Is there room for punctuated equilibrium in macroevolution?

A lineage perspective on hominin taxonomy and evolution

An uncritical reliance on the phylogenetic species concept has led paleoanthropologists to become increasingly typological in their delimitation of new species in the hominin fossil record. As a practical matter, this approach identifies species as diagnosably distinct groups of fossils that share a unique suite of morphological characters but, ontologically, a species is a metapopulation lineage segment that extends from initial divergence to eventual extinction or subsequent speciation. Working from first principles of species concept theory, it is clear that a reliance on morphological diagnosabilty will systematically overestimate species diversity in the fossil record; because morphology can evolve within a lineage segment, it follows that early and late populations of the same species can be diagnosably distinct from each other. We suggest that a combination of morphology and chronology provides a more robust test of the single-species null hypothesis than morphology alone.

Exploring the patterns of evolution: Core thoughts and focus on the saltational model

The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.

Punctuated equilibrium at 50: Anything there for evolutionary anthropology? Yes; definitely

The theory of punctuated equilibrium (PE) was developed a little over 50 years ago to explain long-term, large-scale appearance and disappearance of species in the fossil record. A theory designed specifically for that purpose cannot be expected, out of the box, to be directly applicable to biocultural evolution, but in revised form, PE offers a promising approach to incorporating not only a wealth of recent empirical research on genetic, linguistic, and technological evolution but also large databases that document human biological and cultural diversity across time and space. Here we isolate the fundamental components of PE and propose which pieces, when reassembled or renamed, can be highly useful in evolutionary anthropology, especially as humanity faces abrupt ecological challenges on an increasingly larger scale.

Fitting and evaluating univariate and multivariate models of within-lineage evolution

The nature of phenotypic evolution within lineages is central to many unresolved questions in paleontology and evolutionary biology. Analyses of evolutionary time-series of ancestor-descendant populations in the fossil record are likely to make important contributions to many of these debates. However, the limited number of models that have been applied to these types of data may restrict our ability to interpret phenotypic evolution in the fossil record. Using uni- and multivariate models of trait evolution that make different assumptions regarding the dynamics of the adaptive landscape, I evaluate contrasting hypotheses to explain evolution of size in the radiolarian Eucyrtidium calvertense and armor in the stickleback Gaserosteus doryssus. Body size evolution in E. calvertense is best explained by a model where the lineage evolves as a consequence of a shift in the adaptive landscape that coincides with the initiation of neosympatry with its sister lineage. Multivariate evolution of armor traits in a stickleback lineage (Gasterosteus doryssus) show evidence of adaptation towards independent optima on the adaptive landscape at the same time as traits change in a correlated fashion. The fitted models are available in a the R package evoTS, which builds on the commonly used paleoTS framework.

Accelerated body size evolution in upland environments is correlated with recent speciation in South American freshwater fishes

Speciation rates vary greatly among taxa and regions and are shaped by both biotic and abiotic factors. However, the relative importance and interactions of these factors are not well understood. Here we investigate the potential drivers of speciation rates in South American freshwater fishes, the most diverse continental vertebrate fauna, by examining the roles of multiple biotic and abiotic factors. We integrate a dataset on species geographic distribution, phylogenetic, morphological, climatic, and habitat data. We find that Late Neogene-Quaternary speciation events are strongly associated with body-size evolution, particularly in lineages with small body sizes that inhabit higher elevations near the continental periphery. Conversely, the effects of temperature, area, and diversity-dependence, often thought to facilitate speciation, are negligible. By evaluating multiple factors simultaneously, we demonstrate that habitat characteristics associated with elevation, as well as body size evolution, correlate with rapid speciation in South American freshwater fishes. Our study emphasizes the importance of integrative approaches that consider the interplay of biotic and abiotic factors in generating macroecological patterns of species diversity.

