Genetics, Vol. 166, 1611-1629, April 2004, Copyright © 2004

Recombination and Migration of Cryphonectria hypovirus 1 as Inferred From Gene Genealogies and the Coalescent

Ignazio Carbonea, Yir-Chung Liub, Bradley I. Hillmanc, and Michael G. Milgroomb
a Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695,
b Department of Plant Pathology, Cornell University, Ithaca, New York 14853
c Department of Plant Pathology, Rutgers University, New Brunswick, New Jersey 08901

Corresponding author: Michael G. Milgroom, 334 Plant Science Bldg., Cornell University, Ithaca, NY 14853., mgm5{at}cornell.edu (E-mail)

Communicating editor: S. TAVARÉ

Genealogy-based methods were used to estimate migration of the fungal virus Cryphonectria hypovirus 1 between vegetative compatibility types of the host fungus, Cryphonectria parasitica, as a means of estimating horizontal transmission within two host populations. Vegetative incompatibility is a self/non-self recognition system that inhibits virus transmission under laboratory conditions but its effect on transmission in nature has not been clearly demonstrated. Recombination within and among different loci in the virus genome restricted the genealogical analyses to haplotypes with common mutation and recombinational histories. The existence of recombination necessitated that we also use genealogical approaches that can take advantage of both the mutation and recombinational histories of the sample. Virus migration between populations was significantly restricted. In contrast, estimates of migration between vegetative compatibility types were relatively high within populations despite previous evidence that transmission in the laboratory was restricted. The discordance between laboratory estimates and migration estimates from natural populations highlights the challenges in estimating pathogen transmission rates. Genealogical analyses inferred migration patterns throughout the entire coalescent history of one viral region in natural populations and not just recent patterns of migration or laboratory transmission. This application of genealogical analyses provides markedly stronger inferences on overall transmission rates than laboratory estimates do.




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