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The Major Features of Evolution.
... Instead, we aim to draw attention to two fundamental elements of this process, ecological opportunity and key innovations (Gillespie et al. 2020). The concept of ecological opportunity as the driving factor in adaptive radiation stems from the early work of Simpson (1953). Ecological opportunity refers to the availability of ecological resources or niche space that were either unoccupied or previously used by competitors (Simpson 1953;Stroud andLosos 2016, De-Kayne et al. 2024). ...
... The concept of ecological opportunity as the driving factor in adaptive radiation stems from the early work of Simpson (1953). Ecological opportunity refers to the availability of ecological resources or niche space that were either unoccupied or previously used by competitors (Simpson 1953;Stroud andLosos 2016, De-Kayne et al. 2024). While Simpson (1953) suggested that ecological opportunities emerge from geographic, ecological, and evolutionary access to new niches that collectively determine a new "adaptive zone," the existence of the space by itself does not generate adaptive radiation. ...
... Ecological opportunity refers to the availability of ecological resources or niche space that were either unoccupied or previously used by competitors (Simpson 1953;Stroud andLosos 2016, De-Kayne et al. 2024). While Simpson (1953) suggested that ecological opportunities emerge from geographic, ecological, and evolutionary access to new niches that collectively determine a new "adaptive zone," the existence of the space by itself does not generate adaptive radiation. Instead, a radiating lineage must gain access to new niches geographically through colonization, ecologically by using resources for which competition is reduced, and evolutionarily by having the adaptations to use such resources in the first place (i.e., enter a new "adaptive zone"; see also Donoghue and Sanderson 2015). ...
Neotropical ecosystems are renowned for numerous examples of adaptive radiation in both plants and animals resulting in high levels of biodiversity and endemism. However, we still lack a comprehensive review of the abiotic and biotic factors that contribute to these adaptive radiations. To fill this gap, we delve into the geological history of the region, including the role of tectonic events such as the Andean uplift, the formation of the Isthmus of Panama, and the emergence of the Guiana and Brazilian Shields. We also explore the role of ecological op- portunities created by the emergence of new habitats, as well as the role of key innovations, such as novel feeding strategies or reproductive mechanisms. We discuss different examples of adaptive radiation, including classic ones like Darwin’s finches and Anolis lizards, and more recent ones like bromeliads and lupines. Finally, we propose new examples of adaptive radiations mediated by ecological interactions in their geological context. By doing so, we provide insights into the complex interplay of factors that contributed to the remarkable diversity of life in the Neotropics and highlight the importance of this region in understanding the origins of biodiversity.
... The study of evolutionary radiations has fascinated biologists for a long time (e.g. Osborn, 1902;Simpson, 1953;Simões et al., 2016). Different kinds of radiations have been proposed over the time (Bouchenak-Khelladi et al., 2015;Givnish, 2015;Simões et al., 2016;Czekanski-Moir and Rundell, 2019), amongst which adaptive, geographic, and climatic are amongst the most investigated (Simões et al., 2016). ...
... Different kinds of radiations have been proposed over the time (Bouchenak-Khelladi et al., 2015;Givnish, 2015;Simões et al., 2016;Czekanski-Moir and Rundell, 2019), amongst which adaptive, geographic, and climatic are amongst the most investigated (Simões et al., 2016). Adaptive radiations were long regarded as the only existing category of radiations (Simpson, 1953;Simões et al., 2016). In adaptive radiations, an increase in species diversification (due to the increased diversity of ecological roles) is associated with a growth of ecomorphological adaptative forms (Simpson, 1953;Stroud and Losos, 2016). ...
... Adaptive radiations were long regarded as the only existing category of radiations (Simpson, 1953;Simões et al., 2016). In adaptive radiations, an increase in species diversification (due to the increased diversity of ecological roles) is associated with a growth of ecomorphological adaptative forms (Simpson, 1953;Stroud and Losos, 2016). This takes place when ecological space is made available by the reduced competition with other species (e.g. ...
... One significant deviation from this view came in 1953 when G.G. Simpson considered the possible effect that genetic drift may have had on morphological evolution in the fossil record (Simpson, 1953). Simpson introduced the theoretical model of adaptive zones for driving rapid evolution, hypothesizing that these zones were dominated by stabilizing selection, but that genetic drift may have played an important role when these adaptive zones were crossed (Simpson, 1953). ...
... One significant deviation from this view came in 1953 when G.G. Simpson considered the possible effect that genetic drift may have had on morphological evolution in the fossil record (Simpson, 1953). Simpson introduced the theoretical model of adaptive zones for driving rapid evolution, hypothesizing that these zones were dominated by stabilizing selection, but that genetic drift may have played an important role when these adaptive zones were crossed (Simpson, 1953). Loosely mirroring Wright's 'shifting balance theory' for genotypes (Wright, 1932), this hypothesis represented a direct application of population genetics theory to the fossil record. ...
... In 1976, R. Lande developed a theory of evolution, building on the Breeder's equation (Equation 1 in Lande, 1976), that incorporated aspects of the neutral theory within a quantitative genetic framework to allow for the evaluation of univariate phenotypic outcomes in fossil populations under models of random genetic drift or natural selection, marking a turning point in evolutionary studies. This classic paper also provided the first iteration of a test for the null hypothesis of genetic drift based on rates of evolution and effective population size, as well as a model for testing Simpson's (1953) proposal of adaptive zones in macroevolution (Lande, 1976). An additional noteworthy point in this paper that Lande highlights are the difficulties inherent in the estimation of heritability for fossil populations. ...
The Journal of Human Evolution (JHE) was founded 50 years ago when much of the foundation for how we think about human evolution was in place or being put in place, providing the main framework for how we consider our origins today. Here, we will explore historical developments, including early JHE outputs, as they relate to our understanding of the relationship between phenotypic variation and evolutionary process, and use that as a springboard for considering our current understanding of these links as applied to human evolution. We will focus specifically on how the study of variation itself has shifted us away from taxonomic and adaptationist perspectives toward a richer understanding of the processes shaping human evolutionary history, using literature searches and specific test cases to highlight this. We argue that natural selection, gene exchange, genetic drift, and mutation should not be considered individually when considering the production of hominin diversity. In this context, we offer suggestions for future research directions and reflect on this more complex understanding of human evolution and its broader relevance to society. Finally, we end by considering authorship demographics and practices in the last 50 years within JHE and how a shift in these demographics has the potential to reshape the science of human evolution going forward.
... Characterizing how variation in the tempo and mode of evolution has structured the phenotypic diversity of extant species is a central goal of macroevolution [1][2][3] . However, studies are typically limited to a handful of traits [4][5][6] , providing incomplete information. ...
... Evidence for early establishment of the morphospace of living birds is clear for some skeletal parts, including beaks and the combined skeletal morphology. However, we find little evidence for early partitioning of that morphospace, contrary to more specific predictions of 'niche-filling' models 1,9 . Nevertheless, early divergence among broad environmental types may have caused an early divergence of evolutionary modes, suggesting an important role for environmental divergence in structuring the radiation of crown-group birds. ...
... And to what extent are patterns of morphological evolution shaped by interactions among species, versus environmental factors? Environmental and among-species drivers are conceptually unified under the widespread 'niche-filling' narrative, in which environment controls the availability of ecological niches and interactions among species drive partitioning of those niches, with direct effects on morphological evolution 1,[9][10][11] . This hypothesis predicts early establishment of a broad phenotypic space during evolutionary radiations into new adaptive zones (for example, ref. 12 ), as well as early partitioning of that space into subgroup-specific subspaces (for example, ref. 13 ). ...
Characterizing how variation in the tempo and mode of evolution has structured the phenotypic diversity of extant species is a central goal of macroevolution1–3. However, studies are typically limited to a handful of traits4–6, providing incomplete information. We analyse morphological diversification in living birds, an ecologically diverse group⁷, documenting structural scales from ‘pan-skeletal’ proportions down to the localized three-dimensional shape changes of individual bones. We find substantial variation in evolutionary modes among avian subgroups and among skeletal parts, indicating widespread mosaicism and possible differences in the structure of the macroevolutionary landscape across Earth’s main environments. Water-linked groups, especially Aequorlitornithes (waterbirds), have repeatedly explored a large portion of their total morphospace, emphasizing variation in body proportions and in the shape of bones close to the body core, which are functionally related to the mechanics of locomotion⁸. By contrast, landbirds (Inopinaves) evolved distinct, group-specific body forms early in the aftermath of the K-Pg and subsequently emphasized local shape variation, especially in the head and distal limb bones, which interact more directly with the environment. Passerines, which comprise more than half of all bird species, show a conservative evolutionary dynamic that resulted in low disparity across all skeletal parts. Evidence for early establishment of the morphospace of living birds is clear for some skeletal parts, including beaks and the combined skeletal morphology. However, we find little evidence for early partitioning of that morphospace, contrary to more specific predictions of ‘niche-filling’ models1,9. Nevertheless, early divergence among broad environmental types may have caused an early divergence of evolutionary modes, suggesting an important role for environmental divergence in structuring the radiation of crown-group birds.