Kobayashi T. Population dynamics models for various forms of adaptation

Adaptability to changing environments is one of the universal characteristics of living organisms. Because individual modes of adaptation are diverse, a unified understanding of these diverse modes is essential to comprehend adaptation. Adaptations can be categorized from at least two perspectives with respect to information. One is the passivity and activity of adaptation and the other is the type of information transmission. In Darwinian natural selection, organisms are selected among randomly generated traits under which individual organisms are passive in the sense that they do not process any environmental information. On the other hand, organisms can also adapt by sensing their environment and changing their traits. This is an active adaptation in that it makes use of environmental information. In terms of information transfer, adaptation through phenotypic heterogeneity, such as bacterial bet-hedging, is intragenerational in which traits are not passed on to the next generation. In contrast, adaptation through genetic diversity is intergenerational. The theory of population dynamics enables us to unify these various modes of adaptations and their properties can be analyzed qualitatively and quantitatively using techniques from quantitative genetics and information thermodynamics. In addition, such methods can be applied to situations where organisms can learn from past experiences and pass them on from generation to generation. In this work, we introduce the unified theory of biological adaptation based on population dynamics and show its potential applications to evaluate the fitness value of information and to analyze experimental lineage tree data. Finally, we discuss future perspectives for its development. This review article is an extended version of the Japanese article in SEIBUTSU BUTSURI Vol. 57, p. 287-290 (2017).

How we study cryptic species and their biological implications: A case study from marine shelled gastropods

Methodological and biological considerations are intertwined when studying cryptic species. A potentially large component of modern biodiversity, the frequency of cryptic species among taxonomic groups is not well documented. The term "cryptic species" is imprecisely used in scientific literature, causing ambiguity when interpreting their evolutionary and ecological significance. This study reviews how cryptic species have been defined, discussing implications for taxonomy and biology, and explores these implications with a case study based on recently published literature on extant shelled marine gastropods. Reviewed gastropods were recorded by species. Records of cryptic gastropods were presented by authors with variable levels of confidence but were difficult to disentangle from inherent biases in the study effort. These complexities notwithstanding, most gastropod species discussed were not cryptic. To the degree that this review's sample represents extinct taxa, the results suggest that a high proportion of shelled marine gastropod species are identifiable for study in the fossil record. Much additional work is needed to provide a more adequate understanding of the relative frequency of cryptic species in shelled marine gastropods, which should start with more explicit definitions and targeted case studies.

Conceptual and empirical bridges between micro- and macroevolution

Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.

Detecting punctuated evolution in SARS-CoV-2 over the first year of the pandemic

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) evolved slowly over the first year of the Coronavirus Disease 19 (COVID-19) pandemic with differential mutation rates across lineages. Here, we explore how this variation arose. Whether evolutionary change accumulated gradually within lineages or during viral lineage branching is unclear. Using phylogenetic regression models, we show that ~13% of SARS-CoV-2 genomic divergence up to May 2020 is attributable to lineage branching events (punctuated evolution). The net number of branching events along lineages predicts ~5% of the deviation from the strict molecular clock. We did not detect punctuated evolution in SARS-CoV-1, possibly due to the small sample size, and in sarbecovirus broadly, likely due to a different evolutionary process altogether. Punctuation in SARS-CoV-2 is probably neutral because most mutations were not positively selected and because the strength of the punctuational effect remained constant over time, at least until May 2020, and across continents. However, the small punctuational contribution to SARS-CoV-2 diversity is consistent with the founder effect arising from narrow transmission bottlenecks. Therefore, punctuation in SARS-CoV-2 may represent the macroevolutionary consequence (rate variation) of a microevolutionary process (transmission bottleneck).

Microstructural and crystallographic evolution of palaeognath (Aves) eggshells

The avian palaeognath phylogeny has been recently revised significantly due to the advancement of genome-wide comparative analyses and provides the opportunity to trace the evolution of the microstructure and crystallography of modern dinosaur eggshells. Here, eggshells of all major clades of Palaeognathae (including extinct taxa) and selected eggshells of Neognathae and non-avian dinosaurs are analysed with electron backscatter diffraction. Our results show the detailed microstructures and crystallographies of (previously) loosely categorized ostrich-, rhea-, and tinamou-style morphotypes of palaeognath eggshells. All rhea-style eggshell appears homologous, while respective ostrich-style and tinamou-style morphotypes are best interpreted as homoplastic morphologies (independently acquired). Ancestral state reconstruction and parsimony analysis additionally show that rhea-style eggshell represents the ancestral state of palaeognath eggshells both in microstructure and crystallography. The ornithological and palaeontological implications of the current study are not only helpful for the understanding of evolution of modern and extinct dinosaur eggshells, but also aid other disciplines where palaeognath eggshells provide useful archive for comparative contrasts (e.g. palaeoenvironmental reconstructions, geochronology, and zooarchaeology).

Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary

Background

An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates.

Results

We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML.

Conclusions

We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02015-8.

