Cospeciation and horizontal transmission of avian sarcoma and leukosis virus gag genes in galliform birds

Abstract

In a study of the evolution and distribution of avian retroviruses, we found avian sarcoma and leukosis virus (ASLV) gag genes in 26 species of galliform birds from North America, Central America, eastern Europe, Asia, and Africa. Nineteen of the 26 host species from whom ASLVs were sequenced were not previously known to contain ASLVs. We assessed congruence between ASLV phylogenies based on a total of 110 gag gene sequences and ASLV-host phylogenies based on mitochondrial 12S ribosomal DNA and ND2 sequences to infer coevolutionary history for ASLVs and their hosts. Widespread distribution of ASLVs among diverse, endemic galliform host species suggests an ancient association. Congruent ASLV and host phylogenies for two species of Perdix, two species of Gallus, and Lagopus lagopus and L. mutus also indicate an old association with vertical transmission and cospeciation for these ASLVs and hosts. An inference of horizontal transmission of ASLVs among some members of the Tetraoninae subfamily (grouse and ptarmigan) is supported by ASLV monophyletic groups reflecting geographic distribution and proximity of hosts rather than host species phylogeny. We provide a preliminary phylogenetic taxonomy for the new ASLVs, in which named taxa denote monophyletic groups.

FIG. 1

Primer locations within avian retrovirus gag genes sequenced and number of amino acid changes relative to the Gag polyprotein. Nucleotide and amino acid position numbers are relative to those of the published RSV genome (27). The known functional domains of assembly (L) and membrane binding (M) are indicated above the gag gene diagram. (A) Fragment 1 indicates the region sequenced for 102 retrovirus clones, and fragment 2 indicates the region sequenced for 40 retrovirus clones. Numbers below the diagram are nucleotide positions, starting at the 3′ base of primers. (B) Graphical representation of the number of amino acid changes over the region sequenced. Amino acid changes were determined from phylogenetic tree branch lengths as described in the text.

FIG. 2

Unrooted NJ tree constructed using Kimura's two-parameter corrected distances, showing the relationship of 85 retroviral sequences based on 720 nucleotide sites from fragment 1 (Fig. 1A) of the gag gene. Bootstrap values are presented for the earliest divergences. An NJ tree using all 112 retroviral sequences has essentially the same topology; we removed 27 taxa representing multiple clones from single individuals from the analysis shown for clarity. Viral sequences are named for their host species (see Table 1 for abbreviations) and a number that identifies clones from the same host individual. When clones were sequenced from multiple individuals from a single species, a letter identifies the individual.

FIG. 3

MP analysis of 61 gag retroviral sequences for fragment 1 isolated from 20 species of galliform birds (see Table 1 for sequence abbreviations and host species). This phylogeny is one of 24 equally parsimonious trees and is based on 654 characters, of which 378 are parsimony informative. Variation in the 24 trees was limited to the relative position of clones from the same individual within groups that remain monophyletic. Bootstrap values greater than 50 are shown on branches (100 replicates). This tree is midpoint rooted.

FIG. 4

Strict consensus of 16 equally parsimonious trees for ASLV gag gene fragment 2 (Fig. 1, GAG.F1-GAG.R2) amplified from 16 species and one subspecies of galliform birds. Of 1,537 nucleotide characters, 557 are parsimony informative. Bootstraps followed by decay indices are indicated on branches, the latter denoting the number of additional steps required to collapse a particular node. Nodes with bootstrap values less than 50 are indicated by a dash. Biogeographic labels are given where ASLV relationships reflect geographic proximity of host species rather than host phylogeny to emphasize inferred independent colonizations (Table 2). An inferred duplication event is also indicated. Roman numerals for clades correspond to those in Fig. 2 and 3.

FIG. 5

Unrooted MP analysis of ASLV gag DNA sequences isolated from birds in the genus Gallus. This phylogeny is based on 1,165 characters (fragment 2) of which 95 are parsimony informative. This is one of two equally parsimonious hypotheses. Bootstrap values above 50 are shown on branches (100 replicates). ML analysis using the GTR model yields the same topology. Sequences GAGA and GAVA are newly sequenced elements from two individuals (A and B) of Gallus gallus and Gallus varius, respectively. gag sequences for the following viruses were obtained from databases: avian leukemia virus, subgroup A (ALV); exogenous avian leukosis virus, subgroup J (HPRS-103); avian myelocytomatosis virus (AVMY); avian retrovirus IC10 (AVRE); RSV (Prague), subgroup C (RSVP); RSV (Schmidt-Ruppin), subgroup D (RSV); FUSV; myeloblastosis-associated virus 1 (MAVT1); myeloblastosis-associated virus 2 (MAVT2); avian sarcoma virus Y73 (Y73); avian sarcoma virus UR2 (ASVUR2); Rous sarcoma-defective endogenous virus, subgroup E (EV1); chicken provirus RAV-0, subgroup E (RAV0) (accession numbers are listed in Materials and Methods).

FIG. 6

Inferred phylogeny for ASLV hosts in the avian order Galliformes based on MP analyses of 2,075 characters (703 informative sites) from the mitochondrial 12S rDNA and ND2 genes, with a waterfowl species (Aythya americana, redhead) as the outgroup. See Table 1 for bird species common names and corresponding ASLV names. Numbers on branches are bootstrap values based on 100 replicate searches and decay indices, respectively. Underlined host taxa were negative for retrovirus infection using our PCR primers.