Comparison of ligand-binding residue positions between extant and reconstructed ancestral sequences also suggests that PXR may represent the gene ancestral to extant mammalian CARs and PXRs.
We noted that the ectopic cells with sc-SOPE-lacZ staining in Bx-Gal4>UAS-Rel-VP16 flies were close to the positions of extant SOPs (seen in Figure 4A) suggesting that they have arisen from cells of the proneural clusters originally expressing ac-sc (Figure 4B).
The 36-OTU dataset comprised only frogs, with Ascaphus and Leiopelma, which occupy the most basal positions among extant anurans (e.g., [ 58]), used as outgroups.
If this is the case, the exonic regions flanking the extant introns of discordant positions should also have higher GC contents than the exonic sequences flanking conserved introns.
This would, however, require an anterior migration of this organ compared to its position in extant monitors (Figure 9A).
This broad distribution has led to the current interpretation that the terminal mouth is an ancestral ecdysozoan character [ 29, 42] that has been secondarily located to a ventral position in extant adult onychophorans and arthropods [ 79].
Complicating the evaluation of these hypotheses is the positioning of extant river dolphins as successive sister-groups to Delphinoidea in some phylogenetic hypotheses based solely on living species; thus according to parsimony optimization, it is unclear whether these similarities are convergent or are homologs with subsequent reversals in Delphinoidea and/or Ziphiidae.
The long stem branch of the complex is atypical within the rest of Agabini, and as there are no known species worldwide that could be more closely related to it [ 28], it appears that the A. brunneus complex has a very isolated position amongst extant Agabini.
Only the differential costs of contrasting relationships among extant taxa, irrespective of the positions of extinct taxa, were noted.
The GC content of exonic sequences flanking extant introns at discordant intron positions compared with those flanking conserved intron sites of the same species; Table S7.
