DOI: 10.5061/dryad.0k6djhb6h
title: Simulated data for: Patch biogeography under intermittent barriers: Macroevolutionary consequences of microevolutionary processes

description: The processes that generate biodiversity start on a microevolutionary
 scale, where each individual’s history can impact the species’ history.
 This manuscript presents a theoretical study that examines the
 macroevolutionary patterns that emerge from the microevolutionary dynamics
 of populations inhabiting two patches. The model is neutral, meaning that
 neither survival nor reproduction depends on a fixed genotype, yet
 individuals must have minimal genetic similarity to reproduce. We used
 historical sea level oscillation over the past 800 thousand years to
 hypothesize periods when individuals could migrate from one patch to
 another. In our study, we keep track of each speciation and extinction
 event, build the complete and extant phylogenies, and characterize the
 macroevolutionary patterns regarding phylogeny balance, acceleration of
 speciation, and crown age. We also evaluate ecological patterns: richness,
 beta diversity, and species distribution symmetry. The balance of the
 complete phylogeny can be a sign of the speciation mode, contrasting
 speciation induced by migration and isolation (vicariance). The
 acceleration of the speciation process is also affected by the
 geographical barriers and the duration of the isolation period, with high
 isolation times leading to accelerated speciation. We report the
 correlation between ecological and macroevolutionary patterns and show
 that it decreases with the time spent in isolation. We discuss, in light
 of our results, the challenge of integrating present-time community
 ecology with macroevolutionary patterns.
description: # Simulated data for: Patch biogeography under intermittent barriers:
 Macroevolutionary consequences of microevolutionary processes Dataset DOI:
 [10.5061/dryad.0k6djhb6h](https://doi.org/10.5061/dryad.0k6djhb6h) ##
 Description of the data and file structure This repository contains a
 single main folder "ArticleData.tar.gz" containing 3
 sub-folders: (i) Phylogenies - contains one script to generate the data
 and another to build the phylogenies as seen in Figure 2 of the main
 text.  (ii) Results - contains the statistical data of phylogenies used in
 the manuscript and the script to generate Figures 3 to 6.  (iii)
 Statistics - contains a script to generate proper statistical data from a
 set of phylogenies. Obs: All R scripts contain the packages required to
 function correctly. #### File: ArticleData.tar.gz #### PHYLOGENIES Folder
 contains (1) One ".cpp" file: C++ source code
 "phylo_patches.cpp" Requires the GSL scientific library: Ubuntu
 system installation through tthe erminal: (C++) ~ sudo apt-get install
 build-essential (GSL) ~ sudo apt-get install gsl-bin (GSL) ~ sudo apt-get
 install libgsl-dev Ubuntu systems compilation through the terminal: \~ c++
 -o3 phylo_patches.cpp -o [executable_name] -lm -lgsl -lgslcblas After
 compilation, we will get an executable.Execution asks for terminal input
 of parameters in the following sequence: N - number of trees to be
 generated M - mean migration rate T - isolation time For example,
 ./[executable_name] 2 0.08 80 Produces the following "data.txt":
 Pop200_Isol80_Mig0.08_MS1_.txt Pop200_Isol80_Mig0.08_Temporal1_.txt
 Pop200_Isol80_Mig0.08_MS2_.txt Pop200_Isol80_Mig0.08_Temporal2_.txt (2)
 One "R" file: R script "Trees.R". Execution needs 3
 parameters input on the script's subsection "Provide data
 parameters": i) the numbered tree; ii) isolation time; iii) migration
 rate. For example: Provide data parameters tree_number=1 isolation_time=80
 migration=0.002 will generate the complete and extant phylogenies, as in
 the panels of Figure 2 of the main text. #### RESULTS Folder contains (1)
 9 files in ".RData" format: They account for the mean,
 confidence interval (inf & sup), and correlation values of the
 following metrics: 1 Number of speciation events 2 Richness 3
 Beta-diversity 4 Asymmetry 5 Balance 6 Alpha-value 7 Phylogeny age
 "Over_time" files contain the time evolution of Balance and
 Alpha for a given isolation time; "Comp_mean" filescontain aa
 dataframe of the mean values of complete phylogenies, numbered in the
 above order. For example, Comp_mean[[2]] returns the resultant
 "Richness" for each pair of isolation time and migration rate.
 (2) Four "data.txt" files for reference of barriers for
 isolation times 80 & 20%. (3) One R script "Figures.R".
 Together with the aforementioned ".RData", it generates the
 following Figures of the main text: FIGURE DATA 3 Comp_(mean,inf and
 sup).RData 4 Ext_(mean,inf and sup).RData 5 Over_time80 &
 Over_time20.RData 6 Correlation_values.RData #### STATISTICS Contains the
 R script "Data_treatment.R". In the file, one will be asked to:
 (1) Set the directory to "the data.txt" location. (2) Provide
 the total number of trees and a list of isolation_time and
 mean_migration_rate parameters. For example: setwd(~/Data/Phylogenies)
 num_trees = 10 level &lt;- c(80,40,20,0) mig &lt;-
 c(0,0.002,0.005,0.01,0.015,0.02,0.025,0.03,0.035,0.04) Its execution shall
 generate the aforementioned 9 statistical data in ".RData"
 format. #### Code/software All scripts are in C++ or R, containing their
 respective libraries. #### Access information Other publicly accessible
 locations of the data: * This is the only public repository of the data
 Data was derived from the following sources: * All data was generated from
 our own simulations.