Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes)
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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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The phylogeny of LINE2 and Mon-1 is supported by a genomewide transposition-in-transposition (TinT) analysis.
“The phylogeny of LINE2 and Mon-1 was also supported by a genomewide transposition-in-transposition (TinT) analysis 59 (Supplementary Tables 7 and 8).”
From Genome analysis of the platypus reveals unique signatures of evolution (2008) · cites this paper as [59]
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Additional file 5 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530432
Additional file 8 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530441
Additional file 4 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530429
Additional file 1 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530420
Additional file 7 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530438
Additional file 3 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530426
Additional file 6 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530435
Additional file 11 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530411
Additional file 10 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530408
Additional file 2 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530423
Additional file 9 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530444
Additional file 13 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530417
Additional file 12 of Genomic bases underlying the adaptive radiation of core landbirds
Wu, Y., Yan, Y., Zhao, Y., Gu, L., Wang, S., & Johnson, D. H. (2021) · Figshare · doi:10.6084/m9.figshare.16530414
Yousif, P., Abdi, A. A., & Mustafa, S. I. (2026) · Russian Journal of Genetics · doi:10.1134/s1022795425701480
Molecular evolution of primates - featuring mobile elements
Osterholz, M. (2009) · doi:10.53846/goediss-327
- Authors
- Kriegs, J., Matzke, A., Churakov, G., Kuritzin, A., Mayr, G., Brosius, J., & Schmitz, J.
- Affiliations
- University of Münster (DE)
- St. Petersburg State Technological Institute (RU)
- Corresponding author
- Kriegs, Jan
- Venue
- BMC Evolutionary Biology
- Published
- 2007
- Volume
- 7
- Issue
- 1
- Pages
- 190
- ISSN
- 1471-2148 (ISSN-L)
- PMC
- PMC2169234
- OpenAlex
- W2154851365
- Cited by
- 82
- References
- 57
- Citations by year
- 2026: 1 · 2022: 3 · 2021: 5 · 2019: 4 · 2018: 2 · 2017: 5 · 2016: 3 · 2015: 4 · 2014: 6 · 2013: 5 · 2012: 12
- FWCI
- 10.13
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Evolutionary Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Publication Server of Goethe University Frankfurt am Main (Goethe University Frankfurt) (submittedVersion, cc-by)
- Funders
- Deutsche Forschungsgemeinschaft
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- Galliformes, game birds, phylogenetic inference, fixation duration, Cracidae, Phasianidae, Megapodiidae, Pavo, grouse, phylogenomics
- MeSH terms
- Animals, DNA Transposable Elements, Phylogeny, Polymerase Chain Reaction, Genome, Sequence Analysis, DNA, Evolution, Molecular, Terminal Repeat Sequences, Galliformes, INDEL Mutation
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