DOI: 10.5061/dryad.504636cd
title: Data from: First dating of a recombination event in mammalian tick-borne flaviviruses

description: The mammalian tick-borne flavivirus group (MTBFG) contains viruses
 associated with important human and animal diseases such as encephalitis
 and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where
 recombination events are frequent, the evolutionary dynamic within the
 MTBFG was believed to be essentially clonal. This assumption was
 challenged with the recent report of several homologous recombinations
 within the Tick-borne encephalitis virus TBEV. We performed a thorough
 analysis of publicly available genomes in this group and found no
 compelling evidence for the previously identified recombinations. However,
 our results show for the first time that demonstrable recombination (i.e.,
 with large statistical support and strong phylogenetic evidences) has
 occurred in the MTBFG, more specifically within the Louping ill virus
 lineage. Putative parents, recombinant strains and breakpoints were
 further tested for statistical significance using phylogenetic methods. We
 investigated the time of divergence between the recombinant and parental
 strains in a Bayesian framework. The recombination was estimated to have
 occurred during a window period of 282 to 76 years before the present. By
 unravelling the temporal setting of the event, we adduce hypotheses
description: ALN1Alignment that contains
 41 complete nucleotide sequences of Tick-borne encephalitis virus and
 three out-groups selected among LGTV and OHFV, retrieved from Genbank in
 January 2011.ALN2Alignment that contains
 28 sequences from ALN1 of known collection dates (from 1937 to 2008), with
 the deletion of out-groups and strains with unusual sampling locations.
 Non coding flanking regions and gap columns were
 removed.ALN2_1Alignment derived from
 ALN2.fas that corresponds to the putative recombinant region
 (204nt).ALN2_2Alignment derived from
 ALN2.fas with the deletion of the putative recombinant
 region.ALN2_CAlignment derived from
 ALN2.fas that corresponds to the C-gene region.ALN2_EAlignment derived from
 ALN2.fas that corresponds to the E-gene region.ALN2_NS1Alignment derived from ALN2.fas that corresponds to the NS1-gene region.ALN2_NS2AAlignment derived from ALN2.fas that corresponds to the NS2A-gene region.ALN2_NS2BAlignment derived from ALN2.fas that corresponds to the NS2B-gene region.ALN2_NS3Alignment derived from ALN2.fas that corresponds to the NS3-gene region.ALN2_NS4AAlignment derived from ALN2.fas that corresponds to the NS4A-gene region.ALN2_NS4BAlignment derived from ALN2.fas that corresponds to the NS4B-gene region.ALN2_NS5Alignment derived from ALN2.fas that corresponds to the NS5-gene region.ALN2_PrMAlignment derived from ALN2.fas that corresponds to the PrM-gene region.ALN3Alignment based on ALN2.fas with the deletion of the E gene and the region of NS3 identified as a possible recombinant fragment.E_161Alignment compiled from the 161 longest E-sequences from Tick-borne encephalitis virus species available in Genbank (1033 to 1491 nt in length) endowed with sampling dates (from 1931 to 2008) retrieved in January 2011.Beast_inference1_CBeast xml file used in Beast inference 1 for the C-gene.Beast_inference1_EBeast xml file used in Beast inference 1 for the E-gene.Beast_inference1_NS1Beast xml file used in Beast inference 1 for the NS1-gene.Beast_inference1_NS2ABeast xml file used in Beast inference 1 for the NS2A-gene.Beast_inference1_NS2BBeast xml file used in Beast inference 1 for the NS2B-gene.Beast_inference1_NS3Beast xml file used in Beast inference 1 for the NS3-gene.Beast_inference1_NS4ABeast xml file used in Beast inference 1 for the NS4A-gene.Beast_inference1_NS4BBeast xml file used in Beast inference 1 for the NS4B-gene.Beast_inference1_NS5Beast xml file used in Beast inference 1 for the NS5-gene.Beast_inference1_PrMBeast xml file used in Beast inference 1 for the PrM-gene.Beast_inference2_ALN2_1Beast xml file used in Beast inference 2 for the putative recombinant region of the genome.Beast_inference2_ALN2_2Beast xml file used in Beast inference 2 for the putative non-recombinant region of the genome.Beast_inference3Beast xml file used in Beast inference 3 based on the 28 full length ORFs with both E-gene and the recombinant fragment omitted.Beast_inference4_E_161Beast xml file used in Beast inference 4 for analysing the 161 longest E-sequences.Figure3_a_BITree file corresponding to result of the Bayesian inference reported in Figure 3a.Figure3_a_MLTree file corresponding to result of the Maximum Likelihood inference reported in Figure 3a.Figure3_b_BITree file corresponding to result of the Bayesian inference reported in Figure 3b.Figure3_b_MLTree file corresponding to result of the Maximum Likelihood inference reported in Figure 3b.Beast_inference4_E_161_treeTree file corresponding to result of the Beast inference 4 described in Figure 5.