Do key innovations unlock diversification? A case-study on the morphological and ecological impact of pharyngognathy in acanthomorph fishes

Key innovations may allow lineages access to new resources and facilitate the invasion of new adaptive zones, potentially influencing diversification patterns. Many studies have focused on the impact of key innovations on speciation rates, but far less is known about how they influence phenotypic rates and patterns of ecomorphological diversification. We use the repeated evolution of pharyngognathy within acanthomorph fishes, a commonly cited key innovation, as a case study to explore the predictions of key innovation theory. Specifically, we investigate whether transitions to pharyngognathy led to shifts in the rate of phenotypic evolution, as well as shifts and/or expansion in the occupation of morphological and dietary space, using a dataset of 8 morphological traits measured across 3,853 species of Acanthomorpha. Analyzing the 6 evolutionarily independent pharyngognathous clades together, we found no evidence to support pharyngognathy as a key innovation; however, comparisons between individual pharyngognathous lineages and their sister clades did reveal some consistent patterns. In morphospace, most pharyngognathous clades cluster in areas that correspond to deeper-bodied morphologies relative to their sister clades, while occupying greater areas in dietary space that reflects a more diversified diet. Additionally, both Cichlidae and Labridae exhibited higher univariate rates of phenotypic evolution compared with their closest relatives. However, few of these results were exceptional relative to our null models. Our results suggest that transitions to pharyngognathy may only be advantageous when combined with additional ecological or intrinsic factors, illustrating the importance of accounting for lineage-specific effects when testing key innovation hypotheses. Moreover, the challenges we experienced formulating informative comparisons, despite the ideal evolutionary scenario of multiple independent evolutionary origins of pharyngognathous clades, illustrates the complexities involved in quantifying the impact of key innovations. Given the issues of lineage specific effects and rate heterogeneity at macroevolutionary scales we observed, we suggest a reassessment of the expected impacts of key innovations may be warranted.     

Cultural Transmission and the Diffusion of Innovations: Adoption Dynamics Indicate That Biased Cultural Transmission Is the Predominate Force in Behavioral Change

In challenging the pervasive model of individual actors as cost-benefit analysts who adapt their behavior by learning from the environment, this article analyzes the temporal dynamics of both environmental (individual) learning and biased cultural transmission processes by comparing these dynamics with the robust "5-shaped" curves that emerge from the diffusion of innovations literature. The analysis shows three things: (1) that environmental learning alone never produces the 5-shaped adoption dynamics typically observed in the spread of novel practices, ideas, and technologies; (2) that biased cultural transmission always produces the S-shaped temporal dynamics; and (3) that a combination of environmental learning and biased cultural transmission can generate 5-dynamics but only when biased cultural transmission is the predominate force in the spread of new behaviors. These findings suggest that biased cultural transmission processes are much more important to understanding the diffusion of innovations and sociocultural evolution than is often assumed by most theorists. [ diffusion of innovations, cultural transmission, learning, cultural evolution ]     

Modern termites inherited the potential of collective construction from their common ancestor

Animal collective behaviors give rise to various spatial patterns, such as the nests of social insects. These structures are built by individuals following a simple set of rules, slightly varying within and among species, to produce a large diversity of shapes. However, little is known about the origin and evolution of the behavioral mechanisms regulating nest structures. In this study, we discuss the perspective of inferring the evolution of collective behaviors behind pattern formations using a phylogenetic framework. We review the collective behaviors that can be described by a single set of behavioral rules, and for which variations of the environmental and behavioral parameter values produce diverse patterns. We propose that this mechanism could be at the origin of the pattern diversity observed among related species, and that, when they are placed in the proper conditions, species have the behavioral potential to form patterns observed in related species. The comparative analysis of shelter tube construction by lower termites is consistent with this hypothesis. Although the use of shelter tubes in natural conditions is variable among species, most modern species have the potential to build them, suggesting that the behavioral rules for shelter tube construction evolved once in the common ancestor of modern termites. Our study emphasizes that comparative studies of behavioral rules have the potential to shed light on the evolution of collective behaviors.     

Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis

Phylogenetic evidence for biological traits that increase the net diversification rate of lineages (key innovations) is most commonly drawn from comparisons of clade size. This can work well for ancient, unreversed traits and for correlating multiple trait origins with higher diversification rates, but it is less suitable for unique events, recently evolved innovations, and traits that exhibit homoplasy. Here I present a new method for detecting the phylogenetic signature of key innovations that tests whether the evolutionary history of the candidate trait is associated with shorter waiting times between cladogenesis events. The method employs stochastic models of character evolution and cladogenesis and integrates well into a Bayesian framework in which uncertainty in historical inferences (such as phylogenetic relationships) is allowed. Applied to a well-known example in plants, nectar spurs in columbines, the method gives much stronger support to the key innovation hypothesis than previous tests.     

