Erratum to: Ploidy tug-of-war: Evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen ((2017), 71, 4, (1025-1038), 10.1111/evo.13205);Ploidy tug-of-war: Evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen

Evolution

Volumn 71, Issue 4, 2017, Pages 1025-1038

  Gerstein, Aleeza C ^a,b   Lim, Heekyung ^a   Berman, Judith ^a,b,c   Hickman, Meleah A ^a,d  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

^d EMORY UNIVERSITY   (United States)

Author keywords

Adaptation; chromosomal evolution; fitness; mutations; selection experimental; selection natural

Indexed keywords

EVOLUTIONARY BIOLOGY; FITNESS; FUNGAL DISEASE; GENETIC ANALYSIS; MUTATION; NATURAL SELECTION; NUTRIENT LIMITATION; PHOSPHORUS; PLOIDY;

CANDIDA ALBICANS;

CANDIDA ALBICANS; DIPLOIDY; EVOLUTION; FUNGAL GENOME; GENETICS; GENOME SIZE; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; HAPLOIDY; HUMAN; NUTRITION; PHYSIOLOGY; POLYPLOIDY;

BIOLOGICAL EVOLUTION; CANDIDA ALBICANS; DIPLOIDY; GENE-ENVIRONMENT INTERACTION; GENOME SIZE; GENOME, FUNGAL; GENOTYPE; HAPLOIDY; HUMANS; NUTRITIONAL PHYSIOLOGICAL PHENOMENA; POLYPLOIDY;

EID: 85016508290     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.13280     Document Type: Erratum

References (77)

