DOI: 10.5061/dryad.dv41ns25x
title: Data from: Rapid radiations outweigh reticulations during the evolution of a 750-million-year-old lineage of cyanobacteria

description: This is the genomic and phylogenetic data used and generated in our study
 on Nostoc evolution and species boundaries. It contains
 the sequence data, alignments, and tree files from our phylogenomic
 analyses and the raw outputs from the analyses of phylogenetic conflict.
description: # Data from: Rapid radiations outweigh reticulations during the evolution
 of a 750-million-year-old lineage of cyanobacteria This repository
 contains the genomic and phylogenetic data that we used in our study on
 *Nostoc* evolution and species boundaries. Both archives contain
 directories in the structure that I used during the computational analyses
 as documented in the code for this project (available from
 [GitHub](https://github.com/cjpardodelahoz/nostoc)). Below is a detailed
 description of the contents of the two files. ## Genomes The
 `cyano_genomes.zip` archive contains three directories with two different
 versions of the genomes we used in the study: * `set103/` contains the
 fasta files for the 151 genomes that we used for phylogenetic analyses. In
 this version of the files the genomes are not sorted by putative
 chromosome or putative plasmid. Rather, all the genomic content is a
 single fasta. The `label_key.csv` contains a key linking the file names
 with the taxa that they correspond to. Note that all of these genomes are
 also available from NCBI. The accessions are listed in Data S1A of the
 manuscript. * `set12c/` and `set12p/` both contain fasta files for the
 same 151 genomes, but in this version the contigs are sorted into putative
 chromosome (`set12c/`) and putative plasmids (`set12p/`). We used the
 chromosome files for the FastANI, PopCOGenT, and GTDB analyses. ##
 Phylogenetic data The `phylogenetics.zip` archive contains two directories
 with the essential data to reproduce our phylogenomic analyses.
 `phylogenetics/set200/` has files and output for the divergence time
 estimation at the Nostocales level and `phylogenetics/set103/` has the
 files and output for phylogenetic analyses of *Nostoc*, based on the
 `cyano_genomes/set103` genome files. ***NOTE:*** the wASTRAL and *rbcLX*
 trees and alignments are also available in the [T-BAS
 platform](https://guide-tbas.cifr.ncsu.edu/tbas) where you can also [do
 phylogenetic placement of
 new](https://github.com/cjpardodelahoz/nostoc/blob/main/tbas_tutorial/README.md) *[Nostoc](https://github.com/cjpardodelahoz/nostoc/blob/main/tbas_tutorial/README.md)* [sequences](https://github.com/cjpardodelahoz/nostoc/blob/main/tbas_tutorial/README.md). ### Data and output from divergence time estimation on Nostocales – `phylogenetics/set200/` * `set200.treefile`: topology used for divergence time estimation of nostocales * `seqs/` * `*faa`: amino acid sequence files for each of the 1648 loci from the nostocales_odb_10 database of orthologs used by BUSCO. These are the loci we used in [our previous paper on phylogenomics of nostocalean cyanobacteria](https://lutzonilab.org/wp-content/uploads/Ancient_Rapid_Radiation_Nostocales.pdf) * `alignments/` * `single/` * `*aln.faa`: aligned amino acid sequences for the 1648 loci. * `*ng.faa`: aligned amino acid sequences for the 1648 loci after trimmming sites with gaps. * `concat/` * `concat_ng_1_part.phy`: concatenated alignment of the 1648 loci with no gaps and in phylip format for divergence time estimation. * `mcmctree_templates/`: This directory contains template files to setup the control and model files needed to run MCMCTRee. * `lg.dat`: The amino acid substitution matrix for the LG model. * `mcmctree-outBV.ctl`: Template for control file to get in.BV for MCMCTree run. * `mcmctree.ctl`: Control file template for mcmc sampling. * `divtime/` * `1_part` * `mcmc`: output from posterior sampling. * `c[1..3]/`: a folder for each of three chains * `FigTree.tre`: Tree file with 95% HPD of posterior age estimates * `mcmc_c[1..3].txt`: Posterior sampling for the internode ages, rate parameters and likelihoods. * `prior`: output from prior sampling * `c[1..3]/`: a folder for each of three chains * `FigTree.tre`: Tree file with 95% HPD of prior age estimates * `mcmc_c[1..3].txt`: Prior sampling for the internode ages, rate parameters and likelihoods. ### Data and output for phylogenomic analyses of *Nostoc* – `phylogenetics/set103/` * `seqs/` * `*faa`: amino acid sequence files for each of the 1899 loci from the nostocales_odb_10 database of orthologs used by BUSCO. The 1517 loci we used for analyses are a subset of these. * `*fna`: nucleotide sequence files for each of the 1899 loci from the nostocales_odb_10 database of orthologs used by BUSCO. * `16s.fas`: file with 16 rDNA sequences. * `trnl.fas`: file with trnL sequences. * `alignments/` * `single/` * `*aln.faa`: aligned amino acid sequences for the 1898 loci. * `*ng.faa`: aligned amino acid sequences for the 1898 loci after trimmming sites with gaps. * `*ng.fna`: aligned nucleotide sequences for the 1898 loci after trimmming sites with gaps. * `16s_aln.*`: aligned 16S sequences in nexus and fasta formats. * `trnl_aln.*`: aligned trnL sequences in nexus and fasta formats. * `*codon_partition`: codon partition files used for model selection and phylogenetic inference. * `concat/` * `concat_ng.fna`: concatenated nucelotide alignment of 1519 loci after trimming sites with gaps. * `codon_partition_concat_ng_na`: codon partition file used for model selection in the concatenated ML inference. * `divtime/` * `1_part` * `mcmc`: output from posterior sampling. * `c[1..3]/`: a folder for each of three chains * `FigTree.tre`: Tree file with 95% HPD of posterior age estimates * `mcmc_c[1..3].txt`: Posterior sampling for the internode ages, rate parameters and likelihoods. * `prior`: output from prior sampling * `c[1..3]/`: a folder for each of three chains * `FigTree.tre`: Tree file with 95% HPD of prior age estimates * `mcmc_c[1..3].txt`: Prior sampling for the internode ages, rate parameters and likelihoods. * `conflict/` * `single_vs_concat/`: output from topological comparisons between gene trees and concatenated ML tree. * `discovista_out/` * `single.metatable.results.csv`: DiscoVista output. Each row in the matrix corresponds to a gene tree. The "ID" column indicates the locus and each of the remaning columns corresponds to a topological bipartition in the species tree. The cells of the matrix indicate whether the bipartition was recovered in the gene tree with strong or weak support. * `single_vs_wastral/`: output from topological comparisons between gene trees and weighted-Astral tree. * `discovista_out/` * `single.metatable.results.csv`: DiscoVista output. Each row in the matrix corresponds to a gene tree. The "ID" column indicates the locus and each of the remaning columns corresponds to a topological bipartition in the species tree. The cells of the matrix indicate whether the bipartition was recovered in the gene tree with strong or weak support.