Neutralism versus selectionism: Chargaff's second parity rule, revisited

Area of Science:

• Genetics
• Molecular Biology
• Evolutionary Biology

Background:

• Chargaff's second parity rule (PR2) regarding DNA base frequencies remains functionally contentious.
• Previous interpretations, like Galtier and Lobry's, favored neutral hypotheses for PR2 based on thermophile base composition (GC%).
• Forsdyke's selective PR2 hypothesis proposes mutations enhance local recombination efficiency, facilitating DNA strand separation.

Purpose of the Study:

• To re-evaluate the functional interpretation of Chargaff's second parity rule (PR2).
• To investigate the role of DNA base order versus base composition in evolutionary pressures.
• To test Forsdyke's selective PR2 hypothesis against neutral models.

Main Methods:

• Utilized novel technology to mask base composition's influence on nucleic acid folding energy.
• Analyzed DNA base order for local, within-species recombination roles.
• Applied principles consistent with Chargaff's cluster rule and relative oligonucleotide frequencies (k-mer analysis).

Main Results:

• Evidence supports a local, within-species role for DNA base order in initiating recombination.
• Forsdyke's selective PR2 hypothesis is consistent with findings.
• Base composition (GC%) primarily reflects genome-wide evolutionary pressure, not solely temperature adaptation.
• The thermoadaptive role of "purine-loading" in open reading frames was identified.

Conclusions:

• Findings challenge anti-selectionist arguments and support a selective basis for PR2.
• DNA base order, not just composition, plays a crucial role in recombination and evolution.
• Provides a theoretical basis for alignment-free taxonomic analyses using k-mer analysis.