Abstract
Nucleotide variation was surveyed in 21 subrepeat arrays from the ribosomal DNA intergenic spacer of three Daphnia pulex populations. Eighteen of these arrays contained four subrepeats. Contrary to expectations, each of the four positions within the array had a different consensus sequence. However, gene conversion, involving sequences less than the length of a subrepeat, had occurred between subrepeats in different positions. Three arrays had more than four subrepeats and were undoubtedly generated by unequal crossing over between standard-length arrays. The data strongly suggested that most unequal exchanges between arrays are intrachromosomal and that they occur much less frequently than unequal exchanges at the level of the entire rDNA repeat. Strong associations among variants at different positions allowed the recognition of five groups of arrays, two of which were found in more than one population. Five of the seven individuals surveyed had arrays from more than one group. Analysis of the distribution of nucleotide variation suggested that the populations were quite divergent, a result that is concordant with previous surveys of allozyme and mitochondrial DNA variation. It was suggested that some of the subrepeat array types are quite old, at least predating the recolonization of pond habitats in the midwestern United States after the last glaciation.
Full Text
The Full Text of this article is available as a PDF (1.1 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Baldridge G. D., Dalton M. W., Fallon A. M. Is higher-order structure conserved in eukaryotic ribosomal DNA intergenic spacers? J Mol Evol. 1992 Dec;35(6):514–523. doi: 10.1007/BF00160212. [DOI] [PubMed] [Google Scholar]
- Baldridge G. D., Fallon A. M. Primary structure of the ribosomal DNA intergenic spacer from the mosquito, Aedes albopictus. DNA Cell Biol. 1992 Jan-Feb;11(1):51–59. doi: 10.1089/dna.1992.11.51. [DOI] [PubMed] [Google Scholar]
- Crease T. J., Lynch M., Spitze K. Hierarchical analysis of population genetic variation in mitochondrial and nuclear genes of Daphnia pulex. Mol Biol Evol. 1990 Sep;7(5):444–458. doi: 10.1093/oxfordjournals.molbev.a040618. [DOI] [PubMed] [Google Scholar]
- Crease T. J. Sequence of the intergenic spacer between the 28S and 18S rRNA-encoding genes of the crustacean, Daphnia pulex. Gene. 1993 Dec 8;134(2):245–249. doi: 10.1016/0378-1119(93)90101-8. [DOI] [PubMed] [Google Scholar]
- Cross N. C., Dover G. A. Tsetse fly rDNA: an analysis of structure and sequence. Nucleic Acids Res. 1987 Jan 12;15(1):15–30. doi: 10.1093/nar/15.1.15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dover G. Molecular drive: a cohesive mode of species evolution. Nature. 1982 Sep 9;299(5879):111–117. doi: 10.1038/299111a0. [DOI] [PubMed] [Google Scholar]
- Elder J. F., Jr, Turner B. J. Concerted evolution at the population level: pupfish HindIII satellite DNA sequences. Proc Natl Acad Sci U S A. 1994 Feb 1;91(3):994–998. doi: 10.1073/pnas.91.3.994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hibner B. L., Burke W. D., Eickbush T. H. Sequence identity in an early chorion multigene family is the result of localized gene conversion. Genetics. 1991 Jul;128(3):595–606. doi: 10.1093/genetics/128.3.595. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Landsberger N., Cancelli S., Carettoni D., Barigozzi C., Badaracco G. Nucleotide variation and molecular structure of the heterochromatic repetitive AluI DNA in the brine shrimp Artemia franciscana. J Mol Evol. 1992 Dec;35(6):486–491. doi: 10.1007/BF00160209. [DOI] [PubMed] [Google Scholar]
- Lassner M., Dvorak J. Preferential homogenization between adjacent and alternate subrepeats in wheat rDNA. Nucleic Acids Res. 1986 Jul 11;14(13):5499–5512. doi: 10.1093/nar/14.13.5499. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Linares A. R., Bowen T., Dover G. A. Aspects of nonrandom turnover involved in the concerted evolution of intergenic spacers within the ribosomal DNA of Drosophila melanogaster. J Mol Evol. 1994 Aug;39(2):151–159. doi: 10.1007/BF00163804. [DOI] [PubMed] [Google Scholar]
- Long E. O., Dawid I. B. Repeated genes in eukaryotes. Annu Rev Biochem. 1980;49:727–764. doi: 10.1146/annurev.bi.49.070180.003455. [DOI] [PubMed] [Google Scholar]
- Lynch M., Crease T. J. The analysis of population survey data on DNA sequence variation. Mol Biol Evol. 1990 Jul;7(4):377–394. doi: 10.1093/oxfordjournals.molbev.a040607. [DOI] [PubMed] [Google Scholar]
- Lynch M. The consequences of fluctuating selection for isozyme polymorphisms in Daphnia. Genetics. 1987 Apr;115(4):657–669. doi: 10.1093/genetics/115.4.657. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Seperack P., Slatkin M., Arnheim N. Linkage disequilibrium in human ribosomal genes: implications for multigene family evolution. Genetics. 1988 Aug;119(4):943–949. doi: 10.1093/genetics/119.4.943. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Takaiwa F., Kikuchi S., Oono K. The complete nucleotide sequence of the intergenic spacer between 25S and 17S rDNAs in rice. Plant Mol Biol. 1990 Dec;15(6):933–935. doi: 10.1007/BF00039432. [DOI] [PubMed] [Google Scholar]
- Tautz D., Tautz C., Webb D., Dover G. A. Evolutionary divergence of promoters and spacers in the rDNA family of four Drosophila species. Implications for molecular coevolution in multigene families. J Mol Biol. 1987 Jun 5;195(3):525–542. doi: 10.1016/0022-2836(87)90181-1. [DOI] [PubMed] [Google Scholar]
- Williams S. M., Furnier G. R., Fuog E., Strobeck C. Evolution of the ribosomal DNA spacers of Drosophila melanogaster: different patterns of variation on X and Y chromosomes. Genetics. 1987 Jun;116(2):225–232. doi: 10.1093/genetics/116.2.225. [DOI] [PMC free article] [PubMed] [Google Scholar]