... The concept was first introduced in 1949 by Alden Miller [1], who suggested that a phenotypic feature might arise which allows a lineage to exploit the environment in a novel way, and thus enter a 'new ecologic sphere'. George Gaylord Simpson expanded upon this idea, proposing that the acquisition of a novel trait can be critical to occupying a new 'adaptive zone' [2]. Both workers considered that the evolution of such traits could potentially be a core component of adaptive radiation: once a key innovation provided access to new resources, natural selection would favor increased adaptation, and subsequent speciation would provide the opportunity for descendants to diversify and specialize on different resources owing to ample ecological opportunity [3]. ...
... In the three decades following Miller's seminal article, key innovations were widely considered to be adaptations central to accessing previously unobtainable portions of the ecological spectrum ( Figure 1A) (e.g., [2,[8][9][10]). Discussions focused on identifying plausible case studies aimed at understanding how the evolution of novel morphological traits could explain shifts to new ecological niches [11,12]. However, as evolutionary biology became increasingly quantitative with the rise of phylogenetic approaches, the largely qualitative idea of a 'key innovation' proved difficult to address in a hypothesis-testing framework. ...
... Simpson publishes "On the Major Features of Evolution," terming the "adaptive zone" [2] 1963 Mayr argues for an integrative key innovation biology in "Animal Species and Evolution" [41] 1984 Fürsich and Jablonski present fossil evidence that key innovations do not always result in "radiation" [24] 1988 Table S2 in the supplemental information online), including loess-smoothed line with 95% standard error. The 21st century has been marked with a steadily increasing availability of well-sampled molecular phylogenies and new phylogenetic methods for estimating macroevolutionary dynamics (e.g., [17]), coincident with a climbing popularity of studies on 'key innovations' and the operational redefinition of the term by many. ...
The idea of ‘key innovations’ has long been influential in theoretical and empirical approaches to understanding adaptive diversification. Despite originally revolving around traits inducing major ecological shifts, the key innovation concept itself has evolved, conflating lineage diversification with trait-dependent ecological shifts. In this opinion article we synthesize the history of the term, clarify the relationship between key innovations and adaptive radiation, and propose a return to the original concept of key innovations: the evolution of organismal features which permit a species to occupy a previously inaccessible ecological state. Ultimately, we suggest an integrative approach to studying key innovations, necessitating experimental approaches of form and function, natural history studies of resource use, and phylogenetic comparative perspectives.
... Here we propose the Clade Replacement Theory (CRT) based on long-debated processes and patterns documented in the literature (e.g., Benton 1987;Simpson 1953) and formalize it as a plausible framework to make testable predictions on ADE patterns emerging from the ecoevolutionary context and history of a biological system. We first enumerate the theories and evidence supporting different ADE patterns, and describe the differences in how the relationship between species age and extinction probability is estimated based on living or extinct species. ...
... Thus, key innovations may have an exaptation condition, by which it would enable the surrogate clade to take advantage of a new selective regime not present yet (Wellborn and Langerhans 2015;Gould and Vrba 1982). As suggested by Simpson (1953), a clade must have geographic, evolutionary, and ecological access for radiation to occur. (Figure 2). ...
There is no scientific consensus about whether and how species’ evolutionary age, or the elapsed time since their origination, might affect their probability of going extinct. Different age-dependent extinction (ADE) patterns have been proposed in theoretical and empirical studies, while the existence of a consistent and universal pattern across the tree of life remains debated. If evolutionary age predicts species extinction probability, then the study of ADE should comprise the elapsed time and the ecological process acting on species from their origin to their extinction, or to the present for extant species. Additionally, given that closely related species share traits associated with fitness, evolutionary proximity could generate similar ADE patterns. Considering the historical context and extinction selectivity based on evolutionary relatedness, we build on previous theoretical work to formalize the Clade Replacement Theory (CRT) as a framework that considers the ecological and evolutionary aspects of species age and extinction probability to produce testable predictions on ADE patterns. CRT’s domain is the diversification dynamics of two or more clades competing for environmental space throughout time; and its propositions or derived hypotheses are: i) incumbency effects by an early arriving clade that limit the colonization and the diversification of a younger clade leading to a negative ADE scenario (younger species more prone to extinction than older ones), and, ii) an ecological shift triggered by an environmental change that imposes a new selective regime over the environmental space and leads to a positive ADE scenario (extinction probability increasing with age). From these propositions, we developed the prediction that the ADE scenario would be defined by whether an ecological shift happens or not. We discuss how the CRT could be tested with empirical data and provide examples where it could be applied. We hope this paper will provide a common ground to unify results from different fields and foster new empirical tests of the mechanisms derived here while providing insights into CRT theoretical structuration.
... This research paper delves into the dynamics of rapid evolution with the proposal of a computational model, called Adaptive Radiation Model (ARM), using concepts from Biogeographic Computation and extending the concepts presented in [16]. Habitats are represented using a fundamental conceptual structure called adaptive surface [21,22,23,24,25], which provides the relationship between the phenotypic characteristics of an individual and its respective adaptation to the habitat. Thus, the adaptive surface is a function that has in its domain the phenotypic characteristics of individuals or species in continuous spaces, and returns quantitative and qualitative values related to the adaptation of a species to a habitat. ...
... Although adaptive surfaces were originally studied in the domain of genes, . evaluation measures 6 Simpson suggested [22] a representation of such surfaces in the domain of phenotypes, arguing that the phenotypes represent a direct interaction with the ecosystem. Furthermore, this phenotypic approach allows the representation of characteristics of individuals, species and habitats in continuous spaces. ...
Recent studies have demonstrated that evolution can be observed in a few dozen generations, especially when species occupy a new ecological opportunity due to environmental changes. There are several factors that induce this rapid evolution and are related to the phenotype and its response to the environment. This response is then determined by phenotypic variation, because if patterns of diversity in a population produce a rapid response to an environmental change, then rapid adaptation to the new environment can occur. This paper aims to investigate patterns of evolution of species in an artificial ecosystem, and to highlight some patterns that promote rapid evolution. Understanding how rapid evolution occurs is not only of fundamental importance in understanding evolutionary processes and species conservation, but also to provide support for improving the resolution of certain types of problems, especially those in which the solution is time-variant. To achieve the objectives of this paper, a computational model of Adaptive Radiation was designed using the concepts of Biogeographic Computing, an area of knowledge that studies ecosystems as information processors, a fundamental principle of Natural Computing. Habitats are represented by adaptive surfaces, which in turn are composed of different ecological opportunities. The results show, for example, that dramatic changes in ecosystems can lead to a rapid response and a rapid adaptation to new ecological opportunities, mainly because of the emergent and self-sustaining behaviour promoted by the continuous speciation, extinction and adaptation of species. This emergent dynamic supports the thesis that rapid environmental changes can lead to rapid evolution. This behaviour, in turn, is highly desired when considering time-varying problem solving. If solutions to a problem are changing over time, sometimes it is necessary to rapidly find new solutions.
... El vínculo entre adaptación y diversificación surge desde los estudios de Darwin y Wallace quienes evidenciaron variantes adaptativas a nivel geográfico entre especies cercanamente emparentadas. Osborn (1902) acuñó el término de radiación adaptativa, mientras que Simpson (1953) lo establece como: ''Divergencia más o menos simultánea de numerosas líneas del mismo tipo adaptativo ancestral''. Además, propuso dos de sus características singulares: i) oportunidad ecológica, entendida como los factores externos que posibilitan el surgimiento de nuevos nichos ecológicos; y ii) atributos o innovaciones clave, que son atributos intrínsecos que favorecen la diversificación mediante la adaptación a distintos nichos ecológicos. ...
... Se puede pensar que la evolución del hábito carnívoro está asociada tanto con atributos clave como con oportunidad ecológica (sensu Simpson, 1953). Los ambientes pobres en nutrientes que resultan limitantes para la mayoría de las plantas no carnívoras podrían abrirse a la colonización de especies que pudieran obtener beneficio en estas condiciones mediante las adaptaciones necesarias. ...
... For instance, when transitioning from a terrestrial to a buoyant environment, different lineages independently evolved similar adaptations to be able to survive in the new habitat, such as streamlined body plans, dorsal nares and similar locomotory systems [5,[12][13][14][15]. These secondary aquatic adaptations in tetrapods are often interpreted as examples of Dollo's Law, which predicts the irreversibility of the loss of complex characters [16]. Technically, these transitions are either irreversible or just extremely unlikely to be reversed, but for simplicity, we will refer to them hereafter as irreversible. ...
