Neophenogenesis: a developmental theory of phenotypic evolution

An important task for evolutionary biology is to explain how phenotypes change over evolutionary time. Neo-Darwinian theory explains phenotypic change as the outcome of genetic change brought about by natural selection. In the neo-Darwinian account, genetic change is primary; phenotypic change is a secondary outcome that is often given no explicit consideration at all. In this article, we introduce the concept of neophenogenesis: a persistent, transgenerational change in phenotypes over evolutionary time. A theory of neophenogenesis must encompass all sources of such phenotypic change, not just genetic ones. Both genetic and extra-genetic contributions to neophenogenesis have their effect through the mechanisms of development, and developmental considerations, particularly a rejection of the commonly held distinction between inherited and acquired traits, occupy a central place in neophenogenetic theory. New phenotypes arise because of a change in the patterns of organism-environment interaction that produce development in members of a population. So long as these new patterns of developmental interaction persist, the new phenotype(s) will also persist. Although the developmental mechanisms that produce the novel phenotype may change, as in the process known as "genetic assimilation", such changes are not necessary in order for neophenogenesis to occur, because neophenogenetic theory is a theory of phenotypic, not genetic, change.     

Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions

During development, signaling networks control the formation of multicellular patterns. To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear. Here, we describe a computational approach to predict and analyze the phenotypic diversity that is accessible to a developmental signaling network. Applying this framework to vulval development in C. elegans, we demonstrate that quantitative changes in the regulatory network can render ~500 multicellular phenotypes. This phenotypic capacity is an order-of-magnitude below the theoretical upper limit for this system but yet is large enough to demonstrate that the system is not restricted to a select few outcomes. Using metrics to gauge the robustness of these phenotypes to parameter perturbations, we identify a select subset of novel phenotypes that are the most promising for experimental validation. In addition, our model calculations provide a layout of these phenotypes in network parameter space. Analyzing this landscape of multicellular phenotypes yielded two significant insights. First, we show that experimentally well-established mutant phenotypes may be rendered using non-canonical network perturbations. Second, we show that the predicted multicellular patterns include not only those observed in C. elegans, but also those occurring exclusively in other species of the Caenorhabditis genus. This result demonstrates that quantitative diversification of a common regulatory network is indeed demonstrably sufficient to generate the phenotypic differences observed across three major species within the Caenorhabditis genus. Using our computational framework, we systematically identify the quantitative changes that may have occurred in the regulatory network during the evolution of these species. Our model predictions show that significant phenotypic diversity may be sampled through quantitative variations in the regulatory network without overhauling the core network architecture. Furthermore, by comparing the predicted landscape of phenotypes to multicellular patterns that have been experimentally observed across multiple species, we systematically trace the quantitative regulatory changes that may have occurred during the evolution of the Caenorhabditis genus.     

Brain evolution and development: adaptation,allometry and constraint

Phenotypic traits are products of two processes: evolution and development. But how do these processes combine to produce integrated phenotypes? Comparative studies identify consistent patterns of covariation, or allometries, between brain and body size, and between brain components, indicating the presence of significant constraints limiting independent evolution of separate parts. These constraints are poorly understood, but in principle could be either developmental or functional. The developmental constraints hypothesis suggests that individual components (brain and body size, or individual brain components) tend to evolve together because natural selection operates on relatively simple developmental mechanisms that affect the growth of all parts in a concerted manner. The functional constraints hypothesis suggests that correlated change reflects the action of selection on distributed functional systems connecting the different sub-components, predicting more complex patterns of mosaic change at the level of the functional systems and more complex genetic and developmental mechanisms. These hypotheses are not mutually exclusive but make different predictions. We review recent genetic and neurodevelopmental evidence, concluding that functional rather than developmental constraints are the main cause of the observed patterns.     

THE EVOLUTION OF PHENOTYPIC CORRELATIONS AND “DEVELOPMENTAL MEMORY”

Development introduces structured correlations among traits that may constrain or bias the distribution of phenotypes produced. Moreover, when suitable heritable variation exists, natural selection may alter such constraints and correlations, affecting the phenotypic variation available to subsequent selection. However, exactly how the distribution of phenotypes produced by complex developmental systems can be shaped by past selective environments is poorly understood. Here we investigate the evolution of a network of recurrent nonlinear ontogenetic interactions, such as a gene regulation network, in various selective scenarios. We find that evolved networks of this type can exhibit several phenomena that are familiar in cognitive learning systems. These include formation of a distributed associative memory that can “store” and “recall” multiple phenotypes that have been selected in the past, recreate complete adult phenotypic patterns accurately from partial or corrupted embryonic phenotypes, and “generalize” (by exploiting evolved developmental modules) to produce new combinations of phenotypic features. We show that these surprising behaviors follow from an equivalence between the action of natural selection on phenotypic correlations and associative learning, well‐understood in the context of neural networks. This helps to explain how development facilitates the evolution of high‐fitness phenotypes and how this ability changes over evolutionary time.     

