Does variation in genome sizes reflect adaptive or neutral processes? new clues from Passiflora

PLoS ONE

Volumn 6, Issue 3, 2011, Pages

  Yotoko, Karla S C ^a   Dornelas, Marcelo C ^b   Togni, Pakisa D ^c   Fonseca, Tamara C ^b   Salzano, Francisco M ^c   Bonatto, Sandro L ^d   Freitas, Loreta B ^c  

^a FEDERAL UNIVERSITY OF VIÇOSA   (Brazil)

^b UNIVERSITY OF CAMPINAS   (Brazil)

^c FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^d PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DECALOBA; ENVIRONMENTAL CHANGE; EVOLUTIONARY ADAPTATION; GENETIC CORRELATION; GENETIC TRAIT; GENOME SIZE; MOLECULAR PHYLOGENY; NONHUMAN; PASSION FRUIT; PHYLOGENETIC TREE; PLANT; SPECIES COMPARISON; ADAPTATION; FLOWER; GENETIC VARIABILITY; GENETICS; HISTOLOGY; MOLECULAR EVOLUTION; PLANT GENOME;

DECALOBA; PASSIFLORA;

ADAPTATION, PHYSIOLOGICAL; EVOLUTION, MOLECULAR; FLOWERS; GENETIC VARIATION; GENOME, PLANT; PASSIFLORA;

EID: 79953155335     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018212     Document Type: Article

References (63)

