Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus.

Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish, Gasterosteus doryssus. This lineage appeared and, over approximately 8000 generations, evolved significant reduction of 12 of 16 traits related to armour, swimming and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reproductively isolated, benthic-limnetic ecotypes of extant Gasterosteus aculeatus. Therefore, we infer that reproductive isolation was evolving. However, local extinction of G. doryssus lineages shows how young, isolated, speciating populations often disappear, supporting Darwin's explanation for missing evidence and revealing a mechanism behind morphological stasis. Extinction may also account for limited sustained divergence within the stickleback species complex and help reconcile speciation rate variation observed across time scales.

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.

Macroevolution, differentiation trees, and the growth of coding systems.

An open process of evolution of multicellular organisms is based on the rearrangement and growth of the program of differentiation that underlies biological morphogenesis. The maintenance of the final (adult) stable non-equilibrium state (stasis) of a developmental system determines the direction of the evolutionary process. This state is achieved via the sequence of differentiation events representable as differentiation trees. A special type of morphogenetic code, acting as a metacode governing gene expression, may include electromechanical signals appearing as differentiation waves. The excessive energy due to the incorporation of mitochondria in eukaryotic cells resulted not only in more active metabolism but also in establishing the differentiation code for interconnecting cells and forming tissues, which fueled the evolutionary process. The "invention" of "continuing differentiation" distinguishes multicellular eukaryotes from other organisms. The Janus-faced control, involving both top-down control by differentiation waves and bottom-up control via the mechanical consequences of cell differentiations, underlies the process of morphogenesis and results in the achievement of functional stable final states. Duplications of branches of the differentiation tree may be the basis for continuing differentiation and macroevolution, analogous to gene duplication permitting divergence of genes. Metamorphoses, if they are proven to be fusions of disparate species, may be classified according to the topology of fusions of two differentiation trees. In the process of unfolding of morphogenetic structures, microevolution can be defined as changes of the differentiation tree that preserve topology of the tree, while macroevolution represents any change that alters the topology of the differentiation tree.

'Evolutionary poker': an agent-based model of interactome emergence and epistasis tested against Lenski's long-term E. coli experiments.

A simple agent-based model is presented that produces results matching the experimental data found by Lenski's group for ≤50,000 generations of Escherichia coli bacteria under continuous selective pressure. Although various mathematical models have been devised previously to model the Lenski data, the present model has advantages in terms of overall simplicity and conceptual accessibility. The model also clearly illustrates a number of features of the evolutionary process that are otherwise not obvious, such as the roles of epistasis and historical contingency in adaptation and why evolution is time irreversible ('Dollo's law'). The reason for this irreversibility is that genomes become increasingly integrated or organized, and this organization becomes a novel selective factor itself, against which future generations must compete. Selection for integrated or synergistic networks, systems or sets of mutations or traits, not for individual mutations, confers the main adaptive advantage. The result is a punctuated form of evolution that follows a logarithmic occurrence probability, in which evolution proceeds very quickly when interactomes begin to form but which slows as interactomes become more robust and the difficulty of integrating new mutations increases. Sufficient parameters exist in the game to suggest not only how equilibrium or stasis is reached but also the conditions in which it will be punctuated, the factors governing the rate at which genomic organization occurs and novel traits appear, and how population size, genome size and gene variability affect these.

Using Punctuated Equilibrium Theory: Policy Momentum in Traditional Medicare Telehealth Reimbursement During COVID-19.

This article seeks to understand the changes in federal health care policy that led to greater telehealth adoption during COVID-19 pandemic. For decades, telehealth was identified as a possibility for increasing health care access, but the policies needed for greater telehealth reimbursement were stalled until the public health emergency was declared. Applying the dynamic concepts within punctuated equilibrium theory (PET) model to traditional fee-for-service Medicare policy, the influential factors are identified and specify how policy change occurred as a response to the pandemic, resulting in swift and large-scale changes in Medicare telehealth reimbursement requirements and widespread telehealth adoption. The model also explains how the same forces that led to Medicare policy response are at work to maintain and broaden or contract and limit the future of telehealth reimbursement as the public health emergency recedes.