Spore germination and isozyme patterns in the apomictic fern Cyrtotnium falcatum

Progeny from a plant of the apomictic species Cyrtomium falcatum were examined by protein electrophoresis. These progeny were produced from spores originating in sporangia with differing spore numbers. Analysis of zymograms indicates that variant banding patterns were exhibited in 16.1% of the progeny sampled. These anomalous phenotypes suggest that some apomictically reproducing plants can produce genetically variable progeny.     

Endocrinology of human female sexuality,mating, and reproductive behavior

Hormones orchestrate and coordinate human female sexual development, sexuality, and reproduction in relation to three types of phenotypic changes: life history transitions such as puberty and childbirth, responses to contextual factors such as caloric intake and stress, and cyclical patterns such as the ovulatory cycle. Here, we review the endocrinology underlying women's reproductive phenotypes, including sexual orientation and gender identity, mate preferences, competition for mates, sex drive, and maternal behavior. We highlight distinctive aspects of women's sexuality such as the possession of sexual ornaments, relatively cryptic fertile windows, extended sexual behavior across the ovulatory cycle, and a period of midlife reproductive senescence—and we focus on how hormonal mechanisms were shaped by selection to produce adaptive outcomes. We conclude with suggestions for future research to elucidate how hormonal mechanisms subserve women's reproductive phenotypes.     

Neuroethological approaches to the study of motor development in chicks: achievements and challenges.

Chicks and chick embryos provide a useful model system for the study of issues related to the development of motor behaviors. EMG and kinematic analyses of leg movements have been used to provide new data on the organization of embryonic motility. These data suggest that the circuitry needed to produce a basic, coordinated motor pattern is available early in development. This circuitry then appears to be retained throughout life. Evidence from analysis of EMG patterns and leg deafferentation studies suggest that the output of this basic circuit can be modulated by sensory input to produce the motor patterns of later behaviors, such as hatching and walking. If the same circuitry is present throughout life, then mechanisms for initiation and termination of particular behaviors must be available to ensure that specific behaviors are turned on and off at appropriate times. For example, hatching can be turned on by a specific sensory signal: proprioceptive signals from the bent neck. In addition to reviewing current research on the development of chick motor behaviors, methodological considerations and suggestions for future research are presented.     

Bone marrow derived macrophages have polyamine and ectoenzyme phenotypes distinct from resident macrophages

Several prototype macrophage (MO) populations were compared for differences in ectoenzyme phenotype and polyamine content. Resident peritoneal MO and Corynebacterium parvum (CP)-activated peritoneal MO expressed unique ectoenzyme phenotypes, while bone marrow derived MO (BMDMO), obtained from stem cells after 7 days in culture with colony stimulating factor, and thioglycollate (TG)-elicited peritoneal MO exhibited a similar ectoenzyme phenotype. All of the MO populations, however, differed in polyamine accumulation patterns. These results suggest that ectoenzyme phenotypes do not serve as completely selective markers of MO differentiation. Moreover, BMDMO do not resemble steady state tissue peritoneal MO but appear to resemble inflammatory MO in several respects. Therefore activated BMDMO do not appear to provide an accurate model system for their continued use in studies to characterize the development of resident tissue MO.     

Neuroethological approaches to the study of motor development in chicks: Achievements and challenges

Chicks and chick embryos provide a useful model system for the study of related to the development of motor behaviors. EMG and kinematic analyses of leg movements have been used to provide new data on the organization of embryonic motility. These data suggest that the circuitry needed to produce a basic, coordinated motor pattern is available early in development. This circuitry then appears to be retained throughout life. Evidence from analysis of EMG patterns and leg deafferentation studies suggest that the output of this basic circuit can be modulated by sensory input to produce the motor patterns of later behaviors, such as hatching and walking. If the same circuitry is present throughout life, then mechanisms for initiation and termination of particular behaviors must be available to ensure that specific behaviors are turned on and off at appropriate times. For example, hatching can be turned on by a specific sensory signal: proprioceptive signals from the bent neck. In addition to reviewing current research on the development of chick motor behaviors, methodological considerations and suggestions for future research are presented. © 1992 John Wiley & Sons, Inc.     

