\label{fig:aftp}
 \end{center}
 \end{figure}
 Not all of the patients studied in refs.~\citealp{shankarappa_consistent_1999} and
@@ -52,7 +55,7 @@ and ACH19768 from ref.~\citealp{bunnik_autologous_2008} showed clear signs of
 compartimentalization (population structure) during infection, which would have
 been an irreparable confounder for our analysis. The difference is clear if
 PCA is performed on all sequences from a ``compartimentalized'' patient, p7.
-This is shown in \figurename~\ref{fig:aftp7}: late sequences subdivide in two
+This is shown in \figurename~\ref{fig:aftp}: late sequences subdivide in two
 well-defined clusters -- this characteristic is absent from all the patient
 sequences used in our main analysis. On the right, allele frequency trajectories from the same
 patient are plotted: evidently, no derived allele is fixed after 1000 days
@@ -62,8 +65,6 @@ but this is an effect of population structure rather than any
 of the processes discussed in the main text (time-dependent selection, competition
 of mutants within the same epitope).
 
-\clearpage
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Nonsynonymous changes outside of variable regions are deleterious}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
index 7f5adb2..002385e 100644 (file)
@@ -394,8 +394,11 @@ deleterious mutations to reach the frequency threshold of 0.25.
 To map the parameter range of the model that is compatible with the data, we
 repeatedly simulated the evolution with random choices for the deleterious
 effect of synonymous mutations, the fraction of synonymous mutations that are
-deleterious, the fitness effect of adaptive mutations (escape rate) and the frequency of
-escapes. Among all simulations, we select the ones that show $A_\text{syn}$ and
+deleterious, the escape rate and the frequency of new escapes. Note that the
+escape rate is sum of two factors: (a) the beneficial effect due to the ability to
+evade the immune system minus (b) the fitness side costs in terms of structure,
+stability, etc.
+Among all simulations, we select the ones that show $A_\text{syn}$ and
 $P_\text{interm}$ as observed in the data, i.e., a large depression in fixation
 probability of synonymous mutations but, simulteneously, a moderately high
 synonymous diversity. Specifically, \FIG{simsfig} shows parameter combinations