Agenda governamental brasileira: prioridades e mudanças na dinâmica da atenção sobre a distribuição orçamentária da União (2000-2021) / Agenda del gobierno brasileño: prioridades y cambios en la dinámica de atención a la distribución del presupuesto federal (2000-2021) / Brazilian policy agenda: priorities and changes in the dynamics of attention on the federal budget distribution (2000-2021)

Resumo Os estudos sobre agenda governamental têm adotado diversos indicadores para mensurar a atenção e as prioridades dos governos, a fim de analisar os processos de formulação e mudança de políticas públicas. Com base nas prerrogativas da teoria do equilíbrio pontuado sobre os padrões de mudanças na dinâmica das políticas, a distribuição do orçamento público tem se destacado como um dos instrumentos que melhor expressam os níveis de atenção e as prioridades dos governos em diferentes setores. Nesse contexto, alinhado a uma agenda internacional, este estudo busca investigar o padrão da atenção governamental acerca da distribuição orçamentária no Brasil. Assim, o objetivo deste trabalho é mapear a dinâmica da atenção governamental sobre a disposição do orçamento aprovado da União ao longo das últimas duas décadas (2000-2021), identificando os níveis percentuais de atenção aos diferentes setores de políticas públicas ao longo do tempo e os fatores conjunturais e institucionais que balizam os níveis de atenção governamental na classificação orçamentária. Para isso, foi formulado um banco de dados do orçamento aprovado de 2000 a 2021, no qual as 814 combinações de funções e subfunções de gastos foram codificadas em 21 setores, conforme metodologia do comparative agenda project (CAP). Os resultados indicam que a atenção governamental sobre essa distribuição opera sob um padrão majoritariamente incremental no decorrer do tempo, mas permeado por pontuações no equilíbrio em políticas setoriais específicas, comprovando a teoria do equilíbrio pontuado (punctuated equilibrium theory [PET]) no cenário nacional. De igual modo, apontam para a necessidade de mais estudos setoriais que expliquem as causas e os efeitos das pontuações na atenção governamental, suas relações com mudanças na agenda legislativa e os impactos de momentos de crises institucionais na definição de prioridades na distribuição orçamentária, apontados como agendas futuras a partir deste trabalho.

Resumen Los estudios sobre la agenda gubernamental adoptaron varios indicadores para medir la atención y las prioridades de los gobiernos a los efectos de analizar los procesos de formulación y cambio de políticas públicas. Desde las prerrogativas de la teoría del equilibrio puntuado sobre los patrones de cambios en la dinámica de las políticas, la distribución del presupuesto público se ha destacado como uno de los instrumentos que mejor expresan los niveles de atención y las prioridades de los gobiernos de los diferentes sectores. En ese contexto, de acuerdo con una agenda internacional, este estudio busca investigar cuál es el patrón de atención gubernamental respecto a la distribución presupuestaria en Brasil. Así, el objetivo de este trabajo es mapear la dinámica de atención gubernamental sobre la distribución del presupuesto federal aprobado en las últimas dos décadas (2000-2021), identificando (i) cuáles son los niveles porcentuales de atención a los diferentes sectores de las políticas públicas a lo largo del tiempo y (ii) los factores coyunturales e institucionales que orientan los niveles de atención del gobierno en la clasificación presupuestaria federal. Para ello, se creó una base de datos del presupuesto aprobado de 2000 a 2021, en la que se codificaron las 814 combinaciones de funciones y subfunciones del gasto en 21 sectores, según la metodología del Proyecto de Agenda Comparada (CAP). Los resultados indican que la atención del gobierno sobre la distribución del presupuesto opera en un patrón mayoritariamente incremental en el tiempo, pero permeado por puntajes de equilibrio en políticas sectoriales específicas, demostrando así la teoría del equilibrio puntuado a nivel nacional. Asimismo, señalan la necesidad de mayores estudios sectoriales que expliquen las causas y efectos de los puntajes en la atención del gobierno, sus relaciones con los cambios en la agenda legislativa y los impactos de los momentos de crisis institucional en la definición de prioridades en la distribución presupuestaria, identificadas como futuras agendas a partir de este trabajo.

