Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes)

Abstract

Background: The phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last decades as new data and analytical methods became available. Analyzing presence/absence patterns of retroposed elements avoids the problems of homoplastic characters inherent in other methodologies. In gamebirds, chicken repeats 1 (CR1) are the most prevalent retroposed elements, but little is known about the activity of their various subtypes over time. Ascertaining the fixation patterns of CR1 elements would help unravel the phylogeny of gamebirds and other poorly resolved avian clades.

Results: We analyzed 1,978 nested CR1 elements and developed a multidimensional approach taking advantage of their transposition in transposition character (TinT) to characterize the fixation patterns of all 22 known chicken CR1 subtypes. The presence/absence patterns of those elements that were active at different periods of gamebird evolution provided evidence for a clade (Cracidae + (Numididae + (Odontophoridae + Phasianidae))) not including Megapodiidae; and for Rollulus as the sister taxon of the other analyzed Phasianidae. Genomic trace sequences of the turkey genome further demonstrated that the endangered African Congo Peafowl (Afropavo congensis) is the sister taxon of the Asian Peafowl (Pavo), rejecting other predominantly morphology-based groupings, and that phasianids are monophyletic, including the sister taxa Tetraoninae and Meleagridinae.

Conclusion: The TinT information concerning relative fixation times of CR1 subtypes enabled us to efficiently investigate gamebird phylogeny and to reconstruct an unambiguous tree topology. This method should provide a useful tool for investigations in other taxonomic groups as well.

Figure 1

Principle behind the TinT method. Examples of directed insertions of CR1 elements active at different periods. (A) Shows three different CR1 subytpes, active at non-overlapping periods and their resultant TinTs (in box below). As indicated by blue arrows, the youngest element (C2) inserted into both older subtypes (D2 and C4). D2 was active after C4 became inactive and inserted into the latter (red arrow). (B) Example of CR1 subtypes active at overlapping and non-overlapping periods. Only elements that were active during overlapping periods (C2 and B2) had the opportunity to insert each into the other. As the activity period of the B2 element only partially overlapped that of the C2, fewer insertions occurred in the B2-C2 direction (indicated by the thinner arrow). (C) Example of three CR1 subtypes active at overlapping periods. Note that the activity of C4 does not overlap that of F0, thus there was no opportunity for C4 to insert directly into F0. Again, fewer insertions of older elements into younger ones are indicated by thinner arrows.

Figure 2

Comparison of TinT relative times of activity and the main divergences of the galliform tree. (A) Cumulative TinT of CR1 elements on a relative timescale during gamebird evolution. The graph shows the cumulative maximum probabilities of activities for nested CR1 retropositions that were fixed in the ancestral lineage of the chicken genome. (B) A simplified galliform tree showing the main divergences from the lineage leading to the chicken (in red). The CR1 subtypes depicted above the various branch points were identified by presence/absence analysis in species on the corresponding internal branches in this study and by Kaiser et al. [12]. The elements within the shadowed areas connecting (A) and (B) that were apparently active on specific branches of the galliform tree were dominating in corresponding peaks of the cumulative TinT graph.

Figure 3

Retroposed elements as landmarks of galliform evolution. Gray balls represent single retroposition events revealed by our search for CR1 and LTR elements in chicken and turkey sequence databases. Filled gray circles denote markers published by Kaiser et al. [12]. Supported splitting points are labeled with Arabic numerals. Triangles denote branches supported by indel markers (amount given by numbers above) present in the same loci as the retroposed elements. The taxa shown represent only those from which we sampled CR1 elements and LTRs. Significantly supported splitting points are indicated with * p < 0.05, **p < 0.0001.