The complex phylogenetic relationships of a 4mC/6mA DNA methyltransferase in prokaryotes

[Display omitted] •We reconstructed a gene tree 4mC/6mA DNA Methyltransferases (MTases).•The highly supported gene tree shows a complex history for this protein family.•Complexities are especially due to many horizontal gene transfers.•Rates of 4mC methylation show phylogenetic signal based on the gene tree.•These broadly-occurring MTases likely arose after life split from a common ancestor. DNA methyltransferases are proteins that modify DNA via attachment of methyl groups to nucleobases and are ubiquitous across the bacterial, archaeal, and eukaryotic domains of life. Here, we investigated the complex evolutionary history of the large and consequential 4mC/6mA DNA methyltransferase protein family using phylogenetic reconstruction of amino acid sequences. We present a well-supported phylogeny of this family based on systematic sampling of taxa across superphyla of bacteria and archaea. We compared the phylogeny to a current representation of the species tree of life and found that the 4mC/6mA methyltransferase family has a strikingly complex evolutionary history that likely began sometime after the last universal common ancestor of life diverged into the bacterial and archaeal lineages and probably involved many horizontal gene transfers within and between domains. Despite the complexity of its evolutionary history, we inferred that only one significant shift in molecular evolutionary rate characterizes the diversification of this protein family.