The SCHIZOID gene regulates differentiation and cell division in Arabidopsis thaliana shoots

 Cell division and cell differentiation are key processes in shoot development. The Arabidopsis thaliana (L.) Heynh. SCHIZOID (SHZ) gene appears to influence cell differentiation and cell division in the shoot. The shz-2 mutant is notable in that distinct phenotypes develop, depending on the environment in which the plants are grown. When shz-2 mutants are grown in petri dishes, callus develops from the petiole and hypocotyl. In contrast, when the mutants are grown on soil, shoots appear externally stunted with malformed leaves. However, detailed examination of soil-grown mutants shows that the two phenotypes are related. Soil-grown mutants form adventitious meristems, produce a large amount of vascular tissues and have aberrant cell divisions in the meristem. Cells with abnormal cell-division patterns were found in the apical and vascular meristems, suggesting SHZ influences cell division. Development of callus in petri dishes, development of adventitious meristems and aberrations in leaves on soil suggest that SHZ influences cell differentiation. The distinct, but related phenotypes on soil and in petri dishes suggests that SHZ normally functions to regulate differentiation and/or cell division in a manner that is responsive to environmental conditions. Received: 30 July 1999 / Accepted: 22 September 1999     

Heliconius wing patterns: an evo-devo model for understanding phenotypic diversity

Evolutionary Developmental Biology aims for a mechanistic understanding of phenotypic diversity, and present knowledge is largely based on gene expression and interaction patterns from a small number of well-known model organisms. However, our understanding of biological diversification depends on our ability to pinpoint the causes of natural variation at a micro-evolutionary level, and therefore requires the isolation of genetic and developmental variation in a controlled genetic background. The colour patterns of Heliconius butterflies (Nymphalidae: Heliconiinae) provide a rich suite of naturally occurring variants with striking phenotypic diversity and multiple taxonomic levels of variation. Diversification in the genus is well known for its dramatic colour-pattern divergence between races or closely related species, and for Müllerian mimicry convergence between distantly related species, providing a unique system to study the development basis of colour-pattern evolution. A long history of genetic studies has showed that pattern variation is based on allelic combinations at a surprisingly small number of loci, and recent developmental evidence suggests that pattern development in Heliconius is different from the eyespot determination of other butterflies. Fine-scale genetic mapping studies have shown that a shared toolkit of genes is used to produce both convergent and divergent phenotypes. These exciting results and the development of new genomic resources make Heliconius a very promising evo-devo model for the study of adaptive change.     

RNA induction and inheritance of epigenetic cardiac hypertrophy in the mouse

Epigenetic regulation shapes normal and pathological mammalian development and physiology. Our previous work showed that Kit RNAs injected into fertilized mouse eggs can produce heritable epigenetic defects, or paramutations, with relevant loss-of-function pigmentation phenotypes, which affect adult phenotypes in multiple succeeding generations of mice. Here, we illustrate the relevance of paramutation to pathophysiology by injecting fertilized mouse eggs with RNAs targeting Cdk9, a key regulator of cardiac growth. Microinjecting fragments of either the coding region or the related microRNA miR-1 led to high levels of expression of homologous RNA, resulting in an epigenetic defect, cardiac hypertrophy, whose efficient hereditary transmission correlated with the presence of miR-1 in the sperm nucleus. In this case, paramutation increased rather than decreased expression of Cdk9. These results highlight the diversity of RNA-mediated epigenetic effects and may provide a paradigm for clinical cases of familial diseases whose inheritance is not fully explained in Mendelian terms.     

Evolution and molecular mechanisms of adaptive developmental plasticity

Aside from its selective role in filtering inter-individual variation during evolution by natural selection, the environment also plays an instructive role in producing variation during development. External environmental cues can influence developmental rates and/or trajectories and lead to the production of distinct phenotypes from the same genotype. This can result in a better match between adult phenotype and selective environment and thus represents a potential solution to problems posed by environmental fluctuation. The phenomenon is called adaptive developmental plasticity. The study of developmental plasticity integrates different disciplines (notably ecology and developmental biology) and analyses at all levels of biological organization, from the molecular regulation of changes in organismal development to variation in phenotypes and fitness in natural populations. Here, we focus on recent advances and examples from morphological traits in animals to provide a broad overview covering (i) the evolution of developmental plasticity, as well as its relevance to adaptive evolution, (ii) the ecological significance of alternative environmentally induced phenotypes, and the way the external environment can affect development to produce them, (iii) the molecular mechanisms underlying developmental plasticity, with emphasis on the contribution of genetic, physiological and epigenetic factors, and (iv) current challenges and trends, including the relevance of the environmental sensitivity of development to studies in ecological developmental biology, biomedicine and conservation biology.     