Copper technology in the Arabah during the Iron Age and the role of the indigenous population in the industry

Following the Egyptian withdrawal in the mid-12^th century BCE from their involvement in the Arabah copper production, and after an additional period of organization, the degree of copper efficiency and production at Timna and Faynan increased in the Early Iron Age (11^th–9^th centuries), rendering the region the largest and most advanced smelting centre in the Levant. The existing paradigm offered as an explanation for this technical and commercial success is based on extraneous influence, namely, the campaign of Pharaoh Sheshonq I near the end of the 10^th century BCE that spurred a renewed Egyptian involvement in the Arabah copper industry. An alternative paradigm is suggested here, viewing the advances in Arabah copper technology and production as a linear development and the outcome of continuous and gradual indigenous improvements on the part of local craftsmen, with no external intervention. Behind these outstanding technical achievements stood excellent managerial personnel, supported by an innovative technical team. They employed two techniques for copper-production optimization that can be defined based on concepts taken from the world of modern industrial engineering: (i) "trial and error", in which the effect of each production variable was tested individually and separately, and (ii) "scaling-up", in which the size of some production elements (i.e., tuyère) was increased by using existing techniques which required minimum developmental costs and experimental risks.

Linking population-level and microevolutionary processes to understand speciation dynamics at the macroevolutionary scale

Although speciation dynamics have been described for several taxonomic groups in distinct geographic regions, most macroevolutionary studies still lack a detailed mechanistic view on how or why speciation rates change. To help partially fill this gap, we suggest that the interaction between the time taken by a species to geographically expand and the time populations take to evolve reproductive isolation should be considered when we are trying to understand macroevolutionary patterns. We introduce a simple conceptual index to guide our discussion on how demographic and microevolutionary processes might produce speciation dynamics at macroevolutionary scales. Our framework is developed under different scenarios: when speciation is mediated by geographical or resource-partitioning opportunities, and when diversity is limited or not. We also discuss how organismal intrinsic properties and different overall geographical settings can influence the tempo and mode of speciation. We argue that specific conditions observed at the microscale might produce a pulse in speciation rates even without a pulse in either climate or physical barriers. We also propose a hypothesis to reconcile the apparent inconsistency between speciation measured at the microscale and macroscale, and emphasize that diversification rates are better seen as an emergent property. We hope to bring the reader's attention to interesting mechanisms to be further studied, to motivate the development of new theoretical models that connect microevolution and macroevolution, and to inspire new empirical and methodological approaches to more adequately investigate speciation dynamics either using neontological or paleontological data.

Neo-darwinism still haunts evolutionary theory: A modern perspective on Charlesworth, Lande, and Slatkin (1982)

The Modern Synthesis (or "Neo-Darwinism"), which arose out of the reconciliation of Darwin's theory of natural selection and Mendel's research on genetics, remains the foundation of evolutionary theory. However, since its inception, it has been a lightning rod for criticism, which has ranged from minor quibbles to complete dismissal. Among the most famous of the critics was Stephen Jay Gould, who, in 1980, proclaimed that the Modern Synthesis was "effectively dead." Gould and others claimed that the action of natural selection on random mutations was insufficient on its own to explain patterns of macroevolutionary diversity and divergence, and that new processes were required to explain findings from the fossil record. In 1982, Charlesworth, Lande, and Slatkin published a response to this critique in Evolution, in which they argued that Neo-Darwinism was indeed sufficient to explain macroevolutionary patterns. In this Perspective for the 75th Anniversary of the Society for the Study of Evolution, we review Charlesworth et al. in its historical context and provide modern support for their arguments. We emphasize the importance of microevolutionary processes in the study of macroevolutionary patterns. Ultimately, we conclude that punctuated equilibrium did not represent a major revolution in evolutionary biology - although debate on this point stimulated significant research and furthered the field - and that Neo-Darwinism is alive and well.

Model-Based Inference of Punctuated Molecular Evolution

In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a rate that can vary (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary timescale. Here, we develop a model, which we call the Relaxed Clock with Spikes model, combining basal, clock-like molecular substitutions with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) cooccurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular substitutions and from variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.

Heterogeneous relationships between rates of speciation and body size evolution across vertebrate clades

Several theories predict that rates of phenotypic evolution should be related to the rate at which new lineages arise. However, drawing general conclusions regarding the coupling between these fundamental evolutionary rates has been difficult due to the inconsistent nature of previous results combined with uncertainty over the most appropriate methodology with which to investigate such relationships. Here we propose and compare the performance of several different approaches for testing associations between lineage-specific rates of speciation and phenotypic evolution using phylogenetic data. We then use the best-performing method to test relationships between rates of speciation and body size evolution in five major vertebrate clades (amphibians, birds, mammals, ray-finned fish and squamate reptiles) at two phylogenetic scales. Our results provide support for the long-standing view that rates of speciation and morphological evolution are generally positively related at broad macroevolutionary scales, but they also reveal a substantial degree of heterogeneity in the strength and direction of these associations at finer scales across the vertebrate tree of life.

