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Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments

Daniel T. Haydon^1,

¹ Department of Zoology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
² Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa
³ Department of Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA

Correspondence
Daniel T. Haydon
D.Haydon{at}bio.gla.ac.uk

We have applied tests for detecting recombination to genes of foot-and-mouth disease virus (FMDV). Our approach estimated summary statistics of linkage disequilibrium (LD), which are sensitive to recombination. Using the genealogical relationships, rate heterogeneity and mutation parameters estimated from individual sets of aligned gene sequences, we simulated matching RNA sequence datasets without recombination. These simulated datasets allowed for recurrent mutations at any site to mimic homoplasy in virus sequence data and allow construction of null distributions for LD parameters expected in the absence of recombination. We tested for recombination in two ways: by comparing LD in observed data with corresponding null distributions obtained from simulated data; and by testing for a negative relationship between observed LD between pairs of polymorphic nucleotide sites and inter-site distance. We applied these tests to six FMDV datasets from four serotypes and found some evidence for recombination in all of them.

Present address: Division of Environmental and Evolutionary Biology, University of Glasgow, Glasgow G12 8QQ, UK.

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