1. Abbey, D. A., J. Funt, M. N. Lurie-Weinberger, D. A. Thompson, A. Regev, C. L. Myers, and J. Berman. 2014. YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens. Genome Med. 6:1–15.
2. Adams, J., and P. Hansche. 1974. Population studies in microorganisms I. Evolution of diploidy in Saccharomyces cerevsiae. Genetics 76:327–338.
3. Albertin, W., and P. Marullo. 2012. Polyploidy in fungi: evolution after whole-genome duplication. Proc. R. Soc. B Biol. Sci. 279:2497–2509.
4. Amberg, D. C., D. J. Burke, and J. N. Strathern. 2005. Methods in yeast genetics: a Cold Spring Harbor laboratory course manual. Cold Spring. New York.
5. Bates, D., M. Maechler, B. Bolker, and S. Walker. 2015. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67:1–48.
6. Bennett, R. J., and A. D. Johnson. 2003. Completion of a parasexual cycle in Candida albicans by induced chromosome loss in tetraploid strains. EMBO J. 22:2502–2515.
7. Chang, F.-M., T.-Y. Ou, W.-N. Cheng, M.-L. Chou, K.-C. Lee, Y.-P. Chin, C.-P. Lin, K.-D. Chang, C.-T. Lin, and C.-H. Su. 2014. Short-term exposure to fluconazole induces chromosome loss in Candida albicans: an approach to produce haploid cells. Fungal Genet. Biol. 70:68–76.
8. de Mendiburu, F. 2015. agricolae: statistical procedures for agricultural research. R package version 1.2-3. Available at https://CRAN.R-project.org/package=agricolae.
9. de Godoy, L., J. V. Olsen, J. Cox, M. L. Nielsen, N. C. Hubner, F. Fröhlich, T. C. Walther, et al. 2008. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455:1251–1254.
10. Diezmann, S., C. J. Cox, G. Schönian, R. J. Vilgalys, and T. G. Mitchell. 2004. Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis. J. Clin. Microbiol. 42:5624–5635.
11. Ezov, T. K., E. Boger-Nadjar, Z. Frenkel, I. Katsperovski, S. Kemeny, E. Nevo, A. Korol and Y. Kashi. 2006. Molecular-genetic biodiversity in a natural population of the yeast Saccharomyces cerevisiae from ”evolution canyon”: Microsatellite polymorphism, ploidy and controversial sexual status. Genetics 174:1455–1468.
12. Elser, J. J., D. R. Dobberfuhl, and N. A. MacKay. 1996. Organism size, life history, and N:P stoichiometry toward a unified view of cellular and ecosystem processes. BioScience 46:674–684.
13. Elser, J. J., K. Acharya, M. Kyle, J. Cotner, W. Makino, T. Markow, T. Watts, S. Hobbie, W. Fagan, J. Schade et al. 2003. Growth rate-stoichiometry couplings in diverse biota. Ecol. Lett. 6:936–943.
14. Elser, J. J., M. E. S. Bracken, E. E. Cleland, D. S. Gruner, W. S. Harpole, H. Hillebrand, J. T. Ngai, E. W. Seabloom, J. B. Shurin, and J. E. Smith. 2007. Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems. Ecol. Lett. 10:1135–1142.
15. Galitski, T., A. Saldanha, C. Styles, E. Lander, and G. Fink. 1999. Ploidy regulation of gene expression. Science 285:251–254.
16. Gerstein, A. C. 2012. Mutational effects depend on ploidy level: all else is not equal. Biol. Lett. 9:20120614.
17. Gerstein, A. C., and S. P. Otto. 2009. Ploidy and the causes of genomic evolution. J. Hered. 100:571–581.
18. Gerstein, A. C., and S. P. Otto 2011. Cryptic fitness advantage: diploids invade haploid populations despite lacking any apparent advantage as measured by standard fitness assays. PLoS ONE 6:e26599.
19. Gerstein, A.C. and J. Berman. 2015. Shift and adapt: the costs and benefits of karyotype variations. Current opinion in Microbiology 26:130-136.
20. Gerstein, A. C., H.-J. E. Chun, A. Grant, and S. P. Otto. 2006. Genomic convergence toward diploidy in Saccharomyces cerevisiae. PLoS Genet 2:e145.
21. Gerstein, A. C., R. M. McBride, and S. P. Otto. 2008. Ploidy reduction in Saccharomyces cerevisiae. Biology Letters 4:91–94.
22. Gerstein, A. C., L. A. Cleathero, M. A. Mandegar, and S. P. Otto. 2010. Haploids adapt faster than diploids across a range of environments. J. Evol. Biol. 24:531–540.
23. Gerstein, A. C., M. S. Fu, L. Mukaremera, Z. Li, K. L. Ormerod, J. A. Fraser, J. Berman, and K. Nielsen. 2015. Polyploid titan cells produce haploid and aneuploid progeny to promote stress adaptation. MBio 6:e01340–e01315.
24. Gillum, A. M., E. Y. Tsay, and D. R. Kirsch. 1984. Isolation of the Candida albicans gene for orotidine-5′-phosphate decarboxylase by complementation of S. cerevisiae ura3 and E. coli pyrF mutations. Mol. Gen. Genet. 198:179–182.
