Of the comparing the new genotypes out of drones to the a couple of phased haplotypes of the king, we obtain mosaic drone chromosomes in which genotype stops transform ranging from a couple haplotypes of queen. Cut-off size is the actual interval ranging from a couple stop indicators of that it cut off. Cut off changing will be the result of often CO otherwise gene transformation. Such as early in the day knowledge [8,45] a lot of system lengths of gene sales was more below ten kb; we think of this a safe upper bound. That’s i determine prevents comprising ?10 kb as the consequence of gene conversion rates (in addition to CO-associated gene sales and you will NCO gene conversions), while you are reduces having period >ten kb is actually known as CO incidents. To check on to have robustness i and working many tolerance selections from so you’re able to 20 kb getting CO and gene transformation (Contour S5 for the Even more file 1). We also consider an upper limit out of 100 kb.

Which is, in the event the 1 and you may 2 depict the 2 maternal haplotypes, brand new king was:

To identify if or not gene sales situations is actually from the crossing over or even more more than likely caused by NCO events, we think about the genomic context of the conversion process enjoy. When the a good CO enjoy has actually an associated regional gene conversion next i anticipate indeed there becoming you to definitely highest take off (brand new CO feel) having upstream or downstream with the, a couple then brief blocks close to each other.

Notice then the a couple of italicized quick stops beside the big stop (see Contour S4 inside A lot more document step 1 having a real example). When the upcoming we see one or two quick stops one exists alongside each other and then have close to a beneficial CO experiences regarding the same take to, he could be considered as you to definitely CO-relevant gene conversion process event. Proximity contained in this framework implies that the greater amount of faraway cut off (22) is no over ten kb regarding side of the newest CO take off, that is, the fresh new course of brand new take off marked inside red-colored are less than ten kb (period is defined as the duration of the block, which is the interval ranging from one or two border indicators within this cut-off). Although not, in this case, we cannot discriminate what type of these two short prevents are the newest converted one to. Any kind of putative gene transformation occurrences is actually up coming known as NCO gene conversion rates and you will believed becoming caused by an NCO knowledge (for decision tree pick Shape S16 during the Additional document step 1). Such as for instance, assuming the latest physical distances are appropriate, a gene transformation far from good CO you may appear to be this:

That is categorized given that a great NCO gene conversion experiences. To possess robustness i plus enquire about the effects regarding relaxing that it ten kb distance presumption, making it possible for CO gene transformation situations to get inside a hundred kb regarding a CO stop.

Remember that this technique, since it doesn’t come with tetrad data, never without difficulty care for easy gene conversions on the crossing-over. Including, if a queen are:

where the gene conversion duration is actually italicized. All of our measures, examining one haploid drone by yourself, would telephone call which as a whole CO enjoy and you can miss out the effortless gene sales feel. For this reason haploid drone/spunk entering almost certainly underestimates what amount of gene sales associated with the crossing-over.

Character out-of recombination events for the workers

Six workers from colony III were also sequenced. Unlike drones, workers are diploid, one haplotype from the sequenced queen and the other from an unknown drone. To separate the queen haplotype from the foreign drone, we considered two scenarios: (1) for each marker in colony III, if this site is homozygous in the worker, then the genotype from the queen haplotype is easily determined as this homozygous one; (2) if this site is called a heterozygous SNP, and if this hetSNP (for example, A/T) is the same as the ple, A/T), then we cannot decide which one is from the queen; and if this hetSNP (for example, G/T) is not the same as the e as the marker (T) is determined to come from the queen. Then we found that one main source of false positives is that hetSNP may be falsely called as homoSNP in workers, due to low read quality or uneven distribution of reads in each genotype. So gene conversion events were not identified in workers. Finally, 309,218 markers per worker are identified to map recombination events. We are reasonably confident that our methods minimize miscalling owing to CNVs in workers. In the two haplotypes of workers, one is from the queen and one from a foreign drone, and we only identify COs in the queen haplotype. When we screened for markers, the hetSNPs introduced by CNVs in this queen we detected in the drones were removed. As gay hookup bars Windsor in addition we only analyzed COs in workers (tract length >10 kb), while most of the CNVs (>90%) we detected are <10 kb, we suggest that CNVs have minimal influence on our analysis in workers.