Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish

Mol Biol Evol. 2013 Jun;30(6):1384-96. doi: 10.1093/molbev/mst053. Epub 2013 Mar 21.


A functional understanding of processes involved in adaptive divergence is one of the awaiting opportunities afforded by high-throughput transcriptomic technologies. Functional analysis of coexpressed genes has succeeded in the biomedical field in identifying key drivers of disease pathways. However, in ecology and evolutionary biology, functional interpretation of transcriptomic data is still limited. Here, we used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify modules of coexpressed genes in muscle and brain tissue of a lake whitefish backcross progeny. Modules were connected to gradients of known adaptive traits involved in the ecological speciation process between benthic and limnetic ecotypes. Key drivers, that is, hub genes of functional modules related to reproduction, growth, and behavior were identified, and module preservation was assessed in natural populations. Using this approach, we identified modules of coexpressed genes involved in phenotypic divergence and their key drivers, and further identified a module part specifically rewired in the backcross progeny. Functional analysis of transcriptomic data can significantly contribute to the understanding of the mechanisms underlying ecological speciation. Our findings point to bone morphogenetic protein and calcium signaling as common pathways involved in coordinated evolution of trophic behavior, trophic morphology (gill rakers), and reproduction. Results also point to pathways implicating hemoglobins and constitutive stress response (HSP70) governing growth in lake whitefish.

Keywords: Coregonus cupleaformis; coexpression networks; ecological speciation; gill raker; microarray; phenotype.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Brain / metabolism
  • Brain Chemistry
  • Cluster Analysis
  • Female
  • Fish Proteins / genetics
  • Fish Proteins / metabolism
  • Gene Expression Profiling
  • Gene Regulatory Networks*
  • Genetic Speciation
  • Male
  • Muscles / chemistry
  • Muscles / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Phenotype
  • Principal Component Analysis
  • Salmonidae / classification
  • Salmonidae / genetics*
  • Salmonidae / metabolism


  • Fish Proteins