RecPD: A Recombination-aware measure of phylogenetic diversity
Fig 1
Outline of the RecPD methodology: Calculating recombination adjusted phylogenetic diversities of feature distributions by employing ancestral state reconstructions.
(A) Tip states are assigned to a given species phylogenetic tree based on presence (teal), or absence (red) of the gene family of interest. (B) Ancestral node states are inferred using one of there ancestral state reconstruction methods and assigned to either presence (teal), absence (red), or split (blue) states, the latter which indicate potential gain/loss events. (C) Branches are assigned to presence states if they join consecutive presence or split nodes/tips (teal), otherwise they are assigned to absence (red). (D) Gene-family lineages are identified, and split state nodes are assigned to gains (teal) or losses (red). Branches descended from the phylogenetic tree root node where no ancestral presence nodes were identified are assigned to absence (grey). RecPD is then calculated as the sum of gene family lineage branch-lengths normalized by the total branch-lengths of the phylogenetic tree.