Data from: Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist

While there is compelling evidence for the impact of endosymbiotic gene
transfer (EGT; transfer from either mitochondrion or chloroplast to the
nucleus) on genome evolution in eukaryotes, the role of interdomain
transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear.
Lateral gene transfers (LGTs) have been argued to be potential sources of
phylogenetic information, particularly for reconstructing deep nodes that
are difficult to recover with traditional phylogenetic methods. We sought
to identify interdomain LGTs by using a phylogenomic pipeline that
generated 13 465 single gene trees and included up to 487 eukaryotes, 303
bacteria and 118 archaea. Our goals include searching for LGTs that unite
major eukaryotic clades, and describing the relative contributions of LGT
and EGT across the eukaryotic tree of life. Given the difficulties in
interpreting single gene trees that aim to capture the approximately 1.8
billion years of eukaryotic evolution, we focus on presence–absence data
to identify interdomain transfer events. Specifically, we identify 1138
genes found only in prokaryotes and representatives of three or fewer
major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata,
Opisthokonta, SAR and orphan lineages). The majority of these genes have
phylogenetic patterns that are consistent with recent interdomain LGTs
and, with the notable exception of EGTs involving photosynthetic
eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest
that LGTs have probably occurred throughout the history of eukaryotes, but
that ancient events are not maintained unless they are associated with
endosymbiotic gene transfer among photosynthetic lineages.