Erratum: The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms (BMC Evolutionary Biology (2015) 15 (244) DOI: 10.1186/s12862-015-0473-3);The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms

BMC Evolutionary Biology

Volumn 15, Issue 1, 2015, Pages

  Tiley, George P ^a   Burleigh, Gordon ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOSPERM; COMPARATIVE STUDY; GENE EXPRESSION; GENETIC STRUCTURE; GENETIC VARIATION; GENOME; HOMOLOGY; MOLECULAR ECOLOGY; PHYLOGENETICS; PROTEIN; RECOMBINATION;

CODON (ANGIOSPERM); MAGNOLIOPHYTA;

CHLOROPLAST DNA; PLANT DNA;

ANGIOSPERM; EVOLUTION; GENETICS; GENOMICS; MOLECULAR EVOLUTION; PHYLOGENY; REPRODUCTIVE ISOLATION;

ANGIOSPERMS; BIOLOGICAL EVOLUTION; DNA, CHLOROPLAST; DNA, PLANT; EVOLUTION, MOLECULAR; GENOMICS; PHYLOGENY; REPRODUCTIVE ISOLATION;

EID: 84941645639     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/s12862-015-0525-8     Document Type: Erratum

References (119)

1. Fisher RA. The distribution of gene ratios for rare mutations. Proc Roy Soc Edinb. 1930;50:205-20.
2. McVean G, Awadalla P, Fearnhead P. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics. 2002;160:1231-41.
3. Stumpf MPH, McVean G. Estimating recombination rates from population-genetic data. Nat Rev Genet. 2003;4:959-68.
4. Wang Y, Rannala B. Bayesian inference of fine-scale recombination rates using population genomic data. Phil Trans R Soc B. 2008;363:3921-30.
5. Lynch M. The origins of eukaryotic gene structure. Mol Biol Evol. 2006;23:450-68.
6. Cavalier-Smith T. Eukaryotic gene numbers, non-coding DNA and genome size. In: Cavalier-Smith T, editor. The Evolution of Genome Size. London: John Wiley and Sons Ltd; 1985. p. 69-104.
7. Rees H, Durrant A. Recombination and genome size. Theor Appl Genet. 1986;73:72-6.
8. Narayan R, McIntyre FK. Chromosomal DNA variation, genomic constraints and recombination in Lathyrus. Genetica. 1989;79:45-52.
9. Martini E, Diaz RL, Hunter N, Keeney S. Crossover homeostasis in yeast. Cell. 2006;126:285-95.
10. Ross-Ibarra J. Genome size and recombination in angiosperms: a second look. J Evol Biol. 2007;20:800-6.
11. Langley CH, Montgomery E, Hudson R, Kaplan N, Charlesworth B. On the role of unequal exchange in the containment of transposable element copy number. Genet Res. 1998;52:223-35.
12. Bennetzen JL. Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica. 2002;115:29-36.
13. Bennetzen JL, Ma J, Devos KM. Mechanisms of recent genome size variation in flowering plants. Ann Bot. 2005;95:127-32.
14. Devos KM, Brown JKM, Bennetzen JL. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 2002;12:1075-79.
15. International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010;463:763-8.
16. Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 2009;19:243-54.
17. Gaut BS, Wright SI, Rizzon C, Dvorak J, Anderson LK. Recombination: an underappreciated factor in the evolution of plant genomes. Nat Rev Genet. 2007;8:77-84.
18. Anderson LK, Lai A, Stack SM, Rizzon C, Gaut BS. Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Res. 2006;16:115-22.
19. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005;436:793-800.
20. Dvorak J, Yang ZL, You FM, Luo MC. Deletion polymorphism in wheat chromosome regions with contrasting recombination rates. Genetics. 2004;168:1665-75.
21. Wright SI, Agrawal N, Bureau TE. Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Res. 2003;13:1897-903.
22. Marais G. Biased gene conversion: Implications for genome and sex evolution. Trends Genet. 2003;19:330-8.
23. Lesecque Y, Mouchiroud D, Duret L. GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance. Mol Biol Evol. 2013;30:1409-19.
24. Loewe L, Charlesworth B. Background selection in single genes may explain patterns of codon bias. Genetics. 2007;175:1381-93.
25. Marais G, Mouchiroud D, Duret L. Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci U S A. 2001;98:5688-92.
26. Lartillot N. Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes. Mol Biol Evol. 2013;30:489-502.
27. Fullerton SM, Carvalho AB, Clark AG. Local rates of recombination are positively correlated with GC content in the human genome. Mol Biol Evol. 2001;18:1139-42.
28. Meunier J, Duret L. Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol. 2004;21:984-90.
