These estimates are a lot lower than this new projected decrease in ?80% when you look at the ref
a estimates (with a corresponding decrease in pa) (Tables 1 and 2). This suggests that future investigations, in which it eter estimates, should include gene conversion in sweep models. Consistent with the effect of the presence or absence of gene conversion, use of the higher estimate of the gene conversion rate from ref. 22 gave smaller estimates of the effect of BGS and larger ? estimates than Green Bay escort reviews when the lower value of ref. 23 was used (Figs. 3 and 4). These findings reflect the fact that, as has long been known, noncrossover gene conversion is a major source of intragenic recombination events in Drosophila (34), and affects the extent of associations between polymorphic variants within genes (43). Inclusion of gene conversion increases the effective rate of recombination in a gene, so that larger selective effects of mutations are needed to explain a given reduction in diversity at linked sites. Ignoring BGS increases the estimates of both ?a and ?u when gene conversion is included in the model, although the order of magnitude of the ? estimates is not changed if gene conversion and/or BGS are ignored. Curiously, omission of UTR effects had only a small effect on the estimates of the NS sweep parameters (Table 1).
Our results also suggest that selection at linked sites causes a large reduction in synonymous site variability relative to the expectation in the absence of such selection (Table 1 and Figs. 3 and 4), but that this effect is greatly mitigated by a high rate of gene conversion. For the standard model (with BGS, UTR effects, and a low rate of gene conversion), the mean reduction in ?S below the null expectation was ?24%; without BGS, the reduction was 21%, and omitting UTRs reduced it to 16%. 14, the most comprehensive previous analysis of this question. The discrepancy does not primarily reflect the inclusion of gene conversion in our model, because omission of gene conversion increased our estimated net reduction only to 26% (Table 1, row 5).
Our model considers only the effects of selective events in genes themselves, which are likely to be the main contributors to correlations between ?S and KA; it must therefore underestimate the overall effect of hitchhiking on diversity. A chromosome-wide diversity reduction of ?45% for an autosome due to BGS alone was estimated in ref. 12; use of this in SI Appendix, Eq. S16c, together with the estimated rate of coalescence due to sweeps of 0.26 (obtained by equating the predicted value of ?S/?0 = 0.793 for sweeps in the absence of BGS to the right-hand side of SI Appendix, Eq. S16c), gives a net mean reduction in diversity of ?60%. Further reductions would be caused by sweeps of strongly selected mutations in other genomic regions; the combined effects of these and BGS across genes (13) may well be important in determining the overall pattern of variability across the genome.
S facing rates from crossing over in shape dos out of ref
We have assessed the extent to which our model of intragenic hitchhiking effects can explain the well-established relation between ?S and recombination (9) by applying the estimates of BGS and SSWs for the low gene conversion rate to predictions of the mean ?S for different values of the rate of crossing over. For values around one-eighth of that of the standard value of 1 cM per Mb, the slope of ?S against this measure of the rate of crossing over was ?4 ? 10 ?3 , and approached 1.1 ? 10 ?3 for a rate of 2 cM per Mb (this covers most of the range for the plot of autosomal ? 18). The estimated multiple regression coefficient for ?S on crossing-over rate for mel-yak was ?8.4 ? 10 ?3 ± 0.2. It seems clear, therefore, that intragenic effects can account for only part of the relation between diversity and rate of crossing over.