DOI: 10.5281/zenodo.14166043
title: Supplemental Information for The Archean origin of assimilatory sulfate metabolisms provides novel insight into redox conditions of early Earth environments

description: Supplemental Information for The Archean origin of assimilatory sulfate metabolisms provides novel insight into redox conditions of early Earth environments.

The following is a list of files contained in the SI dataset.

Data S1. 401 sequence trimmed and subsampled final alignment file.

S1_payette_SM_MIT_EAPS_2025_sat_04042024_RmEmptyColumns.fa.phy.dedupe.EDITRmCamp.phy4.txt

Data S2. 414 sequence untrimmed alignment file.

S2_payette_SM_MIT_EAPS_2025_sat_04042024.fa.phy.txt

Data S3. 414 sequence trimmed alignment file.

S3_payette_SM_MIT_EAPS_2025_sat_04042024_RmEmptyColumns.fa.phy.dedupe.txt 

Data S4. Preliminary COG#2046 NCBI sequences recruited in FASTA format.

S4_payette_SM_MIT_EAPS_2025_sat_COG2046_sequences_combined.txt

Data S5. Minimal Ancestor Deviation (MAD) Rooted Maximum Likelihood newick extended format tree with coded tip labels (Appendix Table S2).

S5_payette_SM_MIT_EAPS_2025_sat_09092024_EDITRmCamp.phy.treefile.MADrooted.rooted

Data S6. Original unrooted Maximum Likelihood newick extended format tree with coded tip labels and bootstrap supports on bipartitions (SH-aLRT/UFBoot).

S6_payette_SM_MIT_EAPS_2025_sat_09092024_EDITRMCamp.phy.treefile 

Data S7. IQ-Tree Tree reconstruction output/log file containing substitution model finder AIC/BIC tests.

S7_payette_SM_MIT_EAPS_2025_sat_09092024_EDITRmCamp.phy.iqtree

Data S8. Chronogram tree for Combined calibrations UGAM branch rate model with all calibrations.

S8_payette_SM_MIT_EAPS_2025_sat_09092024_lg_rootcal_Combined_allEuk_Cyano2_UGAM_noBD_post.treefile

Data S9. Original Combined calibrations UGAM chronogram data.

S9_payette_SM_MIT_EAPS_2025_sat_09092024_lg_rootcal_Combined_allEuk_Cyano2_UGAM_noBD_post.1_sample.chronogram

Data S10. Phylobayes Label tree in extended newick format with internal node labels.

S10_payette_SM_MIT_EAPS_2025_sat_09092024_lg_rootcal_Combined_allEuk_Cyano2_UGAM_noBD_post.1_sample.labels

Data S11. Zip file containing Phylobayes chronograms and datedist files for molecular clock analyses.

S11_payette_SM_MIT_EAPS_2025_Appendix_S11_sat_phylobayes_chronograms_files.zip

Data S12. Large expanded diversity tree for sat/ATPS/met3 protein family (2089 sequences).

S12_payette_SM_MIT_EAPS_2025_Appendix_S12_sat_expanded_diversity.fasta

Data S13. Large expanded diversity sequence FASTA for sat/ATPS/met3 protein family (2089 sequences).

S13_payette_SM_MIT_EAPS_2025_Appendix_S13_sat_expanded_diversity_GINSi.treefile.rooted.figTree

Data S14. A zip file for the figures in The Archean origin of assimilatory sulfate metabolisms provides novel insight into redox conditions of early Earth environments.

S14_payette_SM_MIT_EAPS_2025_sulfate_assimilation_figure_files.zip

Figure 1. Maximum Likelihood (ML) tree cartoon representation of the sat (sulfate adenylyltransferase)/met3/ATP sulfurylase gene family (E.C.2.7.7.4).

Figure 2. Crown sat/ATPS protein family divergence date age estimates (probability densities) under different calibrations with a uniform tree process and LG substitution model (Table 1).

Figure 3. Geobiological timeline in billions of years (Ga).

Appendix Figure S1. Rooted Maximum Likelihood (IQ-Tree) phylogenetic tree run under LG+R10 model, with branch lengths on internal nodes, with tip labels (sequences), by taxonomic name (Table S2).

Appendix Figure S2. Expanded Rooted maximum Likelihood (IQ-Tree) phylogenetic tree run under LG+R10 model with sequence labels (tips), by taxonomic name and color coding for calibration groups.

Appendix Figure S3. Maximum Likelihood (IQ-Tree) phylogenetic tree run under LG+R10 model with bootstraps supports on each bipartition (SH-aLRT/UFBoot) and tip labels (sequences) coded by ID (Table 2).

Appendix Figure S4. Phylobayes chronogram tree for UGAM branch rate model with all combined calibrations (Table 1).

Appendix Figure S5. Parfrey chronogram tree annotated with calibration groups used in this analysis. Modified from Parfrey et al., 2011.

Appendix Figure S6. Large expanded diversity tree for sat/ATPS/met3 protein family, 2089 tips with phylum labels, colored coded.

Appendix Figure S7. Large expanded diversity tree for sat/ATPS/met3 protein family, 2089 tips with Accession Id No. labels, colored by phylum.