DOI: 10.5061/dryad.sj3tx96bd
title: Code and sequence data pertaining to: A phylogenomic perspective on interspecific competition

description: Evolutionary processes may have substantial impacts on community assembly,
 but evidence for phylogenetic relatedness as a determinant of
 interspecific interaction strength remains mixed. In this perspective, we
 consider a possible role for discordance between gene trees and species
 trees in the interpretation of phylogenetic signal in studies of community
 ecology. Modern genomic data show that the evolutionary histories of many
 taxa are better described by a patchwork of histories that vary along the
 genome rather than a single species tree. If a subset of genomic loci
 harbor trait-related genetic variation, then the phylogeny at these loci
 may be more informative of interspecific trait differences than the genome
 background. We develop a simple method to detect loci harboring
 phylogenetic signal and demonstrate its application through a proof of
 principle analysis of Penicillium genomes and pairwise interaction
 strength. Our results show that phylogenetic signal that may be masked
 genome-wide could be detectable using phylogenomic techniques and may
 provide a window into the genetic basis for interspecific interactions.
description: Fungal sequences and interaction strengths were obtained from
 fungal isolates as described in Louw et al.
description: # Code and sequence data pertaining to: A phylogenomic perspective on
 interspecific competition 
 ## Directory Structure The top-level directory is ILSSimsDryad and is
 deposited through Zenodo [here](https://doi.org/10.5281/zenodo.10211291).
 The two data directories are also deposited on Dryad. The folder
 ILSSimsDryad/src contains the source code for our simulations. The folder
 ILSSimsDryad/obsData contains the observed data (sequences, gene trees,
 and competition coefficients) for our study. The folder
 ILSSimsDryad/conceptPlot contains the scripts for recreating our figures.
 See below for more detailed descriptions of each folder. The instructions
 below assume that the user is already inside the top-level directory,
 ILSSimsDryad. ### CODE This software implements analyses in Louw et al
 2023, "A phylogenomic perspective on interspecific competition",
 forthcoming in Ecology Letters. The bioRxiv preprint of the corresponding
 manuscript is available at
 The
 code requires DendroPy to run most of the analyses:
 The source code is available in the src
 folder. You can install it by running "python setup.py install
 --user" from the command line. Once you've installed the source,
 the code in the scripts folder implements the analyses in the figures. The
 visualizations were made using ggplot and code for these is available in
 the conceptPlot folder. To rerun all the analyses, uncomment the lines in
 scripts/run_disc_sims.sh and rerun all the code. ### DATA Gene tree files
 for the eight penicillium species are stored in obsData/Gene_Trees
 Sequence data corresponding to these trees is available in
 obsData/Single_Copy_Orthologue_Sequences. The files in the subfolder
 obsData/Single_Copy_Orthologue_Sequences/Single_Copy_Spec_Labels remove
 the sequence ID and contain only species identifiers, but are otherwise
 the same as the fasta files in obsData/Single_Copy_Orthologue_Sequences/.
 Output from FungiFun v.2 (tests for pathway enrichment) is available in
 the folder obsData/enrichment in CSV format. RCC values (competitive
 index) are available in obsData/RCCdata.txt. The three distinct numbers
 per species pair represent experimental replicates. We averaged the three
 replicates per pair for analyses in our study. Orthologs have ID numbers
 in the file names that correspond to the Orthogroup/Gene numbers in Tables
 1 and S1 in our manuscript. The Gene ID numbers in Table S4 correspond to
 the IDs in the Penicillium chrysogenum reference genome (taxonomy ID
 500485), available at uniprot.org/uniprotkb?query=(taxonomy_id:500485).
 Single_Copy_Spec_Labels ### PLOTS Figure 1 is a conceptual figure, we do
 not provide code to recreate it. To remake Figure 2, run the code in
 conceptPlot/DiscordanceNullPower.R from within conceptPlot To remake
 Figures 3 and 4, run the code in conceptPlot/NullandEmpRDist.R from within
 conceptPlot To remake Figure 5, run the code in conceptPlot/Fig5Updated.R
 from within conceptPlot #### Scripts and python code Command lines
 corresponding to each the underlying analyses for these figures are
 included in scripts/run_disc_sims.sh. To run part of the analysis,
 uncomment the corresponding line and execute the script as
 ./run_disc_sims.sh while inside the scripts directory. The source code for
 our simulations is stored in src/coalAssoc/simAndInfer.py