Revisiting a Landmark Study System: No Evidence for a Punctuated Mode of Evolution in Metrarabdotos

Is speciation generally a "special time" in morphological evolution, or are lineage-splitting events just "more of the same" where the end product happens to be two separate lineages? Data on evolutionary dynamics during anagenetic and cladogenetic events among closely related lineages within a clade are rare, but the fossil record of the bryozoan genus Metrarabdotos is considered a textbook example of a clade where speciation causes rapid evolutionary change against a backdrop of morphological stasis within lineages. Here, we point to some methodological and measurement theoretical issues in the original work on Metrarabdotos. We then reanalyze a subset of the original data that can be meaningfully investigated using quantitative statistical approaches similar to those used in the original studies. We consistently fail to find variation in the evolutionary process during within-lineage evolution compared with cladogenetic events: the rates of evolution, the strength of selection, and the directions traveled in multivariate morphospace are not different when comparing evolution within lineages and at speciation events in Metrarabdotos, and genetic drift cannot be excluded as a sufficient explanation for the morphological differentiation within lineages and during speciation. Although widely considered the best example of a punctuated mode of evolution, morphological divergence and speciation are not linked in Metrarabdotos.

The paradox behind the pattern of rapid adaptive radiation: how can the speciation process sustain itself through an early burst?

Rapid adaptive radiation poses a distinct question apart from speciation and adaptation: what happens after one speciation event? That is, how are some lineages able to continue speciating through a rapid burst? This question connects global macroevolutionary patterns to microevolutionary processes. Here we review major features of rapid radiations in nature and their mismatch with theoretical models and what is currently known about speciation mechanisms. Rapid radiations occur on three major diversification axes - species richness, phenotypic disparity, and ecological diversity - with exceptional outliers on each axis. The paradox is that the hallmark early stage of adaptive radiation, a rapid burst of speciation and niche diversification, is contradicted by most existing speciation models which instead predict continuously decelerating speciation rates and niche subdivision through time. Furthermore, while speciation mechanisms such as magic traits, phenotype matching, and physical linkage of co-adapted alleles promote speciation, it is often not discussed how these mechanisms could promote multiple speciation events in rapid succession. Additional mechanisms beyond ecological opportunity are needed to understand how rapid radiations occur. We review the evidence for five emerging theories: 1) the 'transporter' hypothesis: introgression and the ancient origins of adaptive alleles, 2) the 'signal complexity' hypothesis: the dimensionality of sexual traits, 3) the connectivity of fitness landscapes, 4) 'diversity begets diversity', and 5) flexible stem/'plasticity first'. We propose new questions and predictions to guide future work on the mechanisms underlying the rare origins of rapid radiation.

Developmental bias in the fossil record

The role of developmental bias and plasticity in evolution is a central research interest in evolutionary biology. Studies of these concepts and related processes are usually conducted on extant systems and have seen limited investigation in the fossil record. Here, I identify plasticity-led evolution (PLE) as a form of developmental bias accessible through scrutiny of paleontological material. I summarize the process of PLE and describe it in terms of the environmentally mediated accumulation and release of cryptic genetic variation. Given this structure, I then predict its manifestation in the fossil record, discuss its similarity to quantum evolution and punctuated equilibrium, and argue that these describe macroevolutionary patterns concordant with PLE. Finally, I suggest methods and directions towards providing evidence of PLE in the fossil record and conclude that such endeavors are likely to be highly rewarding.

Darwin review: angiosperm phylogeny and evolutionary radiations

Darwin's dual interests in evolution and plants formed the basis of evolutionary botany, a field that developed following his publications on both topics. Here, we review his many contributions to plant biology—from the evolutionary origins of angiosperms to plant reproduction, carnivory, and movement—and note that he expected one day there would be a ‘true’ genealogical tree for plants. This view fuelled the field of plant phylogenetics. With perhaps nearly 400 000 species, the angiosperms have diversified rapidly since their origin in the Early Cretaceous, often through what appear to be rapid radiations. We describe these evolutionary patterns, evaluate possible drivers of radiations, consider how new approaches to studies of diversification can contribute to our understanding of angiosperm diversity, and suggest new directions for further insight into plant evolution.

