Body-axis organization in tetrapods: a model-system to disentangle the developmental origins of convergent evolution in deep time

Convergent evolution is a central concept in evolutionary theory but the underlying mechanism has been largely debated since On the Origin of Species. Previous hypotheses predict that developmental constraints make some morphologies more likely to arise than others and natural selection discards those of the lowest fitness. However, the quantification of the role and strength of natural selection and developmental constraint in shaping convergent phenotypes on macroevolutionary timescales is challenging because the information regarding performance and development is not directly available. Accordingly, current knowledge of how embryonic development and natural selection drive phenotypic evolution in vertebrates has been extended from studies performed at short temporal scales. We propose here the organization of the tetrapod body-axis as a model system to investigate the developmental origins of convergent evolution over hundreds of millions of years. The quantification of the primary developmental mechanisms driving body-axis organization (i.e. somitogenesis, homeotic effects and differential growth) can be inferred from vertebral counts, and recent techniques of three-dimensional computational biomechanics have the necessary potential to reveal organismal performance even in fossil forms. The combination of both approaches offers a novel and robust methodological framework to test competing hypotheses on the functional and developmental drivers of phenotypic evolution and evolutionary convergence.     

Collective Fluctuations in the Dynamics of Adaptation and Other Traveling Waves

The dynamics of adaptation are difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from random genetic drift arising in a vanguard of particularly fit individuals of the population. Several approaches have been developed to analyze the crucial role of genetic drift on the expected dynamics of adaptation, including the mean fitness of the entire population, or the fate of newly arising beneficial deleterious mutations. However, little is known about how genetic drift causes fluctuations to emerge on the population level, where it becomes palpable as variations in the adaptation speed and the fitness distribution. Yet these phenomena control the decay of genetic diversity and variability in evolution experiments and are key to a truly predictive understanding of evolutionary processes. Here, we show that correlations induced by these emergent fluctuations can be computed at any arbitrary order by a suitable choice of a dynamical constraint. The resulting linear equations exhibit fluctuation-induced terms that amplify short-distance correlations and suppress long-distance ones. These terms, which are in general not small, control the decay of genetic diversity and, for wave-tip dominated (“pulled”) waves, lead to anticorrelations between the tip of the wave and the lagging bulk of the population. While it is natural to consider the process of adaptation as a branching random walk in fitness space subject to a constraint (due to finite resources), we show that other traveling wave phenomena in ecology and evolution likewise fall into this class of constrained branching random walks. Our methods, therefore, provide a systematic approach toward analyzing fluctuations in a wide range of population biological processes, such as adaptation, genetic meltdown, species invasions, or epidemics.     

Evolutionary walks through a land plant morphospace

A model for mimicking land plant evolution is here expanded and re-evaluated. The model consists of (1) a morphospace containing on the order of 10⁹ phenotypic variants, (2) 15 different fitness landscapes, each defined on the basis of performing one or more of four tasks (i.e. maximizing light interception, mechanical stability and reproduction, and minimizing total surface area), and (3) an algorithm driving a search through fitness landscapes for more fit variants. The model is used to predict the effects of the number of simultaneously performed tasks ('complexity'), abrupt changes in environmental conditions (mimicked by random replacement of one fitness landscape with another), and developmental barriers (mimicked by barring searches from entering specific subdomains in the morphospace) on number and accessibility of variants occupying fitness maxima. The model predicts that (1) the number and accessibility of fitness peaks will increase (while the difference between the relative fitness of peaks and valleys will decrease) in proportion to functional complexity, (2) abrupt shifts in landscapes will increase rather than decrease phenotypic diversity, and (3) obstructed searches have an equal or higher probability of reaching fitness peaks than unfettered searches. These results follow axiomatically from the way hypothetical variants are spatially ordered in the morphospace, the manner in which relative fitness is defined, and the protocol used to locate fitness peaks. A critique of the model's predictions and desiderata for future research are provided.     

