Abstract
Polyploidy has been an extremely common phenomenon in the evolutionary history of angiosperms. Despite this there are few data available to evaluate the effects of polyploidy on genetic diversity and to compare the relative effects of drift and selection in polyploids and related diploids. We investigated DNA sequence diversity at four nuclear loci (adh1, glb1, c1, and waxy) from the tetraploid Zea perennis and the closely related diploid Z. diploperennis. Contrary to expectations, we detected no strong evidence for greater genetic diversity in the tetraploid, or for consistent differences in the effects of either drift or selection between the tetraploid and the diploid. Our failure to find greater genetic diversity in Z. perennis may result from its relatively recent origin or demographic factors associated with its origin. In addition to comparing genetic diversity in the two species, we constructed genealogies to infer the evolutionary origin of Z. perennis. Although these genealogies are equivocal regarding the mode of origin, several aspects of these genealogies support an autotetraploid origin. Consistent with previous molecular data the genealogies do not, however, support the division of Zea into two sections, the section Zea and the section Luxuriantes.
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- Akashi H. Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. Genetics. 1999 Jan;151(1):221–238. doi: 10.1093/genetics/151.1.221. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Barrier M., Baldwin B. G., Robichaux R. H., Purugganan M. D. Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications. Mol Biol Evol. 1999 Aug;16(8):1105–1113. doi: 10.1093/oxfordjournals.molbev.a026200. [DOI] [PubMed] [Google Scholar]
- Buckler E. S., 4th, Holtsford T. P. Zea systematics: ribosomal ITS evidence. Mol Biol Evol. 1996 Apr;13(4):612–622. doi: 10.1093/oxfordjournals.molbev.a025621. [DOI] [PubMed] [Google Scholar]
- Cronn R. C., Small R. L., Wendel J. F. Duplicated genes evolve independently after polyploid formation in cotton. Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14406–14411. doi: 10.1073/pnas.96.25.14406. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Doebley J., Renfroe W., Blanton A. Restriction site variation in the zea chloroplast genome. Genetics. 1987 Sep;117(1):139–147. doi: 10.1093/genetics/117.1.139. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eyre-Walker A., Gaut R. L., Hilton H., Feldman D. L., Gaut B. S. Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4441–4446. doi: 10.1073/pnas.95.8.4441. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fu Y. X., Li W. H. Statistical tests of neutrality of mutations. Genetics. 1993 Mar;133(3):693–709. doi: 10.1093/genetics/133.3.693. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Galitski T., Saldanha A. J., Styles C. A., Lander E. S., Fink G. R. Ploidy regulation of gene expression. Science. 1999 Jul 9;285(5425):251–254. doi: 10.1126/science.285.5425.251. [DOI] [PubMed] [Google Scholar]
- Gaut B. S., Clegg M. T. Molecular evolution of alcohol dehydrogenase 1 in members of the grass family. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2060–2064. doi: 10.1073/pnas.88.6.2060. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gaut B. S., Clegg M. T. Molecular evolution of the Adh1 locus in the genus Zea. Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5095–5099. doi: 10.1073/pnas.90.11.5095. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hanson M. A., Gaut B. S., Stec A. O., Fuerstenberg S. I., Goodman M. M., Coe E. H., Doebley J. F. Evolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci. Genetics. 1996 Jul;143(3):1395–1407. doi: 10.1093/genetics/143.3.1395. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hudson R. R., Kreitman M., Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics. 1987 May;116(1):153–159. doi: 10.1093/genetics/116.1.153. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Iltis H. H., Doebley J. F., M R. G., Pazy B. Zea diploperennis (Gramineae): A New Teosinte from Mexico. Science. 1979 Jan 12;203(4376):186–188. doi: 10.1126/science.203.4376.186. [DOI] [PubMed] [Google Scholar]
- Mason-Gamer R. J., Weil C. F., Kellogg E. A. Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol Biol Evol. 1998 Dec;15(12):1658–1673. doi: 10.1093/oxfordjournals.molbev.a025893. [DOI] [PubMed] [Google Scholar]
- Masterson J. Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science. 1994 Apr 15;264(5157):421–424. doi: 10.1126/science.264.5157.421. [DOI] [PubMed] [Google Scholar]
- Moody M. E., Mueller L. D., Soltis D. E. Genetic variation and random drift in autotetraploid populations. Genetics. 1993 Jun;134(2):649–657. doi: 10.1093/genetics/134.2.649. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Otto S. P., Whitton J. Polyploid incidence and evolution. Annu Rev Genet. 2000;34:401–437. doi: 10.1146/annurev.genet.34.1.401. [DOI] [PubMed] [Google Scholar]
- Postlethwait J. H., Yan Y. L., Gates M. A., Horne S., Amores A., Brownlie A., Donovan A., Egan E. S., Force A., Gong Z. Vertebrate genome evolution and the zebrafish gene map. Nat Genet. 1998 Apr;18(4):345–349. doi: 10.1038/ng0498-345. [DOI] [PubMed] [Google Scholar]
- Purugganan M. D., Wessler S. R. Molecular evolution of magellan, a maize Ty3/gypsy-like retrotransposon. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11674–11678. doi: 10.1073/pnas.91.24.11674. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
- Sawyer S. A., Dykhuizen D. E., Hartl D. L. Confidence interval for the number of selectively neutral amino acid polymorphisms. Proc Natl Acad Sci U S A. 1987 Sep;84(17):6225–6228. doi: 10.1073/pnas.84.17.6225. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Seoighe C., Wolfe K. H. Extent of genomic rearrangement after genome duplication in yeast. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4447–4452. doi: 10.1073/pnas.95.8.4447. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Small R. L., Wendel J. F. Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium). Genetics. 2000 Aug;155(4):1913–1926. doi: 10.1093/genetics/155.4.1913. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Song K., Lu P., Tang K., Osborn T. C. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7719–7723. doi: 10.1073/pnas.92.17.7719. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 1983 Oct;105(2):437–460. doi: 10.1093/genetics/105.2.437. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989 Nov;123(3):585–595. doi: 10.1093/genetics/123.3.585. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wolfe K. H., Li W. H., Sharp P. M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci U S A. 1987 Dec;84(24):9054–9058. doi: 10.1073/pnas.84.24.9054. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wright S. The Distribution of Gene Frequencies in Populations of Polyploids. Proc Natl Acad Sci U S A. 1938 Sep;24(9):372–377. doi: 10.1073/pnas.24.9.372. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zimmer E. A., Jupe E. R., Walbot V. Ribosomal gene structure, variation and inheritance in maize and its ancestors. Genetics. 1988 Dec;120(4):1125–1136. doi: 10.1093/genetics/120.4.1125. [DOI] [PMC free article] [PubMed] [Google Scholar]