plosone-phylo
pone.0022099.g001.png
The assessment of possible OGDs on the tree.
The calculation of OGDs involves the assessment of the likelihood of the placement of every branch of the unrooted tree at every possible position for each of the gene families separately. 1) The branch leading to Species A and B is to be assessed and is pruned. It is then replaced at every possible position on the remaining tree (I to V above) and the likelihood of each is assessed. 2) When all likelihoods have been assessed the expected likelihood weight (ELW) of each is calculated. If any placement except the original position receives an ELW of at least 0.65 (implying high support) this is considered a putative transfer event (as in IV above). The branch with the best placement is considered the donor and the recipient is the branch that was assessed at each position (A and B above). 3) To be considered an OGD the path-length distance of the original position of the clade to its best placement is calculated. If this distance is greater than 0.4 (thereby avoiding the possibility of wrongly identifying phylogenetic uncertainty as an OGD), the placement is considered a putative OGD.
pone.0022099.g001.png
The assessment of possible OGDs on the tree.
The calculation of OGDs involves the assessment of the likelihood of the placement of every branch of the unrooted tree at every possible position for each of the gene families separately. 1) The branch leading to Species A and B is to be assessed and is pruned. It is then replaced at every possible position on the remaining tree (I to V above) and the likelihood of each is assessed. 2) When all likelihoods have been assessed the expected likelihood weight (ELW) of each is calculated. If any placement except the original position receives an ELW of at least 0.65 (implying high support) this is considered a putative transfer event (as in IV above). The branch with the best placement is considered the donor and the recipient is the branch that was assessed at each position (A and B above). 3) To be considered an OGD the path-length distance of the original position of the clade to its best placement is calculated. If this distance is greater than 0.4 (thereby avoiding the possibility of wrongly identifying phylogenetic uncertainty as an OGD), the placement is considered a putative OGD.