The Distribution of Fitness Effects of Beneficial Mutations in Pseudomonas aeruginosa

Understanding how beneficial mutations affect fitness is crucial to our understanding of adaptation by natural selection. Here, using adaptation to the antibiotic rifampicin in the opportunistic pathogen Pseudomonas aeruginosa as a model system, we investigate the underlying distribution of fitness effects of beneficial mutations on which natural selection acts. Consistent with theory, the effects of beneficial mutations are exponentially distributed where the fitness of the wild type is moderate to high. However, when the fitness of the wild type is low, the data no longer follow an exponential distribution, because many beneficial mutations have large effects on fitness. There is no existing population genetic theory to explain this bias towards mutations of large effects, but it can be readily explained by the underlying biochemistry of rifampicin–RNA polymerase interactions. These results demonstrate the limitations of current population genetic theory for predicting adaptation to severe sources of stress, such as antibiotics, and they highlight the utility of integrating statistical and biophysical approaches to adaptation.     

The genetics of adaptation to novel environments: selection on germination timing in Arabidopsis thaliana

When studying selection during adaptation to novel environments, researchers have often paid little attention to an organism’s earliest developmental stages. Despite this lack of attention, early life history traits may be under strong selection during colonization, as the expression of adaptive phenotypes at later points is contingent upon early survival. Moreover, the timing of early developmental transitions can constrain the timing of later transitions, with potentially large effects on fitness. In this issue, Huang et al. (2010) underscore the importance of early life history traits in the adaptation of Arabidopsis thaliana to old‐field sites in North America. Using a new population of mapped recombinant inbred lines, the authors examined germination timing and total lifetime fitness of A. thaliana while varying site latitude, dispersal season, and maternal photoperiod. Huang et al. (2010) discovered several Quantitative Trait Loci (QTL) with large effects on fitness that colocalized with QTL for field germination timing and seed dormancy—demonstrating that fitness is genetically associated with these early life history traits, and that these loci are likely under strong selection during adaptation to novel environments. In the epistatic interactions of some loci, recombinant genotypes outperformed parental genotypes, supporting the potentially adaptive role of recombination. This study provides elegant evidence that traits expressed early in an organism’s development can play an important role during adaptive evolution.     

Relationship between fluctuating asymmetry and fitness within and between stressed and unstressed populations of the wolf spider Pirata piraticus

Although developmental instability, measured as fluctuating asymmetry (FA), is expected to be positively related to stress and negatively to fitness, empirical evidence is often lacking or contradictory when patterns are compared at the population level. We demonstrate that two important properties of stressed populations may mask such relationships: (i) a stronger relationship between FA and fitness, resulting in stronger selection against low quality (i.e. developmental unstable) individuals and (ii) the evolution of adaptive responses to environmental stress. In an earlier study, we found female wolf spiders Pirata piraticus from metal exposed populations to be characterized by both reduced clutch masses and increased egg sizes, the latter indicating an adaptive response to stress. By studying the relationship between these two fitness related traits and levels of FA at individual level, we here show a significant negative correlation between FA and clutch mass in metal stressed populations but not in unstressed reference populations. As a result, levels of population FA may be biased downward under stressful conditions because of the selective removal of developmentally unstable (low quality) individuals. We further show that females that produced larger eggs in stressed populations exhibited lower individual FA levels. Such interaction between individual FA and fitness with stress may confound the effect of metal stress on FA, resulting in an absence of relationships between FA, fitness and stress at the population level.     