... Stem pinnipeds, from Oligocene, displayed paddle-like limbs, but yet relying more on terrestrial environments than extant pinnipeds [60]. Dollo's Law postulates that once a complex trait is lost, it cannot be regained [16,18,61,62]. The law is also thought to be generally true in cases such as tooth loss [22,55,56] (but see [60]), or loss of ability to fly in birds [18,64]. ...
Secondary transitions to aquatic environments are common among vertebrates, and aquatic lineages display several adaptations to this realm, some of which might make these transitions irreversible. At the same time, discussions about secondary transitions often focus only on the marine realm, comparing fully terrestrial with fully aquatic species. This, however, captures only a fraction of land-to-water transitions, and freshwater and semi-aquatic groups are often neglected in macroevolutionary studies. Here, we use phylogenetic comparative methods to unravel the evolution of different levels of aquatic adaptations across all extant mammals, testing if aquatic adaptations are irreversible and if they are related to relative body mass changes. We found irreversible adaptations consistent with Dollo's Law in lineages that rely strongly on aquatic environments, while weaker adaptations in semi-aquatic lineages, which still allow efficient terrestrial movement, are reversible. In lineages transitioning to aquatic realms, including semi-aquatic ones, we found a consistent trend towards an increased relative body mass and a significant association with a more carnivorous diet. We interpret these patterns as the result of thermoregulation constraints associated with the high thermal conductivity of water leading to body mass increase consistently with Bergmann's rule and to a prevalence of more nutritious diets.
... Nonetheless, there remains considerable uncertainty about the macroevolutionary dynamics that characterize adaptive radiations. An oft-hypothesized pattern of adaptive radiations is an 'early burst' in 58 ecomorphological change as lineages rapidly adapt to new niches, followed by a slowing of evolutionary rates as ecological opportunity diminishes (Simpson 1944, Simpson 1953 ...
... The observed macroevolutionary patterns of phyllostomid molars are consistent with predictions of the hierarchical adaptive radiation hypothesis (Osborn 1902, Simpson 1944, Simpson 1953, Slater and Friscia 306 2019). The phyllostomid radiation involved (i) a dramatic higher-level radiation of lineages into novel, diet-affiliated adaptive zones and (ii) lower-level radiations of lineages within adaptive zones. ...
Adaptive radiations are bursts in biodiversity that lead to the origin of new evolutionary lineages and phenotypes. However, adaptive radiations typically occur over millions of years and it is unclear how the macroevolutionary dynamics that underpin them vary through time and among groups of organisms. Phyllostomid bats radiated extensively for diverse diets –from insects to vertebrates, fruit, nectar, and blood– and we use their molars as a model system to examine the dynamics of adaptive radiations. Three-dimensional shape analyses of lower molars of Noctilionoidea (Phyllostomidae and close relatives) indicate that different diet groups exhibit distinct morphotypes. Comparative analyses further reveal that phyllostomids are a striking example of a hierarchical radiation; their initial, higher-level diversification involved an ‘early burst’ in molar morphological disparity as lineages invaded new diet-affiliated adaptive zones, followed by subsequent lower-level diversifications within adaptive zones involving less dramatic morphological changes. We posit that strong selective pressures related to initial shifts to derived diets may have freed molars from morpho-functional constraints associated with the ancestral molar morphotype. Then, lineages with derived diets (frugivores and nectarivores) diversified considerably within broad adaptive zones, likely reflecting finer-scale niche partitioning. The observed early burst pattern is only evident when examining molar traits that are strongly linked to diet, highlighting the importance of ecomorphological traits in comparative studies. Our results support the hypothesis that adaptive radiations are commonly hierarchical and involve different tempos and modes at different phylogenetic scales, with early bursts being more common at broader scales.
SIGNIFICANCE STATEMENT
Many groups of organisms are exceptionally diverse in their ecology, morphology, and number of species. But there is debate as to whether these groups commonly achieved this diversity through ‘bursts’ in diversification early in their history. Phyllostomid bats are one of the most ecologically diverse mammalian families and a classic example of an adaptive radiation. We use their molar shapes, which correlate with diet, as a model for examining macroevolutionary patterns during diversifications. We find that phyllostomids experienced a two-step process of diversification; the first step involved a rapid burst, whereas the second involved finer-scale changes as lineages filled ecological niches. We posit that this is a common, yet underappreciated, pattern during the early histories of many diverse clades.
... -G.G. Simpson (1953) Understanding the origin and persistence of phenotypic, ecological, and species diversity, and how this diversity changes through time, is a fundamental aim of evolutionary biology. To achieve this, researchers have undertaken both theoretical and empirical investigations in a variety of biological systems. ...
Understanding the processes that drive phenotypic diversification and underpin speciation is key to elucidating how biodiversity has evolved. Although these processes have been studied across a wide array of clades, adaptive radiations (ARs), which are systems with multiple closely related species and broad phenotypic diversity, have been particularly fruitful for teasing apart the factors that drive and constrain diversification. As such, ARs have become popular candidate study systems for determining the extent to which ecological features, including aspects of organisms and the environment, and inter- and intraspecific interactions, led to evolutionary diversification. Despite substantial past empirical and theoretical work, understanding mechanistically how ARs evolve remains a major challenge. Here, we highlight a number of understudied components of the environment and of lineages themselves, which may help further our understanding of speciation and AR. We also outline some
substantial remaining challenges to achieving a detailed understanding of adaptation, speciation, and the role of ecology in these processes. These major challenges include identifying
factors that have a causative impact in promoting or constraining ARs, gaining a more holistic understanding of features of organisms and their environment that interact resulting in
adaptation and speciation, and understanding whether the role of these organismal and environmental features varies throughout the radiation process. We conclude by providing perspectives on how future investigations into the AR process can overcome these challenges, allowing us to glean mechanistic insights into adaptation and speciation
... This clarification is critical in predicting how organisms will respond to environmental change. Parallel evolution, the repeated evolution of traits in related lineages in response to similar environmental conditions (Simpson 1953), has historically been used as strong supporting evidence for natural selection (Endler 1986;Schluter and Nagel 1995;Schluter et al. 2004;Wake et al. 2011;Bolnick et al. 2018). Consistent and directional changes in traits described as parallel evolution are indicative of natural selection because it is highly unlikely that these repeated patterns would emerge based on chance alone (Endler 1986;Schluter and Nagel 1995;Schluter et al. 2004;Wake et al. 2011). ...
The parallel evolution of lateral plates and body shape in the threespine stickleback (Gasterosteus aculeatus) is an iconic example of adaptation. We test a case of contemporary evolutionary transition in a recently isolated population of marine G. aculeatus in British Columbia, Canada. We investigate Ectodysplasin (Eda) genotypes, plate counts, neutral genetic divergence, and whole-body phenotypes to determine the genetic and phenotypic distance between this population and nearby comparative populations. Our focal population is in the process of adapting both genetically and phenotypically to a freshwater environment, and we provide an example of the genetic basis for parallel evolution on a contemporary timescale. The frequency of Eda genotypes and lateral plate phenotypes in our focal population is not consistent with those of marine or fully freshwater populations. Although our focal population is genetically distinct from nearby marine populations, these fish still more closely resemble marine populations in overall body shape while demonstrating an intriguing intermediate phenotype. Eda frequency and lateral plate phenotype change faster than body shape in response to freshwater conditions, suggesting that the pace of adaptation differs across traits in response to the same environmental conditions. Our results further bolster the case for G. aculeatus as a key model of contemporary evolution.
... Our results suggest that different methodologies and taxonomic samples do not necessarily explain previously reported region-specific macroevolutionary patterns; rather, complexity in explanatory factors of skeletal diversity is a key feature of Carnivora. The ability of individual skeletal components to adapt to specific ecological factors independently from each other may have contributed to the clade's hierarchical [64,65] evolution. As previously hypothesized [28,38], the restriction of carnassial shear to the P4/m1 pair may have been the key innovation that facilitated the initial carnivoran diversification early in the clade's evolutionary history. ...
The diversity of vertebrate skeletons is often attributed to adaptations to distinct ecological factors such as diet, locomotion, and sensory environment. Although the adaptive evolution of skull, appendicular skeleton, and vertebral column is well studied in vertebrates, comprehensive investigations of all skeletal components simultaneously are rarely performed. Consequently, we know little of how modes of evolution differ among skeletal components. Here, we tested if ecological and phylogenetic effects led to distinct modes of evolution among the cranial, appendicular and vertebral regions in extant carnivoran skeletons. Using multivariate evolutionary models, we found mosaic evolution in which only the mandible, hindlimb and posterior (i.e. last thoracic and lumbar) vertebrae showed evidence of adaptation towards ecological regimes whereas the remaining skeletal components reflect clade-specific evolutionary shifts. We hypothesize that the decoupled evolution of individual skeletal components may have led to the origination of distinct adaptive zones and morphologies among extant carnivoran families that reflect phylogenetic hierarchies. Overall, our work highlights the importance of examining multiple skeletal components simultaneously in ecomorphological analyses. Ongoing work integrating the fossil and palaeoenvironmental record will further clarify deep-time drivers that govern the carnivoran diversity we see today and reveal the complexity of evolutionary processes in multicomponent systems.
