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README.md

BarnesClark2017-Salamanders

Title of Manuscript: 65 Million Years of Change in Temperature and Topography Explain Evolutionary History in Eastern North American Plethodontid Salamanders

Authors:

DOI Number of Manuscript: 10.1086/691796

Code Repositories

This repository contains source code for the salamander speciation model described in the aforementioned manuscript.

Abstract

For many taxa and systems, species richness peaks at mid-elevations. One potential explanation for this pattern is that large-scale changes in climate and geography have, over evolutionary time, selected for traits that are favored under conditions found in contemporary mid-elevation regions. To test this hypothesis, we used records of historical temperature and topographic changes over the past 65 Myr to construct a general simulation model of Plethodontid salamander evolution in eastern North America. We then explore possible mechanisms constraining species to mid-elevation bands by using the model to predict Plethodontid evolutionary history and contemporary geographic distributions. Our results show that models which incorporate both temperature and topographic changes are better able to predict these patterns, suggesting that both processes may have played an important role in driving Plethodontid evolution in the region. Additionally, our model (whose annotated source code is included as a supplement) represents a proof of concept to encourage future work that takes advantage of recent advances in computing power to combine models of ecology, evolution, and earth history to better explain the abundance and distribution of species over time.

Compilation

The program can be produced simply by running make in the root directory. OpenMP is required for compilation.

Running make will produce an executable called salamander.exe.

Entering the src directory and running make test will generate test.exe, which can be used to verify some parts of the code.

Running the Program

salamander.exe can be run without arguments. In this mode it prints out the format of its configuration file. An example configuration file is included at params/z_example_param.param.

Running with a configuration file, as in

./salamander.exe params/z_example_param.param

generates several output files in the output directory.

Output Files

The output files are in CSV format and contain self-documenting headers. The .tre files contain the salamanders' phylogenies in Newick format.

Data Files

The data directory contains the temperature time series referred to in the manuscript. The file is ordered such that the most recent data points at at the top. The intervals between lines are 1,000 years and the data series begins 65 Mya.