Evolution of fitnesses and allele frequencies in a population with spatially heterogeneous selection pressures

The level of gene flow considerably influences the outcome of evolutionary processes in structured populations with spatial heterogeneity in selection pressures; low levels of gene flow may allow local adaptation whereas high levels of gene flow may oppose this process thus preventing the stable maintenance of polymorphism. Indeed, proportions of fitness space that successfully maintain polymorphism are substantially larger in spatially heterogenous populations with lower to moderate levels of gene flow when compared to single-deme models. Nevertheless, the effect of spatial heterogeneity on the evolutionary construction of polymorphism is less clear. We have investigated the levels of polymorphism resulting from a simple two-deme construction model, which incorporates recurrent mutation as well as selection. We further compared fitness properties, stability of equilibria, and frequency distribution patterns emerging from the construction approach and compared these to the static fitness-space approach. The construction model either promotes or constrains the level of polymorphisms, depending on the levels of gene flow. Comparison of the fitness properties resulting from both approaches shows that they maintain variation in different parts of fitness space. The part of fitness space resulting from construction is more stable than that implied by the ahistoric fitness-space approach. Finally, the equilibrium allele-frequency distribution patterns vary substantially with different levels of gene flow, underlining the importance of correctly sampling spatial structure if these patterns are to be used to estimate population-genetic processes.     

The ontogenetic complexity of developmental constraints

Developmental constraint is a theoretically important construct bridging ontogenetic and evolutionary studies. We propose a new operationalization of this notion that exploits the unusually rich measurement structure of landmark data. We represent landmark configurations by their partial warps, a basis for morphospace that represents a set of localized features of form. A finding of developmental constraint arises from the interplay between age-varying means and age-specific variances in these subspaces of morphospace. Examination of variances and means in 16 ventral skull landmarks in the cotton rat S. fulviventer at ages 1, 10, 20, and 30 days yielded three types of developmental constraint: canalization (constraint to relatively constant form age by age); chreods (reduction of variance orthogonal to the mean trajectory over ages); and opposition (reduction of age-specific variance along the mean trajectory over ages). While canalization and chreodic constraints have been noted previously, the oppositional type of constraint appears novel. Only one of our characters, relative length and orientation of the incisive foramen, appears to be canalized. Although skull growth becomes increasingly integrated through ontogeny, our characters display a remarkable spatiotemporal complexity in patterns of variance reduction. The specific assortment of constraints observed may be related to the precociality of Sigmodon. We suggest that Waddington's diagrammatic presentation of the “epigenetic landscape” may be misleading in quantitative studies of developmental regulation.     

Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes

Morphospaces—representations of phenotypic characteristics—are often populated unevenly, leaving large parts unoccupied. Such patterns are typically ascribed to contingency, or else to natural selection disfavoring certain parts of the morphospace. The extent to which developmental bias, the tendency of certain phenotypes to preferentially appear as potential variation, also explains these patterns is hotly debated. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. Upon random mutations, some RNA SS shapes (the frequent ones) are much more likely to appear than others. By using the RNAshapes method to define coarse-grained SS classes, we can directly compare the frequencies that noncoding RNA SS shapes appear in the RNAcentral database to frequencies obtained upon a random sampling of sequences. We show that: 1) only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored; 2) remarkably small numbers of random sequences are needed to produce all the RNA SS shapes found in nature so far; and 3) perhaps most surprisingly, the natural frequencies are accurately predicted, over several orders of magnitude in variation, by the likelihood that structures appear upon a uniform random sampling of sequences. The ultimate cause of these patterns is not natural selection, but rather a strong phenotype bias in the RNA genotype–phenotype map, a type of developmental bias or “findability constraint,” which limits evolutionary dynamics to a hugely reduced subset of structures that are easy to “find.”     

