Cophylogenetic

Cophylogenetics, or cospeciation studies, is a field of evolutionary biology that examines the phylogenies of two interacting groups of organisms, such as hosts and their parasites or symbionts, to determine how closely their evolutionary histories align. The goal is to identify patterns of coevolution and to infer the processes that shape them.

Two broad methodological approaches are used in cophylogenetics. Event-based reconciliation methods aim to explain the parasite or symbiont tree from the host tree by assigning evolutionary events such as cospeciation, host-switching, duplication, and lineage loss, often with a cost-minimization framework. Notable tools for this approach include Jane, CoRe-PA, and eMPRess. Global-fit methods, such as ParaFit and PACo, test for overall congruence between trees and known associations without explicitly inferring a sequence of events.

Analyses typically require robust, well-supported phylogenies for both interacting groups and a matrix of host–symbiont associations. Dating and time-calibrated trees can help interpret the timing of divergence events and potential cospeciation versus host-switching scenarios.

Common outcomes of cophylogenetic studies include evidence for cospeciation, where speciation events in hosts are mirrored by their partners; host-switching, where a lineage shifts to a new host; duplication events within a lineage; and sorting or lineage loss. Classic examples include the coevolutionary history of fig trees and their fig wasps, and the aligned diversification of pocket gophers and their chewing lice. Cophylogenetics has applications in understanding coevolutionary dynamics across systems, with implications for ecology, disease evolution, and conservation, while also facing challenges from incomplete sampling, phylogenetic uncertainty, and timing mismatches.