29. Paape T, Zhou P, Branca A, Briskine R, Young N, Tiffin P. Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome. Genome Biol Evol. 2012;4:726-37.
30. Marais G, Charlesworth B, Wright SI. Recombination and base composition: The case of the highly self-fertilizing plant Arabidopsis thaliana. Genome Biol. 2004;5:R45.
31. Pessia E, Popa A, Mousset S, Rezvoy C, Duret L, Marais G. Evidence for widespread GC-biased gene conversion in eukaryotes. Genome Biol Evol. 2012;4:787-94.
32. Zhang L, Kosakovsky Pond S, Gaut BS. A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa. J Mol Evol. 2001;52:144-56.
33. Muller HJ. The relation of recombination to mutational advance. Mutat Res. 1964;1:2-9.
34. Crow JF, Kimura M. Evolution in sexual and asexual populations. Am Nat. 1965;99:439-50.
35. Felsenstein J. The evolutionary advantage of recombination. Genetics. 1974;78:737-56.
36. Hill WG, Robertson A. The effect of linkage on limits to artificial selection. Genet Res. 1966;8:269-94.
37. Charlesworth B, Morgan MT, Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics. 1993;134:1289-303.
38. Campos JL, Halligan DL, Haddrill PR, Charlesworth B. The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster. Mol Biol Evol. 2014;31:1010-28.
39. Tenaillon MI, Sawkins MC, Anderson LK, Stack SM, Doebley J, Gaut BS. Patterns of diversity and recombination along chromosome 1 of maize (Zea mays spp. mays L.). Genetics. 2002;162:1401-13.
40. Wright SI, Foxe JP, DeRose-Wilson L, Kawabe A, Looseley M, Gaut BS, et al. Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata. Genetics. 2006;174:1421-30.
41. Baudry E, Kerdelhué C, Innan H, Stephan W. Species and recombination effects on DNA variability in the tomato genus. Genetics. 2001;158:1725-35.
42. Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, Przeworski M, et al. PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science. 2010;327:836-40.
43. Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, et al. Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc Natl Acad Sci U S A. 2012;109:16240-5.
44. Bauer E, Falque M, Walter H, Bauland C, Camisan C, Campo L, et al. Intraspecific variation of recombination rate in maize. Genome Biol. 2013;14:R103.
45. Yang L, Gaut BS. Factors that contribute to rate variation among Arabidopsis genes. Mol Biol Evol. 2011;28:2359-69.
46. Zhang L, Gaut BS. Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome? Genome Res. 2003;13:2533-40.
47. Akhunov ED, Goodyear AW, Geng S, Qi L-L, Echalier B, Gill BS, et al. The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res. 2003;13:753-63.
48. Rizzon C, Ponger L, Gaut BS. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comp Bio. 2006;doi: 10.1371/journal.pcbi.0020115.
49. Lynch M, Force A. The probability of duplicate gene preservation by subfunctionalization. Genetics. 2000;154:459-73.
50. Xue C, Huang R, Liu S, Fu Y. Recombination facilitates neofunctionalization of duplicate genes via originalization. BMC Genet. 2010;11:46.
51. Lynch M, O'Hely M, Walsh B, Force A. The probability of a newly arisen gene duplicate. Genetics. 2001;159:1789-04.
52. Chakravarti A, Lasher LK, Reefer JE. A maximum likelihood method for estimating genome length using genetic linkage data. Genetics. 1991;128:175-82.
53. Hall MC, Willis JH. Transmission ratio distortion in intraspecific hybrids of Mimulus guttatus: implications for genomic divergence. Genetics. 2005;170:375-86.
54. Dumont BL, Payseur BA. Evolution of the genomic rate of recombination in mammals. Evolution. 2008;62:276-94.
55. Jinks-Robertson S, Petes TD. High-frequency meiotic gene conversion between repeated genes on nonhomologous chromosomes in yeast. Proc Natl Acad Sci U S A. 1985;82:3350-4.
56. Kupiec M, Petes TD. Meiotic recombination between repeated transposable elements in Saccharomyces cerevisiae. Mol Cell Biol. 1988;8:2942-54.
57. Lichten M, Borts RH, Haber JE. Meiotic gene conversion and crossing over between dispersed homologous sequences occurs frequently in Saccharomyces cerevisiae. Genetics. 1987;115:233-46.
58. Goldman AS, Lichten M. The efficiency of meiotic recombination between dispersed sequences in Saccharomyces cerevisiae depends upon their chromosomal location. Genetics. 1996;144:43-55.
