Figure 6

Evaluation of C. heterostrophus NPS2 and A. nidulans SidC with the PDH algorithm (possible duplication history). A. i) Unrooted maximum likelihood phylogeny of C. heterostrophus NPS2 A domains, the duplication tree resulting from rooting the phylogeny at position b (top) and inferred partially ordered duplication history (below). ii) Unrooted maximum likelihood phylogeny of C. heterostrophus NPS2 C domains, the duplication tree resulting from rooting the phylogeny at position c, and partially ordered duplication history (bottom). iii) and iv) Representation of the series of three tandem duplication events suggested by the partially ordered duplication trees of C domains. Bold and thin lines indicate relationships among modules 1, 3, and 5 and among modules 2, 4 and 6 respectively. If one infers loss of AMP5 and AMP6, relationships among A domains are consistent with the series of three tandem duplication events inferred from the C domain partially ordered duplication history: Step 1) duplication of A module 1, Step 2) duplication of A modules 1 and 2, and Step 3) duplication of A modules 3 and 4. v) Relationships among A and among C domains in partially ordered duplication histories mapped to the domain architecture with predicted domain losses shown in red. B. i) Unrooted maximum likelihood phylogeny of A. nidulans SidC A domains, duplication tree rooted at position b (top) and inferred partially ordered duplication history (bottom). ii) Unrooted maximum likelihood phylogeny of A. nidulans SidC C domains, duplication tree rooted at position c (top) and inferred partially ordered duplication history (bottom). iii) and iv) Representation of the series of three tandem duplication events suggested by the partially ordered duplication trees. Bold and thin lines as in A above. Relationships among A. nidulans SidC A domains are consistent with the series of tandem duplication events predicted by relationships among the C. heterostrophus NPS2 C domains if losses of AMP2, AMP5, and AMP6 are invoked (iii). Relationships among SidC C domains are also consistent with a series of three tandem duplication events if loss of CON2 is invoked (iv). v) Relationships from partially ordered duplication histories mapped to the domain architecture with predicted domain losses shown in red.