Abstract Studies on policy agenda have adopted several indicators to measure the attention and priorities of governments to analyze the processes of policy change and policy dynamics. Based on the Punctuated Equilibrium Theory (PET) applied on the patterns of policy change, the distribution of the public budget has stood out as one of the instruments that best express the levels of attention and priority for governments in different sectors. This study seeks to investigate the pattern of government attention on the federal budget distribution in Brazil. Thus, this work maps the dynamics of government attention on the distribution of the federal approved budget over the last two decades (2000-2021), identifying (i) what are the percentage levels of attention to the different sectors of public policies over time and (ii) the conjunctural and institutional factors that guide the levels of government attention in the budget distribution of the federal government in Brazil. A database of the federal approved budget from 2000 to 2021 was created, in which the 814 combinations of expenditure functions and subfunctions were coded into 21 sectors according to the methodology of the Comparative Agenda Project (CAP). The results indicate that government attention on the distribution of the Brazilian federal budget operates in a mostly incremental pattern over time, permeated by punctuations in specific sectoral policies, thus proving the Punctuated Equilibrium Theory at the national level. As for future research agenda, the study shows the need for further sectoral studies that explain the causes and effects of changes on government attention, their relationships with the legislative agenda, and the impacts of moments of institutional crisis in defining priorities in budget distribution.

The relationship between volume of newspaper coverage and policy action for nutrition issues in Australia: a content analysis.

OBJECTIVES: Unhealthy diets are a leading risk factor for the global burden of disease. Research suggests that comprehensive, population-level solutions are required to attenuate this problem, though such policies have not been adopted. Increased media attention may lead to government-led policy action through issue definition and agenda setting. The aim of this study was to analyse which nutrition policy issues are covered in print media, and whether media attention correlated with relevant policy actions in Australia. STUDY DESIGN/METHODS: A content analysis was conducted on newspaper articles published between 1999 and 2019 from 11 major Australian metropolitan newspapers. RESULTS: Of the policy issues identified, few received meaningful media attention. Of those with peaks in media attention, only fortification and labelling issues coincided with government-led policy actions, while regulating junk-food advertising to children, sugar-sweetened beverage taxation, and the formulation of a National Nutrition Policy did not result in policy outcomes. CONCLUSIONS: Given the limited coverage of nutrition policy issues, the relationship between media attention and policy actions for the captured issues may not be determinable. In addition, factors including social, political, and historical contexts may be stronger influences on policymaking than media attention. Although this study did not demonstrate a relationship between media attention and policy action because of low coverage of nutrition issues, it did identify the media are generally reporting nutrition policy issues with a positive public health framing. Promoting favourable coverage of nutrition policy issues is still an important tool for advocacy globally. Moving forward, increasing the volume of coverage of nutrition issues should be an advocacy priority.

Bursts of Genomic Instability Potentiate Phenotypic and Genomic Diversification in Saccharomyces cerevisiae.

