We originated SSH before RNASeq technology became feasible for our study so the SSH experiments were not originally designed to complement the RNAseq experiments.
For example (Figure 4), we see that sharks originated before whales, but cannot tell from the cladogram how long before.
This founder mutation appeared in all single cell clones and thus most likely it originated before we started this experiment.
As this founder mutation appeared in all single cell clones most probably it originated before we started to do this experiment.
Since 3 of the retrogenes are also older than the radiation of the Drosophila genus, we cannot infer if they originated before or after the neighborhoods.
We analyzed only genes that originated before the split between the Sophophora and Drosophila subgenus to avoid the confounding effect from new genes that are usually enriched in the X chromosome if testis-biased expressed (as described in [ 3]).
We found that, despite having originated before Brassicaceae radiation, MIR168a and MIR168b paralogs have been maintained, most likely as functional, throughout Brassicacea evolution, with MIR168b having undergone a partial sub-functionalization.
If we assume, however, that Archaea is a derived lineage from gram-positive bacteria [ 36, 37], then HTPG proteins originated before the origin of Archaea, but were subsequently lost in this lineage.
Since this pattern is restricted to orphans that most likely originated before the chromosomal fusion, we argue that the change in chromosomal environment has affected the function of orphan genes, most likely via expression differences.
Whether these subtypes of element families originated before or after the origin of soybean as a distinct species is unknown.
We also found that the old miRNA genes that originated before the divergence of Drosophila species (>60 Ma) have been under strong functional constraints, whereas young miRNA genes generated ∼10 Ma evolve in a more or less neutral fashion.
