Patterns of sequence variability and divergence at the diminutive gene region of Drosophila melanogaster

Complex patterns suggest an ancestral selective sweep

Jeffrey Jensen, Vanessa L Bauer DuMont, Adeline B. Ashmore, Angela Gutierrez, Charles F. Aquadro

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

To identify putatively swept regions of the Drosophila melanogaster genome, we performed a microsatellite screen spanning a 260-kb region of the X chromosome in populations from Zimbabwe, Ecuador, the United States, and China. Among the regions identified by this screen as showing a complex pattern of reduced heterozygosity and a skewed frequency spectrum was the gene diminutive (dm). To investigate the microsatellite findings, nucleotide sequence polymorphism data were generated in populations from both China and Zimbabwe spanning a 25-kb region and encompassing dm. Analysis of the sequence data reveals strongly reduced nucleotide variation across the entire gene region in both the non-African and the African populations, an extended haplotype pattern, and structured linkage disequilibrium, as well as a rejection of neutrality in favor of selection using a composite likelihood-ratio test. Additionally, unusual patterns of synonymous site evolution were observed at the second exon of this locus. On the basis of simulation studies as well as recently proposed methods for distinguishing between selection and nonequilibrium demography, we find that this "footprint" is best explained by a selective sweep in the ancestral population, the signal of which has been somewhat blurred via founder effects in the non-African samples.

Original languageEnglish (US)
Pages (from-to)1071-1085
Number of pages15
JournalGenetics
Volume177
Issue number2
DOIs
StatePublished - Oct 2007
Externally publishedYes

Fingerprint

Drosophila melanogaster
Zimbabwe
Microsatellite Repeats
Population
Genes
China
Founder Effect
Ecuador
Linkage Disequilibrium
X Chromosome
Haplotypes
Sequence Analysis
Exons
Nucleotides
Demography
Genome

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Patterns of sequence variability and divergence at the diminutive gene region of Drosophila melanogaster : Complex patterns suggest an ancestral selective sweep. / Jensen, Jeffrey; DuMont, Vanessa L Bauer; Ashmore, Adeline B.; Gutierrez, Angela; Aquadro, Charles F.

In: Genetics, Vol. 177, No. 2, 10.2007, p. 1071-1085.

Research output: Contribution to journalArticle

Jensen, Jeffrey ; DuMont, Vanessa L Bauer ; Ashmore, Adeline B. ; Gutierrez, Angela ; Aquadro, Charles F. / Patterns of sequence variability and divergence at the diminutive gene region of Drosophila melanogaster : Complex patterns suggest an ancestral selective sweep. In: Genetics. 2007 ; Vol. 177, No. 2. pp. 1071-1085.
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