Simulated data for: Patch biogeography under intermittent barriers: Macroevolutionary consequences of microevolutionary processes
Data files
Feb 18, 2026 version files 140.13 KB
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ArticleData.tar.gz
136.34 KB
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README.md
3.79 KB
Abstract
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.
Dataset DOI: 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 <- c(80,40,20,0) mig
<- 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.