25. Giovannoni, S. J., J. C. Thrash, and Ben Temperton. 2014. Implications of streamlining theory for microbial ecology. 8:1553–1565.
26. Glazunov, A. V., A. V. Boreĭko, and A. Esser. 1989. Relative competitiveness of haploid and diploid yeast cells growing in a mixed population. Mikrobiologiia 58:769–777.
27. Gregory, T. R., and B. Mable. 2005. Polyploidy in animals. The evolution of the genome. Pp. 427–517. Elsevier Academic Press. Cambridge, Massachusetts.
28. Gresham, D. 2006. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311:1932–1936.
29. Gresham, D., M. Desai, C. Tucker, H. Jenq, D. Pai, A. Ward, C. DeSevo, D. Botstein, and M. Dunham. 2008. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet 4:e1000303.
30. Gómez, A., J. A. López, B. Pintos, E. Camafeita, and M. Á. Bueno. 2009. Proteomic analysis from haploid and diploid embryos of Quercus suber L. identifies qualitative and quantitative differential expression patterns. Proteomics 9:4355–4367.
31. Harrison, B. D., J. Hashemi, M. Bibi, R. Pulver, D. Bavli, Y. Nahmias, M. Wellington, G. Sapiro, and J. Berman. 2014. A tetraploid intermediate precedes aneuploid formation in yeasts exposed to fluconazole. PLoS Biol 12:e1001815.
32. Hessen, D. O., P. D. Jeyasingh, M. Neiman, and L. J. Weider. 2010. Genome streamlining and the elemental costs of growth. Trends Ecol. Evol. 25:75–80.
33. Hickman, M. A., G. Zeng, A. Forche, M. P. Hirakawa, D. Abbey, B. D. Harrison, Y.-M. Wang, C.-H. Su, R. J. Bennett, Y. Wang et al. 2013. The “obligate diploid” Candida albicans forms mating-competent haploids. Nature 494:55–59.
34. Hickman, M. A., C. Paulson, A. M. Dudley, and J. Berman. 2015. Parasexual ploidy reduction drives population heterogeneity through random and transient aneuploidy in Candida albicans. Genetics. 200:781–794.
35. Homann, O. R., J. Dea, S. M. Noble, and A. D. Johnson. 2009. A phenotypic profile of the Candida albicans regulatory network. PLoS Genet 5:e1000783.
36. Janbon, G., F. Sherman, and E. Rustchenko. 1998. Monosomy of a specific chromosome determines L-sorbose utilization: a novel regulatory mechanism in Candida albicans. Proc. Natl. Acad. Sci. USA 95:5150–5155.
37. Jeyasingh, P. D., P. Roy Chowdhury, M. W. Wojewodzic, D. Frisch, D. O. Hessen, and L. J. Weider. 2015. Phosphorus use and excretion varies with ploidy level in Daphnia. J. Plankton Res. 37:1210–1217.
38. Kellis, M., B. W. Birren, and E. S. Lander. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevsiae. Nature 428:617–624.
39. Kilkenny, B. C., and C. Hinshelwood. 1951. The utilization of carbon sources by certain yeast strains. Proc. R. Soc. Lond. Biol. 138:375–385.
40. Kuznetsova, A., B. Brockhoff, and H. B. Christensen, 2016. lmerTest: tests in linear mixed effects models. R package version 2.0-30. Available at https://CRAN.R-project.org/package=lmerTest.
41. Lewis, W., Jr. 1985. Nutrient scarcity as an evolutionary cause of haploidy. Am. Nat. 125:692–701.
42. Li, B.-Z., J.-S. Cheng, M.-Z. Ding, and Y.-J. Yuan. 2010. Transcriptome analysis of differential responses of diploid and haploid yeast to ethanol stress. Journal of Biotechnology 148:194–203.
43. Mable, B. 2001. Ploidy evolution in the yeast Saccharomyces cerevisiae: a test of the nutrient limitation hypothesis. J. Evol. Biol. 14:157–170.
44. Magasanik, B., and C. A. Kaiser. 2002. Nitrogen regulation in Saccharomyces cerevisiae. Gene 290:1–18.
45. Marr, K. A., T. C. White, J. A. van Burik, and R. A. Bowden. 1997. Development of fluconazole resistance in Candida albicans causing disseminated infection in a patient undergoing marrow transplantation. Clin. Infect. Dis. 25:908–910.
46. Muzzey, D., G. Sherlock, and J. S. Weissman. 2014. Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans. Genome Res. 24:963–973.
47. Neiman, M., A. D. Kay, and A. C. Krist. 2013a. Can resource costs of polyploidy provide an advantage to sex? Heredity 110:152–159.
48. Neiman, M., A. D. Kay, and A. C. Krist 2013b. Sensitivity to phosphorus limitation increases with ploidy level in a New Zealand snail. Evolution 67:1511–1517.
49. Neiman, M., M. J. Beaton, D. O. Hessen, P. D. Jeyasingh, and L. J. Weider. 2017. Endopolyploidy as a potential driver of animal ecology and evolution. Biol. Rev. Camb. Philos. Soc. 92:234–247.
50. Odds, F. C. 1988. Candida and candidosis: a review and bibliography. 2nd ed. Bailliere Tindall, London.
