Molecular Biology and Evolution, Vol 13, 261-277, Copyright © 1996 by Society for Molecular Biology and Evolution
EN Moriyama and JR Powell
We have summarized and analyzed all available nuclear DNA sequence
polymorphism studies for three species of Drosophila, D. melanogaster (24
loci), D. simulans (12 loci), and D. pseudoobscura (5 loci). Our major
findings are: (1) The average nucleotide heterozygosity ranges from about
0.4% to 2% depending upon species and function of the region, i.e., coding
or noncoding. (2) Compared to D. simulans and D. pseudoobscura (which are
about equally variable), D. melanogaster displays a low degree of DNA
polymorphism. (3) Noncoding introns and 3' and 5' flanking DNA shows less
polymorphism than silent sites within coding DNA. (4) X-linked genes are
less variable than autosomal genes. (5) Transition (Ts) and transversion
(Tv) polymorphisms are about equally frequent in non-coding DNA and at
fourfold degenerate sites in coding DNA while Ts polymorphisms outnumber Tv
polymorphisms by about 2:1 in total coding DNA. The increased Ts
polymorphism in coding regions is likely due to the structure of the
genetic code: silent changes are more often Ts's than are replacement
substitutions. (6) The proportion of replacement polymorphisms is
significantly higher in D. melanogaster than in D. simulans. (7) The level
of variation in coding DNA and the adjacent noncoding DNA is significantly
correlated indicating regional effects, most notably recombination. (8)
Surprisingly, the level of polymorphism at silent coding sites in D.
melanogaster is positively correlated with degree of codon usage bias. (9)
Three proposed tests of the neutral theory of DNA polymorphisms have been
performed on the data: Tajima's test, the HKA test, and the
McDonald-Kreitman test. About half of the loci fail to conform to the
expectations of neutral theory by one of the tests. We conclude that many
variables are affecting levels of DNA polymorphism in Drosophila, from
properties of nucleotides to population history and, perhaps, mating
structure. No simple, all encompassing explanation satisfactorily accounts
for the data.
ORIGINAL ARTICLE
Intraspecific nuclear DNA variation in Drosophila
Department of Biology, Yale University, New Haven, Connecticut 06520- 8104, USA.
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M. A. Jensen, B. Charlesworth, and M. Kreitman Patterns of Genetic Variation at a Chromosome 4 Locus of Drosophila melanogaster and D. simulans Genetics, February 1, 2002; 160(2): 493 - 507. [Abstract] [Full Text] [PDF]
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V. Dvornyk, A. Sirvio, M. Mikkonen, and O. Savolainen Low Nucleotide Diversity at the pal1 Locus in the Widely Distributed Pinus sylvestris Mol. Biol. Evol., February 1, 2002; 19(2): 179 - 188. [Abstract] [Full Text] [PDF]
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K. J. Schmid and C. F. Aquadro The Evolutionary Analysis of ""Orphans"" From the Drosophila Genome Identifies Rapidly Diverging and Incorrectly Annotated Genes Genetics, October 1, 2001; 159(2): 589 - 598. [Abstract] [Full Text] [PDF]
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J. Parsch, C. D. Meiklejohn, and D. L. Hartl Patterns of DNA Sequence Variation Suggest the Recent Action of Positive Selection in the janus-ocnus Region of Drosophila simulans Genetics, October 1, 2001; 159(2): 647 - 657. [Abstract] [Full Text] [PDF]
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C. M. Bergman and M. Kreitman Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences Genome Res., August 1, 2001; 11(8): 1335 - 1345. [Abstract] [Full Text] [PDF]
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D. A. Filatov, V. Laporte, C. Vitte, and D. Charlesworth DNA Diversity in Sex-Linked and Autosomal Genes of the Plant Species Silene latifolia and Silene dioica Mol. Biol. Evol., August 1, 2001; 18(8): 1442 - 1454. [Abstract] [Full Text] [PDF]
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M. I. Tenaillon, M. C. Sawkins, A. D. Long, R. L. Gaut, J. F. Doebley, and B. S. Gaut Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) PNAS, July 19, 2001; (2001) 151244298. [Abstract] [Full Text] [PDF]
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J. Rozas, M. Gullaud, G. Blandin, and M. Aguade DNA Variation at the rp49 Gene Region of Drosophila simulans: Evolutionary Inferences From an Unusual Haplotype Structure Genetics, July 1, 2001; 158(3): 1147 - 1155. [Abstract] [Full Text] [PDF]
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B. C. Verrelli and W. F. Eanes Clinal Variation for Amino Acid Polymorphisms at the Pgm Locus in Drosophila melanogaster Genetics, April 1, 2001; 157(4): 1649 - 1663. [Abstract] [Full Text]
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P. Andolfatto Contrasting Patterns of X-Linked and Autosomal Nucleotide Variation in Drosophila melanogaster and Drosophila simulans Mol. Biol. Evol., March 1, 2001; 18(3): 279 - 290. [Abstract] [Full Text]
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M. Przeworski, J. D. Wall, and P. Andolfatto Recombination and the Frequency Spectrum in Drosophila melanogaster and Drosophila simulans Mol. Biol. Evol., March 1, 2001; 18(3): 291 - 298. [Abstract] [Full Text]
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D. Bensasson, D. A. Petrov, D.-X. Zhang, D. L. Hartl, and G. M. Hewitt Genomic Gigantism: DNA Loss Is Slow in Mountain Grasshoppers Mol. Biol. Evol., February 1, 2001; 18(2): 246 - 253. [Abstract] [Full Text]
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 D. Nurminsky, D. D. Aguiar, C. D. Bustamante, and D. L. Hartl Chromosomal Effects of Rapid Gene Evolution in Drosophila melanogaster Science, January 5, 2001; 291(5501): 128 - 130. [Abstract] [Full Text]
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G. A. T. McVean and J. Vieira Inferring Parameters of Mutation, Selection and Demography From Patterns of Synonymous Site Evolution in Drosophila Genetics, January 1, 2001; 157(1): 245 - 257. [Abstract] [Full Text]
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K. Ashton, A. P. Wagoner, R. Carrillo, and G. Gibson Quantitative Trait Loci for the Monoamine-Related Traits Heart Rate and Headless Behavior in Drosophila melanogaster Genetics, January 1, 2001; 157(1): 283 - 294. [Abstract] [Full Text]
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