From d27a81820df914267b8f760ff0568e8996552a59 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 15 Jul 2025 16:24:57 +0200 Subject: [PATCH 1/4] Suggested edits to main.tex --- main.tex | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/main.tex b/main.tex index 9471535..826287a 100644 --- a/main.tex +++ b/main.tex @@ -166,7 +166,7 @@ \subsubsection*{BEAST2 - Bayesian Evolutionary Analysis Sampling Trees2} \subsubsection*{BEAUti2 - Bayesian Evolutionary Analysis Utility} -BEAUti2 is the successor of BEAUti, a graphical user interface tool that makes it easy to generate BEAST2 XML configuration files (these files are necessary to specify and run MCMC analyses). +BEAUti2 is a graphical user interface tool that makes it easy to generate BEAST2 XML configuration files (these files are necessary to specify and run MCMC analyses). It is provided as a part of the BEAST2 package so you do not need to install it separately. Both BEAST2 and BEAUti2 are written in Java, meaning that these programs can not only be integrated at their codebase level, but that they are also cross-platform: the exact same code runs on all platforms. Although the screenshots used in this tutorial have been taken on a Mac OS X computer, both BEAST2 and BEAUti2 will have the same layout and functionality under other operating systems like Windows and Linux. @@ -225,7 +225,7 @@ \subsection{Installing dependencies} \end{figure} This tutorial will also make use of a few other packages; -these are \texttt{sampled-ancestors} and \texttt{morph-models}. +these are \texttt{SA} (implementing sampled ancestor trees) and \texttt{MM} (implementing models of morphological character evolution). The first implements speciation and fossilization models (for evaluating the probability of phylogenies themselves), and the second implements models for the evolution of discrete morphological characters. %These packages have a dedicated tutorial (here \textcolor{red}{[https://taming-the-beast.org/tutorials/Total-Evidence-Tutorial/]}) and will not be discussed further in the present exercise. The SA and MM packages have two dedicated tutorials on the Taming the BEAST website (\href{https://taming-the-beast.org/tutorials/FBD-tutorial/}{Divergence Time Estimation tutorial} and \href{https://taming-the-beast.org/tutorials/Total-Evidence-Tutorial/}{Total Evidence tutorial}) and will not be discussed further in the present exercise. @@ -258,7 +258,7 @@ \section{Practical Part \uppercase\expandafter{\romannumeral 1}: Bayesian phylo The following two sections will walk you through the required steps for setting up a couple of different analyses. The first shall carry out Bayesian inference of divergence times using continuous morphology only; the main player here is the Brownian model implemented in the \texttt{contraband} package. In the second analysis we will set up an integrative model with components for each type of data (described above) -- this will be a full-blown total-evidence dating analysis with all the data we have. -Like in other tutorials, we will use BEAUti2 as a tool for specifying BEAST2 .XML files for running our analyses. +Like in other tutorials, we will use BEAUti2 as a tool for specifying BEAST2 XML files for running our analyses. %\subsection{Phylogenetic inference with Brownian motion} %We start by opening BEAUti2 and loading the continuous morphology data available for our carnivoran species. @@ -289,7 +289,7 @@ \subsubsection{Loading the Carnivoran Continuous data}\label{load-continuous-dat %Clicking ``Ok'' should now populate the table with the fossil ages extracted from the species names. \subsubsection{Setting the fossil ages (Tip Dates)}\label{parse-fosill-age} -Since the data set contains fossil species, we will need to open the "Tip Dates" panel and then select the "Use tip dates" checkbox to specify the fossil ages. This can be done in multiple ways. In our case, we can obtain the date information from the species names. We can tell BEAUti to use these by clicking the \emph{Auto-configure} button. The fossil ages appear following the second underscore "\_" in the species name. To extract these times, select "use everything", then select "after last" from the drop-down box to the right, and input "\_" (without the quotes) in the text box immediately to the right, as shown in the figure below \autoref{fig:example2}. Clicking "OK" should now populate the table with the fossil ages extracted from the species names. +Since the data set contains fossil species, we will need to open the "Tip Dates" panel and then select the "Use tip dates" checkbox to specify the fossil ages. This can be done in multiple ways. In our case, we can obtain the