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Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence.

Kosmas Hench1, Marta Vargas2, Marc P Höppner3

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Summary
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Speciation with gene flow is hindered by recombination. This study reveals that linkage disequilibrium, crucial for species origin, can evolve without physical gene linkage in Caribbean hamlets, driven by visual mating preferences.

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Speciation research

Background:

  • Recombination between genes for mate choice and ecological traits impedes speciation with gene flow.
  • Linkage disequilibrium (LD) evolution is a key step in the origin of species.
  • Hamlets (reef fishes) exhibit reproductive isolation via visually-based assortative mating, differing primarily in color patterns.

Purpose of the Study:

  • To investigate the genomic basis of speciation in hamlets.
  • To determine if linkage disequilibrium can evolve without physical linkage between genes influencing speciation.
  • To identify genomic regions associated with species divergence in hamlets.

Main Methods:

  • Full-genome analysis of closely related hamlet species.
  • Identification of differentiated genomic intervals.
  • Analysis of genes involved in visual traits and development.

Main Results:

  • Four narrow genomic intervals showed consistent differentiation among sympatric hamlet species despite low overall genomic divergence.
  • These intervals contain genes related to pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1), and visual opsins (SWS, LWS).
  • Islands of long-distance and inter-chromosomal linkage disequilibrium evolved in these regions as species diverged.

Conclusions:

  • Speciation with gene flow can occur through the evolution of linkage disequilibrium even without physical gene linkage.
  • The genomic architecture of species differences in hamlets, particularly involving visual traits, facilitates LD evolution.
  • This study provides insights into the genetic mechanisms driving the origin of species in the face of ongoing gene flow.