Second, intron-rich ancestors are likely to have had significant AS.
Complementing the results of gene-rich ancestors is the finding that ongoing gene loss on diverging branches is a major contributor to genome evolution (Snel et al. 2002; Makarova et al. 2006; Csűrös and Miklós 2009; David and Alm 2010).
Remarkably, intron-rich ancestors were reconstructed even for those major groups of eukaryotes that currently consist entirely of intron-poor forms such as the alveolates that apparently evolved via differential, lineage-specific, extensive intron loss 54.
This non-adaptive population genetic perspective on the evolution of introns and eukaryotic gene architecture is compatible with the results of empirical reconstruction according to which the general (perhaps counter-intuitive) trend is evolution of intron-poor genomes in multiple lineages from intron-rich ancestors (see Figure 2).
Second, many reconstruction studies on the evolution of gene architecture have suggested intron-rich ancestors of major eukaryotic lineages (Roy 2006; Carmel et al. 2007b; Carmel, Wolf, et al. 2007), leading to the proposal that intron losses, rather than gains, dominated the evolution of eukaryotic genes (Csuros et al. 2011).
This demonstrates, according to many authors, that introns have been inserted in eukaryotes, at a very early stage of their evolution, so that all extant eukaryotes stem from an intron-bearing, and potentially intron-rich ancestor [10], [11], [12].
Two notable examples are the reconstruction of the complex archaeal ancestor and the intron-rich ancestor of eukaryotes.
For instance, an extensive lineage-specific loss of introns in an intron-rich ancestor is suggested to happened in some chromalveolate lineages [ 35].
Nevertheless, the existence of an intron-rich ancestor of eukaryotes is strongly supported by a high rate of shared intron positions between animals, fungi and plants [ 22, 23, 36].
Conservation of intron position, exon phase and exon length between insect OXPHOS genes and their counterparts in Fugu, Zebrafish and human strongly suggest descent from a common intron-rich ancestor in 55 out of 68 orthologous gene clusters.
This may suggest that the last common ancestor of protostomes gained the intron-rich ancestor of PsGEF, and some of these ancient introns have been lost, and some new introns have been gained in each species, as demonstrated with, for example, nuclear OXPHOS genes [ 30].
