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The genotype–phenotype distinction: from Mendelian genetics to 21st century biology

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It is a well-established fact that language is not only our servant, when we wish to express–or even to conceal–our thoughts, but that it may also be our master, overpowering us by means of the notions attached to the current words. This fact is the reason why it is desirable to create a new terminology in all cases where new or revised conceptions are being developed. Old terms are mostly compromised by their application in antiquated or erroneous theories and systems, from which they carry splinters of inadequate ideas, not always harmless to the developing insight. (Johannsen, 1911, p. 132)

Abstract

The Genotype-Phenotype (G-P) distinction was proposed in the context of Mendelian genetics, in the wake of late nineteenth century studies about heredity. In this paper, we provide a conceptual analysis that highlights that the G-P distinction was grounded on three pillars: observability, transmissibility, and causality. Originally, the genotype is the non-observable and transmissible cause of its observable and non-transmissible effect, the phenotype. We argue that the current developments of biology have called the validity of such pillars into question. First, molecular biology has unveiled the putative material substrate of the genotype (qua DNA), making it an observable object. Second, numerous findings on non-genetic heredity suggest that some phenotypic traits can be directly transmitted. Third, recent organicist approaches to biological phenomena have emphasized the reciprocal causality between parts of a biological system, which notably applies to the relation between genotypes and phenotypes. As a consequence, we submit that the G-P distinction has lost its general validity, although it can still apply to specific situations. This calls for forging new frameworks and concepts to better describe heredity and development.

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Notes

  1. Two conceptions of heredity can be distinguished in the nineteenth century: a phenomenal (statistical) one, according to which heredity is merely a measurable resemblance, and a physiological one, which interprets heredity as a process of material transmission (Gayon 1992; 2000). The phenomenal approach only measures resemblances between parents and offspring without any consideration for underlying processes. In this paper, we leave it aside.

  2. This differential view of the genotype–phenotype causal relationship was recently reaffirmed (Orgogozo et al. 2015), notably to prevent naïve interpretations according to which genes alone would be the causes of traits.

  3. The effects of interactions — of genes with other genes (epistasis) and of genes with the environment (norms of reactions) — also increased the complexity of the G-P relations, insofar as they imply a many-to-many relation between the genotype and the phenotype (see Orgogozo et al. 2015; De Vienne, this issue).

  4. Trans-generationally inherited epigenetic marks are sometimes referred to as “epigenotypes” (e.g. Hofmeister et al. 2017). We note a similar trajectory of this concept with that of the genotype. Waddington originally coined the term “epigenotype” to mean something rather abstract: “the set of organizers [i.e. genes] and organizing relations” (Waddington 1939 [2016]) or, in a slightly different sense, the complex of developmental processes that link the genotype and phenotype (Waddington 1942; see Boisseau, in press). The epigenotype came to be interpreted in a molecular way following the development of molecular biology. (Haig 2012).

  5. Strictly speaking, originally the phenotype is a relational notion that supposes a corresponding genotype (Gayon and Petit 2018, p. 326). From this point of view, talking about the transmission of phenotypes is improper, and presupposes an inflexion of the original Mendelian meaning. A more Mendelian notion is that of “posthumous phenotypes” (Lehmann 2008; see Pocheville 2010), that is, phenotypes that extend beyond the generation time.

  6. Note that conditions of existence concern a different level of explanation than causation. Conditions of existence explain the possibility of existence of a given system, while causation explains how differences make differences on some predicates (Bernard 1865; Woodward 2003; Pearl 2009; see also Stewart 2004). Thus, the reciprocal determination of conditions of existence does not per se invalidate any putative G-P causal asymmetry.

  7. Mutational assimilation, which refers to the fact that phenotypes can induce a specific kind of variation in the genotype (qua DNA sequence) at the level of the individual, is different from genetic assimilation (sensu Waddington), which occurs at the level of the population (Pigliucci et al. 2006).

  8. As a reviewer noticed, a different strategy would be to take a step back from a causal theory of inheritance and espouse statistical concepts such as those of heritable and non-heritable variation, as dissected by ANOVA in quantitative genetics (e.g. Danchin and Wagner 2010). Although not unrelated to underlying causal theories of inheritance, such statistical concepts do not map straightforwardly to causal concepts (as genotype and phenotype are), and a proper discussion of such intricacies would deserve a paper of its own. We note that the extreme sensitivity of ANOVA to frequency distributions of variables brings such a statistical approach closer to a description of contingent situations than to a theory of biological variation (Lewontin 1974).

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Acknowledgements

We thank Dominique De Vienne, Andràs Paldi, Francesca Merlin, Lounès Chikhi, Paul-Antoine Miquel, Alexis Boisseau, Jonathan Racine, Mathilde Tahar, Emmanuelle Maciel, and three anonymous reviewers for insightful comments on earlier versions of the manuscript.

Funding

GP was supported by an ANR grant (Envirobiosoc, ANR-19-CE26-0018) to Francesca Merlin.

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  1. Institut d’Histoire et de Philosophie des Sciences et des Techniques, CNRS/Université Paris 1 Panthéon-Sorbonne, Paris, France

    Gaëlle Pontarotti & Matteo Mossio

  2. Université de Toulouse, Laboratoire Évolution et Diversité Biologique, UMR 5174, CNRS, IRD, UPS, Toulouse, France

    Arnaud Pocheville

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Pontarotti, G., Mossio, M. & Pocheville, A. The genotype–phenotype distinction: from Mendelian genetics to 21st century biology. Genetica 150, 223–234 (2022). https://doi.org/10.1007/s10709-022-00159-5

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  • DOI: https://doi.org/10.1007/s10709-022-00159-5

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