Parasitoid-Host Cophylogenetic Analyses
When cospeciation between parasites and their hosts occurs, we expect congruence between parasitoid and host phylogenies and a 1:1 relationship between the interacting species, demonstrating strong host specialization (Balbuena, Míguez-Lozano, & Blasco-Costa, 2013; Fahrenholz, 1913; Legendre, Desdevises, & Bazin, 2002; Page, 2003). Given the degree of host flexibility observed within Eadyaparasitoids (Peixoto et al., 2018; Ridenbaugh et al., 2018), cospeciation with their hosts was not expected. To test this, two cophylogenetic methods were used, an event-based and distance-based method. The former compares parasitoid and beetle tree topologies and their associations to reconstruct cospeciation, duplication, host switch, losses, and failure-to-diverge events, while the later uses distance matrices produced from the parasitoid and beetle phylogenies and their associations to statistically test for congruences between the two topologies. In the event-based reconstruction cospeciation events occur when the parasite speciates in unison with the host. Duplication events are when speciation in the parasite occurs independently from the host. Host switching is the result of a duplication event in which the parasite jumps to a new host lineage. Loss and failure-to-diverge events are very similar in that both occur when the host speciates, but the parasite does not. However, in loss events the parasite only remains on one of the new host lineages, and in failure-to-diverge events the parasite remains on both host lineages. For the event-based analysis Jane 4 (Conow, Fielder, Ovadia, & Libeskind-Hadas, 2010) was used, with the genetic algorithm set to run for 200 generations with a population size of 5000 using two different cost models. The first model was the default cost model for Jane, with cospeciation set to 0, duplication and host switching set to 2, and all other event types set to 1. An alternative model was used with cospeciation set to -10 and all other events set to default to test the algorithms sensitivity to the cost settings. For this method the input was trees drawn by hand using the tree editor within Jane 4 and with clades collapsed for each species to control for the potential overestimation of cospeciation events due to sampling bias (Bass, 2019). For the distance-based method, a PACo analysis (Balbuena et al., 2013) was used as implemented in R (R Core Team, 2016) using the R package “PACo” (Hutchinson, Cagua, Balbuena, Stouffer, & Poisot, 2017). PACo was run for 10,000 permutations with the r0 randomization algorithm from the R package “vegan” (Oksanen et al., 2016).