Inference of Ancestral Recombination Graphs through Topological Data Analysis
Fig 10
Barcode ensemble and partially reconstructed tARG of a sample of 112 Darwin’s finches.
The barcode ensemble is shown in (A), based on 140 homozygous SNPs present in a 9 megabase scaffold. In total, 13 recombination/gene flow events are captured in the barcode ensemble, with different genetic scales. Bars are colored according to the position of the corresponding recombination breakpoint in the genome, as depicted in (C). We also indicate the number of recombination events detected at each genomic interval, as well as some of the orthologous genes present at regions where recombination events are detected. The reconstructed tARG is presented in (B). Loops in the reconstructed tARG are outlined using the same code of colors. We have also included leaf nodes that do not participate in any recombination event, using a nearest neighbour algorithm based on genetic distance. Edge lengths are arbitrary.