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Related Experiment Videos

Polymorphism and divergence at a Drosophila pseudogene locus

J K Pritchard1, S W Schaeffer

  • 1Department of Biology, Pennsylvania State University, University Park 16802, USA.

Genetics
|September 1, 1997
PubMed
Summary
This summary is machine-generated.

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The study on Drosophila melanogaster larval cuticle protein pseudogene (Lcp psi) found high divergence between species but low within-species variation. This suggests background selection, a mechanism limiting genetic diversity in non-recombining regions.

Area of Science:

  • Evolutionary genetics
  • Molecular evolution
  • Drosophila research

Background:

  • The larval cuticle protein (Lcp) gene cluster in Drosophila melanogaster includes functional genes and a pseudogene (Lcp psi).
  • Understanding pseudogene evolution provides insights into selective pressures and genetic variation within species.

Purpose of the Study:

  • To investigate nucleotide substitution rates and levels of variation at the Lcp psi locus in Drosophila.
  • To test hypotheses regarding synonymous vs. nonsynonymous substitution rates, variation levels compared to functional genes, and correlation between intraspecific polymorphism and interspecific divergence.

Main Methods:

  • Nucleotide sequencing of a 630-bp fragment of Lcp psi in 10 D. melanogaster strains and a 458-bp fragment from D. simulans.
  • Analysis of synonymous and nonsynonymous substitution rates.

Related Experiment Videos

  • Application of the Hudson, Kreitman, and Aguade (HKA) test to compare polymorphism and divergence.
  • Comparison with the Adh 5' flanking region.

    • Main Results:

    • Synonymous and nonsynonymous substitution rates were equivalent.
    • Extremely high nucleotide divergence (Jukes-Cantor distance = 0.149 +/- 0.150) was observed between D. melanogaster and D. simulans.
    • Lower levels of within-species polymorphism (theta = 0.001 +/- 0.001) were found at Lcp psi compared to many functional loci.
    • The HKA test indicated lower-than-expected polymorphism at Lcp psi relative to divergence, especially when compared to the Adh 5' flanking region.

    Conclusions:

    • The Lcp psi locus exhibits high interspecific divergence but low intraspecific polymorphism.
    • The low polymorphism is likely due to background selection, a process prevalent in regions of infrequent recombination.
    • Pseudogene evolution is influenced by complex evolutionary forces, including purifying selection acting on linked functional sites.