Towards a genetic architecture of cryptic genetic variation and genetic assimilation: the contribution of K. G. Bateman

A theoretical perspective on Waddington's genetic assimilation experiments

Genetic assimilation is the process by which a phenotype that is initially induced by an environmental stimulus becomes stably inherited in the absence of the stimulus after a few generations of selection. While the concept has attracted much debate after being introduced by C. H. Waddington 70 y ago, there have been few experiments to quantitatively characterize the phenomenon. Here, we revisit and organize the results of Waddington's original experiments and follow-up studies that attempted to replicate his results. We then present a theoretical model to illustrate the process of genetic assimilation and highlight several aspects that we think require further quantitative studies, including the gradual increase of penetrance, the statistics of delay in assimilation, and the frequency of unviability during selection. Our model captures Waddington's picture of developmental paths in a canalized landscape using a stochastic dynamical system with alternative trajectories that can be controlled by either external signals or internal variables. It also reconciles two descriptions of the phenomenon-Waddington's, expressed in terms of an individual organism's developmental paths, and that of Bateman in terms of the population distribution crossing a hypothetical threshold. Our results provide theoretical insight into the concepts of canalization, phenotypic plasticity, and genetic assimilation.

Canalization and genetic assimilation: Reassessing the radicality of the Waddingtonian concept of inheritance of acquired characters

Genetic assimilation is often mixed up with the Baldwin effect. For Waddington, genetic assimilation was both a phenomenon and a specific mechanism of adaptive evolution which was grounded in the concept of canalization. This theoretical link between canalization and genetic assimilation, which was pivotal in Waddington's view, has been weakened since the early 1960s. The aim of the present article is to emphasize the specificity and to reassess the possible radicality of Waddington's proposal. What he claimed to have elaborated was an actual and genuine mechanism of inheritance of acquired characters that did not rely on soft Lamarckian inheritance. Consequently his "theory" of genetic assimilation, unlike the Baldwin effect, might not be as easily integrated in the framework of the Modern Synthesis.

The flexible stem hypothesis: evidence from genetic data

Phenotypic plasticity, the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions, is widely observed in the wild. It is believed to facilitate evolution and, under the "flexible stem hypothesis", it is thought that an ancestral plastic species can be at the origin of sister lineages with divergent phenotypes fixed by genetic assimilation of alternative morphs. We review here the genetic mechanisms underlying such phenomenon. We show several examples in which the same gene shows transcriptional plasticity in response to environmental factors and divergence of expression within or between species. Thus, the same gene is involved both in the plasticity of a trait and in the evolution of that trait. In a few cases, it can be traced down to cis-regulatory variation in this gene and, in one case, in the very same regulatory sequence whose activity is modulated by the environment. These data are compatible with the "flexible stem hypothesis" and also suggest that the evolution of the plasticity of a trait and the evolution of the trait are not completely uncoupled as they often involve the same locus. Furthermore, the "flexible stem hypothesis" implies that it is possible to canalize initially plastic phenotypes. Several studies have shown that it was possible through modification of chromatin regulation or hormonal signalling/response. Further studies of phenotypic plasticity in an evolutionary framework are needed to see how much the findings described in this review can be generalized.

Diverse genetic architectures lead to the same cryptic phenotype in a yeast cross

Cryptic genetic variants that do not typically influence traits can interact epistatically with each other and mutations to cause unexpected phenotypes. To improve understanding of the genetic architectures and molecular mechanisms that underlie these interactions, we comprehensively dissected the genetic bases of 17 independent instances of the same cryptic colony phenotype in a yeast cross. In eight cases, the phenotype resulted from a genetic interaction between a de novo mutation and one or more cryptic variants. The number and identities of detected cryptic variants depended on the mutated gene. In the nine remaining cases, the phenotype arose without a de novo mutation due to two different classes of higher-order genetic interactions that only involve cryptic variants. Our results may be relevant to other species and disease, as most of the mutations and cryptic variants identified in our study reside in components of a partially conserved and oncogenic signalling pathway.

Cryptic genetic variants may not individually show discernible phenotypic effects, but collectively, these polymorphisms can lead to unexpected, genetically complex traits that might be relevant to evolution and disease. Here, the authors use large yeast populations to comprehensively dissect the genetic bases of 17 independent occurrences of a phenotype that arises due to combinations of epistatically interacting cryptic variants.

