Host

1. a) MTB b) Extinction c) Host switching A A 1 1 (2) B B (2) (2) C C 3 3 D D 4 4 E E 5 5 A 1 d) Sampling problem a) Missing the boat (MTB): the founder population of host B lacked parasites. B (2) C b) Extinction of parasite 2 among the ancestors of host B. 3 c) Sequential colonization of hosts (A-E) by parasites (1-5) that coincides with host phylogeny, but never colonized host B. D 4 E 5 d) Parasite 2 is present on host B but has not been detected because of low density or variable distribution. A 1 B C 3 D 4 E 5 Host Parasite Explaining the hypothesized absence of parasite 2 from host B (adapted from Fig.1 Paterson et al., 2000. 49:383-399)

2. A host A 1 a) Host b) Parasite B 2 host C C host B 3 c) Reconciliation (spread) 1 A d) Reconciliation (stacked) 1 A B 3 B 2 C 2 C A Reconciling incongruent host and parasite trees (adapted from Fig. 2 Paterson et al., 2000. 49:383-399) 3 B Host (a) and parasite (b) cladograms showing conflict (parasite taxa 1 and 2 are sister taxa but their hosts A and C are not). C Reconciliation analysis reconstructs the evolutionary events (cospeciation, intrahost speciation, and sorting events) necessary to produce the observed host and parasite cladograms. Reconciling these host and parasite trees assuming maximum cospeciation requires one intrahost speciation ( ) (duplication) and three sorting events ( ). Spread (c) and stacked (d) trees are merely different ways of representing the reconciliation tree and contain the same information.