DOI: 10.5061/dryad.bnzs7h4hq
title: Data from: Stochastic character mapping, Bayesian model selection, and biosynthetic pathways shed new light on the evolution of habitat preference in cyanobacteria

description: Cyanobacteria are the only prokaryotes to have evolved oxygenic
 photosynthesis paving the way for complex life. Studying the evolution and
 ecological niche of cyanobacteria and their ancestors is crucial for
 understanding the intricate dynamics of biosphere evolution. These
 organisms frequently deal with environmental stressors such as salinity
 and drought, and they employ compatible solutes as a mechanism to cope
 with these challenges. Compatible solutes are small molecules that help
 maintain cellular osmotic balance in high-salinity environments, such as
 marine waters. Their production plays a crucial role in salt tolerance,
 which, in turn, influences habitat preference. Among the five known
 compatible solutes produced by cyanobacteria (sucrose, trehalose,
 glucosylglycerol, glucosylglycerate, and glycine betaine), their synthesis
 varies between individual strains. In this study, we work in a Bayesian
 stochastic mapping framework, integrating multiple sources of information
 about compatible solute biosynthesis in order to predict the ancestral
 habitat preference of Cyanobacteria. Through extensive model selection
 analyses and statistical tests for correlation, we identify
 glucosylglycerol and glucosylglycerate as the most significantly
 correlated with habitat preference, while trehalose exhibits the weakest
 correlation. Additionally, glucosylglycerol, glucosylglycerate, and
 glycine betaine show high loss/gain rate ratios, indicating their
 potential role in adaptability, while sucrose and trehalose are less
 likely to be lost due to their additional cellular functions. Contrary to
 previous findings, our analyses predict that the last common ancestor of
 Cyanobacteria (living at around 3180 Ma) had a 97% probability of a high
 salinity habitat preference and was likely able to synthesize
 glucosylglycerol and glucosylglycerate. Nevertheless, cyanobacteria likely
 colonized low-salinity environments shortly after their origin, with an
 89% probability of the first cyanobacterium with low-salinity habitat
 preference arising prior to the Great Oxygenation Event (2460 Ma).
 Stochastic mapping analyses provide evidence of cyanobacteria inhabiting
 early marine habitats, aiding in the interpretation of the geological
 record. Our age estimate of ~2590 Ma for the divergence of two major
 cyanobacterial clades (Macro- and Microcyanobacteria) suggests that these
 were likely significant contributors to primary productivity in marine
 habitats in the lead-up to the Great Oxygenation Event, and thus played a
 pivotal role in triggering the sudden increase in atmospheric oxygen.
description: Please see the associated manuscript for more information about
 the data and methods.
description: # Data from: Stochastic character mapping, Bayesian model selection, and
 biosynthetic pathways shed new light on the evolution of habitat
 preference in cyanobacteria
 [https://doi.org/10.5061/dryad.bnzs7h4hq](https://doi.org/10.5061/dryad.bnzs7h4hq) This repository contains Supplementary Information for the manuscript **"Stochastic Character Mapping, Bayesian Model Selection, and Biosynthetic Pathways Shed New Light on the Evolution of Habitat Preference in Cyanobacteria"** *By G. Bianchini, M. Hagemann, and P. Sánchez-Baracaldo* Information about the methods used to obtain these data is available in the main manuscript. ## Description of the data and file structure The file `Supplementary_Information.docx` contains Supplementary Tables S1-S10, Supplementary Figures S1-S14, as well as additional information supplementing the main manuscript. The file `Character_states.tsv` contains presence/absence data for compatible solutes in the cyanobacterial strains analysed, as well as habitat preference states. The repository also contains the following 7 folders: 1. `Sequences` This folder contains the sequences for compatible solute genes and for the markers included in the phylogenomic dataset. For each sequence file, unaligned sequences are provided along with manually trimmed alignments. Sequences are provided in NEXUS and FASTA formats for convenience. 2. `Phylogeny` This folder contains the partition file and the script file used to run the phylogenomic analysis. 3. `Molecular_clock` This folder contains the data files and script necessary to run the molecular clock analysis. 4. `Stochastic_mapping` This folder contains the data files necessary to run the stochastic mapping analyses and the output of each analysis. This folder has 3 subfolders: 4.1. `Stochastic_mapping/All_independent` This folder contains files for the analyses where all characters were analysed independently. 4.2. `Stochastic_mapping/GG_GGA_Habitat` This folder contains files for the analysis where habitat preference was conditioned on GG and GGA. 4.3. `Stochastic_mapping/Suc_GG_GGA_GB_Habitat` This folder contains files for the analysis where habitat preference was conditioned on Suc, GG, GGA, and GB. 5. `Source_code` This folder contains the source code for scripts used to produce Figures 1, 4, 5, and S14. All necessary data files for each figure are provided as well. The source code is provided as a "Solution" that can be opened using Microsoft Visual Studio (but the actual source code is also accessible from the `Program.cs` file corresponding to each figure). 6. `Tree_files` This folder contains the phylogenetic tree files used to produce Figures 3 and S2-S13, in NEXUS format. These files can be opened using TreeViewer in order to reproduce the full figures. 7. `Supplementary_figures` This folder contains Figures S1-S13 in PDF format. Additional information is provided by the `README.txt` files provided in some of the subfolders of this repository.