... Readily measurable and the most frequently used key morphological parameter, the body size of an organism profoundly affects every aspect of life history, including biological, physiological, and ecological traits (Calder 1984;McKinney 1990;McNamara 1990;Kingsolver and Pfennig 2004;Cardillo et al. 2005;Roy 2008;Smith et al. 2016;Waller and Svensson 2017;Salamon et al. 2021). As a result, body-size evolution has been a focus of interest among palaeontologists and biologists for decades (Simpson 1953;Bonner 1988Bonner , 2006Payne et al. 2009;Baker et al. 2015;Gotanda et al. 2015;Smith et al. 2016 and references therein), and the fossil record offers an excellent dataset to investigate the long term evolutionary body-size trend across a wide range of skeletonised taxa (Heim et al. 2015;Smith et al. 2016). Cope's rule (Cope 1887), which postulates an evolutionary increase of body size in descendants compared to ancestors, is one such long-term evolutionary trend that received unprecedented attention (e.g. ...
An organism’s body size is interlinked with several ecological and physiological parameters and, therefore, has been widely used to detect and describe long-term macroevolutionary trends. One of those long-term trends is Cope’s rule, a tendency to increase size over time. In the present study, we document long-term evolutionary trends in the body size of the Middle Jurassic – Early Cretaceous bivalves from the Kutch basin, India. It appears that the body size of the Kutch bivalves did not follow any gradual increasing trend or Cope’s rule. Our data suggest a fluctuating pattern of change in bivalve body size from the Bathonian to the Aptian. The repeated transgressive-regressive cycles in the Mesozoic may have resulted in temporally volatile adaptive landscapes and adaptive optima, which may explain the observed patterns of change in bivalve body size. This oscillating pattern in body size is evident at higher (class and order) and lower taxonomic levels (family and genus). The most significant increase in bivalve size occurred across the Jurassic – Cretaceous boundary. We argue that a high abundance of certain groups, ecological interactions, and taphonomy may explain this significant increase in bivalve body size.
... While the landscape metaphor holds a prominent place in evolutionary thinking, it is not without critics. One criticism concerns the metaphor's multiple forms: one describing individual fitness as a function of genotypes, another as a function of phenotypes (Simpson, 1953), and yet another describing a population's mean fitness as a function of its genetic structure (Pigliucci and Kaplan, 2006). Except in a few special cases, the axes are not rigorously defined, but rather depict some sort of distance between types. ...
... Lower α rates implied lower variance and greater homoplasy. Under EB, we generated matrices emulating scenarios of character evolution expected in events of adaptive radiations (sensu Simpson, 1953). This Gaussian, time-varying process was controlled by multiple decay beta (β) rates slowing variance over time (Table 1). ...
Quantitative traits are a source of evolutionary information often difficult to handle in cladistics. Tools exist to analyze this kind of data without subjective discretization, avoiding biases in the delimitation of categorical states. Nonetheless, the ability of continuous characters to accurately infer relationships is incompletely understood, particularly under parsimony analysis. This study evaluates the accuracy of phylogenetic reconstructions from simulated matrices of continuous characters evolving under alternative evolutionary processes and analyzed by parsimony. We generated 100 trees to simulate 9,000 matrices containing 26 terminals and 100 continuous characters evolving under: Brownian-Motion (BM), Ornstein-Uhlenbeck (OU) and Early-Burst (EB) processes assuming variable parametrizations. Our comparisons of cladograms revealed that matrices analyzed by parsimony carry phylogenetic signals to infer relationships, but the accuracy is higher for matrices simulated under BM, regardless of the parameterization schemes. Implementation of equal or implied weighting with multiple penalization strengths against homoplasies did not affect cladogram inferences. Accuracy of continuous characters in resolving relationships is skewed toward apical nodes of the trees. Our simulations provide controlled tests of the usefulness of quantitative traits in phylogenetics, specifically under neutral evolution, and demonstrate their effectiveness in estimating shallower nodes among recently diverged species, regardless of parameters and weighting schemes.
... Any higher taxon, like a species, is maximally adapted to a certain range of environments alias the adaptive zone of a taxon (Simpson, 1953b, as restricted by Van Valen, 1971). These environments define the area of ecological optimum for this taxon, in which it diversifies in course of time. ...
The geographic characteristic of plant macroevolution is manifested in general in neither even, nor random distribution of the archaic and advanced representatives of a higher taxon in its range. The explanatory concepts proposed are still contradictory. Besides, they are poorly testable, because they concern too long-time intervals during which multiple major changes in both the environment and the ranges of taxa can have occurred; these changes usually continue untraceable in fossil records. The tribe Senecioneae in the Succulent Karoo is best suited for studying the geographic patterns of plant macroevolution for the following reasons: i) the environment of the Succulent Karoo has resulted from unidirectional climate change over 10 million years (accordingly, large fluctuations of the taxon ranges there are highly unlikely); ii) the phylogeny of the tribe Senecioneae is quite fully recognized (and it is not distorted by extinctions, at least at the level of genera); iii) Senecioneae are completely allochthonous in the Succulent Karoo (accordingly, interpretation of results becomes easier and simpler). The archaic genera of Senecioneae are as numerous in the Succulent Karoo as the highly advanced ones, whereas the mid-advanced genera are completely absent there. Such a genus composition of the tribe in the area concerned cannot be explained by the cradle and museum concept, since this area is outside of center of origin/diversification of Senecioneae. The zonal stratification concept is inapplicable to this case, since the climate of the Succulent Karoo was changing unidirectional all the time without noticeable fluctuations. All other concepts proposed are also inapplicable, as they treat the emerging of archaism gradient(s) in the taxon range, but not a deficiency/absence of mid-advanced representatives of a higher taxon in a territory occupied by its archaic and highly advanced members. The absence of mid-advanced members of Senecioneae in the Succulent Karoo could be explained as follows. Any higher taxon very rarely and at long time intervals acquires traits that enable it to spread to areas which greatly differ in their environments from the center of origin/diversification of this taxon. All new subordinate taxa that originate during these time intervals remain confined in the center of origin/diversification of the higher taxon. Accordingly, only archaic and most advanced representatives of this higher taxon would be found faraway its center of origin/diversification.
... Однако биота в своей основе не просто совокупность видов, а система потенциальных адаптивных зон определённых экологических форм на уровне отдельных видов, родов, семейств. Следует учесть, что адаптивная зона по Симпсону (Simpson 1953) представляет собой теоретический конструкт. Эти формы не нужно путать с жизненными. ...
Постулируется наличие в биологической эволюции двух основных составляющих, двух пространств – эволюционного и экологического. Каждое пространство имеет свои закономерности и свой набор категорий. Важнейшей, ключевой категорией эволюционного пространства является архетип. Каждый эволюционный таксон имеет свой архетип, отражающий тип его организации. Можно говорить об архетипах уровня типа, класса, отряда. Здесь понятия таксона вышеперечисленных уровней принципиально отличается от такового в рамках экологического пространства – семейства, рода, вида. В последнем случае семейство и род следует рассматривать как объединение видов, имеющих общего предка. Под архетипом, в отличие от плана строения, следует понимать комплекс тех новшеств, которые лежат в основе сформировавшегося нового таксона. Архетип формируется и развивается независимо от внешних условий. Показана роль биоты в процессе видообразования, которую следует рассматривать как систему адаптивных зон определенных экологических форм на уровне отдельных видов. родов. семейств Элементами биоты являются процессы видообразования и вымирания видов, родов, семейств. Показана роль географического фактора в процессах на уровне эволюционного пространства.
... However, biota is basically not just a collection of species but a system of potential adaptive zones of certain ecological forms at the level of individual species, genera, and families. It should be noted that according to Simpson (Simpson 1953) the adaptive zone is a theoretical construct. These forms should not be confused with life forms. ...
The presence of two main elements, two spaces – evolutionary space and an ecological space – within biological evolution has been postulated in the article. Each space has its own patterns and its own set of categories. The most important, key category of evolutionary space is an archetype. Each evolutionary taxon has its own archetype reflecting the type of its organization. One can speak of archetypes at the level of Phylum, Class, Order. Here, the concepts of taxon at the above levels are fundamentally different from those within ecological space - Family, Genus, Species. In the latter case, the Gamily and Genus should be considered as a unity of species that have a common ancestor. An archetype, in contrast to a structural plan, should be understood as a complex of those innovations that lie within the formed new taxon. The archetype is formed and develops regardless of external conditions. The role of biota in the process of speciation, which should be considered as a system of adaptive zones of certain ecological forms at the level of individual species, genera, and families, has been presented in the article. The elements of biota are the processes of speciation and extinction of species, genera, and families. The role of the geographical factor in processes at the level of evolutionary space has been established.