How microbial cells leverage their phenotypic potential to survive in a changing environment is a complex biological problem, with important implications for pathogenesis and species evolution. Stochastic phenotype switching, a particularly fascinating adaptive approach observed in numerous species across the tree of life, introduces phenotypic diversity into a population through mechanisms which have remained difficult to define. Here we describe our investigations into the mechanistic basis of colony morphology phenotype switching which occurs in populations of a pathogenic isolate of Saccharomyces cerevisiae, YJM311. We observed that clonal populations of YJM311 cells produce variant colonies that display altered morphologies and, using whole genome sequence analysis, discovered that these variant clones harbored an exceptional collection of karyotypes newly altered by de novo structural genomic variations (SVs). Overall, our analyses indicate that copy number alterations, more often than changes in allelic identity, provide the causative basis of this phenotypic variation. Individual variants carried between 1 and 16 de novo copy number variations, most of which were whole chromosomal aneuploidies. Notably, we found that the inherent stability of the diploid YJM311 genome is comparable to that of domesticated laboratory strains, indicating that the collections of SVs harbored by variant clones did not arise by a chronic chromosomal instability (CIN) mechanism. Rather, our data indicate that these variant clones acquired such complex karyotypic configurations simultaneously, during stochastic and transient episodes of punctuated systemic genomic instability (PSGI). Surprisingly, we found that the majority of these highly altered variant karyotypes were propagated with perfect fidelity in long-term passaging experiments, demonstrating that high aneuploidy burdens can often be conducive with prolonged genomic integrity. Together, our results demonstrate that colony morphology switching in YJM311 is driven by a stochastic process in which genome stability and plasticity are integrally coupled to phenotypic heterogeneity. Consequently, this system simultaneously introduces both phenotypic and genomic variation into a population of cells, which can, in turn perpetuate population diversity for many generations thereafter.

Catastrophe risk can accelerate unlikely evolutionary transitions.

Intelligent life has emerged late in Earth's habitable lifetime, and required a preceding series of key evolutionary transitions. A simple model (the Carter model) explains the late arrival of intelligent life by positing these evolutionary transitions were exceptionally unlikely 'critical steps'. An alternative model (the neocatastrophism hypothesis) proposes that intelligent life was delayed by frequent catastrophes that served to set back evolutionary innovation. Here, we generalize the Carter model and explore this hypothesis by including catastrophes that can 'undo' an evolutionary transition. Introducing catastrophes or evolutionary dead ends can create situations in which critical steps occur rapidly or in clusters, suggesting that past estimates of the number of critical steps could be underestimated. If catastrophes affect complex life more than simple life, the critical steps will also exhibit a pattern of acceleration towards the present, suggesting that the increase in biological complexity over the past 500 Myr could reflect previously overlooked evolutionary transitions. Furthermore, our results have implications for understanding the different explanations (critical steps versus neo-catastrophes) for the evolution of intelligent life and the so-called Fermi paradox-the observation that intelligent life appears rare in the observable Universe.

Further illusions: On key evolutionary mechanisms that could never fit with Modern Synthesis.

In light of illusions of the Modern Synthesis (MS) listed by Noble (2021a), MS's key concept, that gradual accumulation of gene mutations within microevolution leads to macroevolution, requires reexamination too. In this article, additional illusions of the MS are identified therein caused by the absence of system information and correct history. First, the MS lacks distinction among the two basic types of information: genome-defined system and gene-defined parts-information, as its treatment was based mostly on gene information. In contrast, it is argued here that system information is maintained by species-specific karyotype code, and macroevolution is based on the whole genome information package rather than on specific genes. Linking the origin of species with system information shows that the creation and accumulation of the latter in evolution is the fundamental question omitted from the MS. Second, modern evidence eliminates the MS's preferred theory that present evolutionary events can be linearly extrapolated to the past to reconstruct Life's history, wrongly assuming that most of the fossil record supports the gradual change while ignoring the true karyotype/genome patterns. Furthermore, stasis, as the most prominent pattern of the deep history of Life, remains a puzzle to the MS, but can be explained by the mechanism of karyotype-preservation-via-sex. Consequently, the concept of system-information is smoothly integrated into the two-phased evolutionary model that paleontology requires (Eldredge and Gould, 1972). Finally, research on genome-level causation of evolution, which does not fit the MS, is summarized. The availability of alternative concepts further illustrates that it is time to depart from the MS.

