Figure 1
From: Feline immunodeficiency virus (FIV) envrecombinants are common in natural infections
Maximum likelihood (ML) tree based on the 708 bp fragment (span 3 as identified by GARD) of the env sequences and their recombination history as inferred by GARD. The data include 47 entire env nucleotide sequences (representative of a total of 355 sequences from Chicago and Memphis), 15 full length env sequences derived from GenBank: Aomori 1 [D37816], Aomori 2 [D37817.1], FIV C [AF474246.1], Dixon [L00608.1], Dutch [X60725], Fukuoka [D37815.1], Sendai 1 [D37813.1], Shizuoka [D37811.1], UK2 [X69494.1], UK8 [X69496.1], USIL2489 [U11820.1], Yokohama [D37812.1], Petaluma [M25381.1], PPR [M36968.1], Leviano [FJ374696.1], three V3-V5 region sequences representing Clade E: LP3 [D84496], LP20 [D84498], LP24 [D84500] and one shorter 504 bp in length RUS14 [EF447297] sequence. Taxa with inconsistent clade assignment are represented with an asterisk (P8, P21). Non-monophyletic taxa from cat M5 are marked with a triangle. The tree is based on an HKY model, rooted on FIV C sequence and is drawn to scale, with branch lengths measured in substitutions per site. Only bootstrap values above 80 are shown. * represents bootstrap values of 100.