These are used to make Figure 4B, hence gift ideas a relatively looks-100 % free (immediately after smoothing) mono-tonic matchmaking between them parameters

a comparable consequently they are breakpoints with the high GC blogs because asked in the event that CO breakpoints was where CO-associated gene conversion process was acting?

As to the next question, we indeed find that brand new breakpoint places possess high GC articles than just its surrounding nations and that the brand new closely close re also-gions enjoys high GC-content compared to genome mediocre or perhaps the randomly artificial research (Contour 4A and you can Contour S10 in the More document step one).

I notice too that from the extreme GC content this new lso are-combination rate tends to be more otherwise underestimated

In both we dissect the genome into 10 kb non-overlapping windows of which there are 19,297. First, we ask about the raw correlation between GC% and cM/Mb for these windows, which as expected is positive and significant (Spearman’s rho = 0.192; P <10-15). Second, we wish to know the average effect of increasing one unit in either parameter on the other. Given the noise in the data (and given that current recombination rate need not imply the ancestral recombination rate) we approach this issue using a smoothing approach. We start by rank ordering all windows by GC content and then dividing them into blocks of 1% GC range, after excluding windows with more than 10% ‘N’. The resulting plot is highly skewed by bins with very high GC (55% to 58%) as these have very few data points (Additional file 1: Figure S10E) (the same outliers likely effect the raw correlation too). Re-moving these three results in a more consistent trend

(Additional file 1: Figure S10F). This also suggests that below circa 20% GC the recombination rate is zero (Additional file 1: Figure S10F). Removing those with GC <20% and, more generally, any bins with fewer than 100 windows (all bins with GC < 20% have fewer than 100 windows) leaves 18,680 (96.8%) of the windows, these having a GC content between approximately 20% and 51%.

Because of the observation, we estimate that normally a-1 cm/ Mb rise in recombination rate was of an increase in GC blogs of around 0.5%. Con-versely a-1% boost in GC stuff corresponds to a roughly 2 cM/Mb escalation in recombination price. I finish that because of the visible rareness away from NCO gene conversion process, no less than throughout the bee genome, extrapola-tion from GC articles to help you mediocre crossing-more price hence seems to be justifiable, about for GC content more than 20%. This could reflect a great discordance anywhere between newest and you will early in the day re also-consolidation prices.

Crossing-over price is additionally of this nucleotide range, gene density, and chatrandom dating site you will backup amount variation re-gions (Figure S11-S13 from inside the A lot more file 1) . Offered the removal of hetSNPs off studies the second result is maybe not trivially a great CNV associated artifact. The fine-measure analyses show a confident correlation between nucleotide diversity and you will recombination speed at all this new scales regarding 10, one hundred, 200, otherwise five-hundred kb series screen (Contour S11 for the Even more document step 1). This bolsters early in the day analyses, certainly one of and this advertised the brand new trend however, think it is getting non-significant, whenever you are various other reported a trend ranging from population hereditary rates out-of recombination and you may gen-etic variety. Brand new pattern accords to the sense one re also-consolidation causes reduced Slope-Robertson interference for this reason permitting significantly lower rates off hitchhiking and you may straight back-floor solutions, thus helping greater assortment. We along with find a robust negative relationship ranging from recombin-ation and gene density (Figure S12 in Even more document step one) and you will a strong self-confident relationship between recombination together with duration of multi-content regions during the some window versions (Figure S13 into the Additional document step one). New relationship which have CNVs was in keeping with a job to possess low-allelic re-integration promoting duplications and deletions thru uneven crossing-over .