... However, by testing for correlations between molecular and morphological evolutionary rates, we can better understand the dynamics of the morphological clock. While a broad link between molecular and morphological change is expected (Simpson 1953), the rate of phenotypic mutation has been observed to be orders of magnitude larger than that of genotypic mutations in eukaryotic organisms (Bürger et al. 2006). The higher rate of phenotypic mutations might be caused by a lack of selective pressure to reduce the rate of mutation below a certain threshold, effectively rendering phenotypic mutation rates independent of genotypic mutation rates (Bürger et al. 2006). ...
... Second, we hypothesize (H2) that high global and regional species richness in our 151 key clade is the result of high in-situ diversification rates, rather than high immigration rates or 152 early colonization times. Specifically, we expect that temperate systems provided novel 153 ecological opportunities or 'adaptive zones' (Simpson 1953) for increased diversification rates 154 6 UNOFFICIAL UNOFFICIAL with limited immigration from tropical regions and relatively recent and similar colonization 155 times across areas. This scenario down weights models assuming gradual diversity accumulation 156 over time, since it explicitly suggests late origination and provides little time for temperate 157 diversity to differentially increase among areas. ...
The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change.
We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes.
Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in - situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae.
The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in - situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in - situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.
... The challenges associated with grass processing have been previously suggested to drive changes in tooth morphology in clades evolving in grasslands. In particular, hypsodonty (high crowned teeth) has been interpreted as an adaptation to abrasive diets such as dusty grasses, and often regarded as a response to the emergence of grasslands in the Miocene (Simpson, 1953;Williams and Kay, 2001). Marmots diverged in a different dimension of tooth morphology: cross-sectional shape and area. ...
... Табл. 4-11), с информацией по радиоуглеродному датированию, 14C (приведены калиброванные даты; использовалась кривая intCal20 ), геохронология позднего плейстоцена и голоцена с использованием данных прокта GICC05 Andersen et al. 2006;Svensson et al. 2008 , with information on 14C dating (provided "экологической ниши" Симпсона (Simpson 1953 Способ оценки взаимного положения выборок опирается на "экспертно-визуальный" подход, основанный на анализе графических результатов применения статистических методов снижения размерности (главные компоненты); в качестве вспомогательного метода использовался линейный регрессионный анализ. Для большей наглядности применения экспертно-визуального подхода можно привести способ визуализации результатов анализа формы объектов, реализованный в прикладной программе tpsRelw (Rohlf 2015 (i) 3Д-модель референсного объекта (Приложение 1: п. 3), который будет выполнять роль трехмерной основы для представления различий между двумя совмещенными целевыми объектами (target1, target2). ...
Late Quaternary communities of shrews, Soricidae, from Ural and Far East Regions of Russia: A protocol for the multifactorial morphospace building //
The current paper is a preliminary attempt to a protocol development for analysis of the Late Pleistocene and Holocene paleocommunities of soricid use modern approaches for the morphological data analysis. First, we assessed the abilities of fossil soricid collections from Ural and Far East localities to provide a complex interregional analysis of the phenotype variation. Thus, for the first time in a linked context the study describes species list and chronological position of Ural and Far East shrew fossil samples in terms of inter- and intraregional comparisons for revealing general and particular responses of paleocommunities on the climatic fluctuations. Second, under the modern approaches, we prepared 182 three-dimensional models of hemimandibles or isolated m1 and build the morphospace of m1 shape for seven Sorex species from the Upper Pleistocene layer MKl-13 and Middle Holocene layer MKl-7 of Medvezhyi Klyk Cave (South Primor'e, Russia). There were recent samples from East Siberia (Yakutia) and north part of the Far East (Magadanskaya Oblast' and Khabarovsky Kray; 'cold' habitats) and South Primor'e ('warm' habitats) including into morphospace for actualization of eventual responses of the fossil samples for Late Quaternary climate fluctuations. Our analysis revealed: (i) a weak reaction of m1 shape of the almost all species on the 'cold' and 'warm' environmental conditions, except S. daphaenodon and S. caecutiens; (ii) two groups of species, namely 'generalized' and 'specialized' by the m1 shape in corresponding the idea of distribution of trophic niches among coexisted shrews; (iii) a diagnostic character for the fossil samples of S. unguiculatus and S. isodon.
... The rapid evolution of phenotypically and ecologically diverse species from a common ancestor, known as organismic radiations, are often fueled by adaptation to ecological opportunities that include diffusion into new habitats and extinction of interspeci c competitors (Schluter, 2000;Simpson, 1944Simpson, , 1953. There are cases in aquatic systems, although infrequent, where multiple sympatric lineages have each radiated into several species or morphs (Johnson et al., 1996). ...
The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remains understudied. The Laurentian Great Lakes provide a unique system of two lineages that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex radiated rapidly prior to the Last Glacial Maximum (80–90 ka), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Salvelinus namaycush , following a brief time lag, which we hypothesize to be driven by predator prey dynamics. Diversification of prey into deepwater created ecological opportunities for the predators, facilitating their demographic expansion through an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation.
... adaptive landscape) is one of the most powerful lines of evidence for deterministic evolution (Losos 2011). Studies demonstrating convergent evolution in similar habitats (Rundle et al. 2000;Collar et al. 2010;Mahler et al. 2014) and dietary regimes (Grant and Grant 1989;Rüber and Adams 2001;Davis and Betancur-R 2017) are common in evolutionary biology, largely because these are key ecological axes that exert strong selective pressures (Simpson 1953;Mayr 1963;Schluter 2000;Losos and Ricklefs 2009). ...
Migration can have a profound influence on rates and patterns of phenotypic evolution. Diadromy is the migration between marine and freshwater habitats for feeding and reproduction that can require individuals to travel tens to thousands of kilometers. The high energetic demands of diadromy are predicted to select for ecomorphological traits that maximize swimming and locomotor efficiency. Intraspecific studies have shown repeated instances of divergence among diadromous and nondiadromous populations in locomotor and foraging traits, which suggests that at a macroevolutionary scale diadromous lineages may experience convergent evolution onto one or multiple adaptive optima. We tested for differences in rates and patterns of phenotypic evolution among diadromous and nondiadromous lineages in Clupeiformes, a clade that has evolved diadromy more than 10 times. Our results show that diadromous clupeiforms show convergent evolution for some locomotor traits and faster rates of evolution, which we propose are adaptive responses to the locomotor demands of migration. We also find evidence that diadromous lineages show convergence into multiple regions of multivariate trait space and suggest that these respective trait spaces are associated with differences in migration and trophic ecology. However, not all locomotor traits and no trophic traits show evidence of convergence or elevated rates of evolution associated with diadromy. Our results show that long-distance migration influences the tempo and patterns of phenotypic evolution at macroevolutionary scales, but there is not a single diadromous syndrome.
... Ecological opportunity is a necessary phenomenon for adaptive radiation to occur. Simpson (1953) proposed that ecological opportunity could become accessible for organisms in four ways: ...
... Their conflicts over the shape of adaptive landscapes; the importance of drift; and whether ge netic features, such as dominance (Mayo and Bürger 1997), are adaptations; are still actively debated by those working on evolvability today (Frank 2012). Similarly, the idea that clades (Simpson 1953;Vermeij 1987;Jablonski, chapter 17) or traits (Armbruster, chapter 15) differ in their ability to evolve is of longstanding importance in macroevolutionary studies. In evo-devo research, an impor tant precursor to evolvability research is the Eu ro pean structuralist tradition exemplified by the work of Waddington (1957) and Riedl (1977Riedl ( , 1978. ...
Essays on evolvability from the perspectives of quantitative and population genetics, evolutionary developmental biology, systems biology, macroevolution, and the philosophy of science.
Evolvability—the capability of organisms to evolve—wasn't recognized as a fundamental concept in evolutionary theory until 1990. Though there is still some debate as to whether it represents a truly new concept, the essays in this volume emphasize its value in enabling new research programs and facilitating communication among the major disciplines in evolutionary biology. The contributors, many of whom were instrumental in the development of the concept of evolvability, synthesize what we have learned about it over the past thirty years. They focus on the historical and philosophical contexts that influenced the emergence of the concept and suggest ways to develop a common language and theory to drive further evolvability research.
The essays, drawn from a workshop on evolvability hosted in 2019–2020 by the Center of Advanced Study at the Norwegian Academy of Science and Letters, in Oslo, provide scientific and historical background on evolvability. The contributors represent different disciplines of evolutionary biology, including quantitative and population genetics, evolutionary developmental biology, systems biology, and macroevolution, as well as the philosophy of science. This plurality of approaches allows researchers in disciplines as diverse as developmental biology, molecular biology, and systems biology to communicate with those working in mainstream evolutionary biology. The contributors also discuss key questions at the forefront of research on evolvability.
