This article is about introns in the nuclear genes coding for mitochondrial proteins. The existence of these introns and these nuclear genes is in line with a nuclear origin of these genes, especially when the intron positions are conserved. The current article assumes (wrongly, imo) that the genes are of bacterial origin and proposes that the conserved intron positions are caused by parallel intron gain. Somehow they changed the fundamental paradigm of the experiment, conserved intron positions cannot have arisen by chance, into the opposite namely that conserved intron positions occurred by chance.
For me, the basic results are 1) MRP and CRP exhibit extensive homology, 2) they show conserved intron positions in line with a common descent, 3) MRPs and CRP between themselves contain considerable number of conserved introns.
From the abstract: In this paper, we tried to gain insights into intron evolution from a novel perspective by comparing the gene structures of cytoplasmic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs), which are held to be of archaeal and bacterial origin, respectively. We analyzed 25 homologous pairs of CRP and MRP genes that together had a total of 527 intron positions. We found that all 12 of the intron positions shared by CRP and MRP genes resulted from parallel intron gains and none could be considered to be “conserved,” i.e., descendants of the same ancestor. This was supported further by the high frequency of proto-splice sites at these shared positions; proto-splice sites are proposed to be sites for intron insertion. Although we could not definitively disprove that spliceosomal introns were already present in the last universal common ancestor, our results lend more support to the idea that introns were gained late. At least, our results show that MRP genes were intronless at the time of endosymbiosis. The parallel intron gains between CRP and MRP genes accounted for 2.3% of total intron positions, which should provide a reliable estimate for future inferences of intron evolution.
Here you can see the several assumptions that are made. Interestingly, they say they only need one clear example of conserved intron positition. They find >10, but then do a parsimony analyses that syas that they are not real conserved intron position.
Mitochondrial ribosomes are considered to be of bacterial origin (that is, they are a product of endosymbiosis), as evidenced by the considerable homology that exists between mitochondrial ribosomal proteins (MRPs) and bacterial RPs [21,22]. Cytoplasmic ribosomal proteins (CRPs), on the other hand, are thought to have evolved independently from archaea, although there is sufficient homology between MRPs and CRPs to allow a comparison of their gene structures. Like most mitochondrial genes, MRP genes were transferred to the nuclear genome after endosymbiosis  and, like their cellular counterparts, contain spliceosomal introns. Thus, by comparing the intron/exon structures of MRP and CRP genes, it may be possible to determine whether spliceosomal introns existed in their last common ancestor. If at least one clear case of intron position conservation is found (i.e., introns at this position are descendants of the same ancestral intron), then it can be concluded that spliceosomal introns existed in the last common ancestor of CRP and MRP genes (introns-early).
A total of 79 MRP genes were found in the human genome [21,22]. Of these, 43 were homologous to bacterial genes, and among these 43, 25 were homologous to eukaryotic CRP genes. We compared the gene structures of these 25 homologous pairs. The multiple sequence alignments showed that, out of the total of 527 intron positions, only 12 (2.3%) were shared by CRP and MRP genes; i.e., an intron was present at each of these positions in at least one CRP gene and in at least one MRP gene (Figure 1B, Figure S1, and Dataset S1).
Here they basically state that there sample is too small. Also, I cannot relate to the parsimony approach since I don’t think evolution is parsimonious and it is a highly anthropomorf and teleological term.
The maximum parsimony method was used to infer the most parsimonious scenarios of these nine shared positions. We recently proposed a maximum likelihood approach for inferring the evolution of introns; however, we believe that maximum parsimony is the best choice for the current dataset because maximum likelihood uses only patterns of intron position in the conserved regions of the multiple sequence alignment, and our dataset is not large enough to make valid statistical inferences using this method.
Figure 4 has made it to my gallery of Trees of Life, and a nice illustration of how people deal with evolution.