Data from: Ancient horizontal gene transfer and the last common ancestors

Background: The genomic history of prokaryotic organismal lineages is
marked by extensive non-vertical inheritance of genes, with horizontal
gene transfer (HGT) between many groups of organisms at all taxonomic
levels. These HGT events have played an essential role in the origin and
distribution of biological innovations. Analyses of ancient gene families
show that HGT existed in the distant past, even at the time of the
organismal last universal common ancestor (LUCA). Most gene transfers
originated in lineages that have since gone extinct. Therefore, one cannot
assume that the last common ancestors of each gene were all present in the
same cell representing the cellular ancestor of all extant life. Results:
An ancient population of organisms existing as part of a diverse ecosystem
at the time of LUCA would likely be sharing genetic material between
lineages. If these other lineages persisted for some time, HGT with the
descendants of LUCA could have continued into the bacterial and archaeal
lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein
families support the hypothesis that the molecular common ancestors of the
most ancient gene families did not all coincide in space and time. This is
most apparent in the evolutionary histories of seryl-tRNA synthetase and
threonyl-tRNA synthetase protein families, each containing highly
divergent “rare” forms, as well as the sparse phylogenetic distributions
of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of
glycyl-tRNA synthetase. These topologies and phyletic distributions are
consistent with horizontal transfers from ancient, likely extinct branches
of the tree of life. Conclusions: Of all the organisms that may have
existed at the time of LUCA, by definition only one lineage is survived by
known progeny; however, this lineage retains a genomic record of
heterogeneous genetic origins. The evolutionary histories of
aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting
this signal, as they are intimately associated with some of the earliest
biochemical processes to evolve, have undergone several ancient HGT
events, and contain many sites with low substitution rates allowing deep
phylogenetic reconstruction. We conclude that some aaRS families contain
groups that diverge before LUCA. We propose that these ancient gene
variants be described by the term “hypnologs”, reflecting their ancient,
reticulate origin from a time in life history that has been all but
erased.