In This Article Expand or collapse the "in this article" section Identifying the Genomic Basis Underlying Phenotypic Variation

  • Introduction
  • Journals
  • Importance of Assessing the Appropriate Traits
  • Nature of Molecular Change
  • Early Success in Laboratory Model Organisms
  • Transitioning from the Lab to the Field
  • Establishing Techniques in Nontraditional Model Organisms
  • From Phenotype to Genotype in Cichlids—A Ten-Plus-Year Endeavor
  • The Challenge of Resolving the Genotype–Phenotype Map
  • The Challenge of Finding the Missing Heritability
  • The Challenge of a Systems Approach to Phenotypic Variation

Evolutionary Biology Identifying the Genomic Basis Underlying Phenotypic Variation
Kara Powder, Craig Albertson
  • LAST REVIEWED: 25 August 2022
  • LAST MODIFIED: 26 April 2018
  • DOI: 10.1093/obo/9780199941728-0106


Since the Modern Synthesis and the identification of the structure of DNA, evolutionary biologists have sought to determine the DNA changes that result in divergent phenotypes on which natural selection can act. In particular, we aim to understand (i) the number and effect size of genes, (ii) the interaction between genetic loci (G×G, or epistasis) and between genes and the environment (G×E), and (iii) the molecular nature of genetic variations that underlie phenotypic variation. With this knowledge, we can then ask myriad questions related to the origin and maintenance of biodiversity including if similar genes underlie convergent phenotypes, if certain classes of genes or changes regulate phenotypic divergence, and what are the genetic origins of novel traits. Here, we define the genomic basis of variation as an unbiased examination of the genome itself. Forward genetics, whereby researchers begin with phenotypic variation and work toward the underlying genotypic variation, exemplifies such an approach. We do not include pure transcriptomics studies in our survey as this rich body of literature can stand on its own. Similarly, we exclude studies that utilize only a candidate gene approach, as this is not an unbiased design. Genome editing techniques such as the CRISPR/Cas9 system have been fruitful in model and non-model organisms alike in linking genotype to phenotype. However, a review of such reverse genetic techniques and work is beyond our focus, which is on forward genetic approaches. As we highlight, gene editing, transcriptomic, and candidate gene approaches can be used to corroborate genomic data.


As technologies improve and genomic methods become accessible to a wider range of investigators, the list of applicable journals has become much larger. As such, it is not practical or possible to list all journals that have papers on this topic. We therefore only give a small sample of example journals. Highly integrated studies including detailed functional analysis of genetic changes, are often published in journals such as Nature, Science, and Proceedings of the National Academy of Sciences USA. PLoS Genetics and Genetics publish studies that are focused on genetic analysis of evolutionarily relevant phenotypes. Genetic/genomic analyses are also appearing more frequently in leading journals in evolution including Evolution, Journal of Evolutionary Biology, and Molecular Biology and Evolution.

  • Evolution. 1947–.

    One of the leading journals in evolutionary biology, this journal is published by the Society for the Study of Evolution and includes those studies focused on the genetic basis of evolution.

  • Genetics. 1916–.

    The flagship journal for the Genetics Society of America, publishing papers and methodology in the genetics and genomics of both model and non-model organisms.

  • Journal of Evolutionary Biology. 1988–.

    Published by the European Society for Evolutionary Biology, this journal integrates all areas of evolutionary biology.

  • Molecular Biology and Evolution. 1983–.

    The journal of the Society of Molecular Biology and Evolution specifically focused on the interface between molecules (e.g., genes) and evolution, publishing methods, results, and theory.

  • Nature. 1869–.

    Publishes high-impact research and commentary in genetics and evolutionary biology that is of broad interest to the scientific community.

  • PLoS Genetics. 2005–.

    One of the leading journals in genetics and genomics, including studies focused on the basis of evolutionarily relevant phenotypes.

  • Proceedings of the National Academy of Sciences USA. 1915–.

    PNAS is a comprehensive multidisciplinary journal including studies in evolutionary biology and genetics.

  • Science. 1880–.

    The flagship journal of the American Association for the Advancement of Science publishes high impact work in evolutionary biology that is of broad interest to the scientific community.

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