Environmental mismatch results in emergence of cooperative behavior in a passerine bird

A major problem in the evolution of maternal effects is explaining the origin and persistence of maternally induced phenotypes that lower offspring fitness. Recent work focuses on the relative importance of maternal and offspring selective environments and the mismatch between them. However, an alternative approach is to directly study the origin and performance of offspring phenotypes resulting from mismatch. Here, we capitalize on a detailed understanding of the ecological contexts that provide both the cue and the functional context for expression of maternally induced offspring phenotypes to investigate the consequences of environmental mismatch. In western bluebirds, adaptive integration of offspring dispersal and aggression is induced by maternal competition over nest cavities. When nest cavities are locally abundant, mothers produce nonaggressive offspring that remain in their natal population, and when nest cavities are scarce, mothers produce aggressive dispersers. However, a few offspring neither disperse nor breed locally, instead helping at their parent’s nest, and as a result these offspring have unusually low fitness. Here, we investigate whether females produce helpers to increase their own fitness, or whether helpers result from a mismatch between the cues mothers experience during offspring production and the breeding environment that helpers later encounter. We found that producing helpers does not enhance maternal fitness. Instead, we show that helpers, which were the least aggressive of all returning sons in the population, were most common when population density increased from the time sons were produced to the time of their reproductive maturity, suggesting that the helper phenotype emerges when cues of resource competition during offspring development do not match the actual level of competition that offspring experience. Thus, environmental mismatch might explain the puzzling persistence of maternally induced phenotypes that decrease offspring fitness.     

Differential gene expression and phenotypic plasticity in behavioural castes of the primitively eusocial wasp, Polistes canadensis

Understanding how a single genome can produce a variety of different phenotypes is of fundamental importance in evolutionary and developmental biology. One of the most striking examples of phenotypic plasticity is the female caste system found in eusocial insects, where variation in reproductive (queens) and non-reproductive (workers) phenotypes results in a broad spectrum of caste types, ranging from behavioural through to morphological castes. Recent advances in genomic techniques allow novel comparisons on the nature of caste phenotypes to be made at the level of the genes in organisms for which there is little genome information, facilitating new approaches in studying social evolution and behaviour. Using the paper wasp Polistes canadensis as a model system, we investigated for the first time how behavioural castes in primitively eusocial insect societies are associated with differential expression of shared genes. We found that queens and newly emerged females express gene expression patterns that are distinct from each other whilst workers generally expressed intermediate patterns, as predicted by Polistes biology. We compared caste-associated genes in P. canadensis with those expressed in adult queens and workers of more advanced eusocial societies, which represent four independent origins of eusociality. Nine genes were conserved across the four taxa, although their patterns of expression and putative functions varied. Thus, we identify several genes that are putatively of evolutionary importance in the molecular biology that underlies a number of caste systems of independent evolutionary origin.     

Predictive adaptive responses and human evolution

The importance of a single genotype being able to produce different phenotypes in different environments (phenotypic plasticity) is widely recognized in evolutionary theory and its adaptive significance is clear. In most cases, the developing organism responds to an environmental cue by producing a selectively and immediately appropriate phenotype. One subset of phenotypic responses to environmental stimuli, however, does not necessarily provide an immediate selective advantage. Rather, these kinds of responses, which we call 'predictive adaptive responses' (PARs), act primarily to improve fitness at a later stage of development. We argue that PARs have had an important role in human evolution, and that their recognition and interpretation has major significance for public health.     

Proto-oncogenes in mammalian development.

The phenotypic analysis of mice carrying germline mutations in protooncogenes is beginning to provide convincing genetic evidence for the important role that these genes play in mammalian development and differentiation. Two approaches are being taken to elucidate the biological function of proto-oncogenes in vivo. The first involves the molecular analysis of existing mouse developmental mutants, while the second approach involves the generation of specific germline mutations by gene targeting using homologous recombination in embryonic stem cells. Several key points have already emerged from these genetic approaches. First, many proto-oncogenes are important to more than one cell lineage and function both during embryogenesis and in the adult. Second, the patterns of expression of these genes provide only a guide to their biological function. Third, mutant phenotypes are generally less severe than would be expected from their expression patterns, suggesting that there may be functional overlap between two or more members of a gene family.