Bursts of amino acid replacements in protein evolution

Evolution can occur both gradually and through alternating episodes of stasis and rapid changes. However, the prevalence and magnitude of fluctuations of the rate of evolution remain obscure. Detecting a rapid burst of changes requires a detailed record of past evolution, so that events that occurred within a short time interval can be identified. Here, we use the phylogenies of the Baikal Lake amphipods and of Catarrhini, which contain very short internal edges which make this task feasible. We detect six salient bursts of evolution of individual proteins during such short time periods, each involving between six and 38 amino acid substitutions. These bursts were extremely unlikely to have occurred neutrally, and were apparently caused by positive selection. On average, in the course of a time interval required for one synonymous substitution per site, a protein undergoes a strong burst of rapid evolution with probability at least approximately 0.01.

Speciation Rate Is Independent of the Rate of Evolution of Morphological Size, Shape, and Absolute Morphological Specialization in a Large Clade of Birds

Whether ecological differences between species evolve in parallel with lineage diversification is a fundamental issue in evolutionary biology. These processes might be connected if conditions that favor the proliferation of species, such as release from competitors, facilitate the evolution of novel ecological relationships. Despite this, phylogenetic studies do not consistently identify such a connection. Conversely, if higher diversity caused species to become increasingly specialized ecologically, then lineage diversification might become dissociated from ecological diversification. In this analysis, we ask whether the rate of lineage diversification in a large clade of birds is correlated with morphological specialization and with rates of morphological evolution. We find that morphological variation is related to species richness within clades but that rates of morphological evolution are decoupled from the rate of lineage diversification. Additionally, morphological specialization within lineages is independent of the rate at which lineages diversify, with the results apparently robust against false negative inference. This dissociation is likely a consequence of the major ecomorphological differences between avian clades arising early in their evolutionary history, with comparatively little variation added subsequently, while avian diversification has been driven predominantly by geographic isolation and sexual selection. Accordingly, biodiversity appears to be limited by the extent to which taxa can subdivide exploited regions of ecological space and not just overall ecological opportunity.

Key questions and challenges in angiosperm macroevolution

Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid diversification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm diversification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day biodiversity. We present six key questions that explore the origin and diversification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include diversification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for sampling bias and heterogeneity of macroevolutionary processes through time and among lineages; (2) the need for large and standardized synthetic databases of morphological variation; and (3) continuous effort on sampling the fossil record, but with a revolution in current paleobotanical practice.

Floral evolution by simplification in Monanthotaxis (Annonaceae) and hypotheses for pollination system shifts

Simplification by reduction has occurred many times independently in the floral evolution of angiosperms. These reductions have often been attributed to changes in reproductive biology. In the angiosperm plant family Annonaceae, most species have flowers with six petals, and many stamens and carpels. In the genus Monanthotaxis several deviations from this pattern have been observed, including flowers that contain three petals and three stamens only. New DNA sequences were generated for 42 specimens of Monanthotaxis. Five chloroplast markers and two nuclear markers for 72 out of 94 species of Monanthotaxis were used to reconstruct a phylogeny of the genus, which revealed several well-supported, morphologically distinct clades. The evolution of four quantitative and two qualitative floral characters was mapped onto this phylogeny, demonstrating a reduction in flower size and number of flower parts in Monanthotaxis. A large variation in stamen forms and numbers, strong correlations between petal size, stamen and carpel number, combined with a non-gradual mode of evolution and the sympatric co-occurrence of Monanthotaxis species from different clades suggest that the high diversity in the African rainforest of this genus is caused by switches in pollination systems.

Conserving Phylogenetic Diversity Can Be a Poor Strategy for Conserving Functional Diversity

For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policy makers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and features (functional diversity [FD]), which may be valuable for a number of reasons. The claim that PD-maximized ("maxPD") sets of taxa will also have high FD is often taken at face value and in cases where researchers have actually tested it, they have done so by measuring the phylogenetic signal in ecologically important functional traits. The rationale is that if traits closely mirror phylogeny, then saving the maxPD set of taxa will tend to maximize FD and if traits do not have phylogenetic structure, then saving the maxPD set of taxa will be no better at capturing FD than criteria that ignore PD. Here, we suggest that measuring the phylogenetic signal in traits is uninformative for evaluating the effectiveness of using PD in conservation. We evolve traits under several different models and, for the first time, directly compare the FD of a set of taxa that maximize PD to the FD of a random set of the same size. Under many common models of trait evolution and tree shapes, conserving the maxPD set of taxa will conserve more FD than conserving a random set of the same size. However, this result cannot be generalized to other classes of models. We find that under biologically plausible scenarios, using PD to select species can actually lead to less FD compared with a random set. Critically, this can occur even when there is phylogenetic signal in the traits. Predicting exactly when we expect using PD to be a good strategy for conserving FD is challenging, as it depends on complex interactions between tree shape and the assumptions of the evolutionary model. Nonetheless, if our goal is to maintain trait diversity, the fact that conserving taxa based on PD will not reliably conserve at least as much FD as choosing randomly raises serious concerns about the general utility of PD in conservation.

