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Molecular Evolution of a Sex-Linked Inversion Polymorphism in Zebra Finches.

Peter D Price¹, Jake Pepper¹, Thea F Rogers²

¹Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK.

Genome Biology and Evolution

|March 5, 2026

Summary

Supergenes suppress recombination to control complex traits. In zebra finches, long-term suppression on Z-linked haplotypes increases mutation load without compensatory expression evolution.

Keywords:

balancing selection inversions sperm competition supergene zebra finch

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Dissection and Downstream Analysis of Zebra Finch Embryos at Early Stages of Development

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Published on: June 21, 2014

Area of Science:

Evolutionary Biology
Genomics
Molecular Evolution

Background:

Supergenes, regions with suppressed recombination, are crucial for maintaining complex traits.
Understanding the long-term molecular impacts of recombination suppression is an evolutionary challenge.
Inversion polymorphisms are a common mechanism for suppressing recombination in supergenes.

Purpose of the Study:

To investigate the molecular evolution of Z-linked haplotypes within a supergene in zebra finches (Taeniopygia guttata).
To assess the impact of recombination suppression on sequence divergence and purifying selection.
To examine the relationship between gene expression and sequence divergence in the context of suppressed recombination.

Main Methods:

Analysis of DNA sequences from A and B haplotypes of a sex-linked inversion polymorphism.
Assessment of purifying selection efficacy on coding sequences.
Examination of gene expression levels and their correlation with sequence divergence.

Main Results:

Evidence of reduced purifying selection efficacy on the coding sequences of Z-linked haplotypes.
An observed increase in mutational load within these haplotypes.
No positive association found between gene expression and sequence divergence, indicating a lack of compensatory expression evolution.

Conclusions:

Long-term recombination suppression in zebra finch supergenes leads to relaxed purifying selection and accumulation of deleterious mutations.
The absence of compensatory expression evolution suggests that genetic load increases without adaptive gene regulation.
These findings provide insights into the molecular evolution of complex traits controlled by supergenes.