ChromEvol: Assessing the pattern of chromosome number evolution and the inference of polyploidy along a phylogeny

Molecular Biology and Evolution

Volumn 31, Issue 7, 2014, Pages 1914-1922

  Glick, Lior ^a   Mayrose, Itay ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

base number; chromEvol; chromosome numbers; polyploidy; software; whole genome duplication

Indexed keywords

BASE;

ARTICLE; CHROMOSOME NUMBER; COMPUTER PROGRAM; DIPLOIDY; INTRASPECIFIC VARIATION; MOLECULAR EVOLUTION; PHYLOGENY; POLYPLOIDY; BIOLOGICAL MODEL; CHROMOSOME; WEB BROWSER;

CHROMOSOMES; EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY; POLYPLOIDY; SOFTWARE; WEB BROWSER;

EID: 84903695435     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu122     Document Type: Article

References (38)

1. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Autom Control. 119:716-723.
2. Albertin W, Marullo P. 2012. Polyploidy in fungi: Evolution after wholegenome duplication. Proc Biol Sci. 279:2497-2509.
3. Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, et al. 2006. Global trends of wholegenome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444:171-178. (Pubitemid 44722053)
4. Cui L,Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, et al. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Res. 16:738-749. (Pubitemid 43830694)
5. Cusimano N, Sousa A, Renner SS. 2012. Maximum likelihood inference implies a high, not a low, ancestral haploid chromosome number in Araceae, with a critique of the bias introduced by "x". Ann Bot. 109: 681-692.
6. Davies EW. 1953. Polyploidy in Primula farinosa L. Nature 171:659-660.
7. Fawcett JA, Maere S, Van de Peer Y. 2009. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci U S A. 106:5737-5742.
8. Furlong RF, Holland PWH. 2004. Polyploidy in vertebrate ancestry: Ohno and beyond. Biol J Linn Soc Lond. 82:425-430. (Pubitemid 39123331)
9. Galtier N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol Biol Evol. 18:866-873. (Pubitemid 32372956)
10. Goldberg EE, Igic B. 2008. On phylogenetic tests of irreversible evolution. Evolution 62:2727-2741.
11. Goldblatt P. 1980. Polyploidy in angiosperms: Monocotyledons. In: Lewis WH, editor. Polyploidy: Biological relevance. New York: Plenum Press. p. 219-239.
12. Grant V. 1963. The origin of adaptations. New York: Columbia University Press.
13. Guerra M. 2008. Chromosome numbers in plant cytotaxonomy: Concepts and implications. Cytogenet Genome Res. 120:339-350. (Pubitemid 351738040)
14. Guggisberg A, Mansion G, Conti E. 2009. Disentangling reticulate evolution in an arctic-Alpine polyploid complex. Syst Biol. 58: 55-73.
15. Hastings WK. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
16. Kandul NP, Lukhtanov VA, Pierce NE. 2007. Karyotypic diversity and speciation in Agrodiaetus butterflies. Evolution 61:546-559. (Pubitemid 46657683)
17. Li J, Webster MA, Smith MC, Gilmartin PM. 2011. Floral heteromorphy in Primula vulgaris: Progress towards isolation and characterization of the S locus. Ann Bot. 108:715-726.
18. Liu PL, Wan Q, Guo YP, Yang J, Rao GY. 2012. Phylogeny of the genus Chrysanthemum L.: Evidence from single-copy nuclear gene and chloroplast DNA sequences. PLoS One 7:e48970.
19. Maddison WP. 2006. Confounding asymmetries in evolutionary diversification and character change. Evolution 60:1743-1746. (Pubitemid 44815495)
20. Maddison WP, Midford PE, Otto SP. 2007. Estimating a binary character's effect on speciation and extinction. Syst Biol. 56: 701-710. (Pubitemid 47402904)
21. Mast AR, Conti E. 2006. The primrose path to heterostyly. New Phytol. 171:439-442. (Pubitemid 44051299)
22. Matthews BW. 1975. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta. 405: 442-451.
23. Mayrose I, Barker MS, Otto SP. 2010. Probabilistic models of chromosome number evolution and the inference of polyploidy. Syst Biol. 59:132-144.
24. Mayrose I, Zhan SH, RothfelsCJ, Magnuson-FordK, BarkerMS,Rieseberg LH, Otto SP. 2011. Recently formed polyploid plants diversify at lower rates. Science 333:1257.
25. Ohi-Toma T, Sugawara T, Murata H, Wanke S, Neinhuis C, Murata J. 2006. Molecular phylogeny of Aristolochia sensu lato (Aristolochiaceae) based on sequences of rbcL, matK, and phyA genes, with special reference to differentiation of chromosome numbers. Syst Bot. 31:481-492. (Pubitemid 44440931)
26. Peruzzi L. 2013. "x" is not a bias, but a number with real biological significance. Plant Biosyst. 147:1238-1241.
27. Ramsey J, Schemske DW. 1998. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu Rev Ecol Syst. 29: 467-501. (Pubitemid 29033040)
28. Richards J. 2002. Primula. Vol. 346. London: BT Batsford. p. 40.
29. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
30. Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH. 2006. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341-345.
31. Schmidt-Lebuhn AN, de Vos JM, Keller B, Conti E. 2012. Phylogenetic analysis of Primula section Primula reveals rampant non-monophyly among morphologically distinct species. Mol Phylogenet Evol. 65: 23-34.
32. Schultheis LM. 2001. Systematics of Downingia (Campanulaceae) based on molecular sequence data: Implications for floral and chromosome evolution. Syst Bot. 26:603-621. (Pubitemid 32908115)
33. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, dePamphilis CW, Wall PK, Soltis PS. 2009. Polyploidy and angiosperm diversification. Am J Bot. 96:336-348.
34. Stebbins GL. 1938. Cytological characteristics associated with the different growth habits in the dicotyledons. Am J Bot. 25: 189-198.
35. Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y. 2003. Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res. 13:382-390. (Pubitemid 36395395)
36. Wolfe KH. 2001. Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet. 2:333-341. (Pubitemid 33673071)
37. Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH. 2009. The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci U S A. 106:13875-13879.
38. Zhan S, Glick L, Tsigenopoulos C, Otto S, Mayrose I. 2014. Comparative analysis reveals that polyploidy does not decelerate diversification in fish. J Evol Biol. 27:391-403..