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
ALN1
Alignment 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.
ALN2
Alignment 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_1
Alignment derived from ALN2.fas that corresponds to the putative recombinant region (204nt).
ALN2_2
Alignment derived from ALN2.fas with the deletion of the putative recombinant region.
ALN2_C
Alignment derived from ALN2.fas that corresponds to the C-gene region.
ALN2_E
Alignment derived from ALN2.fas that corresponds to the E-gene region.
ALN2_NS1
Alignment derived from ALN2.fas that corresponds to the NS1-gene region.
ALN2_NS2A
Alignment derived from ALN2.fas that corresponds to the NS2A-gene region.
ALN2_NS2B
Alignment derived from ALN2.fas that corresponds to the NS2B-gene region.
ALN2_NS3
Alignment derived from ALN2.fas that corresponds to the NS3-gene region.
ALN2_NS4A
Alignment derived from ALN2.fas that corresponds to the NS4A-gene region.
ALN2_NS4B
Alignment derived from ALN2.fas that corresponds to the NS4B-gene region.
ALN2_NS5
Alignment derived from ALN2.fas that corresponds to the NS5-gene region.
ALN2_PrM
Alignment derived from ALN2.fas that corresponds to the PrM-gene region.
ALN3
Alignment based on ALN2.fas with the deletion of the E gene and the region of NS3 identified as a possible recombinant fragment.
E_161
Alignment 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_C
Beast xml file used in Beast inference 1 for the C-gene.
Beast_inference1_E
Beast xml file used in Beast inference 1 for the E-gene.
Beast_inference1_NS1
Beast xml file used in Beast inference 1 for the NS1-gene.
Beast_inference1_NS2A
Beast xml file used in Beast inference 1 for the NS2A-gene.
Beast_inference1_NS2B
Beast xml file used in Beast inference 1 for the NS2B-gene.
Beast_inference1_NS3
Beast xml file used in Beast inference 1 for the NS3-gene.
Beast_inference1_NS4A
Beast xml file used in Beast inference 1 for the NS4A-gene.
Beast_inference1_NS4B
Beast xml file used in Beast inference 1 for the NS4B-gene.
Beast_inference1_NS5
Beast xml file used in Beast inference 1 for the NS5-gene.
Beast_inference1_PrM
Beast xml file used in Beast inference 1 for the PrM-gene.
Beast_inference2_ALN2_1
Beast xml file used in Beast inference 2 for the putative recombinant region of the genome.
Beast_inference2_ALN2_2
Beast xml file used in Beast inference 2 for the putative non-recombinant region of the genome.
Beast_inference3
Beast 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_161
Beast xml file used in Beast inference 4 for analysing the 161 longest E-sequences.
Figure3_a_BI
Tree file corresponding to result of the Bayesian inference reported in Figure 3a.
Figure3_a_ML
Tree file corresponding to result of the Maximum Likelihood inference reported in Figure 3a.
Figure3_b_BI
Tree file corresponding to result of the Bayesian inference reported in Figure 3b.
Figure3_b_ML
Tree file corresponding to result of the Maximum Likelihood inference reported in Figure 3b.
Beast_inference4_E_161_tree
Tree file corresponding to result of the Beast inference 4 described in Figure 5.