Delineating the longitudinal tumor evolution using organoid models

Cancer is an evolutionary process fueled by genetic or epigenetic alterations in the genome. Understanding the evolutionary dynamics that are operative at different stages of tumor progression might inform effective strategies in early detection, diagnosis, and treatment of cancer. However, our understanding on the dynamics of tumor evolution through time is very limited since it is usually impossible to sample patient tumors repeatedly. The recent advances in in vitro 3D organoid culture technologies have opened new avenues for the development of more realistic human cancer models that mimic many in vivo biological characteristics in human tumors. Here, we review recent progresses and challenges in cancer genomic evolution studies and advantages of using tumor organoids to study cancer evolution. We propose to establish an experimental evolution model based on continuous passages of patient-derived organoids and longitudinal sampling to study clonal dynamics and evolutionary patterns over time. Development and integration of population genetic theories and computational models into time-course genomic data in tumor organoids will help to pinpoint the key cellular mechanisms underlying cancer evolutionary dynamics, thus providing novel insights on therapeutic strategies for highly dynamic and heterogeneous tumors.     

The origin of metazoan development: a palaeobiological perspective

The rapid diversification of early Metazoa remains one of the most puzzling events in the fossil record. Several models have been proposed to explain a critical aspect of this event: the origin of Metazoan development. These include the origin of the eukaryotic cell, environmental triggers, key innovations or selection among cell lineages. Here, the first three hypotheses are evaulated within a phylogenetic framework using fossil, molecular and developmental evidence. Many elements of metazoan development are widely distributed among unicellular eukaryotes, yet only 3 of the 23 multicellular eukaryotic lineages evolved complex development. Molecular evidence indicates the lineage leading to the eukaryotic cell is nearly as old as the eubacterial and archaebacterial lineages, although the symbiotic events established that the eukaryotic cell probably occurred about 1.5 billion years ago. Yet Metazoa did not appear until 1000 to 600 million years ago (Myr), suggesting the origin of metazoan development must be linked to either an environmental trigger, perhaps an increase in atmospheric oxygen, or key innovations such as the development of collagen. Yet the first model fails to explain the unique appearance of complex development in Metazoa, while the latter fails to explain the simultaneous diversification of several ‘protist’ groups along with the Metazoa. A more complete model of the origin of metazoan development combines environmental triggering of a series of innovations, with successive innovations generating radiations of metazoan clades as lineages breached functional thresholds. The elaboration of new cell classes and the appearance of such developmental innovations as cell sheets may have been of particular importance. Evolutionary biologists often implicitly assume that evolution is a uniformitarian, time-homogeneous process without strong temporal asymmetries in evolutionary mechanisms, rate or context. Yet evolutionary patterns do exhibit such asymmetries, raising the possibility that such innovations as metazoan development impose non-uniformities of evolutionary process.     

Fossil mammals and paleoenvironments in the Omo-Turkana Basin

Although best known for its fossil hominins, the Omo-Turkana Basin of Kenya and Ethiopia is the source of one of the best records of vertebrate evolution from the Late Cenozoic of Africa. Located near the heart of the East African Rift Valley, the basin serves as an important frame of reference for the continent. The fossil record from this region plays a key role in our efforts to understand the environmental and ecological context of human evolution in Africa. The Omo-Turkana faunal data shed light on key questions of human evolution: What kinds of environments did early humans inhabit? How did these environments change over time? What is the relationship between faunal change in East Africa and broader patterns of climatic change?     

Environment-sensitive epigenetics and the heritability of complex diseases

Genome-wide association studies have thus far failed to explain the observed heritability of complex human diseases. This is referred to as the "missing heritability" problem. However, these analyses have usually neglected to consider a role for epigenetic variation, which has been associated with many human diseases. We extend models of epigenetic inheritance to investigate whether environment-sensitive epigenetic modifications of DNA might explain observed patterns of familial aggregation. We find that variation in epigenetic state and environmental state can result in highly heritable phenotypes through a combination of epigenetic and environmental inheritance. These two inheritance processes together can produce familial covariances significantly higher than those predicted by models of purely epigenetic inheritance and similar to those expected from genetic effects. The results suggest that epigenetic variation, inherited both directly and through shared environmental effects, may make a key contribution to the missing heritability.     