59. Laliberté E. metacor: Meta-analysis of correlation coefficients. R package version 1.0-2. http://CRAN.R-project.org/package=metacor (2011).
60. Thuriaux P. Is recombination confined to structural genes on the eukaryotic genome? Nature. 1977;4:460-2.
61. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, et al. The Sorghum biocolor genome and the diversification of grasses. Nature. 2009;457:551-6.
62. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, et al. Phytozome: a comparative platform for green plant genomics. Nucl Acids Res. 2012;40(D1):doi: 10.1093/nar/gkr944.
63. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nuc Acids Res. 2004;3:1792-7.
64. Wright F. The 'effective number of codons' used in a gene. Gene. 1990;87:23-9.
65. Comeron JM, Aguadé M. An evaluation of measures of synonymous codon usage bias. J Mol Evol. 1998;47:268-74.
66. Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, et al. Angiosperm phylogeny: 17 genes, 640 taxa. Am J Bot. 2011;98:704-30.
67. Kosakovsky Pond SL, Frost SWD, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005;21:676-9.
68. Hilu JW. Borsch T, Muller K, Soltis DE, Soltis PS, Savolainen, et al. Angiosperm phylogeny based on matK sequence information. Am J Bot. 2003;90:1758-76.
69. Sanderson MJ. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics. 2003;19:301-2.
70. Kellogg EA. Evolutionary history of the grasses. Plant Physiol. 2001;125:1198-205.
71. Magallón S, Castillo A. Angiosperm diversification through time. Am J Bot. 2009;96:349-65.
72. Davis CC, Webb CO, Wurdack KJ, Jaramillo CA, Donoghue MJ. Explosive radiation of Malpighiales supports Mid-Cretaceous origin of modern tropical rain forests. Am Nat. 2005;165:E36-65.
73. Soltis PS, Soltis DE. The origin and diversification of angiosperms. Am J Bot. 2004;91:1614-26.
74. Anderson LC, Bremer K, Friis EM. Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points. Am J Bot. 2005;92:1737-48.
75. Garland T, Harvey PH, Ives AR. Procedures for the analysis of comparative data using independent contrasts. Syst Biol. 1992;41:1832.
76. Midford PE, Garland Jr. T, Maddison WP. PDAP Package of Mesquite. Version 1.16 (2011). http://mesquiteproject.org/pdap-mesquite/
77. Maddison WP, Maddison DR. Mesquite: A modular system for evolutionary analysis. Version 1.1. http://mesquiteproject.org (2006).
78. Blomberg SP, Garland T. Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. J Evol Biol. 2002;15:899-910.
79. Bomberg SP, Garland T, Ives AR. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution. 2003;57:717-45.
80. Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics. 2010;26:1463-4.
81. Felsenstein J. Phylogenies and the comparative method. Am Nat. 1985;125:1-15.
82. Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics. 2004;20:289-90.
83. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/ (2013).
84. Champely S. pwr: Basic functions for power analysis. R package version 1.1.1. http://CRAN.R-project.org/package=pwr (2012).
85. Cohen J. Statistical power analysis for the behavioral sciences. 2nd ed. Hillsdale, NJ: Lawrence Erlbaum; 1988.
86. Lartillot N, Poujol R. A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Mol Biol Evol. 2011;28:729-44.
87. Shearer LA, Anderson LK, de Jong H, Smit S, Goicoechea JL, Roe BA, et al. Fluorescence In Situ Hybridization and optical mapping to correct scaffold arrangement in the tomato genome. G3. 2014;4:1395-405.
88. Betancourt AJ, Presgraves DC. Linkage limits the power of natural selection in Drosophila. Proc Natl Acad Sci U S A. 2002;99:13616-20.
89. Ruffner H, Joazeiro CAP, Hemmati D, Hunter T, Verma IM. Cancer-predisposing mutations within the RING domain of BRCA1: loss of ubiquitin protein ligase activity and protection from radiation hypersensitivity. Proc Natl Acad Sci U S A. 2001;98:5134-9.
90. Wright DA, Townsend JA, Winfrey Jr RJ, Irwin PA, Rajagopal J, Lonosky PM, et al. High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J. 2005;44:693-705.
91. Perry J, Kleckner N, Borner GV. Bioinformatic analyses implicate the collaborating meiotic crossover/chiasma proteins Zip2, Zip3, and Spo22/Zip4 in ubiquitin labeling. Proc Natl Acad Sci U S A. 2005;102:17594-9.