Contributors:J. David Aponte, W. Scott Armbruster, Geir H. Bolstad, Salomé Bourg, Ingo Brigandt, Anne Calof, James M. Cheverud, Josselin Clo, Frietson Galis, Mark Grabowski, Rebecca Green, Benedikt Hallgrímsson, Thomas F. Hansen, Agnes Holstad, David Houle, David Jablonski, Arthur Lander, Arnaud LeRouzic, Alan C. Love, Ralph Marcucio, Michael B. Morrissey, Laura Nuño de la Rosa, Øystein H. Opedal, Mihaela Pavličev, Christophe Pélabon, Jane M. Reid, Heather Richbourg, Jacqueline L. Sztepanacz, Masahito Tsuboi, Cristina Villegas, Marta Vidal-García, Kjetil L. Voje, Andreas Wagner, Günter P. Wagner, Nathan M. Young
... Additionally, dispersal/vicariance events can occur within a relatively short timeframe along these biogeographical boundaries. These dispersal/vicariance events may enhance speciation given ecological opportunity presented by dispersal to new areas or changes in habitat (Simpson, 1953;Yoder et al., 2010) as well as limiting secondary contact and gene flow. These rapid radiations should also increase the probability of incomplete lineage sorting (ILS; Maddison, 1997) resulting in greater phylogenetic uncertainty at those nodes tran- Nuñez et al. ...
North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.
... Our results provide the first insights into how 21 the genomic architecture of clownfishes could relate to their morphological and ecological 22 diversity. Adaptive radiation is an outstanding process considered to play a central role in the 2 buildup of the diversity of life on Earth (Simpson, 1953;Schluter, 2000). It is defined as the 3 rapid diversification of an ancestral species into a multitude of new forms that are adapted to 4 diverse ecological niches (Schluter, 2000). ...
Clownfishes are an iconic group of coral reef fishes that evolved a mutualistic interaction with sea anemones, which triggered the rapid diversification of the group. Following the emergence of this mutualism, clownfishes diversified into different ecological niches and developed convergent phenotypes associated with their host use. The genetic basis of the initial acquisition of the mutualism with host anemones has been described, but the genomic architecture underlying clownfish diversification once the mutualism was established and the extent to which clownfish phenotypic convergence originated through shared genetic mechanisms are still unknown. Here, we investigated these questions by performing comparative genomic analyses on the available genomic data of five pairs of closely related but ecologically divergent clownfish species. We found that clownfish diversification was characterized by bursts of transposable elements, an overall accelerated coding evolution, incomplete lineage sorting and ancestral hybridization events. Additionally, we detected a signature of positive selection in 5.4 % of the clownfish genes. Among them, five presented functions associated with social behavior and ecology, and they represent candidate genes involved in the evolution of the size-based hierarchical social structure so particular to clownfishes. Finally, we found genes with patterns of either relaxation or intensification of purifying selection and signals of positive selection linked with clownfish ecological divergence, suggesting some level of parallel evolution during the diversification of the group. Altogether, this work provides the first insights into the genomic substrate of clownfish adaptive radiation and integrates the growing collection of studies investigating the genomic mechanisms governing species diversification.
... Generation length is also essential to our understanding of evolutionary resiliency to contemporary environmental change (9)(10)(11). When compared on a given interval of time (e.g., years), species with shorter generation times are predicted to evolve faster because they experience more opportunities for shifts in gene frequencies (6,7,12). For example, long-lived organisms are expected to respond more slowly to environmental change than their short-lived counterparts, which in general have been shown to evolve remarkably rapidly (13,14). ...
Variation in evolutionary rates among species is a defining characteristic of the tree of life and may be an important predictor of species' capacities to adapt to rapid environmental change. It is broadly assumed that generation length is an important determinant of microevolutionary rates, and body size is often used as a proxy for generation length. However, body size has myriad biological correlates that could affect evolutionary rates independently from generation length. We leverage two large, independently collected datasets on recent morphological change in birds (52 migratory species breeding in North America and 77 South American resident species) to test how body size and generation length are related to the rates of contemporary morphological change. Both datasets show that birds have declined in body size and increased in wing length over the past 40 y. We found, in both systems, a consistent pattern wherein smaller species declined proportionally faster in body size and increased proportionally faster in wing length. By contrast, generation length explained less variation in evolutionary rates than did body size. Although the mechanisms warrant further investigation, our study demonstrates that body size is an important predictor of contemporary variation in morphological rates of change. Given the correlations between body size and a breadth of morphological, physiological, and ecological traits predicted to mediate phenotypic responses to environmental change, the relationship between body size and rates of phenotypic change should be considered when testing hypotheses about variation in adaptive responses to climate change.
... Te lineage diversity plot for clades 2. [56] and provides evidence that the expansion of one genetic group is gained at the expense of another [57]. We also noted a small increase in the genetic diversity after 2019 was characteristic for clades 2. (Figure 1). ...
Highly pathogenic avian influenza (HPAI) H5 viruses have circulated globally causing incidental human infection with a substantial pandemic threat. The present study investigated the molecular evolution and phylodynamics of hemagglutinin (HA) in avian and human-isolated H5Nx viruses globally circulating since 2000. We investigated the dynamics of amino acid substitution in the HA sequences of avian and human H5Nx viruses and performed a phylogenetic analysis. Our study found that the H5Nx lineages dominantly expanded since 2000 and diverged into multiple sublineages with unique genetic mutations. P185S mutation in HA became a molecular characteristic of dominant H5Nx viruses throughout clades 2.3.4.1 to 2.3.4.4 (2.3.4.1–4). The key mutations, ΔE130 and I155T, and potential N-linked glycosylation at residues 128, 144, and 159 in the HA gene of human-isolated viruses possibly contributed to both the individual and population levels of the H5 evolution and the host adaptation. Our analysis detected heterogeneity in amino acid sites under positive selection in the HA gene of clades 2.3.4.1–4. Accumulated mutations in the HA protein may potentially affect not only the genetic and antigenic diversity of HPAI H5Nx viruses but also increase the functional compatibility with NA subtypes. Given the global spread and incessantly occurring HA mutations of H5Nx viruses, our results emphasize the importance of early identification of HA mutations as well as the need for a comprehensive assessment of H5Nx variants in terms of pandemic preparedness.
... In particular, according to the ecological theory of adaptive radiation (Schluter, 2000), 'ecological opportunity', the diversity of available resources not used by other taxa, is central to explaining why adaptive radiations occur. Lineages often diversify when they colonise habitats where there is little competition for constraining resources (Simpson 1953, Schluter 2000. The concentration on biotic interactions, especially competition for food, that has followed from the idea of ecological opportunity, has meant that the role of abiotic environmental variation has been less well explored. ...
The context and cause of adaptive radiations has been widely described and explored but why rapid evolutionary diversification does not occur in related evolutionary lineages has yet to be understood. One possible answer to this is simply that evolutionary diversification is provoked by environmental diversity, and that some lineages do not encounter the necessary environmental diversity. Three-spined stickleback on the Scottish island of North Uist show enormous diversification, which seems to be associated with the diversity of aquatic habitats. Stickleback on the neighbouring island of South Uist have not been reported to show the same level of evolutionary diversity, despite levels of environmental variation that we might expect to be similar to North Uist. In this study, we compared patterns of morphological and environmental diversity on North and South Uist. Ancestral anadromous stickleback from both islands exhibited similar morphology including size and bony ‘armour’. Resident stickleback showed significant variation in armour traits in relation to pH of water. However, North Uist stickleback exhibited greater diversity of morphological traits than South Uist and this was associated with greater diversity in pH of the waters of lochs on North Uist. Highly acidic and highly alkaline freshwater habitats are missing, or uncommon, on South Uist. Thus, pH appears to act as a causal factor driving the evolutionary diversification of stickleback in local adaptation in North and South Uist. This is consistent with diversification being more associated with ecological constraint than ecological opportunity.
... Ecological and evolutionary outcomes on oceanic islands are influenced by island area, isolation and heterogeneity (MacArthur & Wilson, 1967;Schluter, 2000;Simpson, 1953). These island features themselves change through time (see Figure 1a). ...
Current models of island biogeography treat endemic and non-endemic species as if they were functionally equivalent, focussing primarily on species richness. Thus, the functional composition of island biotas in relation to island biogeographic variables remains largely unknown. Using plant trait data (plant height, leaf area, flower length) for 895 native species in the Canary Islands, we related functional trait distinctiveness and climate rarity for endemic and non-endemic species and island ages. Endemics showed a link to climatically rare conditions that is consistent with island geological change through time. However functional trait distinctiveness did not differ between endemics and non-endemics and remained constant with island age. Thus, there is no obvious link between trait distinctiveness and occupancy of rare climates, at least for the traits measured here, suggesting that treating endemic and non-endemic species as functionally equivalent in island biogeography is not fundamentally wrong.