Multilevel selection and the social transmission of behavior

Many evolutionary models assume that behaviors are caused directly by genes. An implication is that behavioral uniformity should be found only in groups that are genetically uniform. Yet, the members of human social groups often behave in a uniform fashion, despite the fact that they are genetically diverse. Behavioral uniformity can occur through a variety of psychological mechanisms and social processes, such as imitation, consensus decision making, or the imposition of social norms. We present a series of models in which genes code for social transmission rules, which in turn govern the behaviors that are adopted. Transmission rules can evolve in randomly formed groups that concentrate phenotypic variation at the between-group level, favoring the evolution of altruistic behaviors and other group-advantageous traits. In addition, a direct bias toward adopting altruistic behaviors can evolve. Our models begin to show how group selection can be a strong force in human evolution, despite the absence of extreme genetic variation among groups.     

Testing the grain-size model for the evolution of phenotypic plasticity

Phenotypic plasticity is the ability of a genotype to modify its phenotypic characteristics in response to different environments. Theory predicts that adaptive plasticity should primarily evolve in organisms that experience heterogeneous environments. An organism's dispersal rate is a key component in these models, because the degree of dispersal partly determines the extent of environmental heterogeneity. Here, I provide the first large-scale test of the theoretical prediction that phenotypic plasticity evolves in association with dispersal rate using meta-analysis of data from 258 experiments from the literature on plasticity in marine invertebrates. In line with predictions, phenotypic plasticity is generally greater in species with higher dispersal rates, suggesting that dispersal and environmental heterogeneity are important selective agents for evolution of plasticity in marine habitats.     

Simulating the Evolution of the Human Family: Cooperative Breeding Increases in Harsh Environments

Verbal and mathematical models that consider the costs and benefits of behavioral strategies have been useful in explaining animal behavior and are often used as the basis of evolutionary explanations of human behavior. In most cases, however, these models do not account for the effects that group structure and cultural traditions within a human population have on the costs and benefits of its members'' decisions. Nor do they consider the likelihood that cultural as well as genetic traits will be subject to natural selection. In this paper, we present an agent-based model that incorporates some key aspects of human social structure and life history. We investigate the evolution of a population under conditions of different environmental harshness and in which selection can occur at the level of the group as well as the level of the individual. We focus on the evolution of a socially learned characteristic related to individuals'' willingness to contribute to raising the offspring of others within their family group. We find that environmental harshness increases the frequency of individuals who make such contributions. However, under the conditions we stipulate, we also find that environmental variability can allow groups to survive with lower frequencies of helpers. The model presented here is inevitably a simplified representation of a human population, but it provides a basis for future modeling work toward evolutionary explanations of human behavior that consider the influence of both genetic and cultural transmission of behavior.     

上海城市热岛效应形成机制及空间格局

城市热岛效应的产生及演变与城市地表覆被变化、人类社会经济活动密切相关,是城市生态环境状况的综合概括与体现,目前对城市热岛形成、演变的驱动机制、热岛效应与地表覆被变化的定量关系研究大多还是从对某些影响因子的测定入手,缺乏对区域热环境系统全面、综合的评价与分析.近年来,在城市化过程中,人类社会、经济活动的加剧使城市地表热力景观呈现出高度的空间异质性,在利用Landsat 7 ETM+热波段数据反演上海地区地表温度的基础上,应用地统计学方法揭示了不同尺度下上海城市地表温度场空间变异特征及其不同的驱动因子.进而,采用决策树方法构造城市热环境系统的分类和预测模型,建立中心城区地表温度场空间分布及其驱动因素之间的定量关系,挖掘上海城市热岛效应的形成机制,揭示出多种影响因素综合作用下中心城区热环境空间格局差异.研究结果表明,城市热环境形成的驱动因子在空间上呈现出明显的分异性特征,各种影响因素在空间上不同的组合方式将决定城市热岛效应的时空演变趋势.运用决策树方法可以有效地确定在城市内部不同区域影响热环境形成的主导因素,揭示城市热岛形成与演变的成因机制及其空间差异,并可以进一步用来预测分析未来城市地表温度场动态变化的空间分布格局.     

Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor

Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life’s earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA. Cellularity provides motility and permits Darwinian evolution by connecting genetic material and its products, and thus establishing heredity and lineage. Considering the importance of compartmentalization and motility, we propose that the early emergence of cellularity is required for environmental dispersal and diversification during these transitions. Early diversification and the emergence of ecology before LUCA could be an important pre-adaptation for life’s persistence on a changing planet.     

TRENDS IN THE EVOLUTION OF THE EUGLENID PELLICLE

Abstract Trends in the evolution of the euglenid pellicle were described using phylogenetic methods on 18S rDNA, morphological, and combined data from 25 mostly phototrophic taxa. The tree topology from a total‐evidence analysis formed a template for a synthetic tree that took into account conflicting results derived from the partitioned datasets. Pellicle character states that can only be observed with the assistance of transmission and scanning electron microscopy were phylogenetically mapped onto the synthetic tree to test a set of previously established homology statements (inferences made independently from a cladogram). The results permitted us to more confidently infer the ancestral‐derived polarities of character state transformations and provided a framework for understanding the key cytoskeletal innovations associated with the evolution of phototrophic euglenids. We specifically addressed the character evolution of (1) the maximum number of pellicle strips around the cell periphery; (2) the patterns of terminating strips near the cell posterior end; (3) the substructural morphology of pellicle strips; (4) the morphology of the cell posterior tip; and (5) patterns of pellicle pores on the cell surface.     

