In line with our previous work [ 22], the DA1-like genes in soybeans diverged into Class I and Class II (Fig. 1a).
The primordial opsin had already diverged into three classes (rhabdomeric, "photoisomerase-like," and ciliary opsins) before protostomes (including most invertebrates) and deuterostome (including vertebrates) diverged, at least 580 Mya.
Archaea consist of two phyla, Euryarchaeota and Crenarchaeota, which diverged into night classes and eleven orders (Additional file 4).
Moreover, introns 3, 5, and 9 exhibited an evolutionary tendency similar to intron 2, but diverged into different classes (supplementary fig. S4, Supplementary Material online).
We therefore infer that myosin II was derived early in the radiation of the eukaryotes and diverged into two classes in the holozoan lineage (smooth and striated), the latter being secondarily lost in ichthyosporeans and choanoflagellates.
We conclude that these plasmids diverged into two classes based on the locations at which cargo DNA is inserted, that the quorum-sensing and transfer functions are coevolving within but not between the two groups, and that this divergent evolution extends to function.
GABAergic cells fell into four morphological classes but diverged into three physiological classes with strong overlap among BC- and HIPP-like neurons in class P1 and between TML-, ML-, and HIPP-like cells in class P3 (Fig. 4A).
The four similar genes in P. patens subsequently diverged into the three classes of PABP genes present in higher plants today.
Approximately half of the copies retained amino acid sequences similar to the monogonont copies, whereas the rest have diverged into four distinct classes that differ in intron structure and biochemical properties predicted by computational analysis.
Evidence supports the idea that spliceosomal introns were not only present in the stem eukaryote but diverged into at least two distinct classes very early in eukaryotic evolution.
