In particular, for genes transferred within the metazoan lineage, which is densely sampled in terms of mitochondrial genomes, we could classify genes into relatively more ancient and more recent transfers.
Ancient HGT during Hadean/Archaean times is more difficult to study than more recent transfers, although it has been proposed that its role was even more pronounced during earlier times in life's history [ 22].
This arrangement indicates at least two more recent transfers, one from D. melanogaster to D. simulans and/or D. sechellia or even to the ancestor of those sister species (corroborated by the low dS values), and a second from any of these species to Z. tuberculatus.
More recent mitochondrial transfer experiments support the general findings of the nuclear transfer experiments (50, 51).
However, retroviruses infect only eukaryotes and retrotransposons are unknown in prokaryotes, making a more recent horizontal transfer the more likely origin of the retropepsin gene.
Since the conflict we document here is with the virtually independently evolving mitochondrial genome, comparisons with other nuclear genes are necessary to identify a pattern consistent with more recent gene transfer.
The deep coalescence of peptaibol A-domains from all three clades at the common ancestor of Trichoderma and Tolypocladium (Fig. 4) suggests that the presence of peptaibiotics in Tolypocladium is an ancient attribute of Tolypocladium genomes and not a product of a more recent horizontal transfer.
This complex distribution led initial reports to question whether the current pattern was due to ancient paralogy and lineage sorting, more recent horizontal gene transfer (HGT), or a combination of both.
To assess the utility of probability and bootstrap support values mapping for detecting more recent interphylum gene transfer events, we calculated extended datasets for the genome quartet of Synechocystis sp., Chlorobium tepidum, Rhodobacter capsulatus and Rhodopseudomonas palustris (see figure 4 and [ 3]).
Also, there are several more recent successful gene transfers from wild AA genome Oryza species into cultivated rice (Table 2).
Nuclear substitution rates do not appear to be unusually low in Joinvillea [ 35, 36], and therefore this result suggests more recent – and thus independent – transfer of rps14 in Joinvillea compared to grasses.
