Basically, silver (Ag) or Cu is used as an oxidizing electrode, and the metal ions are migrated through the chalcogenide material under a positive bias on the Ag or Cu electrode.
Across all lineages, we identified 80 candidates that may have evolved under positive selection (see Materials and Methods; supplementary table 2, Supplementary Material online).
In Fig. 2 we report a plot of the probability P dN/dS>1) that a codon has dN/dS>1 for rrgA, and sites for which the Bayes-Empirical-Bayes inference (BEB) method [26] (see Materials and Methods section) supports evolution under positive selection are evidenced.
Simulations letting a fraction of sites evolve under positive selection (see Material and Methods) found similar effects.
SET process: (1) Under positive electric field, TE material in the TE/RS-layer interface is oxidized and O2−/Vo is generated; (2) O ions drift to TE or O vacancies drift to BE through the RS layer to form Vo-CF.
Curiously, those SNPs are enriched in genes performing olfactory transduction function (supplementary fig. S8, Supplementary Material online), which are known to be under positive selection in human evolution (Young and Trask 2002).
LRT was significant in all cases, and different sites were detected to be under positive selection (see the supplementary information, Supplementary Material online, for LRT results).
One hundred seven genes had d N/d S values >1, which indicates that they are under positive selection (supplementary fig. S2, Supplementary Material online, the complete gene list can be found in supplementary table S2, Supplementary Material online) (Jordan et al. 2002a).
The number of sites under purifying selection was significantly lower (P < 0.0001) at the ends of the genes than in the middle, as more sites were under positive selection (supplementary fig. S2b, Supplementary Material online).
Comparison of the two gene sets allowed us to detect 772 genes present in both, and this was taken as the final list of genes putatively under positive selection using SM (supplementary table S3, Supplementary Material online).