Coordinated Dispersal and Pre-Isthmian Assembly of the Central American Ichthyofauna

We document patterns of coordinated dispersal over evolutionary time frames in heroine cichlids and poeciliine live-bearers, the two most species-rich clades of freshwater fishes in the Caribbean basin. Observed dispersal rate (DO) values were estimated from time-calibrated molecular phylogenies in Lagrange+, a modified version of the ML-based parametric biogeographic program Lagrange. DO is measured in units of "wallaces" (wa) as the number of biogeographic range-expansion events per million years. DO estimates were generated on a dynamic paleogeographic landscape of five areas over three time intervals from Upper Cretaceous to Recent. Expected dispersal rate (DE) values were generated from alternative paleogeographic models, with dispersal rates proportional to target area and source-river discharge volume, and inversely proportional to paleogeographic distance. Correlations between DO and DE were used to assess the relative contributions of these three biogeographic parameters. DO estimates imply a persistent dispersal corridor across the Eastern (Antillean) margin of the Caribbean plate, under the influence of prevailing and perennial riverine discharge vectors such as the Proto-Orinoco-Amazon river. Ancestral area estimation places the earliest colonizations of the Greater Antilles and Central America during the Paleocene-Eocene (ca. 58-45 Ma), potentially during the existence of an incomplete Paleogene Arc (∼59 Ma) or Lesser Antilles Arc (∼45 Ma), but predating the GAARlandia land bridge (∼34-33 Ma). Paleogeographic distance is the single best predictor of DO. The Western (Central American) plate margin did not serve as a dispersal corridor until the Late Neogene (12-0 Ma), and contributed relatively little to the formation of modern distributions.

Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms

Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity.

Diversity and Coevolutionary Dynamics in High-Dimensional Phenotype Spaces

We study macroevolutionary dynamics by extending microevolutionary competition models to long timescales. It has been shown that for a general class of competition models, gradual evolutionary change in continuous phenotypes (evolutionary dynamics) can be nonstationary and even chaotic when the dimension of the phenotype space in which the evolutionary dynamics unfold is high. It has also been shown that evolutionary diversification can occur along nonequilibrium trajectories in phenotype space. We combine these lines of thinking by studying long-term coevolutionary dynamics of emerging lineages in multidimensional phenotype spaces. We use a statistical approach to investigate the evolutionary dynamics of many different systems. We find (1) that, for a given dimension of phenotype space, the coevolutionary dynamics tend to be fast and nonstationary for an intermediate number of coexisting lineages but tend to stabilize as the evolving communities reach a saturation level of diversity and (2) that the amount of diversity at the saturation level increases rapidly (exponentially) with the dimension of phenotype space. These results have implications for theoretical perspectives on major macroevolutionary patterns such as adaptive radiation, long-term temporal patterns of phenotypic changes, and the evolution of diversity.

Studying the evolutionary significance of thermal adaptation in ectotherms: The diversification of amphibians' energetics

A fundamental problem in evolutionary biology is the understanding of the factors that promote or constrain adaptive evolution, and assessing the role of natural selection in this process. Here, comparative phylogenetics, that is, using phylogenetic information and traits to infer evolutionary processes has been a major paradigm . In this study, we discuss Ornstein-Uhlenbeck models (OU) in the context of thermal adaptation in ectotherms. We specifically applied this approach to study amphibians's evolution and energy metabolism. It has been hypothesized that amphibians exploit adaptive zones characterized by low energy expenditure, which generate specific predictions in terms of the patterns of diversification in standard metabolic rate (SMR). We complied whole-animal metabolic rates for 122 species of amphibians, and adjusted several models of diversification. According to the adaptive zone hypothesis, we expected: (1) to find "accelerated evolution" in SMR (i.e., diversification above Brownian Motion expectations, BM), (2) that a model assuming evolutionary optima (i.e., an OU model) fits better than a white-noise model and (3) that a model assuming multiple optima (according to the three amphibians's orders) fits better than a model assuming a single optimum. As predicted, we found that the diversification of SMR occurred most of the time, above BM expectations. Also, we found that a model assuming an optimum explained the data in a better way than a white-noise model. However, we did not find evidence that an OU model with multiple optima fits the data better, suggesting a single optimum in SMR for Anura, Caudata and Gymnophiona. These results show how comparative phylogenetics could be applied for testing adaptive hypotheses regarding history and physiological performance in ectotherms.

