DOI: 10.5061/dryad.246pr
title: Data from: Reassortment patterns of avian influenza virus internal segments among different subtypes

description: Background: The segmented RNA genome of avian Influenza viruses (AIV)
 allows genetic reassortment between co-infecting viruses, providing an
 evolutionary pathway to generate genetic innovation. The genetic diversity
 (16 haemagglutinin and 9 neuraminidase subtypes) of AIV indicates an
 extensive reservoir of influenza viruses exists in bird populations, but
 how frequently subtypes reassort with each other is still unknown. Here we
 quantify the reassortment patterns among subtypes in the Eurasian avian
 viral pool by reconstructing the ancestral states of the subtypes as
 discrete states on time-scaled phylogenies with respect to the internal
 protein coding segments. We further analyzed how host species, the
 inferred evolutionary rates and the dN/dS ratio varied among segments and
 between discrete subtypes, and whether these factors may be associated
 with inter-subtype reassortment rate. Results: The general patterns of
 reassortment are similar among five internal segments with the exception
 of segment 8, encoding the Non-Structural genes, which has a more
 divergent phylogeny. However, significant variation in rates between
 subtypes was observed. In particular, hemagglutinin-encoding segments of
 subtypes H5 to H9 reassort at a lower rate compared to those of H1 to H4,
 and Neuraminidase-encoding segments of subtypes N1 and N2 reassort less
 frequently than N3 to N9. Both host species and dN/dS ratio were
 significantly associated with reassortment rate, while evolutionary rate
 was not associated. The dN/dS ratio was negatively correlated with
 reassortment rate, as was the number of negatively selected sites for all
 segments. Conclusions: These results indicate that overall selective
 constraint and host species are both associated with reassortment rate.
 These results together identify the wild bird population as the major
 source of new reassortants, rather than domestic poultry. The lower
 reassortment rates observed for H5N1 and H9N2 may be explained by the
 large proportion of strains derived from domestic poultry populations. In
 contrast, the higher rates observed in the H1N1, H3N8 and H4N6 subtypes
 could be due to their primary origin as infections of wild birds with
 multiple low pathogenicity strains in the large avian reservoir.
description: XML of Eurasian
 AIVXML were created in
 BEAUti v1.6.2 for analysis in BEAST v1.7.3 (Drummond & Rambaut, 2007,
 Drummond et al. 2012). For each file, one internal segment of the same 344
 subsampled Eurasian AIV (specified with subtype, host, location and
 isolate dates) was used as input data, labelled with the segment name.
 Files labelled with “original” represent the original time-scaled
 phylogenies of different segments. The substitution, clock and coalescent
 models are provided along with the priors placed on the model parameters.
 The other files labelled “empirical” and “H, N or HN” were generated to
 estimate the transition rate among discrete subtypes (HA, NA or HA-NA
 combined), with the implementation of a discrete trait model and BSSVS
 (Lemey et al. 2009) using empirical trees for each segment. These other
 files contain additional XML code not generated by BEAUTi in order to
 allow the re-use of the previously generated empirical tree
 sets.