Paleontological Patterns, Macroecological Dynamics and the Evolutionary Process

Here we consider evolutionary patterns writ large in the fossil record. We argue that Darwin recognized but downgraded or de-emphasized several of these important patterns, and we consider what a renewed emphasis on these patterns can tell us about the evolutionary process. In particular, one of the key patterns we focus on is the role geographic isolation plays in fomenting evolutionary divergence; another one of the key patterns is stasis of species; the final pattern is turnovers, which exist at several hierarchical scales, including regional ecosystem replacement and pulses of speciation and extinction. We consider how each one of these patterns are related to the dynamic of changing ecological and environmental conditions over time and also investigate their significance in light of other concepts including punctuated equilibria and hierarchy theory. Ultimately, we tie each of these patterns into a framework involving macroecological dynamics and the important role environmental change plays in shaping evolution from the micro- to macroscale.     

Investigating the eco-evolutionary response of microbiomes to environmental change

Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome–functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.     

Self-organized fish schools: an examination of emergent properties

Heterogeneous, "aggregated" patterns in the spatial distributions of individuals are almost universal across living organisms, from bacteria to higher vertebrates. Whereas specific features of aggregations are often visually striking to human eyes, a heuristic analysis based on human vision is usually not sufficient to answer fundamental questions about how and why organisms aggregate. What are the individual-level behavioral traits that give rise to these features? When qualitatively similar spatial patterns arise from purely physical mechanisms, are these patterns in organisms biologically significant, or are they simply epiphenomena that are likely characteristics of any set of interacting autonomous individuals? If specific features of spatial aggregations do confer advantages or disadvantages in the fitness of group members, how has evolution operated to shape individual behavior in balancing costs and benefits at the individual and group levels? Mathematical models of social behaviors such as schooling in fishes provide a promising avenue to address some of these questions. However, the literature on schooling models has lacked a common framework to objectively and quantitatively characterize relationships between individual-level behaviors and group-level patterns. In this paper, we briefly survey similarities and differences in behavioral algorithms and aggregation statistics among existing schooling models. We present preliminary results of our efforts to develop a modeling framework that synthesizes much of this previous work, and to identify relationships between behavioral parameters and group-level statistics.     

The evolution of feeding motor patterns in vertebrates

Despite considerable skepticism, researchers have found that the patterns of muscle activation that control feeding behaviors of lower vertebrates have been surprisingly conserved during evolution. This tendency for conservation among taxa appears in the face of marked flexibility of motor patterns within individuals. One interpretation of these apparently conflicting trends is that the most effective motor pattern for any given feeding situation is the same across substantial phylogenetic distances and morphological differences. The novel evolutionary insight provided by this research is that historical changes to motor patterns are a relatively infrequent source of trophic innovation. The spectacular diversity of feeding abilities and feeding ecology in lower vertebrates is based mostly on axes of variation, and on the innovations in the organization of muscles and the skeletal linkage systems that they drive.     

Global analysis of endothelial cell line proliferation patterns based on nutrient-depletion models: implications for a standardization of cell proliferation assays

It is known that cell populations growing in different environmental conditions may exhibit different proliferation patterns. However, it is not clear if, despite the diversity of the so-observed patterns, inherent cellular growth characteristics of the population can nevertheless be determined. This study quantifies the proliferative behaviour of the permanent endothelial human cell line, Eahy926, and establishes to which extent the estimation of the cell proliferation rate depends on variations of the experimental protocols. Cell proliferation curves were obtained for cells cultured over 16 days and the influences of cell seeding densities, foetal bovine serum content and frequency of culture medium changes were investigated. Quantitative dynamic modelling was conducted to evaluate the kinetic characteristics of this cell population. We proposed successive models and retained a nutrient-depletion toxicity dependant model, which takes into account the progressive depletion of nutrients, as well as the increase of toxicity in the cell culture medium. This model is shown to provide a very good and robust prediction of the experimental proliferation curves, whatever are the considered frequency of culture medium changes and serum concentrations. Thus, the model enables an intrinsic quantification of the parameters driving in vitro EAhy926 proliferation, including proliferation, nutrient consumption and toxicity increase rates, rather independently of the experiments design. We therefore propose that such models could provide a basis for a standardized quantification of intrinsic cell proliferation kinetics.