... among others, Brownian Motion (BM) or single-optima OU models, as detailed in chapter 6). likely at the base of the outstanding diversity of many clades (Simpson 1949;Simpson 1953;Schluter 2000;Stroud and Losos 2016). On the other hand, an arboreal lifestyle poses peculiar functional demands, often unparalleled by other ecologies Nations et al. 2019). ...
Ecomorphological convergence occurs when similar morphological traits are independently evolved by species with the same lifestyle. Novel case studies can help to elucidate the underlying mechanisms of this process. This work addresses some convergent slow arboreal mammals, i.e. two lineages of ‘tree sloths’, the silky anteater, ‘Lorisidae’, two clades of extinct lemurs, i.e. palaeopropithecids and Megaladapis, and the koala. Functional morphological convergences are searched in these taxa, studying their humerus and femur as well as those of their closely related ecologically distinct taxa. For the first time, bones are analyzed at four anatomical levels, i.e. external shape, diaphyseal microstructure and anatomy and epiphyseal trabecular architecture, through phylogenetic comparative methods. Many slow arboreal mammals share a low cortical compactness, probably related to their extremely low metabolic rate and biomechanical demands. Slow arboreal xenarthrans, i.e. ‘tree sloths’ and the silky anteater, exhibit a pattern of incomplete convergence for a set of external and internal anatomical features, possibly explained by the relatively distinct ecology of the silky anteater. On a wider mammalian scale, other traits possibly related to slow arboreal ecology converge in some of the studied taxa, although with complex patterns also explained by other evolutionary processes. Only suspensory taxa significantly contribute to convergence. This thesis highlights the stronger convergence reflected by bone internal structure. By providing potential explanations for convergence in slow arboreal mammals, the inherent complexity of this process is here emphasized.
... Two of the key drivers of these evolutionary diversifications have been argued to be priority effects, an advantage of the first species to colonize a pristine habitat lacking potential competitors (Chase 2003, Fukami 2015 and ecological opportunity, an excess of available resources paired with hardly any competition by other species (Schluter 2000, Losos 2010, Stroud and Losos 2016. One particular striking possibility for priority effects and ecological opportunity is presented after novel environments with previously unutilized resources are colonized (Simpson 1953), as potentially the case for the adaptive radiation of Nicaraguan crater lake Midas cichlid fishes (Barluenga and Meyer 2004, Barluenga et al. 2006, Barluenga and Meyer 2010. ...
... Island biotas have played a significant role in the formulation of evolutionary theory (e.g., Darwin and Murray, 1859;Simpson, 1953;Gavrilets and Losos, 2009;Valente et al., 2020). Limited area and longstanding isolation are key features that make islands ideal settings to study evolutionary radiations and diversification (Losos and Ricklefs, 2009;Warren et al., 2015). ...
Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6–4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes – in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression – can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.
... We further complemented our analysis of disparity with a quantification of the rate of eye size evolution using a Bayesian analyses of macroevolutionary mixtures (BAMM) (Rabosky 2014), with prior parameters set using the R package BAMMtools ). This analysis allowed us to assess evidence for an elevated rate of eye size evolution during the initial radiation as would be predicted by classical adaptive radiation theory (Simpson 1953;Gavrilets and Losos 2009) versus evidence of more recent eye size diversification following more recent ecological opportunities generated by community recovery from glacial scouring events (Dornburg et al. 2017;Parker et al. 2022). We ran two independent analyses for 50 million generations, sampling every 1,000 generations. ...
Evolutionary transitions in water column usage have played a major role in shaping ray-finned fish diversity. However, the extent to which vision-associated trait complexity and water column usage is coupled remains unclear. Here we investigate the relationship between depth niche, eye size, and the molecular basis of light detection across the Antarctic notothenioid adaptive radiation. Using a phylogenetic comparative framework, we integrate sequence analyses of opsin tuning sites with data on eye size and depth occupancy from over two decades of NOAA trawl-based surveys. We find a consistent signature of changes in tuning sites suggestive of shifts in their ability to detect lower wavelengths of light. These represent repeated instances of independent tuning site changes across the notothenioid phylogeny that are generally not associated with habitat depth or species eye size. We further reveal an acceleration in the rate of eye size diversification nearly 20 million years after the initial radiation that has manifested in high levels of eye size divergence among closely related taxa. Collectively, our results strongly support a decoupling of the diversification dynamics between opsin tuning sites, eye size and depth, providing a new perspective of the evolution of the visual system in this iconic adaptive radiation.
The modern discussion of living fossils turns mostly on the persistence of archaic, or ancestral, traits in extant organisms. Prime examples mentioned by Darwin already—who also coined the term “living fossil”—include the platypus and the extant lungfishes. However, the identification of archaic traits in extant organisms requires a basis of comparison, i.e., it requires an estimate of the phylogenetic interrelationships of the living fossil in question. Phylogenetic relationships are determined not on the basis of the persistence of archaic traits, but on the basis of shared derived characters. The identification of persistent traits in an organism requires the same organism to also exhibit advanced, or specialized traits that allow its proper classification. The occurrence of such a mixture of primitive (plesiomorphic) or derived (apomorphic) traits in an organism, or species, is called the heterobathmy of characters. Willi Hennig recognized the heterobathmy of characters as quite a universal phenomenon, and made it the basis of his phylogenetic systematics.
Madagascar is one of the world's foremost biodiversity hotspots with more than 90% of its species endemic to the island. Malagasy carnivorans are one of only four extant terrestrial mammalian clades endemic to Madagascar. Although there are only eight extant species, these carnivorans exhibit remarkable phenotypic and ecological diversity that is often hypothesized to have diversified through an adaptive radiation. Here, we investigated the evolution of skull diversity in Malagasy carnivorans and tested if they exhibited characteristics of convergence and an adaptive radiation. We found that their skull disparity exceeds that of any other feliform family, as their skulls vary widely and capture a large amount of the morphological variation found across all feliforms. We also found evidence of shared adaptive zones in cranial shape between euplerid subclades and felids, herpestids, and viverrids. Lastly, contrary to predictions of adaptive radiation, we found that Malagasy carnivorans do not exhibit rapid lineage diversification and only marginally faster rates of mandibular shape evolution, and to a lesser extent cranial shape evolution, compared to other feliforms. These results reveal that exceptional diversification rates are not necessary to generate the striking phenotypic diversity that evolved in carnivorans after their dispersal to and isolation on Madagascar.
Differentiation of biota according to Cavalier-smith, with emphasis on Opisthokonta Cavalier-Smith, 1987, and belonging clades (Holozoa – Holomycota). This review aims to provide insights into Opisthokonta's evolutionary dynamics and the
differentiation of its primary clades, Holozoa and Holomycota. Cavalier-Smith's classification, rooted in molecular evidence, offers a comprehensive framework for understanding the evolutionary history and relationships within Opisthokonta. By examining the morphological and genetic characteristics of organisms within this superphylum, Cavalier-Smith has reshaped our understanding of eukaryotic diversity and evolution. Through a systematic analysis of literature, this review synthesizes key findings to elucidate the unique features and evolutionary trajectories of Opisthokonta, shedding light on its significance in the broader
context of biological classification and evolutionary biology.
Major ecological transitions are thought to fuel evolutionary radiations, but whether they are contingent on the evolution of certain traits is unclear. We show that the rapid ecological transition of anglerfishes into pelagic habitats during a period of major global warming coincided with the origins of sexual parasitism, in which male anglerfishes temporarily attach or permanently fuse to females to mate. A phylogenomic reconstruction of the evolutionary history of anglerfishes provides a strong inference for the convergent evolution of permanently-fusing deep-sea anglerfishes and their degenerate immune genes. Our results support that sexual parasitism was enabled by the degeneration of adaptive immunity and ancestral sexual size dimorphism. The combination of these traits facilitated the transition of pelagic anglerfishes into novel ecologies available in the deep open oceans after evolving from benthic ancestors. These results show how seemingly unrelated physiological and reproductive traits interact synergistically to drive evolutionary radiation in novel environments.
Dental data are one of the most important sources of information on the evolution of ancient hominids. It preserves information about both the early stages of ontogenesis and the postnatal period of life. It is generally accepted that one of the main evolutionary trend within the genus Homo over the past two million years was reduction of teeth size. This trend substantially accelerated in modern Homo sapiens during the Upper Paleolithic and Neolithic. It is assumed that a number of factors could influence the teeth reduction process. However, no detailed understanding of its patterns, limits and chronological and territorial variability has been revealed so far. In this study, we analyze the variability of the upper second molar sizes in Neanderthals, Denisovans, Homo antecessor, Middle Pleistocene Homo from Sierra de Atapuerca (Gran Dolina), Homo erectus, Middle and Late Pleistocene Homo from China other than H. erectus, and compare them with the characteristics of the modern H. sapiens. The main goal of our analysis was to identify local chronological and geographical patterns in the evolution of the size of the second upper molars and assess their compliance with the general epochal trend. The results of the analysis showed that before the appearance of the Upper Paleolithic H. sapiens, two distinct local trends existed on the territory of Eurasia. The first trend, which can be detected in the European pre-sapiens humans, was a decrease in the molar size of the upper second molars. The second one, which got spread in the Middle Pleistocene in Asia, on the contrary, consisted of a sharp increase of the molar size, which formed the morphological specificity of the Denisovan lineage. No stable geographic differentiations of the size of the upper second molars are observed within H. sapiens sample.
Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations vs. pre-existing variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns of phylogenetic discordance and introgression in Penstemon subgenus Dasanthera , a small and diverse adaptive radiation of plants. We found that magenta hummingbird-adapted flowers have apparently evolved twice from ancestral blue-violet bee-pollinated flowers within this radiation. These apparently independent shifts in flower color are accompanied by a variety of inactivating mutations to a key anthocyanin pathway enzyme, suggesting de novo mutations underlie parallel evolution of this trait. Although patterns of introgression and phylogenetic discordance were heterogenous across the genome, a strong effect of gene density suggests that, in general, natural selection opposes introgression and maintains genetic differentiation in gene-rich genomic regions.
Colonization of a novel habitat is often followed by radiation in the wake of ecological opportunity. Alternatively, some habitats should be inherently more constraining than others if the challenges of that environment have few evolutionary solutions. We examined the push-and-pull of these factors on evolution following habitat transitions, using anglerfishes (Lophiiformes) as a model. Deep-sea fishes are notoriously difficult to study, and poor sampling has limited progress thus far. Here we present a new phylogeny of anglerfishes with unprecedented taxonomic sampling (1,092 loci and 40% of species), combined with three-dimensional phenotypic data from museum specimens obtained with micro-CT scanning. We use these datasets to examine the tempo and mode of phenotypic and lineage diversification using phylogenetic comparative methods, comparing lineages in shallow and deep benthic versus bathypelagic habitats. Our results show that anglerfishes represent a surprising case where the bathypelagic lineage has greater taxonomic and phenotypic diversity than coastal benthic relatives. This defies expectations based on ecological principles since the bathypelagic zone is the most homogeneous habitat on Earth. Deep-sea anglerfishes experienced rapid lineage diversification concomitant with colonization of the bathypelagic zone from a continental slope ancestor. They display the highest body, skull and jaw shape disparity across lophiiforms. In contrast, reef-associated taxa show strong constraints on shape and low evolutionary rates, contradicting patterns suggested by other shallow marine fishes. We found that Lophiiformes as a whole evolved under an early burst model with subclades occupying distinct body shapes. We further discuss to what extent the bathypelagic clade is a secondary adaptive radiation, or if its diversity can be explained by non-adaptive processes.
The Canidae are an ecologically important group of dog-like carnivores that arose in North America and spread across the planet around 10 million years ago. The current distribution patterns of species, coupled with their phylogenetic structure, suggest that Canidae diversification may have occurred at varying rates across different biogeographic areas. However, such extant-only analyses undervalued the rich fossil history of the group because of a limitation in methods development. Current State-dependent Speciation and Extinction (SSE) models are (i) often parameter-rich which hinders reliable application to relatively small clades such as the Caninae (the only extant subclade of the Canidae consisting of 36 extant species); and (ii) often assume as possible states only the states that extant species present. Here we extend the SSE method SecSSE to apply to phylogenies with extinct species as well (111 Caninae species) and compare the results to those of analyses with the extant-species-only phylogeny. The results on the extant-species tree suggest that distinct diversification patterns are related to geographic areas, but the results on the complete tree do not support this conclusion. Furthermore, our extant-species analysis yielded an unrealistically low estimate of the extinction rate. These contrasting findings suggest that information from extinct species is different from information from extant species. A possible explanation for our results is that extinct species may have characteristics (causing their extinction), which may be different from the characteristics of extant species that caused them to be extant. Hence, we conclude that differences in biogeographic areas probably did not contribute much to the variation in diversification rates in Caninae.
A comprehensive study was conducted in the Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, known for its remarkable microbiological diversity and unique physicochemical properties. The ″Archaean Domes ″ (DA) in the CCB are hypersaline, non-lithifying microbial mats. This study focused on analyzing the small domes and circular structures formed in DA through metagenome assembly genomes (MAGs) with the aim of finding new microorganisms and providing information on the tree of life in a place as diverse as the CCB. In total, 329 MAGs were identified, including 52 archaea and 277 bacteria. Remarkably, 30 Archaea and 154 Bacteria could not be classified at the genus level, highlighting the remarkable diversity of CCB. The CCBs showed significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Euryarchaeota, Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, Chloroflexi, Planctomycetes, Candidatus Parvarchaeota, Verrucomicrobia, Balneolaeota, Nitrospirae, and Tenericutes. Subsequently, the MAGs were classified into a phylogenetic tree. In Archaea, monophyletic groups MAGs belonged to the phyla Archaeoglobi, Candidatus Aenigmarchaeota, Candidatus Nanoarchaeota, Candidatus Lokiarchaeota, and Halobacteriota. Among the Bacteria, monophyletic groups were identified as well, including Spirochaetes, Proteobacteria, Planctomycetota, Actinobacteria, Verrucomicrobiota, Bacteroidetes, Bipolaricaulota, Desulfobacterota, and Cyanobacteria. These monophyletic clusters may indicate radiation events that are likely influenced by geographical isolation as well as extreme environmental conditions reported in AD pond like phosphorus deficiency (122:42:1 C:N:P), fluctuating pH and a salinity of 5.28%
Lemurs are a well-known example of adaptive radiation. Since colonizing Madagascar, more than 100 extant lemur species have evolved to fill the variety of ecological niches on the island. However, recent work suggests that lemurs do not exhibit one of the hallmarks of adaptive radiations: explosive speciation rates that decline over time. We test this idea using a phylogenomic dataset with broad taxonomic sampling of lemurs and their sister group, the lorisiforms of Asia and continental Africa. We find higher rates of speciation in Madagascar's lemurs compared to lorisiforms and we confirm that lemurs did not experience an "early burst" of speciation after colonizing Madagascar. Instead, we identify three independent bursts of speciation approximately 15 million years ago that underly much of today's lemur diversity. We demonstrate that the lemur clades with exceptionally high diversification rates have higher rates of introgression. This suggests that hybridization in these primates is not an evolutionary dead-end, but a driving force for diversification. Considering the conservation crisis affecting strepsirrhine primates, with approximately 95% of species being threatened with extinction, this phylogenomic study offers a new perspective for explaining Madagascar's exceptional primate diversity and reveals patterns of speciation, extinction, and gene flow that will help inform future conservation decisions.
Although the clade Crocodylomorpha is represented by few extant species (Crocodylia), it has a rich fossil record. Hundreds of species, adapted to terrestrial, semi-aquatic and marine environments, have existed over more than 200 million years. Numerous studies have attempted to characterize the factors driving the diversification and extinction events of Crocodylomorpha, resulting in ambiguous and even contradictory conclusions, which points to the need for phylogenetically and temporally smaller-scaled studies. Here, we focus on differential survival at the Cretaceous-Palaeo-gene (K-Pg) crisis of Notosuchia, a diverse clade of mostly terrestrial Crocodylomorpha that achieved great diversity during the Cretaceous. More precisely, we tested the effect of body size and palaeotemperatures on notosuchian survival probability during the K-Pg crisis as well as the effect of diet on the evolution of their body size. We find that Notosuchia showed an evolutionary trend towards larger body sizes through time, associated with a shift from an omnivorous to a carnivorous diet. This may explain why sebecids were the only notosuchians to survive the K-Pg crisis. We also corroborate the conclusions of previous studies that detected a Lagerst€ atten effect occurring in the Adamantina Formation (Upper Cretaceous, Brazil, Bauru Group). This work confirms the value of more finely-scaled macroevolutionary studies for understanding the history of a rich and complex group such as Crocodylomorpha.
The general notion of species is one of the most fundamental in biology. But an idea of species is also one of the most persistent unresolved obsessions of biologists, philosophers and theoreticians. This new book investigates the multifaceted problem species as a "conceptual envelope" of that notion. Contemporary conceptualists and evolutionary epistemology allow for a fresh look by analyzing the framework of history viewed as changes ordered by changing philosophical-scientific contexts. In this analysis, the species problem is characterized in a pluralistic non-trivial manner, in contrast to a more monistic "accepted view."
Key Features
- Provides new insights into the persistent species "problem."
- Focuses on conceptual history and identifies pivotal landmarks in the history of the concept of species.
- Argues for a scientific consistency of species pluralism.
- Discusses the "evolving species-hood" in the context of new essentialism.
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