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Address #26 and #40.

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evogytis committed Nov 27, 2017
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@@ -306,7 +306,7 @@ \subsection*{Recombination shapes MERS-CoV diversity}
Amongst other parameters of interest, recombination is expected to interfere with molecular clocks, where transferred genomic regions can give the impression of branches undergoing rapid evolution, or branches where recombination results in reversions appearing to evolve slow.
In addition to its potential to influence tree topology, recombination in molecular sequence data is an erratic force with unpredictable effects.
We suspect that the effects of recombination in MERS-CoV data are reigned in by a relatively small effective population size of the virus in Saudi Arabia (see next section) where haplotypes are fixed or nearly fixed, thus preventing an accumulation of genetic diversity that would then be reshuffled via recombination.
Nevertheless, we choose not to report on any particular estimates for times of common ancestors (tMRCAs), even though these are expected to be somewhat robust for dating human clusters, and we do not report on the evolutionary rate of the virus, even though it appears to fall firmly within the expected range for RNA viruses (data not shown).
Nevertheless, we choose not to report on any particular estimates for times of common ancestors (tMRCAs), even though these are expected to be somewhat robust for dating human clusters, and we do not report on the evolutionary rate of the virus, even though it appears to fall firmly within the expected range for RNA viruses: regression of nucleotide differences to Jordan-N3/2012 genome against sequence collection dates yields a rate of $4.59 \times 10^{-4}$ subs/site/year, Bayesian structured coalescent estimate from primary analysis $9.57 \times 10^{-4}$ (95\% HPDs: $8.28-10.9 \times 10^{-4}$) subs/site/year.
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