Phenotypic Evolution With and Beyond Genome Evolution

DNA does not make phenotypes on its own. In this volume entitled "Genes and Phenotypic Evolution," the present review draws the attention on the process of phenotype construction-including development of multicellular organisms-and the multiple interactions and feedbacks between DNA, organism, and environment at various levels and timescales in the evolutionary process. First, during the construction of an individual's phenotype, DNA is recruited as a template for building blocks within the cellular context and may in addition be involved in dynamical feedback loops that depend on the environmental and organismal context. Second, in the production of phenotypic variation among individuals, stochastic, environmental, genetic, and parental sources of variation act jointly. While in controlled laboratory settings, various genetic and environmental factors can be tested one at a time or in various combinations, they cannot be separated in natural populations because the environment is not controlled and the genotype can rarely be replicated. Third, along generations, genotype and environment each have specific properties concerning the origin of their variation, the hereditary transmission of this variation, and the evolutionary feedbacks. Natural selection acts as a feedback from phenotype and environment to genotype. This review integrates recent results and concrete examples that illustrate these three points. Although some themes are shared with recent calls and claims to a new conceptual framework in evolutionary biology, the viewpoint presented here only means to add flesh to the standard evolutionary synthesis.

Genetic assimilation: a review of its potential proximate causes and evolutionary consequences

BACKGROUND

Most, if not all, organisms possess the ability to alter their phenotype in direct response to changes in their environment, a phenomenon known as phenotypic plasticity. Selection can break this environmental sensitivity, however, and cause a formerly environmentally induced trait to evolve to become fixed through a process called genetic assimilation. Essentially, genetic assimilation can be viewed as the evolution of environmental robustness in what was formerly an environmentally sensitive trait. Because genetic assimilation has long been suggested to play a key role in the origins of phenotypic novelty and possibly even new species, identifying and characterizing the proximate mechanisms that underlie genetic assimilation may advance our basic understanding of how novel traits and species evolve.

SCOPE

This review begins by discussing how the evolution of phenotypic plasticity, followed by genetic assimilation, might promote the origins of new traits and possibly fuel speciation and adaptive radiation. The evidence implicating genetic assimilation in evolutionary innovation and diversification is then briefly considered. Next, the potential causes of phenotypic plasticity generally and genetic assimilation specifically are examined at the genetic, molecular and physiological levels and approaches that can improve our understanding of these mechanisms are described. The review concludes by outlining major challenges for future work.

CONCLUSIONS

Identifying and characterizing the proximate mechanisms involved in phenotypic plasticity and genetic assimilation promises to help advance our basic understanding of evolutionary innovation and diversification.

Transcriptional Derepression Uncovers Cryptic Higher-Order Genetic Interactions

Disruption of certain genes can reveal cryptic genetic variants that do not typically show phenotypic effects. Because this phenomenon, which is referred to as ‘phenotypic capacitance’, is a potential source of trait variation and disease risk, it is important to understand how it arises at the genetic and molecular levels. Here, we use a cryptic colony morphology trait that segregates in a yeast cross to explore the mechanisms underlying phenotypic capacitance. We find that the colony trait is expressed when a mutation in IRA2, a negative regulator of the Ras pathway, co-occurs with specific combinations of cryptic variants in six genes. Four of these genes encode transcription factors that act downstream of the Ras pathway, indicating that the phenotype involves genetically complex changes in the transcriptional regulation of Ras targets. We provide evidence that the IRA2 mutation reveals the phenotypic effects of the cryptic variants by disrupting the transcriptional silencing of one or more genes that contribute to the trait. Supporting this role for the IRA2 mutation, deletion of SFL1, a repressor that acts downstream of the Ras pathway, also reveals the phenotype, largely due to the same cryptic variants that were detected in the IRA2 mutant cross. Our results illustrate how higher-order genetic interactions among mutations and cryptic variants can result in phenotypic capacitance in specific genetic backgrounds, and suggests these interactions might reflect genetically complex changes in gene expression that are usually suppressed by negative regulation.

Some genetic polymorphisms have phenotypic effects that are masked under most conditions, but can be revealed by mutations or environmental change. The genetic and molecular mechanisms that suppress and uncover these cryptic genetic variants are important to understand. Here, we show that a single mutation in a yeast cross causes a major phenotypic change through its genetic interactions with two specific combinations of cryptic variants in six genes. This result suggests that in some cases cryptic variants themselves play roles in revealing their own phenotypic effects through their genetic interactions with each other and the mutations that reveal them. We also demonstrate that most of the genes harboring cryptic variation in our system are transcription factors, a finding that supports an important role for perturbation of gene regulatory networks in the uncovering of cryptic variation. As a final part of our study, we interrogate how a mutation exposes combinations of cryptic variants and obtain evidence that it does so by disrupting the silencing of one or more genes that must be expressed for the cryptic variants to exert their effects. To prove this point, we delete the transcriptional repressor that mediates this silencing and demonstrate that this deletion reveals a similar set of cryptic variants to the ones that were discovered in the initial mutant background. These findings advance our understanding of the genetic and molecular mechanisms that reveal cryptic variation.

