Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse...

Area of Science:

• Evolutionary biology
• Genomics
• Developmental biology

Background:

• Fish fins are crucial appendages that exhibit significant natural diversity across lineages.
• Understanding the genetic basis of fin evolution, particularly reduction, is key to deciphering vertebrate appendage development.

Purpose of the Study:

• To identify genomic changes associated with natural fin diversity, specifically fin reduction, in percomorph fish.
• To investigate the role of conserved regulatory elements in the convergent evolution of reduced fins.

Main Methods:

• Comparative genomics of 36 percomorph fish species with complete or reduced pelvic and caudal fins.
• Identification of conserved genomic regions and analysis of deletions in fin-reduced lineages.
• Functional assays, including enhancer activity in transgenic fish and genome editing, to validate candidate regulatory elements.

Main Results:

• 1,614 genomic regions conserved in fin-complete species are missing in multiple fin-reduced lineages.
• Recurrent deletions near appendage development genes are enriched in fin-reduced species, suggesting convergent genomic evolution.
• The Pitx1 enhancer (PelA) was independently deleted in pelvic-reduced species, and a novel caudal fin enhancer was identified and validated through functional assays.

Conclusions:

• Convergent fin reduction in fish is associated with repeated deletions of regulatory elements near key developmental genes.
• Specific enhancers, like PelA and the novel caudal fin enhancer, play significant roles in the evolution of fin morphology.
• This study provides a framework for linking phenotypes to genotypes across vertebrate evolution and identifies regulatory hotspots driving recurrent evolutionary changes.