Local adaptation across a fertility gradient is influenced by soil biota in the invasive grass, <Emphasis Type="Italic">Bromus inermis</Emphasis>

Biotic soil factors, such as fungi, bacteria and herbivores affect resource acquisition and fitness in plants, yet little is known of their role as agents of selection. Evolutionary responses to these selective agents could be an important mechanism that explains the success of invasive species. In this study, we tested whether populations of the invasive grass Bromus inermis are adapted to their home soil environment, and whether biotic factors influence the magnitude of this adaptation. We selected three populations growing at sites that differed in soil fertility and grew individuals from each population in each soil. To assess whether biotic factors influence the magnitude of adaptation, we also grew the same populations in sterilized field soil. To further examine the role of one element of the soil biota (fungi) in local adaptation, we measured colonization by arbuscular mycorrhizal (AM) and septate fungi, and tested whether the extent of colonization differed between local and foreign plants. In non-sterilized (living) soil, there was evidence of a home site advantage because local plants produced significantly more biomass than at least one of the two populations of foreign plants in all three soil origins. By contrast, there was no evidence of a home site advantage in sterilized soil because local plants never produced significantly more biomass than either population of foreign plants. Fungal colonization differed between local and foreign plants in the living soil and this variation corresponded with biomass differences. When local plants produced more biomass than foreign plants, they were also less intensively colonized by AM fungi. Colonization by septate fungi did not vary between local and foreign plants. Our results suggest that biotic soil factors are important causes of plant adaptation, and that selection for reduced interactions with mycorrhizae could be one mechanism through which adaptation to a novel environment occurs.     

GENETIC CONSTRAINTS ON ADAPTATION TO A CHANGING ENVIRONMENT

Genetic correlations between traits can constrain responses to natural selection. To what extent such correlations limit adaptation depends on patterns of directional selection. I derive the expected rate of adaptation (or evolvability) under randomly changing selection gradients. When directional selection gradients have an arbitrary covariance matrix, the average rate of adaptation depends on genetic correlations between traits, contrary to the isotropic case investigated in previous studies. Adaptation may be faster on average with more genetic correlation between traits, if these traits are selected to change jointly more often than the average pair of traits. However, natural selection maximizes the long‐term fitness of a population, not necessarily its rate of adaptation. I therefore derive the average lag load caused by deviations of the mean phenotype from an optimum, under several forms of environmental changes typically experienced by natural populations, both stochastic and deterministic. Simple formulas are produced for how the G matrix affects long‐term fitness in these contexts, and I discuss how their parameters can be estimated empirically.     

Evolution of Cranial Shape in Caecilians (Amphibia: Gymnophiona)

Insights into morphological diversification can be obtained from the ways the species of a clade occupy morphospace. Projecting a phylogeny into morphospace provides estimates of evolutionary trajectories as lineages diversified information that can be used to infer the dynamics of evolutionary processes that produced patterns of morphospace occupation. We present here a large-scale investigation into evolution of morphological variation in the skull of caecilian amphibians, a major clade of vertebrates. Because caecilians are limbless, predominantly fossorial animals, diversification of their skull has occurred within a framework imposed by the functional demands of head-first burrowing. We examined cranial shape in 141 species, over half of known species, using X-ray computed tomography and geometric morphometrics. Mapping an existing phylogeny into the cranial morphospace to estimate the history of morphological change (phylomorphospace), we find a striking pattern: most species occupy distinct clusters in cranial morphospace that closely correspond to the main caecilian clades, and each cluster is separated by unoccupied morphospace. The empty spaces in shape space are unlikely to be caused entirely by extinction or incomplete sampling. The main caecilian clades have different amounts of morphological disparity, but neither clade age nor number of species account for this variation. Cranial shape variation is clearly linked to phyletic divergence, but there is also homoplasy, which is attributed to extrinsic factors associated with head-first digging: features of caecilian crania that have been previously argued to correlate with differential microhabitat use and burrowing ability, such as subterminal and terminal mouths, degree of temporal fenestration (stegokrotaphy/zygokrotaphy), and eyes covered by bone, have evolved and many combinations occur in modern species. We find evidence of morphological convergence in cranial shape, among species that have eyes covered by bone, resulting in a narrow bullet-shaped head. These results reveal a complex history, including early expansion of morphospace and both divergent and convergent evolution resulting in the diversity we observe today.     