51. Orr, H. A. 2005. The genetic theory of adaptation: a brief history. Nat. Rev. Genet. 6:119–127.
52. Orr, H. A., and S. Otto. 1994. Does diploidy increase the rate of adaptation? Genetics 136:1475–1480.
53. Otto, S. P., and J. Whitton. 2000. Polyploid incidence and evolution. Annu. Rev. Genet. 34:401–437.
54. Pinheiro, J., D. Bates, S. DebRoy, D. Sarkar, and R Core Team. 2016. nlme: linear and nonlinear mixed effects models. Available at http://CRAN.R-project.org/package=nlme.
55. Pontecorvo, G., J. A. Roper, E. Forbes. 1953. Genetic recombination without sexual reproduction in Aspergillus niger. J. Gen. Microbiol. 8:198–210.
56. R Core Team. 2014. R: A Language and Environment for Statistical Computing. Vienna, Austria.
57. Ramsey, J., and Ramsey, T. S. 2014. Ecological studies of polyploidy in the 100 years following its discovery. Phil. Trans. R. Soc. B 369:20130352.
58. Rose, M. D., F. Winston, and P. Hieter. 1990. Methods in yeast genetics, a laboratory course manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
59. Schmoller, K. M., J. J. Turner, M. Kõivomägi, and J. M. Skotheim. 2015. Dilution of the cell cycle inhibitor Whi5 controls budding-yeast cell size. Nature 526:268–272.
60. Schoenfelder, K. P., R. A. Montague, S. V. Paramore, A. L. Lennox, A. P. Mahowald, and D. T. Fox. 2014. Indispensable pre-mitotic endocycles promote aneuploidy in the Drosophila rectum. Development 141:3551–3560.
61. Schoustra, S. E., A. J. M. Debets, M. Slakhorst, and R. F. Hoekstra. 2007. Mitotic recombination accelerates adaptation in the fungus Aspergillus nidulans. PLoS Genet. 3:e68.
62. Seervai, R. N. H., S. K. Jones, M. P. Hirakawa, A. M. Porman, and R. J. Bennett. 2013. Parasexuality and ploidy change in Candida tropicalis. Eukaryot. Cell 12:1629–1640.
63. Selmecki, A. M., Y. E. Maruvka, P. A. Richmond, M. Guillet, N. Shoresh, A. L. Sorenson, S. De, R. Kishony, F. Michor, R. Dowell et al. 2015. Polyploidy can drive rapid adaptation in yeast. Nature 519:349–352.
64. Soltis, D. E., C. J. Visger, D. B. Marchant, and P. S. Soltis. 2016. Polyploidy: pitfalls and paths to a paradigm. Am. J. Bot. 103:1–21.
65. Sterner, R. W., and J. J. Elser. 2002. Ecological stoichiometry: the biology of elements from molecules to the biosphere. Princeton University Press. Princeton, New Jersey.
66. Storchová, Z., and D. Pellman. 2004. From polyploidy to aneuploidy, genome instability and cancer. Nat. Rev. Mol. Cell Biol. 5:45–54.
67. Storchová, Z., A. Breneman, J. Cande, J. Dunn, K. Burbank, E. O'toole, and D. Pellman. 2006. Genome-wide genetic analysis of polyploidy in yeast. Nature 443:541–547.
68. Suzuki, T., S. Nishibayashi, T. Kuroiwa, T. Kanbe, and K. Tanaka. 1982. Variance of ploidy in Candida albicans. J. Bacteriol. 152:893–896.
69. Thompson, J. D., and R. Lumaret. 1992. The evolutionary dynamics of polyploid plants: origins, establishment and persistence. TREE 7:302–307.
70. Venkataram, S., B. Dunn, Y. Li, A. Agarwala, J. Chang, E. R. Ebel, K. Geiler-Samerotte, L. Hérissant, J. R. Blundell, S. F. Levy et al. 2016. Development of a comprehensive genotype-to-fitness map of adaptation-driving mutations in yeast. Cell 166:1585–1596.e22.
71. Vitale, I., G. Manic, L. Senovilla, G. Kroemer, and L. Galluzzi. 2015. Karyotypic aberrations in oncogenesis and cancer therapy. Trends Cancer 1:124–135.
72. Voordeckers, K., J. Kominek, A. Das, A. Espinosa-Cantú, D. De Maeyer, A. Arslan, M. Van Pee, E. van der Zande, W. Meert, Y. Yang et al. 2015. Adaptation to high ethanol reveals complex evolutionary pathways. PLoS Genet. 11:e1005635.
73. Wellington, M., and E. Rustchenko. 2005. 5-Fluoro-orotic acid induces chromosome alterations in Candida albicans. Yeast 22:57–70.
74. Wu, C.-Y., P. A. Rolfe, D. K. Gifford, and G. R. Fink. 2010. Control of transcription by cell size. PLoS Biology 8:e1000523.
75. Wendel, J. F. 2015. The wondrous cycles of polyploidy in plants. Am. J. Bot. 102:1753–1756.
76. Zhu, Y. O., G. Sherlock, and D.A. Petrov. 2016. Whole genome analysis of 132 clinical Saccharomyces cerevisiae strains reveals extensive ploidy variation. G3: Genes| Genomes| Genetics, 6:2421-2434.
77. Zörgö, E., K. Chwialkowska, A. B. Gjuvsland, E. Garré, P. Sunnerhagen, G. Liti, A. Blomberg, S. W. Omholt, and J. Warringer. 2013. Ancient evolutionary trade-offs between yeast ploidy states. PLoS Genet. 9:e1003388.