publications

For an up-to-date list of publications, you can visit my Google Scholar profile. Here is a highly subjective selection of highlights from the group and our collaborators over recent years. * Denotes (co-)corresponding/senior author.

Kay CJ, Spang A, Szollosi GJ, Pisani D, Williams TA*, Donoghue PCJ* (2026). Dated gene duplications elucidate the evolutionary assembly of eukaryotes. Nature 650: 129-140. Link; summary of online coverage.

• Eukaryotes are fairly different from prokaryotes, and there is some debate about the order in which key eukaryotic traits evolved during the prokaryote-to-eukaryote transition. In this study, we used a sequential dating method to estimate the ages of gene duplications along the branches leading from Asgard archaea and Alphaproteobacteria to eukaryotes. The analysis suggested that duplications of archaeal origin tended to be fixed earlier in evolution, suggesting elaboration of eukaryote-like complexity in the archaeal lineage prior to the acquisition of mitochondria through endosymbiosis.
• There was some accessible coverage of this article, for example an interesting overview by John Archibald.

Davin AA*, Woodcroft BJ*, Soo RM, Morel B, Murali R, Schrempf D, Clark JW, Boussau B, Moody ERR, Szantho LL, Richy E, Pisani D, Hemp J, Fischer W, Donoghue PCJ, Spang A, Hugenholtz P*, Williams TA*, Szollosi GJ* (2025). A geological timescale for bacterial evolution and oxygen adaptation. Science 388: 6742. Link; summary of online coverage.

• Relating the evolution of Bacteria to geological time is difficult, because there are few interpretable fossils of single-celled organisms. In this study, we attempted to better calibrate bacterial evolution by linking the origin and spread of oxygen-using metabolisms to the accumulation of oxygen in the Earth’s atmosphere over the past few billion years.

Moody ERRM*, Betts HC, Clark JW, Mahendrarajah TA, Dombrowski N, Alvarez-Carretero S, Szantho LL, Daines S, Boyle R, Chen X, Lane N, Yang Z, Shields GA, Szöllősi GJ, Spang A, Pisani D*, Williams TA*, Lenton TM*, Donoghue PCJ* (2024). The metabolism of the last universal common ancestor and its impact on the early Earth system. Nature Ecology & Evolution 8: 1654-1666. Link; summary of online coverage.

• This paper was a multi-disciplinary effort to understand a bit more about the last universal common ancestor (LUCA), including inferences of its age (likely >4 Ga), gene content, metabolism, and something about the community of other lifeforms in which it might have lived.
• Quanta Magazine had a nice feature on this paper with Ed and Phil.

Harris BJ, Clark JW, Schrempf D, Szöllősi GJ, Donoghue PCJ, Hetherington AM, Williams TA* (2022). Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat Ecol Evol 6: 1634-1643. Link; summary of online coverage.

• We investigated evolutionary relationships among land plants, and found (more) evidence for a sister relationship between vascular plants (like flowering plants, ferns, etc.) and bryophytes (mosses, hornworts and liverworts). We used comparative genomics to suggest that their common ancestor was already rather complex, and that some features of bryophytes that have traditionally been viewed as primitive might actually be the result of reductive evolution.

Coleman GA, Davin AA, Mahendrarajah T, Spang A, Hugenholtz P, Szollosi GJ, Williams TA* (2021). A rooted phylogeny resolves early bacterial evolution. Science 372: eabe0511. Link; summary of online coverage

• Many new bacterial lineages continue to be discovered, and it hasn’t been entirely clear how they relate to the known groups, or even whether a bifurcating tree provides a useful framework for thinking about bacterial diversity, due to extensive horizontal gene transfer. Here, we used phylogenetic reconciliation to try to infer a phylogenetic tree of Bacteria, and to draw inferences about the last bacterial common ancestor. Our analyses supported a deep split between two main groups, Gracilicutes and Terrabacteria, and suggested their common ancestor was already a diderm/double-membraned/Gram-negative cell.

Williams TA*, Cox CJ, Foster PG, Szollosi GJ, Embley TM (2020). Phylogenomics provides robust support for a two-domains tree of life. Nature Ecology & Evolution 4: 138-147. Link; summary of online coverage

• For many years, there was debate about whether a “three domains” or “two domains” tree was the best-supported hypothesis for the tree of life, and in particular, whether eukaryotes branched within, or sister to, the Archaea. This was (yet) another contribution to this debate, using concatenation of a small core of marker genes and supertree analysis of a large number of single-copy genes in eukaryotes and Archaea, finding support for a “two-domains” tree in which eukaryotes branched with Heimdallarchaeota, a lineage within the Asgard archaea. We also reported (very) large differences in the number of inferred substitutions (evolutionary changes) on the tree of life between different phylogenetic models, which may contribute to the differences observed between different studies.

There is also the American Academy of Microbiology’s report on Early Microbial Life, which is aimed at a general (scientific) audience.