Covarion structure in plastid genome evolution: a new statistical test - PubMed (original) (raw)
Covarion structure in plastid genome evolution: a new statistical test
Cécile Ané et al. Mol Biol Evol. 2005 Apr.
Abstract
Covarion models of molecular evolution allow the rate of evolution of a site to vary through time. There are few simple and effective tests for covarion evolution, and consequently, little is known about the presence of covarion processes in molecular evolution. We describe two new tests for covarion evolution and demonstrate with simulations that they perform well under a wide range of conditions. A survey of covarion evolution in sequenced plastid genomes found evidence of covarion drift in at least 26 out of 57 genes. Covarion evolution is most evident in first and second codon positions of the plastid genes, and there is no evidence of covarion evolution in third codon positions. Therefore, the significant covarion tests are likely due to changes in the selective constraints of amino acids. The frequency of covarion evolution within the plastid genome suggests that covarion processes of evolution were important in generating the observed patterns of sequence variation among plastid genomes.
Similar articles
- Phylogenetic substitution models for detecting heterotachy during plastid evolution.
Whelan S, Blackburne BP, Spencer M. Whelan S, et al. Mol Biol Evol. 2011 Jan;28(1):449-58. doi: 10.1093/molbev/msq215. Epub 2010 Aug 19. Mol Biol Evol. 2011. PMID: 20724379 - The complete plastid genome sequence of the haptophyte Emiliania huxleyi: a comparison to other plastid genomes.
Sánchez Puerta MV, Bachvaroff TR, Delwiche CF. Sánchez Puerta MV, et al. DNA Res. 2005;12(2):151-6. doi: 10.1093/dnares/12.2.151. DNA Res. 2005. PMID: 16303746 - Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor.
Deusch O, Landan G, Roettger M, Gruenheit N, Kowallik KV, Allen JF, Martin W, Dagan T. Deusch O, et al. Mol Biol Evol. 2008 Apr;25(4):748-61. doi: 10.1093/molbev/msn022. Epub 2008 Jan 24. Mol Biol Evol. 2008. PMID: 18222943 - Reconstructing evolution: gene transfer from plastids to the nucleus.
Bock R, Timmis JN. Bock R, et al. Bioessays. 2008 Jun;30(6):556-66. doi: 10.1002/bies.20761. Bioessays. 2008. PMID: 18478535 Review. - The role of plastids in plant speciation.
Greiner S, Rauwolf U, Meurer J, Herrmann RG. Greiner S, et al. Mol Ecol. 2011 Feb;20(4):671-91. doi: 10.1111/j.1365-294X.2010.04984.x. Epub 2011 Jan 10. Mol Ecol. 2011. PMID: 21214654 Review.
Cited by
- Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST.
Baele G, Gill MS, Bastide P, Lemey P, Suchard MA. Baele G, et al. Syst Biol. 2021 Jan 1;70(1):181-189. doi: 10.1093/sysbio/syaa037. Syst Biol. 2021. PMID: 32415977 Free PMC article. - Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis.
Ye X, Hu D, Guo Y, Sun R. Ye X, et al. PLoS One. 2019 Jul 30;14(7):e0212325. doi: 10.1371/journal.pone.0212325. eCollection 2019. PLoS One. 2019. PMID: 31361757 Free PMC article. - Further Simulations and Analyses Demonstrate Open Problems of Phylostratigraphy.
Moyers BA, Zhang J. Moyers BA, et al. Genome Biol Evol. 2017 Jun 1;9(6):1519-1527. doi: 10.1093/gbe/evx109. Genome Biol Evol. 2017. PMID: 28637261 Free PMC article. - Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium.
Yang J, Yue M, Niu C, Ma XF, Li ZH. Yang J, et al. Genes (Basel). 2017 Apr 19;8(4):124. doi: 10.3390/genes8040124. Genes (Basel). 2017. PMID: 28422071 Free PMC article. - The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms.
Raman G, Park S. Raman G, et al. Front Plant Sci. 2016 Mar 21;7:341. doi: 10.3389/fpls.2016.00341. eCollection 2016. Front Plant Sci. 2016. PMID: 27047519 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources