Table 2.

Example gene tree-species phylogeny reconciliation analysis using Notung v2.8 (Vernot et al., 2007; Stolzer et al., 2012).

Notung run	Transfer cost	Duplication cost	Loss cost	No. equally parsimonious solutions	Reconciliation score	Recovers Podospora HGT
Figure S1C	-	1.5	1	1	123	no
Figure S1D	3	1.5	1	256	70	yes
Figure S1E	7.5	1.5	1	1	97.5	yes
Figure S1F	15	1.5	1	1	112.5	yes
Figure S1G	17	1.5	1	1	116.5	yes
Figure S1H	19	1.5	1	1	119.5	no
Figure S1I	30	1.5	1	1	123	no

Gene tree of homologous sequences to stcI (a gene in the sterigmatocystin SM cluster, Supplementary Figure S1A) was reconciled to the consensus species phylogeny (Supplementary Figure S1B) using different transfer costs. Only when using a transfer cost over 11.33 times the duplication cost, does Notung no longer predict a HGT from Aspergillus to Podospora anserina. See Supplementary Figure 1 for reconciled trees.