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In this sense, our analysis of dS/dN rate might shed some light on this issue as it is expected for sites that have significant relevance for viral fitness to be functionally constrained (undergoing a negative selection) while those sites that are less restricted to change may be able to evolve adaptively (undergoing positive selection).
M2a has an additional site class that allows sites to evolve adaptively.
As the beta distribution is limited to the interval (0, 1), M7 does not allow sites to evolve adaptively.
Retroposed genes contribute to new gene evolution (Long et al. 2003) and may often evolve adaptively (Long and Langley 1993).
Note that this procedure is conservative because it may eliminate bona fide miRNAs that evolve adaptively (Lyu et al. 2014).
To clarify, my theory does not argue that no degree of selfing can evolve adaptively [ 95, 96].
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Several studies have shown that many loci in cetaceans have gone through adaptive evolution, suggesting that some cetacean organs evolved adaptively while others degenerated.
We find that many historically fast-evolving genes in D. miranda and D. pseudoobscura continue to be evolving adaptively on a more recent timescale and are thus detectable in tests of selection using both patterns of polymorphism and LD.
Furthermore, some NALP genes, including NLRP1, NLRP14, and CIITA, were found to have evolved adaptively.
Since local environmental knowledge is neither static nor does it present a cohesive entity, but is rather evolving adaptively over time, we wanted to use a mapping format that is dynamic and interactive.
The Neanderthal genome project has revealed the sequence of several Neanderthal protein-coding genes that have evolved adaptively recently in modern humans (Burbano et al. 2010; Green et al. 2010).
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