1. Thomas CA, (1971) The genetic organization of chromosomes. Ann Rev Genet 5: 237-256.
2. Cavalier-Smith T, (1978) Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the C-value paradox. J Cell Sci 34: 247-278.
3. Gregory TR, (2004) Macroevolution, hierarchy theory, and the C-value enigma. Paleobiol 30: 179-202.
4. Gaut BS, Ross-Ibarra J, (2008) Selection on major components of angiosmperm genomes. Science 320: 484-486.
5. Bennett MD, Smith JB, (1976) Nuclear DNA amounts in angiosperms. Philos Transac Royal Soc London B 274: 227-274.
6. Albertini AM, Hofer M, Carlos MP, Miller JH, (1982) On the formation of spontaneous deletions: The importance of short sequence homologies in the generation of large deletions. Cell 29: 319-328.
7. Bebenek K, Kunkel TA, (1990) Frameshift errors initiated by nucleotide misincorporation. Proc Natl Acad Sci USA 87: 4946-4950.
8. Kunkel T A, (1990) Misalignment-mediated DNA synthesis errors. Biochemistry 29: 8003-8011.
9. Soltis DE, Soltis PS, (1999) Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol 14: 348-352.
10. Wendel JF, Cronn RC, Johnston JS, Price HJ, (2002) Feast and famine in plant genomes. Genetica 115: 37-47.
11. Cui L, Wall PK, Leeben-Mack J-H, Lindsay BG, Soltis DE, et al. (2006) Widespread genome duplications throughout the history of flowering plants. Genome Res 16: 738-749.
12. Devos KM, Brown JKM, Bennetzen JL, (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075-1079.
13. Kazazian HH Jr, (2004) Mobile elements: Drivers of genome evolution. Science 303: 1626-1632.
14. Hawkins JS, Kim HR, Nason JD, Wing RA, Wendel JF, (2006) Differential lineagespecific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 16: 1252-1261.
15. Bennetzen JL, (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29-36.
16. Ohno S, (1972) So much 'junk' in our genomes. In: Smith HH, editors. Evolution of Genetic Systems Upton Brookhaven Symposia in Biology pp. 366-370.
17. Orgel LE, Crick FHC, (1980) Selfish DNA: the ultimate parasite. Nature 284: 604-607.
18. Petrov DA, (2002) Mutational equilibrium model of genome size evolution. Theor Pop Biol 61: 533-546.
19. Oliver MJ, Petrov F, Ackerly D, Falkowski P, Schofield OM, (2007) The mode and tempo of genome size evolution in eukaryotes. Genome Res 17: 594-601.
20. Gregory TR, (2005) The C-value enigma in plants and animals: A review of parallels and an appeal for partnership. Ann Bot 95: 133-146.
21. Wakamiya I, (1993) Genome size and environmental factors in the genus Pinus. Am J Bot 80: 1235-1241.
22. Chung J, Lee JH, Arumuganathan K, Graef GL, Specht JE, (1998) Relationships between nuclear DNA content and seed and leaf size in soybean. Theor Appl Gen 96: 1064-1068.
23. Jasienski M, Bazzaz FA, (1995) Genome size and high CO2. Nature 376: 559-560.
24. Vinogradov AE, (1995) Nucleotypic effect in homeotherms: Body-mass-corrected basal metabolic rate of mammals is related to genome size. Evolution 49: 1249-1259.
25. Vinogradov AE, (1997) Nucleotypic effect in homeotherms: Body-mass independent resting metabolic rate of passerine birds is related to genome size. Evolution 51: 220-225.
26. Kozlowski J, Konarzewski M, Gawelczyk AT, (2003) Cell size as a link between noncoding DNA and metabolic rate scaling. Proc Natl Acad SciUSA 100: 14080-14085.
27. Beaulieu JM, Leitch IJ, Knight CA, (2007) Genome size evolution in relation to leaf strategy and metabolic rates revisited. Ann Bot 99: 495-505.
28. Ross-Ibarra J, (2007) Genome size and recombination in angiosperms: a second look. J Evol Biol 20: 800-806.
29. Smarda P, Bures P, Horova L, Rotreklova O, (2008) Intrapopulation genome size dynamics in Fetusca pallens. Ann Bot 102: 599-607.
30. Meagher TR, Costich DE, (1994) Sexual dimorphism in nuclear DNA content and floral morphology in populations of Silene latifolia (Caryophyllaceae). Am J Bot 81: 1198-1204.
31. Meagher TR, Costich DE, (2008) 'Junk' DNA and phenotypic evolution in Silene section Siphonomorpha. Genet Res 90: 111-118.
32. Knight CA, Ackerly DD, (2002) Variation in nuclear DNA content across environmental gradients: A quantile regression analysis. Ecol Lett 5: 66-76.
33. Achigan-Dako EG, Fuchs J, Ahanchede A, Blattner FR, (2008) Flow cytometric analysis in Lagenaria siceraria (Cucurbitaceae) indicates correlation of genome size with usage types and growing elevation. Plant Syst Evol 276: 9-19.
34. Knight CA, Beaulieu JM, (2008) Genome size scaling through phenotype space. Ann Bot 101: 759-766.
35. Bennett MD, (1972) Nuclear DNA content and minimum generation time in herbaceous plants. Proc Royal Soc London B 181: 109-135.
36. Bennett MD, (1977) The time and duration of meiosis. Philos Transac Royal Soc London B 277: 201-226.
37. Price HJ, Sparrow AH, Nauman AF, (1973) Correlations between nuclear volume, cell volume and DNA content in meristematic cells of herbaceous angiosperms. Experientia 29: 1028-1029.
38. Wyman J, Laliberte S, Tremblay E, (1997) Nuclear DNA content variation in seeds from 22 half-sib families of jack pine (Pinus banksiana, Pinaceae). Am. J. Bot 84: 1351-1361.
39. Ulmer T, MacDougal JM, (2004) Passiflora: Passionflowers of the World. 430 Portland-Cambridge, Timber Press.
40. Muschner VC, Lorenz AP, Cervi AC, Bonatto SL, Souza-Chies TT, et al. (2003) A first molecular phylogenetic analysis of Passiflora (Passifloraceae). Am J Bot 90: 1229-1238.
41. Hansen AK, Gilbert LE, Simpson BB, Downie SR, Cervi AC, et al. (2006) Phylogenetic relationships and chromosome number evolution in Passiflora. Syst Bot 31: 138-150.
42. Otto FJ, (1990) DAPI staining of fixed cells for high-resolution flow cytometry of nuclear DNA. In: Darzynkiewickz Z, Crissman HA, editors. Methods in cell biology 33 Academic Press: 105-110.
43. Bennett MD, Leitch IJ, (2005) Plant genome size research: a filed in focus. Ann Bot 95: 1-6.
44. Price H, Johnston J, (1996) Analysis of plant DNA content by Feulgen microspectrophotometry and flow cytometry. In: Jauhar P, editors. Methods of genome analysis in plants Boca Raton CRC Press pp. 115-131.
45. Doležel J, Bartoš J, (2005) Plant DNA flow cytometry and estimation of nuclear genome size. Ann Bot 95: 99-110.
46. Roy A, Frascaria N, MacKay J, Bousquet J, (1992) Segregating random amplified polymorphic DNAs (RAPDs) in Betula alleghaniensisis. Theor Appl Genet 85: 173-180.
47. Savolainen V, Chase MW, Hoot S B, Morton CM, Soltis DE et al, (2000) Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst Biol 49: 306-362.
48. Souza-Chies TT, Bittar G, Nadot S, Carter L, Besin E, et al. (1997) Phylogenetic analysis of Iridaceae with parsimony and distance methods using the plastid gene rps4. Plant Syst Evol 204: 109-123.
49. Taberlet P, Gielly L, Patou G, Bouvet J, (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105-1109.
50. Dunn IS, Blattner FR, (1987) Chaperons 36 to 40: Multi-enzyme, high capacity, recombination deficient replacement vectors with polylinkers and polystuffers. Nucl Acids Res 15: 2677-2698.
51. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
52. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
53. Ronquist F, Huelsenbeck JP, (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
54. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves Aldrey JL, (2004) Bayesian phylogenetic analysis of combined data. Syst Biol 53: 47-67.
55. Felsenstein J, (1985) Phylogenies and the comparative method. Am Natl 125: 1-15.
56. Garland T, Midford PE, Jones JA, Dickerman AW, Diaz-Uriarte R, (2006) PDAP: Phenotypic Diversity Analysis Programs.
57. Garland T Jr, Midford PE, Ives AR, (1999) An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral states. Am. Zoolog 39: 374-388.
58. Pagel M, (1997) Inferring evolutionary processes from phylogenies. Zoologica Scripta (Journal of the Royal Swedish Academy) 25th Anniversary Special Issue. Phylogenet. Syst 26: 331-348.
59. Pagel M, (1999) Inferring the historical patterns of biological evolution. Nature 401: 877-884.
60. Pagel M, Meade A, Barker D, (2004) Bayesian estimation of ancestral character states on phylogenies. Syst. Biol 53: 673-684.
61. Rambaut A, Drummond A, (2003) Tracer: MCMC trace analysis tool. University of Oxford.
62. Ashman T-L, Morgan MT, (2004) Explaining phenotypic selection on plant attractive characters: male function, gender balance or ecological context? Proc R Soc London B 271: 553-559.
63. Ashman T-L, Majestic CJ, (2006) Genetic constraints on floral evolution: a review and evaluation of patterns. Heredity 96: 343-352.