Integrating Paleontological and Phylogenetic Approaches to Macroevolution

With proliferation of molecular phylogenies and advances in statistical modeling, phylogeneticists can now address macroevolutionary questions that had traditionally been the purview of paleontology. Interest has focused on three areas at the intersection of phylogenetic and paleontological research: time-scaling phylogenies, understanding trait evolution, and modeling species diversification. Fossil calibrations have long been crucial for scaling phylogenies to absolute time, but recent advances allow more equal integration of extinct taxa. Simulation and empirical studies have shown that fossil data can markedly improve inferences about trait evolution, especially for models with heterogeneous temporal dynamics and in clades for which the living forms are unrepresentative remnants of their larger clade. Recent years have also seen a productive cross-disciplinary conversation about the nature and uncertainties of inferring diversification dynamics. Challenges remain, but the present time represents a flowering of interest in integrating these two views on the history of life.

A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts

When novel sources of ecological opportunity are available, physiological innovations can trigger adaptive radiations. This could be the case of yeasts (Saccharomycotina), in which an evolutionary novelty is represented by the capacity to exploit simple sugars from fruits (fermentation). During adaptive radiations, diversification and morphological evolution are predicted to slow‐down after early bursts of diversification. Here, we performed the first comparative phylogenetic analysis in yeasts, testing the “early burst” prediction on species diversification and also on traits of putative ecological relevance (cell‐size and fermentation versatility). We found that speciation rates are constant during the time‐range we considered (ca., 150 millions of years). Phylogenetic signal of both traits was significant (but lower for cell‐size), suggesting that lineages resemble each other in trait‐values. Disparity analysis suggested accelerated evolution (diversification in trait values above Brownian Motion expectations) in cell‐size. We also found a significant phylogenetic regression between cell‐size and fermentation versatility (R² = 0.10), which suggests correlated evolution between both traits. Overall, our results do not support the early burst prediction both in species and traits, but suggest a number of interesting evolutionary patterns, that warrant further exploration. For instance, we show that the Whole Genomic Duplication that affected a whole clade of yeasts, does not seems to have a statistically detectable phenotypic effect at our level of analysis. In this regard, further studies of fermentation under common‐garden conditions combined with comparative analyses are warranted.

The extended Price equation quantifies species selection on mammalian body size across the Palaeocene/Eocene Thermal Maximum

Species selection, covariation of species' traits with their net diversification rates, is an important component of macroevolution. Most studies have relied on indirect evidence for its operation and have not quantified its strength relative to other macroevolutionary forces. We use an extension of the Price equation to quantify the mechanisms of body size macroevolution in mammals from the latest Palaeocene and earliest Eocene of the Bighorn and Clarks Fork Basins of Wyoming. Dwarfing of mammalian taxa across the Palaeocene/Eocene Thermal Maximum (PETM), an intense, brief warming event that occurred at approximately 56 Ma, has been suggested to reflect anagenetic change and the immigration of small bodied-mammals, but might also be attributable to species selection. Using previously reconstructed ancestor-descendant relationships, we partitioned change in mean mammalian body size into three distinct mechanisms: species selection operating on resident mammals, anagenetic change within resident mammalian lineages and change due to immigrants. The remarkable decrease in mean body size across the warming event occurred through anagenetic change and immigration. Species selection also was strong across the PETM but, intriguingly, favoured larger-bodied species, implying some unknown mechanism(s) by which warming events affect macroevolution.

Species selection and random drift in macroevolution

Species selection resulting from trait-dependent speciation and extinction is increasingly recognized as an important mechanism of phenotypic macroevolution. However, the recent bloom in statistical methods quantifying this process faces a scarcity of dynamical theory for their interpretation, notably regarding the relative contributions of deterministic versus stochastic evolutionary forces. I use simple diffusion approximations of birth-death processes to investigate how the expected and random components of macroevolutionary change depend on phenotype-dependent speciation and extinction rates, as can be estimated empirically. I show that the species selection coefficient for a binary trait, and selection differential for a quantitative trait, depend not only on differences in net diversification rates (speciation minus extinction), but also on differences in species turnover rates (speciation plus extinction), especially in small clades. The randomness in speciation and extinction events also produces a species-level equivalent to random genetic drift, which is stronger for higher turnover rates. I then show how microevolutionary processes including mutation, organismic selection, and random genetic drift cause state transitions at the species level, allowing comparison of evolutionary forces across levels. A key parameter that would be needed to apply this theory is the distribution and rate of origination of new optimum phenotypes along a phylogeny.

