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Autophagy, as a cellular response to nutrient deprivation, is evolutionarily a more ancient event than apoptosis.
Nodes separating these sub-groups could relate to a more ancient event not necessarily linked to a large scale genome duplication.
For example, Arabidopsis thaliana has experienced at least three WGD events two recent events (α and β) since its divergence from other members of the Brassicales clade and a more ancient event shared with most if not all eudicots [ 6].
Instead, they proposed that acanthopterygian pax6a genes originated in a more ancient event, namely the 2R-WGD at the base of vertebrate evolution (fig. 2 A; Ravi et al. 2013).
These figures seem to indicate a genome duplication event in a common ancestor of melon and cucumber as well as another, more ancient event affecting a common ancestor of all the dicotyledonous species we analyzed.
In man, the loss of a functional GLY1 gene appears to be a more ancient event than the loss of TDH because GLY1 genes in both man and chimpanzees have a number of frame-shifts and mutations of functional amino acid residues, whereas the mutated exon 6 splice-acceptor site in human TDH is intact in chimpanzees (data not shown).
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However, compartmentalization may also reflect more ancient events, such as phylogenetic splits [3], [14], [18].
Although our study focuses on these more recent events, we also find evidence for more ancient events.
This approach is conservative and will, compared to including more ancient events, produce less false positive HGT candidates.
The results (Table 5) are presented not only for the recent WGD but also for the more ancient events.
Close examination of the phylogenies show that core genes putatively acquired from the host are a mix of recent and more ancient events.
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