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Generally, sites with a functional divergence score above 0.5 were considered to be functionally divergent in order to identify the maximum number of possible candidate sites for consideration [ 60, 62].
Residues predicted to be functionally divergent in anoctamins were mapped onto topology model of human anoctamin 1.
Residues predicted to be functionally divergent in bestrophin, were mapped onto topology models of human bestrophins 2 and 4, respectively.
We did not detect a significant QTL for CRY2, known to be functionally divergent in Cvi-0, the parent for two of our populations (Bur-0 × Cvi-0 [P10] and Cvi-0 × RRS7 [P17]), reflecting the short-day-dependent nature of the early flowering phenotype conferred by the CRY2Cvi-0 allele.
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In addition, 11 out of 44 positively selected sites detected by LRT in codeml were also found to be functionally divergent between bestrophin paralogues (marked by asterisk in Table 4).
In addition, 24 out of 69 positively selected sites detected under model M3 (discrete) implemented in the codeml program of the PAML v4.0 package were also found to be functionally divergent between OPR paralogues (marked by asterisks in Tables 2 and 3).
Although the homeodomain is a highly conserved motif, it is not invariant; in fact only 17 residues are absolutely conserved between all vertebrate Hox genes in our alignment, suggesting that variable sites could be functionally divergent.
Eleven out of the 44 positively selected sites were also found to be functionally divergent between bestrophins.
This suggests that the honeybee gut bacteria may be functionally divergent despite having highly similar 16S rRNA genes.
Moreover, the difference of gene organization and motif composition between the paralogous pairs suggested that they may be functionally divergent.
The evolutionary relationship among these fish, amphibian and mammalian uroplakins, that seem to be functionally divergent, remains unclear.
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