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More than three billion years ago, the tree of life sprouted. As life diversified, the branches of the tree spread, each fork a common ancestor, each proceeding branch a diverging lineage, and every terminating leaf an extant species. The tree has flourished (despite several harsh prunings) for eons hence. The arboreal analogy seems like a perfect fit to us eukaryotes because the immediately obvious direction of gene transfer is vertical: parents passing their genetic information to their offspring. Because genes are passed down the generations, we can use the similarity or dissimilarity of species’ genomes to construct a phylogenetic tree showing the species’ evolutionary history and relationships. However, genetic relations in the real world are not so neat and sequential. Genes can also be passed through routes other than parent-to-offspring. While the transfer of genetic information outside of reproduction may seem unusual, it is regularly employed by bacteria as an adaptive strategy. If a bacterium receives a totally new gene, the process is called horizontal gene transfer (HGT), but when two bacteria swap different variants (i.e., alleles) of the same gene the process is called homologous recombination. HGT and homologous recombination highlight the shortcomings of the simple analogy of the tree of life. If a phylogeny is constructed in a way that only accounts for vertical transmission, it will falsely interpret HGT events as evolutionary distance between that taxon and its closest relatives. Compounding the issue, homologous recombination can increase genetic variability when it occurs between two distant populations, but it also tends to reduce genetic diversity when it occurs between members of the same population. The latter scenario can cause advantageous versions of a gene to proliferate while driving the disadvantageous ones to extinction. Then, it’s obvious that HGT and homologous recombination can be major actors on the bacterial genome—either by introducing new genes for evolution to act upon or by homogenizing genes in a population after selection. How have both types of gene transfer shaped the evolution of bacteria and the organisms they interact with?

GEMS postdoc Mario Cerón-Romero in Professor Katy Heath’s lab at the University of Illinois Urbana-Champaign is working to develop phylogenetic pipelines that identify HGT and homologous recombination events in the nitrogen-fixing bacteria of the genus Ensifer, which form mutualistic relationships with leguminous plants. The issue of HGT can be resolved by producing a phylogeny not for each taxon, but for each gene (or a set of genes) in each taxon. The majority of these genes will not have been horizontally transferred, producing similar phylogenies to one another which can be combined to create a single consensus tree. This consensus tree is what allows the researchers to identify genes that have undergone HGT; the genes that produced phylogenies differing significantly from the consensus tree are likely to be the result of transfer events. Homologous recombination within a population can also be detected either directly with methods based on identifying identical regions between genomes or indirectly with methods that apply models to infer those events. Cerón-Romero has already improved the consensus species tree by incorporating information about each gene’s location in the genome of Ensifer bacteria—in the chromosome or in the two smaller megaplasmids—and by “rooting” the tree by adding a species distantly related to all others in the tree.

Identifying the transfer events will not only produce a better phylogeny of the species, but will also allow the researchers to understand how these events have impacted the evolutionary trajectory of the bacteria and their symbioses with their host plants. Indeed, some genes associated with mutualistic traits such as nitrogen fixation and nodulation are already known to have evolved through HGT. This project will improve our understanding of these events that, though occurring at the smallest of scales, impact all scales of the symbiotic network.

This summary was written by Luke Hearon, Graduate Student, University of Illinois Urbana-Champaign.