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

Kriegs JO, Matzke A, Churakov G, Kuritzin A, Mayr G, Brosius J, Schmitz J - BMC Evol. Biol. (2007)

Bottom Line: 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.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.This method should provide a useful tool for investigations in other taxonomic groups as well.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Experimental Pathology (ZMBE) University of Münster, Von-Esmarch-Str, 56, D-48149 Münster, Germany. kriegs@uni-muenster.de

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.

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Related in: MedlinePlus

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.
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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.

Mentions: The results show that the various CR1 subtypes differ not only in the median time points on the relative timescale during which they were actively fixed in the genome, but also in the lengths of these time windows, revealing three major peaks of concentrated CR1 activity/fixation (Figure 2A, additional data file 1). The oldest peak is dominated by CR1 subtypes Y4, D, X2, E, C4, Y, F2, D2, and X elements, the middle peak by CR1 subtypes Y2, C3, G, F2, X1, D2, H, Y4, E, and C, and the youngest peak by CR1 subtypes H2, F0, B2, F2, D2, and C2.


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

Kriegs JO, Matzke A, Churakov G, Kuritzin A, Mayr G, Brosius J, Schmitz J - BMC Evol. Biol. (2007)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2169234&req=5

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.
Mentions: The results show that the various CR1 subtypes differ not only in the median time points on the relative timescale during which they were actively fixed in the genome, but also in the lengths of these time windows, revealing three major peaks of concentrated CR1 activity/fixation (Figure 2A, additional data file 1). The oldest peak is dominated by CR1 subtypes Y4, D, X2, E, C4, Y, F2, D2, and X elements, the middle peak by CR1 subtypes Y2, C3, G, F2, X1, D2, H, Y4, E, and C, and the youngest peak by CR1 subtypes H2, F0, B2, F2, D2, and C2.

Bottom Line: 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.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.This method should provide a useful tool for investigations in other taxonomic groups as well.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Experimental Pathology (ZMBE) University of Münster, Von-Esmarch-Str, 56, D-48149 Münster, Germany. kriegs@uni-muenster.de

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.

Show MeSH
Related in: MedlinePlus