Epistatic interactions between ancestral genotype and beneficial mutations shape evolvability in Pseudomonas aeruginosa

The idea that interactions between mutations influence adaptation by driving populations to low and high fitness peaks on adaptive landscapes is deeply ingrained in evolutionary theory. Here, we investigate the impact of epistasis on evolvability by challenging populations of two Pseudomonas aeruginosa clones bearing different initial mutations (in rpoB conferring rifampicin resistance, and the type IV pili gene network) to adaptation to a medium containing l ‐serine as the sole carbon source. Despite being initially indistinguishable in fitness, populations founded by the two ancestral genotypes reached different fitness following 300 generations of evolution. Genome sequencing revealed that the difference could not be explained by acquiring mutations in different targets of selection; the majority of clones from both ancestors converged on one of the following two strategies: (1) acquiring mutations in either PA2449 (gcsR, an l ‐serine‐metabolism RpoN enhancer binding protein) or (2) protease genes. Additionally, populations from both ancestors converged on loss‐of‐function mutations in the type IV pili gene network, either due to ancestral or acquired mutations. No compensatory or reversion mutations were observed in RNA polymerase (RNAP) genes, in spite of the large fitness costs typically associated with mutations in rpoB. Although current theory points to sign epistasis as the dominant constraint on evolvability, these results suggest that the role of magnitude epistasis in constraining evolvability may be underappreciated. The contribution of magnitude epistasis is likely to be greatest under the biologically relevant mutation supply rates that make back mutations probabilistically unlikely.     

Unbeatable strategy, constraint and coevolution, or how to resolve evolutionary conflicts: the case of the fig/wasp mutualism

Constraints and evolution are central for the resolution of conflicts between mutualistic species and for the stability of mutualisms. However, proximal causes of the benevolence of mutualistic species are often unknown. Monoecious fig species and their specific pollinators are in conflict on the use of fig ovaries, which can either produce one seed or host one pollinator larva. Here, I provide new data showing that, probably because of space constraints during the development of both seeds and wasps, ovaries vary in their quality as a substrate for pollinator development depending on their location within the fig inflorescence. This constraint may be responsible for the stability of the fig/wasp mutualism. Moreover, population density of pollinators and density dependent selection on the pollinators could be sufficient to explain the observed highly variable seed/wasp ratios produced by figs.     

The paradox of seed size and adaptation

Correlations between habitat and seed size suggest that this character is adaptive. Mean seed size is a relatively invariant species characteristic and seed size has marked effects upon fitness. These observations have previously led to the conclusion that seed size is under stabilizing selection. This conclusion, originally based mainly on evidence from crop plants grown in controlled environments, is questioned here on the grounds that recent studies of wild plants show marked phenotypic plasticity and low heritability of seed size. If seed size is not readily altered by natural selection in the wild, then its effects on fitness are evidence that this character is a constraint on habitat distribution. Constancy of mean seed size may be due to developmental canalization to a size set by previous selection, rather than a continuing process of stabilizing selection.     

Very low levels of direct additive genetic variance in fitness and fitness components in a red squirrel population

A trait must genetically correlate with fitness in order to evolve in response to natural selection, but theory suggests that strong directional selection should erode additive genetic variance in fitness and limit future evolutionary potential. Balancing selection has been proposed as a mechanism that could maintain genetic variance if fitness components trade off with one another and has been invoked to account for empirical observations of higher levels of additive genetic variance in fitness components than would be expected from mutation–selection balance. Here, we used a long‐term study of an individually marked population of North American red squirrels (Tamiasciurus hudsonicus) to look for evidence of (1) additive genetic variance in lifetime reproductive success and (2) fitness trade‐offs between fitness components, such as male and female fitness or fitness in high‐ and low‐resource environments. “Animal model” analyses of a multigenerational pedigree revealed modest maternal effects on fitness, but very low levels of additive genetic variance in lifetime reproductive success overall as well as fitness measures within each sex and environment. It therefore appears that there are very low levels of direct genetic variance in fitness and fitness components in red squirrels to facilitate contemporary adaptation in this population.     

