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Analysis of Horizontal Gene Transfer Events Can Date Microbial Phylogenies

NEW YORK (GenomeWeb) – The messiness of microbial genomes and their phylogenies can help gauge when different branches of archaea and bacteria arose, according to two new studies.

Microbes swap genes through horizontal gene transfer (HGT), which can lead to complicated phylogenetic trees. But two teams of researchers have shown that tracking gene transfer events can put a timeframe on when they occurred and when various phylogenetic branches arose to reconstruct the history of microbes that otherwise have left little trace of themselves behind. For instance, if one of the species involved in an HGT event has left evidence of itself in the geological record, what's known about when that species was around could put a timestamp on the other's phylogenetic trees.

In one study, researchers led by Gergely Szöllősi from Eotvos Lorand University in Hungary used a set of algorithms they developed to analyze HGT events within archaeal, cyanobacterial, and fungal genomes to determine the order of speciation, as they reported in Nature Ecology & Evolution. In the same journal, a Massachusetts Institute of Technology duo described a similar approach to track the transfer of genes from archaeal methanogens to cyanobacteria to pinpoint the divergence of methanogens.

"Both works highlight how an ingenious toolkit, analysis of HGTs, can be used by evolutionary biologists in the quest to date the tree of life," Queen Mary University of London's Mario dos Reis wrote in an accompanying commentary. He noted, though, that the approach is "still at early stages of development."

In the first paper, Szöllősi and his colleagues applied this approach to a set of homologous gene families from 40 cyanobacterial genomes, 60 archaeal genomes, and 60 fungal genomes. For each gene family, they used a method called amalgamated likelihood estimation (ALE) to construct likely scenarios of gene transfers. With another algorithm, called maximum time consistency (MaxTiC), they then estimated the number of consistent transfers needed to determine a time order of speciation.

They calculated, for instance, that two clusters of methanogens within Euryarchaeota are 3.0 billion years old and 2.8 billion years old, respectively, and are older than the TACK+Lokiarchaeum clade and DPANN Archaea clades.

They also reported that their estimated dates broadly matched with ones determined using the more established molecular clock approach.

"Phylogenetic models of genome evolution have the potential to turn the phylogenetic discord caused by gene transfer into an invaluable source of information for dating the tree of life," Szöllősi and his colleagues wrote.

In a separate paper, Joanna Wolfe and Gregory Fournier from MIT focused specifically on an ancient gene transfer that occurred between archaeal methanogens and the ancestor of cyanobacteria. They used concatenated SMC complex sequences — which encode proteins needed for chromosome condensation — and ribosomal protein sequences from numerous cyanobacteria and Euryachaeota to build a gene tree.

From this, they estimated that methanogens diverged some 3.53 billion years ago, and that methanogenesis likely evolved even earlier than that. "This timing provides independent support for scenarios wherein microbial methane production was important in maintaining temperatures on the early Earth," the pair wrote.

Dos Reis wrote in his commentary that while the method could help calibrate evolutionary trees, it still needs refinement. He noted that the approach Wolfe and Fournier used to reconcile conflicts between species and HGT events on phylogenetic trees — namely, by splitting the ribosomal protein alignment, which evolved with the species tree — is impractical to apply to scenarios with more than one HGT event. He added that he agreed with Szöllősi and his colleagues, who suggested that a Bayesian framework be developed to handle such conflicts.