Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication

Abstract

In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible.

A spectrum of verticality across genes

“…If we break the data down to families, genera, or species, the number of donors grows accordingly (all prokaryotic organisms employed in this study were in the sister group to eukaryotes at least once), such that each gene in eukaryotes would correspond to an individual donation, as some would argue [ 54 ]. But that logic leads straight to the erroneous conclusion that ancestral plastid and mitochondrial genomes were assembled by acquisition one gene at a time [ 55 ] the converse of what they are in plain sight, namely reduced genomes of single bacterial endosymbionts [ 50 ] that underwent reductive evolution by transferring genes to the nucleus. Worse yet, the same problem ensues at the origin of plastids ( Fig 4B , right column), because for photosynthetic eukaryotes again all phyla, including the archaea, appear as donors.…”

Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution

“…A reanalysis of this dataset has argued that the acquisition of genes by LGT may have been a more piecemeal process [ 7 ]. However, the methodological basis of this reanalysis has very recently been challenged as artificially inflating the number of more recent events [ 28 ]. We tested whether the composite genes reported in our study could provide additional (although clearly distinct) elements to the debate regarding the tempo of acquisition of bacterial gene fragments into Haloarchaea.…”

Cytonuclear integration and co-evolution

“…This model offers an explanation for the heterogeneous phylogenetic signals within organellar proteomes and for how eukaryotes may have overcome major early barriers to cytonuclear integration. However, these interpretations have been vehemently disputed by other researchers 169,170 , who argue that the phylogenetic patterns can be explained by: first, the statistical artefacts associated with reconstructing trees for individual genes across such deep timescales, and second, a rampant history of HGT among diverse lineages of bacteria that may have affected the mitochondrial ancestor prior to eukaryogenesis. This ongoing debate highlights one of the central uncertainties about the earliest stages of cytonuclear integration.…”