date information from the species names. We can tell BEAUti to use these by clicking the \emph{Auto-configure} button. The fossil ages appear following the second underscore "\_" in the species name. To extract these times, select "use everything", then select "after last" from the drop-down box to the right, and input "\_" (without the quotes) in the text box immediately to the right, as shown in the figure below \autoref{fig:example2}. Clicking "OK" should now populate the table with the fossil ages extracted from the species names. \begin{figure}[!htbp] \centering @@ -298,6 +298,7 @@ \subsubsection{Setting the fossil ages (Tip Dates)}\label{parse-fosill-age} \label{fig:example2} \end{figure} +Next, make sure that the dropdown box indicates that dates are specified as "Before the present". In the populated table, the two columns \textbf{Date} and \textbf{Height} should now have values between 0.0 and 35.55 in million years (\autoref{fig:example3}). \begin{figure}[!htbp] @@ -315,7 +316,7 @@ \subsubsection{Setting the Brownian motion Model} We want to estimate all these parameters (so check all the ``estimate'' boxes), but for simplicity, we will assume that all characters are evolving at the same rate. Therefore, we want to check the ``One Rate Only'' box. -Parameter values at the start of the MCMC chain can be specified in the text boxes next to their corresponding parameters names; these should not matter for analysis convergence, and we will just use arbitrary, round values (Fig. \ref{fig:example4}). +Parameter values at the start of the MCMC chain can be specified in the text boxes next to their corresponding parameter names; these should not matter for analysis convergence, and we will just use arbitrary, round values (\autoref{fig:example4}). @@ -329,9 +330,10 @@ \subsubsection{Setting the Brownian motion Model} \subsubsection{Setting the Clock model}\label{bm-clock-model} -The morphological clock model we will use in this analysis is the well known uncorrelated log-normal clock \cite{drummond06}, under which each branch of the species tree is assumed to have its own relative evolutionary rate, with rates being identically and independently distributed. +The morphological clock model we will use in this analysis is the well known uncorrelated log-normal clock \citep{drummond06}, under which each branch of the species tree is assumed to have its own relative evolutionary rate, with rates being identically and independently distributed. -%\st{We assume the relative branch-specific rates are independently distributed and follow a LogNormal distribution with a fixed mean of 1. Therefore, we specify a relaxed clock model by selecting "Optimised Relaxed Clock" in the drop-down menu, where the mean clock rate represents the global morphological clock rate that will be estimated by default. The detailed description of the model can be found in} % \cite{douglas2021}. +%We assume the relative branch-specific rates are independently distributed and follow a LogNormal distribution with a fixed mean of 1. +Therefore, we specify a relaxed clock model by selecting "Optimised Relaxed Clock" in the drop-down menu, where the mean clock rate represents the global morphological clock rate that will be estimated by default. The detailed description of the model can be found in \cite{douglas2021}. \begin{figure}[!htbp] \centering @@ -382,7 +384,7 @@ \subsection{Analysing the results} \subsubsection{Analysing the log file using Tracer} First, we can open the \texttt{*.log} file in tracer to check if the -MCMC has converged. The ESS value should be above 200 for almost all +MCMC has converged. An example output file is provided in the "precooked\_runs" folder (\texttt{BM.log}). The ESS value should be above 200 for almost all parameters and especially for the posterior estimates (\autoref{fig:bm_res1}). This is clearly not the case here and this analysis should be run for much longer to reach convergence. \begin{figure}[!htbp] \centering @@ -421,7 +423,7 @@ \subsubsection{Analysing the log file using Tracer} \begin{figure}[!htbp] \centering \includegraphics[width=0.700000\textwidth]{figures/results/BM_clock_sigma.png} - \caption{Comparing the inferrred migration rates.} + \caption{Comparing the inferrred morphological clock.} \label{fig:bm_res5} \end{figure} \end{itemize} @@ -569,15 +571,15 @@ \subsubsection{Specifying the MCMC chain length (MCMC)}\label{specify-the-mcmc-c \subsection{Running the Analysis using BEAST2}\label{run-the-analysis-using-beast2} % -Run the \lstinline!