92. Lynn A, Soucek R, Börner GV. ZMM proteins during meiosis: crossover artists at work. Chromosome Res. 2007;15:591-605.
93. Jantsch V, Pasierbek P, Mueller MM, Schweizer D, Jantsch M, Loidi J. Targeted gene knockout reveals a role in meiotic recombination for ZHP-3, a Zip3-related protein in Caenorhabditis elegans. Mol Cell Biol. 2004;24:7998-8006.
94. Kong A, Thorleifsson G, Stefansson H, Masson G, Helgason A, Gudbjartsson DF, et al. Sequence variants in the RNF212 gene associate with genome-wide recombination rate. Science. 2008;319:1398-401.
95. Jaramillo-Correa JP, Verdu M, Gonzalex-Martinez SC. The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms. BMC Evol Biol. 2010;10:22.
96. Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P. A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 2000;10:908-15.
97. Vitte C, Panaud O. Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol Biol Evol. 2003;20:528-40.
98. Haudry A, Cenci A, Guilhaumon C, Paux E, Poirier S, Santoni S, et al. Mating system and recombination affect molecular evolution in four Triticeae species. Genet Res. 2008;90:97-109.
99. Muyle A, Serres-Giardi L, Ressayre A, Escobar J, Glémin S. GC-biased gene conversion and selection affect GC content in the Oryza genus (rice). Mol Biol Evol. 2011;28:2695-706.
100. Glémin S, Bazin E, Charlesworth D. Impact of mating systems on patterns of sequence polymorphism in flowering plants. Proc Roy Soc London B. 2006;273:3011-9.
101. Escobar JS, Cenci A, Bolognini J, Haudry A, Laurent S, David J, et al. An integrative test of the dead-end hypothesis of selfing evolution in Triticeae (Poaceae). Evolution. 2010;64:2855-72.
102. Gaut BS, Doebley JF. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A. 1997;94:6809-14.
103. Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 2012;485:635-41.
104. Innan H, Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 2010;11:97-108.
105. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, et al. Ancestral polyploidy in seed plants and angiosperms. Nature. 2011;473:97-100.
106. Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McKeal J, et al. A genome triplication associated with early diversification of the core eudicots. Genome Biol. 2012;13:R3.
107. Amborella Genome Project. The Amborella genome and the evolution of flowering plants. Science 2013;342:doi: 10.1126/science.1241089.
108. Kawabe A, Forrest A, Wright SI, Charlesworth D. High DNA sequence diversity in pericentromeric genes of the plant Arabidopsis lyrata. Genetics. 2008;179:985-95.
109. Lercher MJ, Hurst LD. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 2002;18:337-40.
110. Hazzouri KM, Escobar JS, Ness RW, Newmann LK, Randle AM, Kalisz S, et al. Comparative population genomics in Collinsia sister species reveals evidence for reduced effective population size, relaxed selection, and evolution of biased gene conversion with an ongoing mating system shift. Evolution. 2013;67:1263-78.
111. Lanfear R, Kokko H, Eyre-Walker A. Population size and the rate of evolution. Trends Ecol Evol. 2014;29:33-41.
112. Larracuente AM, Sackton TB, Greenberg AJ, Wong A, Singh ND, Sturgill D, et al. Evolution of protein-coding genes in Drosophila. Trends Genet. 2008;24:114-23.
113. Weber CC, Hurst LD. Protein rates of evolution are predicted by double-strand break events, independent of crossing-over rates. Genome Biol Evol. 2009;1:340-9.
114. Schierup MH, Wright SI, Onge K, Hansen TT, Bataillon T, Slotte T. Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol Evol. 2011;3:1210-9.
115. Pál C, Papp B, Hurst LD. Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer. Mol Biol Evol. 2001;18:2323-6.
116. Webster MT, Hurst LD. Direct and indirect consequences of meiotic recombination: implications for genome evolution. Trends Genet. 2012;28:101-9.
117. Slotte T. The impact of linked selection on plant genomic variation. Briefings in Functional Genomics. 2014;13:268-75.
118. Cutter AD, Payseur BA. Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Genet. 2013;14:262-74.
119. Gossman TI, Santure AW, Sheldon BC, Slate J, Zeng K. Highly variable recombinational landscape modulates efficacy of natural selection in birds. Genome Biol Evol. 2014;6:2061-75.