Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses

Table 3 Recombination event 3 and other potential recombination signals in whole genome Gamma-PVs

Estimated Break point positions				Recombinant (Gamma-species)	Parent sequence		Evidence (method with P value < 0.05)	Intra-species or inter species recombination
In Alignment		In Genbank sequence		Recombinant (Gamma-species)	Minor (Gamma-species)	Major (Gamma-species)	Evidence (method with P value < 0.05)	Intra-species or inter species recombination
4446	8018	3631	6426	^HPV4 (γ-1)	HPV130 (γ-10)	Unknown (HPV162)(γ-19)	M,C,S, 3S	Inter-species
				HPV163[T]
				HPV173[T]
				HPV205[T]
				HPV158[T]
				HPV95[T]
				HPV65[T]

N.B Only event 3 is shown in Table 2, all the potential recombinant Gamma-PVs for this event are shown in the recombinant column and the proposed major and minor parents
^ = The recombinant sequence may have been misidentified (one of the identified parents might be the recombinant
Minor Parent = Parent contributing the smaller fraction of sequence
Major Parent = Parent contributing the larger fraction of sequence
Unknown = only one parent and a recombinant need be in the alignment for a recombination event to be detectable the sequence listed as unknown was used to infer the existence of a missing parental sequence
[T] Sequences with trace evidence of the same recombinant event

ISSN: 1471-2164