Recent origin of iron oxidation in extant microbial groups and low clade fidelity of iron metabolisms

Reduced iron was abundant in Earth’s surface environments before their oxygenation, so iron oxidation could have been a common metabolism on the early Earth. Consequently, modern microbial iron oxidation is sometimes seen as a holdover from an earlier biosphere, but the continuity of involved lineages or the metabolic process itself has not been verified. Modern neutrophilic iron oxidizers use cytochrome-porin Cyc2 as the initial electron acceptor in iron oxidation. With the protein as a proxy for the metabolism, we performed a phylogenetic analysis of Cyc2 to understand the evolutionary history of this microbial iron oxidation pathway.
In addition to known iron oxidizers, we identified Cyc2 orthologs in gammaproteobacterial endosymbionts of lucinid bivalves. These bivalves have a robust fossil record and rely on sea-grass meadows that only appear in the Cretaceous, providing a valuable time calibration in the evolutionary history of Cyc2. Our molecular clock analysis shows that extant ..., Cyc2 sequence collection and alignment
The Cyc2 sequence in Chlorobium phaeoferrooxidans str. KB01 (protein accession number WP_076792910.1) as identified by Tsuji et al. (2020) was used to query the NCBI non-redundant protein database for homologous Cyc2 sequences using BLASTp.
Two different datasets of Cyc2 orthologs were assembled, differing in the breadth of the sampling strategy. A broad sample includes the first 500 BLAST hits returned by the search, exhaustively covering the sequence space in and around the main clades of neutrophilic iron oxidizers as well as including any clades containing possible calibration points in the broader protein family. This large sequence set showed multiple suspected misalignments on visual inspection, especially within very distantly related sequences (alignment files in Supplementary Data linked at the end of the manuscript), calling for the cross-validation of results against a smaller dataset including only the descendants of the last common an..., , # Recent origin of modern clades of iron oxidizers and low clade fidelity of iron metabolisms

[https://doi.org/10.5061/dryad.905qfttvf](https://doi.org/10.5061/dryad.905qfttvf)

## Description of the data and file structure

This dataset contains multiple sequence alignments and phylogenetic trees inferred from these alignments as referenced in the paper \"Recent origin of modern clades of iron oxidizers and low clade fidelity of iron metabolisms\".

Multiple sequence alignments are uploaded in the FASTA format (.afa). Phylogenetic trees are in the Newick format. For the maximum-likelihood phylogenetic trees (.figTree) and the Bayesian posterior samples of molecular clock runs (half of the .chronogram files), the Newick-format tree is embedded in a NEXUS file that stores further information about the taxa on the tree for clarity. The NEXUS files can be opened as text files or using a tree visualization program such as [FigTree](http://tree.bio.ed.ac.uk/software/figtree/). The Bayesian pr...,