*.xml! using BEAST2 or use finished runs from the -\emph{precooked-runs} folder. The analysis should take about 6 to 7 +Run the \texttt{*.xml} using BEAST2 or use finished runs from the +\emph{precooked\_runs} folder. The analysis should take about 6 to 7 minutes. % \subsection{Analysing the results} For this section either use the output files from your own analysis or use finished runs from the -\emph{precooked-runs} folder. +\emph{precooked\_runs} folder. \begin{itemize} \item Examine the posterior estimates for the inferred clock models for continuous data, discrete data and molecular sequences in Tracer (\autoref{fig:bm_res6} and \autoref{fig:bm_res7}) From f1b5e0b399c4088bc6a8bf4872cdb6edb45d15b3 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 15 Jul 2025 16:27:03 +0200 Subject: [PATCH 2/4] Add a little explanation to README.md --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 8a48729..47fcf2a 100644 --- a/README.md +++ b/README.md @@ -8,4 +8,7 @@ beastversion: 2.7.7 # Contraband tutorial +This tutorial shows how to use the **contraband** package in **BEAST2** to model continuous trait evolution along a phylogeny with Brownian motion. +Unlike methods that assume a "known", fixed tree, **contraband** lets you estimate the tempo and mode of trait evolution simultaneously with both species relationships and divergence times. + This tutorial is currently only available as a [PDF]( {{site.baseurl}}/tutorials/contraband-tutorial/main.pdf ). \ No newline at end of file From 32671855c37f4abdc61c102033c30c5924c7abc1 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 15 Jul 2025 16:27:29 +0200 Subject: [PATCH 3/4] Rename folders so they will show up on the website --- {precooked-runs => precooked_runs}/BM.log | 0 {precooked-runs => precooked_runs}/ShrinkageBM.log | 0 {precooked-runs => precooked_runs}/carnivora_27_mcc.tree | 0 {precooked-runs => precooked_runs}/carnivora_27_tree.trees | 0 .../carnivora_continuous_27_bm_mcc.tree | 0 .../carnivora_continuous_27_tree_bm.trees | 0 {xmls => xml}/BM.xml | 0 {xmls => xml}/ShrinkageBM.xml | 0 8 files changed, 0 insertions(+), 0 deletions(-) rename {precooked-runs => precooked_runs}/BM.log (100%) rename {precooked-runs => precooked_runs}/ShrinkageBM.log (100%) rename {precooked-runs => precooked_runs}/carnivora_27_mcc.tree (100%) rename {precooked-runs => precooked_runs}/carnivora_27_tree.trees (100%) rename {precooked-runs => precooked_runs}/carnivora_continuous_27_bm_mcc.tree (100%) rename {precooked-runs => precooked_runs}/carnivora_continuous_27_tree_bm.trees (100%) rename {xmls => xml}/BM.xml (100%) rename {xmls => xml}/ShrinkageBM.xml (100%) diff --git a/precooked-runs/BM.log b/precooked_runs/BM.log similarity index 100% rename from precooked-runs/BM.log rename to precooked_runs/BM.log diff --git a/precooked-runs/ShrinkageBM.log b/precooked_runs/ShrinkageBM.log similarity index 100% rename from precooked-runs/ShrinkageBM.log rename to precooked_runs/ShrinkageBM.log diff --git a/precooked-runs/carnivora_27_mcc.tree b/precooked_runs/carnivora_27_mcc.tree similarity index 100% rename from precooked-runs/carnivora_27_mcc.tree rename to precooked_runs/carnivora_27_mcc.tree diff --git a/precooked-runs/carnivora_27_tree.trees b/precooked_runs/carnivora_27_tree.trees similarity index 100% rename from precooked-runs/carnivora_27_tree.trees rename to precooked_runs/carnivora_27_tree.trees diff --git a/precooked-runs/carnivora_continuous_27_bm_mcc.tree b/precooked_runs/carnivora_continuous_27_bm_mcc.tree similarity index 100% rename from precooked-runs/carnivora_continuous_27_bm_mcc.tree rename to precooked_runs/carnivora_continuous_27_bm_mcc.tree diff --git a/precooked-runs/carnivora_continuous_27_tree_bm.trees b/precooked_runs/carnivora_continuous_27_tree_bm.trees similarity index 100% rename from precooked-runs/carnivora_continuous_27_tree_bm.trees rename to precooked_runs/carnivora_continuous_27_tree_bm.trees diff --git a/xmls/BM.xml b/xml/BM.xml similarity index 100% rename from xmls/BM.xml rename to xml/BM.xml diff --git a/xmls/ShrinkageBM.xml b/xml/ShrinkageBM.xml similarity index 100% rename from xmls/ShrinkageBM.xml rename to xml/ShrinkageBM.xml From 3ad589cb358988af4102e222754a8155a229cc71 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 15 Jul 2025 16:31:56 +0200 Subject: [PATCH 4/4] Add license --- LICENSE | 396 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 396 insertions(+) create mode 100644 LICENSE diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..53883b1 --- /dev/null +++ b/LICENSE @@ -0,0 +1,396 @@ +Attribution 4.0 International + +======================================================================= + +Creative Commons Corporation ("Creative Commons") is not a law firm and +does not provide legal services or legal advice. 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