Population admixture,biological invasions and the balance between local adaptation and inbreeding depression

When previously isolated populations meet and mix, the resulting admixed population can benefit from several genetic advantages, including increased genetic variation, the creation of novel genotypes and the masking of deleterious mutations. These admixture benefits are thought to play an important role in biological invasions. In contrast, populations in their native range often remain differentiated and frequently suffer from inbreeding depression owing to isolation. While the advantages of admixture are evident for introduced populations that experienced recent bottlenecks or that face novel selection pressures, it is less obvious why native range populations do not similarly benefit from admixture. Here we argue that a temporary loss of local adaptation in recent invaders fundamentally alters the fitness consequences of admixture. In native populations, selection against dilution of the locally adapted gene pool inhibits unconstrained admixture and reinforces population isolation, with some level of inbreeding depression as an expected consequence. We show that admixture is selected against despite significant inbreeding depression because the benefits of local adaptation are greater than the cost of inbreeding. In contrast, introduced populations that have not yet established a pattern of local adaptation can freely reap the benefits of admixture. There can be strong selection for admixture because it instantly lifts the inbreeding depression that had built up in isolated parental populations. Recent work in Silene suggests that reduced inbreeding depression associated with post-introduction admixture may contribute to enhanced fitness of invasive populations. We hypothesize that in locally adapted populations, the benefits of local adaptation are balanced against an inbreeding cost that could develop in part owing to the isolating effect of local adaptation itself. The inbreeding cost can be revealed in admixing populations during recent invasions.     

Overdominance interacts with linkage to determine the rate of adaptation to a new optimum

Overdominance, or a fitness advantage of a heterozygote over both homozygotes, can occur commonly with adaptation to a new optimum phenotype. We model how such overdominant polymorphisms can reduce the evolvability of diploid populations, uncovering a novel form of epistatic constraint on adaptation. The fitness load caused by overdominant polymorphisms can most readily be ameliorated by evolution at tightly linked loci; therefore, traits controlled by multiple loosely linked loci are predicted to be strongly constrained. The degree of constraint is also sensitive to the shape of the relationship between phenotype and fitness, and the constraint caused by overdominance can be strong enough to overcome the effects of clonal interference on the rate of adaptation for a trait. These results point to novel influences on evolvability that are specific to diploids and interact with genetic architecture, and they predict a source of stochastic variability in eukaryotic evolution experiments or cases of rapid evolution in nature.     

Allometric space and allometric disparity: a developmental perspective in the macroevolutionary analysis of morphological disparity

Here, we advance novel uses of allometric spaces--multidimensional spaces specifically defined by allometric coefficients--with the goal of investigating the focal role of development in shaping the evolution of morphological disparity. From their examination, operational measures of allometric disparity can be derived, complementing standard signals of morphological disparity through an intuitive and process-oriented refinement of established analytical protocols used in disparity studies. Allometric spaces thereby become a promising context to reveal different patterns of evolutionary developmental changes and to assess their relative prevalence and importance. Such spaces offer a novel domain of investigation of phenotypic variation and should help in detecting large-scale trends, thus placing various macroevolutionary phenomena in an explicitly developmental context. Ammonoidea (Cephalopoda) at the Lower-Middle Jurassic transition were chosen as a case study to illustrate this methodological approach. We constructed two phenotypic spaces: a static, adult one (adult morphospace) and a dynamic, developmental one (allometric space). Comparative disparity analyses show a strikingly stable occupation in both spaces, despite extensive change in taxonomic composition. In contrast, disparity analyses of subclades reveal clearly distinct morphological and allometric disparity dynamics. Allometric approaches allow developmental insights into morphological diversification otherwise intractable from the analysis of adult morphospace alone.