A New Method to Reconstruct Recombination Events at a Genomic Scale
Figure 1
Scheme of the recombination detection process for one run of the algorithm.
(A) Input dataset of 10 sequences and 83 SNPs. Colors on sequences represent similar patterns of SNPs, and a change of color along a sequence represents the signal of past recombination events. (B) Recoded matrix. The patterns of SNPs within a column of grain size n (10 SNPs in this example) have been recoded into numbers. Those sequences having the same pattern within a column will be assigned the same number. Between columns, numbers represent completely different patterns. Unique patterns are assigned the number zero and will not be considered. (C) Trees one, two and three, constructed based on the recoded matrix. Going from left to right, the recoded matrix is segmented into sets of compatible [30] columns of patterns. Compatibility of columns is checked using a variant of the four gamete test [31] for multi-allelic markers. Each segment is represented as a tree in which the leaf nodes contain the sequences analyzed and the edges contain the patterns inherited, similar to point mutations. Recurrence is not allowed. (D) Networks 1–2 and 2–3 constructed from consecutive trees one, two and three merged pairwise. All the information contained in the two original trees will be present in the compatible network. Recombinant sequences are leaf nodes descending from nodes having two parents, which means that have inherited patterns from two different nodes (similar to an Ancestral Recombination Graph). (E) Information saved for each detected recombination event: the recombinants sequences and the starting and ending position of the network. For a more detailed description of the algorithm see [12]. In red, the recombination event that will be further studied in Figure 2.