Nested Levels of Adaptive Divergence: The Genetic Basis of Craniofacial Divergence and Ecological Sexual Dimorphism

Exemplary systems for adaptive divergence are often characterized by their large degrees of phenotypic variation. This variation represents the outcome of generations of diversifying selection. However, adaptive radiations can also contain a hierarchy of differentiation nested within them where species display only subtle phenotypic differences that still have substantial effects on ecology, function, and ultimately fitness. Sexual dimorphisms are also common in species displaying adaptive divergence and can be the result of differential selection between sexes that produce ecological differences between sexes. Understanding the genetic basis of subtle variation (between certain species or sexes) is therefore important for understanding the process of adaptive divergence. Using cichlids from the dramatic adaptive radiation of Lake Malawi, we focus on understanding the genetic basis of two aspects of relatively subtle phenotypic variation. This included a morphometric comparison of the patterns of craniofacial divergence between two ecologically similar species in relation to the larger adaptive radiation of Malawi, and male-female morphological divergence between their F2 hybrids. We then genetically map craniofacial traits within the context of sex and locate several regions of the genome that contribute to variation in craniofacial shape that is relevant to sexual dimorphism within species and subtle divergence between closely related species, and possibly to craniofacial divergence in the Malawi radiation as a whole. To enhance our search for candidate genes we take advantage of population genomic data and a genetic map that is anchored to the cichlid genome to determine which genes within our QTL regions are associated with SNPs that are alternatively fixed between species. This study provides a holistic understanding of the genetic underpinnings of adaptive divergence in craniofacial shape.

Eco-evo-devo: the time has come

The major goal of ecological evolutionary developmental biology, also known as "eco-evo-devo," is to uncover the rules that underlie the interactions between an organism's environment, genes, and development and to incorporate these rules into evolutionary theory. In this chapter, we discuss some key and emerging concepts within eco-evo-devo. These concepts show that the environment is a source and inducer of genotypic and phenotypic variation at multiple levels of biological organization, while development acts as a regulator that can mask, release, or create new combinations of variation. Natural selection can subsequently fix this variation, giving rise to novel phenotypes. Combining the approaches of eco-evo-devo and ecological genomics will mutually enrich these fields in a way that will not only enhance our understanding of evolution, but also of the genetic mechanisms underlying the responses of organisms to their natural environments.

Developmental plasticity and the evolution of animal complex life cycles

Metazoan life cycles can be complex in different ways. A number of diverse phenotypes and reproductive events can sequentially occur along the cycle, and at certain stages a variety of developmental and reproductive options can be available to the animal, the choice among which depends on a combination of organismal and environmental conditions. We hypothesize that a diversity of phenotypes arranged in developmental sequence throughout an animal's life cycle may have evolved by genetic assimilation of alternative phenotypes originally triggered by environmental cues. This is supported by similarities between the developmental mechanisms mediating phenotype change and alternative phenotype determination during ontogeny and the common ecological condition that favour both forms of phenotypic variation. The comparison of transcription profiles from different developmental stages throughout a complex life cycle with those from alternative phenotypes in closely related polyphenic animals is expected to offer critical evidence upon which to evaluate our hypothesis.

On the origins of novelty in development and evolution

The origin of novel traits is what draws many to evolutionary biology, yet our understanding of the mechanisms that underlie the genesis of novelty remains limited. Here I review definitions of novelty including its relationship to homology. I then discuss how ontogenetic perspectives may allow us to move beyond current roadblocks in our understanding of the mechanics of innovation. Specifically, I explore the roles of canalization, plasticity and threshold responses during development in generating a reservoir of cryptic genetic variation free to drift and accumulate in natural populations. Environmental or genetic perturbations that exceed the buffering capacity of development can then release this variation, and, through evolution by genetic accommodation, result in rapid diversification, recurrence of lost phenotypes as well as the origins of novel features. I conclude that, in our quest to understand the nature of innovation, the nature of development deserves to take center stage.

A role for genetic accommodation in evolution?

Whether evolutionary change can occur by genetic assimilation, or more generally by genetic accommodation, remains controversial. Here we examine some of the experimental evidence for both phenomena. Several experiments in Drosophila suggest that assimilation is possible, and a new paper shows that a color polyphenism in the tobacco hornworm, Manduca sexta, can evolve by genetic accommodation. We argue that genetic accommodation, including assimilation, is a plausible mechanism in evolution; however, more work is required to test how this mechanism acts and how often it is involved in evolutionary change.