A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology

Directional evolution has played an important role in shaping the morphological, ecological, and molecular diversity of life. However, standard substitution models assume stationarity of the evolutionary process over the time scale examined, thus impeding the study of directionality. Here we explore a simple, nonstationary model of evolution for discrete data, which assumes that the state frequencies at the root differ from the equilibrium frequencies of the homogeneous evolutionary process along the rest of the tree (i.e., the process is nonstationary, nonreversible, but homogeneous). Within this framework, we develop a Bayesian approach for testing directional versus stationary evolution using a reversible-jump algorithm. Simulations show that when only data from extant taxa are available, the success in inferring directionality is strongly dependent on the evolutionary rate, the shape of the tree, the relative branch lengths, and the number of taxa. Given suitable evolutionary rates (0.1-0.5 expected substitutions between root and tips), accounting for directionality improves tree inference and often allows correct rooting of the tree without the use of an outgroup. As an empirical test, we apply our method to study directional evolution in hymenopteran morphology. We focus on three character systems: wing veins, muscles, and sclerites. We find strong support for a trend toward loss of wing veins and muscles, while stationarity cannot be ruled out for sclerites. Adding fossil and time information in a total-evidence dating approach, we show that accounting for directionality results in more precise estimates not only of the ancestral state at the root of the tree, but also of the divergence times. Our model relaxes the assumption of stationarity and reversibility by adding a minimum of additional parameters, and is thus well suited to studying the nature of the evolutionary process in data sets of limited size, such as morphology and ecology.

Multiple phylogenetically distinct events shaped the evolution of limb skeletal morphologies associated with bipedalism in the jerboas

Recent rapid advances in experimental biology have expanded the opportunity for interdisciplinary investigations of the evolution of form and function in non-traditional model species. However, historical divisions of philosophy and methodology between evolutionary/organismal biologists and developmental geneticists often preclude an effective merging of disciplines. In an effort to overcome these divisions, we take advantage of the extraordinary morphological diversity of the rodent superfamily Dipodoidea, including the bipedal jerboas, to experimentally study the developmental mechanisms and biomechanical performance of a remarkably divergent limb structure. Here, we place multiple limb character states in a locomotor and phylogenetic context. Whereas obligate bipedalism arose just once in the ancestor of extant jerboas, we find that digit loss, metatarsal fusion, between-limb proportions, and within-hindlimb proportions all evolved independently of one another. Digit loss occurred three times through at least two distinct developmental mechanisms, and elongation of the hindlimb relative to the forelimb is not simply due to growth mechanisms that change proportions within the hindlimb. Furthermore, we find strong evidence for punctuated evolution of allometric scaling of hindlimb elements during the radiation of Dipodoidea. Our work demonstrates the value of leveraging the evolutionary history of a clade to establish criteria for identifying the developmental genetic mechanisms of morphological diversification.

The Role of Standing Variation in Geographic Convergent Adaptation

The extent to which populations experiencing shared selective pressures adapt through a shared genetic response is relevant to many questions in evolutionary biology. In this article, we explore how standing genetic variation contributes to convergent genetic responses in a geographically spread population. Geographically limited dispersal slows the spread of each selected allele, hence allowing other alleles to spread before any one comes to dominate the population. When selectively equivalent alleles meet, their progress is substantially slowed, dividing the species range into a random tessellation, which can be well understood by analogy to a Poisson process model of crystallization. In this framework, we derive the geographic scale over which an allele dominates and the proportion of adaptive alleles that arise from standing variation. Finally, we explore how negative pleiotropic effects of alleles can bias the subset of alleles that contribute to the species' adaptive response. We apply the results to the malaria-resistance glucose-6-phosphate dehydrogenase-deficiency alleles, where the large mutational target size makes it a likely candidate for adaptation from deleterious standing variation. Our results suggest that convergent adaptation may be common. Therefore, caution must be exercised when arguing that strongly geographically restricted alleles are the outcome of local adaptation. We close by discussing the implications of these results for ideas of species coherence and the nature of divergence between species.