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The photoperiodic cues to initiate certain life-history phases may be under adaptive evolution (Bradshaw and Holzapfel 2001).
* p > 0.05 Recently evolved novel genes were shown to be under adaptive evolution in D. melanogaster lineage species [ 8, 9].
Most of the amino acid sites detected to be under adaptive evolution have been previously identified to have important functional roles.
Cernunnos-XLF is a microcephaly-associated locus newly identified to be under adaptive evolution in humans, and possibly played a role in human brain expansion.
In particular, the C-terminal tail was shown to evolve under more relaxed selective constraints in the four datasets examined and many sites pinpointed to be under adaptive evolution were located in this region.
The possibility that the NAT enzymes could be broadening or changing their substrate specificity in accordance to the high diversity of xenobiotics compounds environmentally available suggests that their metabolic function could be under adaptive evolution and makes them a promising subject for evolutionary analyses.
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In order to infer which site is under adaptive evolution in a specific lineage, we re-ran CODEML with the branch-site model.
If two amino acid sites were under adaptive evolution and these sites were co-evolving, this may indicate their functional/structural dependency.
We performed additional tests using the M7 (beta) and M8 (beta and ω) models to detect amino acid sites that were under adaptive evolution.
They assessed variation in 318 Single nucleotide polymorphisms (SNPs) in a selection of samples from two cod populations (northeast Arctic and Norwegian coastal cod) and identified a number of outlier loci as candidates for being under adaptive evolution.
This may well explain the pattern we observe in the Rubisco, with many of the mutations that are under adaptive evolution and that co-evolve occurring at the interface of the protein dimer where stability is essential for the preservation of enzyme function and integrity.
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