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Basic, all of our remedy for BGS and SSWs assumes on panmixia and you may a stable productive population size

Basic, all of our remedy for BGS and SSWs assumes on panmixia and you may a stable productive population size

In common with other ways to estimating the brand new details from confident choices, we have produced several practically unlikely presumptions. Due to the fact BGS appears to have seemingly absolutely nothing affect the fresh new ? and p quotes (Table step one), area of the real question is the outcome out-of demographic products on SSW quotes. escort girl Denton Inclusion ones difficulties within the methods for quoting selection variables try a challenging situation. Although not, i keep in mind that new spread to a high frequency away from a good favorable mutation in a people spread-over a two-dimensional ecosystem is a lot reduced than in an excellent panmictic society, which suggests there is more chance for recombination to dilute the consequences away from SSWs than just having panmixia (47). This step manage ergo cause all of our ? prices as faster as compared to genuine philosophy, and also the p quotes are big.

Information and techniques

Second, we have assumed “hard” sweeps, based on unique mutations, rather than “soft sweeps” based on recurrent mutations or mutations arising from standing variation (48). If soft sweeps are prevalent in Drosophila, as has recently been argued (49), then the same pattern of bias as from a subdivided population would arise (50, 51). (Note, however, that gene conversion of a favored mutation onto an ancestral haplotype could generate the appearance of a soft sweep.) The opposite would apply to incomplete sweeps (52), if their incidence in a gene is correlated with its KA value. These were omitted from our models because they do not affect KA. However, the lack of evidence for intermediate-frequency NS and synonymous variants in pooled site frequency spectra for the Rwandan population of D. melanogaster, as seen in figure 5 of ref. 33, suggests that incomplete sweeps are relatively infrequent in this population. If favorable mutations do not arise as single events, the estimates of the proportions of favorable mutations are likely to be overestimated as well.

These considerations mean that the estimates of the parameters of positive selection obtained in this and previous studies need to be treated with caution, and will no doubt be revised with future improvements in inference procedures. It seems clear, however, that hitchhiking effects greatly reduce neutral or nearly neutral sequence diversity in genes in normally recombining regions of the Drosophila genome. There is increasing evidence that this is also true for many other organisms (1, 3). Such processes have important implications for attempts to estimate demographic parameters, which usually ignore these complications, as has been pointed out before (53 ? ? –56). This is especially important when selection at linked sites distorts gene genealogies and hence site frequency spectra, because these are the main basis for inferring demographic parameters. There is evidence from our unbinned data for mel-yak that KA is weakly positively correlated with the proportion of singletons at synonymous sites (Spearman partial rank correlation, ? = 0.044, P = 0.002), consistent with increased distortions of the frequency spectra caused by hitchhiking in genes with large KA, as was previously found by Andolfatto (15). The problem of relating the magnitude of these effects to the BGS and SSW models remains to be explored.

Top Research Analyses.

We used polymorphism data for coding sequences of 7,099 autosomal genes, using 17 haploid genomes from the Gikongoro (Rwanda) population of Drosophila melanogaster provided by the Drosophila Population Genomics Project 2 (57), with Drosophila yakuba as an outgroup. The coding sequence data were filtered and analyzed as described in materials and methods in ref. 19. We excluded 225 genes located in the autosomal heterochromatic regions and on chromosome 4, where crossing over is absent (19, 58). We obtained diversity and divergence statistics for synonymous and NS sites, as well as for 5?- and 3?-UTRs for D. melanogaster genes with UTR annotations. For the analyses of UTRs, we followed the annotations of Flybase, version 5.33, masking any UTRs included in coding sequences and excluding UTRs with no available sequence in the outgroup, leaving a dataset of 5,992 genes with 3?- and/or 5?-UTRs. After applying a Kimura two-parameter correction (59), the mean level of divergence of UTR sequences between species, KU, was 0.10, which is intermediate between the mean values for NS sites (KA = 0.038) and synonymous sites (KS = 0.262).

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