Count does not recover major events of gene flux in real biological data

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 birth-and-death phylogenetic models to investigate prokaryote genome evolution to claim that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here we test the ability of Count, a birth-and-death based program, to recover known events of mass acquisition and differential loss using plastid genomes and eukaryotic protein families that were acquired from plastids. Count showed a strong bias towards reconstructed histories having gene acquisitions distributed uniformly across the tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, Count recovered gradual and continuous lateral gene transfer among lineages, even when massive gains followed by gradual differential loss is the true evolutionary process that generated the gene distribution data.