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Noncoding regions underpin avian bill shape diversification at macroevolutionary scales.

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Genomic analysis reveals that regulatory, noncoding DNA changes, not protein-coding genes, drive major bird beak evolution over long timescales. This finding advances our understanding of macroevolutionary processes.

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Developmental biology

Background:

  • Identifying genomic underpinnings of trait evolution is key, but relevance across micro- and macroevolutionary scales is debated.
  • Bird beak shape is a model trait for studying resource use, divergence, and speciation.

Purpose of the Study:

  • To investigate whether genomic regions identified at microevolutionary scales are relevant to macroevolutionary trait changes.
  • To explore the genetic basis of bird beak shape evolution across macroevolutionary timescales.

Main Methods:

  • Integrated geometric morphometrics with evolutionary sequence analyses of 10,322 protein-coding genes and 229,001 genomic regions across 72 bird species.
  • Analyzed molecular rates in relation to rates of beak shape evolution.
  • Examined gene ontology and pathway associations for identified coding and noncoding regions.

Main Results:

  • Identified 1,434 protein-coding genes and 39,806 noncoding regions significantly linked to beak shape evolution rates.
  • Homologs of identified genes and nearby noncoding regions are involved in mammalian craniofacial development and avian beak morphology pathways (BMP, Wnt signaling).
  • Noncoding loci showed significantly reduced overlap with coding loci and stronger associations with beak phenotype, with evidence of recent selection in Darwin's finches.

Conclusions:

  • Genome-wide identification of genotype-phenotype associations is feasible over macroevolutionary time.
  • Regulatory (noncoding) genetic changes appear to be the primary drivers of morphological diversification in bird beaks over macroevolutionary scales, rather than changes in protein-coding genes.