Reconciliation of a gene network and species tree

The phylogenetic trees of genes and the species which they belong to are similar, but distinct due to various evolutionary processes which affect genes but do not create new species. Reconciliations map the gene tree into the species tree, explaining the discrepancies by events including gene duplications and losses. However, when duplicate genes undergo recombination (a phenomenon known as paralog exchange, or non-allelic homologous...