From ebfa62afaf76b343a50e4472220b9d87c769e95c Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Thu, 20 Oct 2016 10:27:57 -0700
Subject: [PATCH] add conclusion slides

---
 simons_genome_diversity_oct_2016.Rnw | 49 ++++++++++++++++++++++------
 1 file changed, 39 insertions(+), 10 deletions(-)

diff --git a/simons_genome_diversity_oct_2016.Rnw b/simons_genome_diversity_oct_2016.Rnw
index 9eb22eb..33fb663 100644
--- a/simons_genome_diversity_oct_2016.Rnw
+++ b/simons_genome_diversity_oct_2016.Rnw
@@ -183,7 +183,7 @@ library("xtable")
 
 \begin{frame}{PCA and Relatedness}
   \begin{center}
-    \includegraphics[width=\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/fig_ed4.png}
+    \includegraphics[width=\textwidth,height=0.6\textheight,keepaspectratio]{genome_diversity_paper/fig_ed4.png}
   \end{center}
   \begin{itemize}
   \item Greatest variation seen in the African populations (orange)
@@ -237,34 +237,63 @@ g
   \end{itemize}
 \end{frame}
 
-\begin{frame}{Cross-coalescence rate}
+\begin{frame}{Selected African cross-coalescence rate/Population Size}
   \begin{center}
-    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2a.png}
-    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2b.png}
+    \includegraphics[width=0.5\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/fig2a.png}
+    \includegraphics[width=0.5\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/fig2d.png}
   \end{center}
+  \begin{itemize}
+  \item Separation began around 200 kya for present-day hunter-gatherers
+  \item Shared ancestors as recently as 100 kya
+  \end{itemize}
 \end{frame}
 
-\begin{frame}{Cross-coalescence rate}
+\begin{frame}{Central African rainforest hunter-gatherer}
   \begin{center}
-    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2c.png}
-    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2d.png}
+    \includegraphics[width=0.5\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/fig2b.png}
+    \includegraphics[width=0.5\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/fig2e.png}
   \end{center}
+  \begin{itemize}
+  \item Within africa separation begins around 100 kya
+  \item Still intermixing between Biaka (CAR, DRC), Bantu, and Luhya (Western Kenya)
+  \end{itemize}
 \end{frame}
 
-\begin{frame}{Effective Population Size}
+\begin{frame}{Ancient, non-african}
   \begin{center}
-    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2e.png}
-    \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig2f.png}
+    \includegraphics[width=0.5\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/fig2c.png}
+    \includegraphics[width=0.5\textwidth,height=0.7\textheight,keepaspectratio]{genome_diversity_paper/fig2f.png}
   \end{center}
+  \begin{itemize}
+  \item Separation begins around 50 kya
+  \end{itemize}
 \end{frame}
 
 \begin{frame}{Best-fitting admixture Graph}
   \begin{center}
     \includegraphics[width=0.5\textwidth,height=0.8\textheight,keepaspectratio]{genome_diversity_paper/fig3.png}
   \end{center}
+  \begin{itemize}
+  \item Present day populations have negligible ancestry from an early
+    dispersal of modern humans out of africa
+  \end{itemize}
 \end{frame}
 
 
+\begin{frame}{Conclusions}
+  \begin{itemize}
+  \item Dispersal of human populations -- little evidence of ancestry
+    from an early dispersal of modern humans
+  \item Possible acceleration in the rate of mutations among non-Africans
+  \item No evidence for species-wide selective sweeps around
+    $\approx 50$ kya (start of modern human behavior in archaeological
+    record) [Did not see that all pairs of modern humans shared a
+    common ancestor $\lt 100$ kya.
+  \item Great resource for additional variants; maybe with H3A?
+  \item Useful for my work with ancestral trees
+  \end{itemize}
+\end{frame}
+
 \section*{References}
 
 \begin{frame}[plain]{References}
-- 
2.39.2