New frontiers in Japanese Forest Policy: Addressing ecosystem disservices in the 21st century.

Forests are a potential solution to numerous global environmental issues, and their restoration is widely pursued. Forty percent of Japan's forests are planted forests. This has caused the common occurrence of forest ecosystem disservices in the country, like-wildlife damage, pollinosis, and driftwood damage. Forest policy processes in Japan are characterized by incrementalism, central mobilization, and hegemony of career civil servants. Responses to forest ecosystem disservices have changed the central mobilization policy pattern. Punctuated equilibrium theory can be applied to several policy processes in Japan, but it provides only limited explanation for policy responses to forest ecosystem disservices. The responses are influenced by national governance and public administration traditions and cultures. It is relevant to expand research on policy responses to forest ecosystem disservices, recognizing that ideal responses may require unusual approaches not within traditional policy making or outside of established policy cultures.

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.

Cladogenesis and replacement in the fossil record of Microsyopidae (?Primates) from the southern Bighorn Basin, Wyoming.

The early Eocene of the southern Bighorn Basin, Wyoming, is notable for its nearly continuous record of mammalian fossils. Microsyopinae (?Primates) is one of several lineages that shows evidence of evolutionary change associated with an interval referred to as Biohorizon A. Arctodontomys wilsoni is replaced by a larger species, Arctodontomys nuptus, during the biohorizon interval in what is likely an immigration/emigration or immigration/local extinction event. The latter is then superseded by Microsyops angustidens after the end of the Biohorizon A interval. Although this pattern has been understood for some time, denser sampling has led to the identification of a specimen intermediate in morphology between A. nuptus and M. angustidens, located stratigraphically as the latter is appearing. Because specimens of A. nuptus have been recovered approximately 60 m above the appearance of M. angustidens, it is clear that A. nuptus did not suffer pseudoextinction. Instead, evidence suggests that M. angustidens branched off from a population of A. nuptus, but the latter species persisted. This represents possible evidence of cladogenesis, which has rarely been directly documented in the fossil record. The improved understanding of both evolutionary transitions with better sampling highlights the problem of interpreting gaps in the fossil record as punctuations.

Evolution in the weak-mutation limit: Stasis periods punctuated by fast transitions between saddle points on the fitness landscape.

A mathematical analysis of the evolution of a large population under the weak-mutation limit shows that such a population would spend most of the time in stasis in the vicinity of saddle points on the fitness landscape. The periods of stasis are punctuated by fast transitions, in lnNe/s time (Ne , effective population size; s, selection coefficient of a mutation), when a new beneficial mutation is fixed in the evolving population, which accordingly moves to a different saddle, or on much rarer occasions from a saddle to a local peak. Phenomenologically, this mode of evolution of a large population resembles punctuated equilibrium (PE) whereby phenotypic changes occur in rapid bursts that are separated by much longer intervals of stasis during which mutations accumulate but the phenotype does not change substantially. Theoretically, PE has been linked to self-organized criticality (SOC), a model in which the size of "avalanches" in an evolving system is power-law-distributed, resulting in increasing rarity of major events. Here we show, however, that a PE-like evolutionary regime is the default for a very simple model of an evolving population that does not rely on SOC or any other special conditions.

Scandalous decisions: explaining shifts in UK medicinal cannabis policy.

BACKGROUND AND AIMS: Opening up access to scheduled drugs such as cannabis in the United Kingdom rarely happens, yet on 1 November 2018 the United Kingdom changed the law to allow cannabis-derived products to be prescribed for medicinal purposes, albeit in tightly controlled circumstances. This followed substantial media interest in the cases of two children with epilepsy. This article focuses upon the role of scandal in bringing about legislative change. METHODS: We used political science and social policy theories (punctuated equilibrium theory and scandal theory) to guide a qualitative content analysis of media articles published in 2018 in UK national newspapers. We focused in particular on the 6-month period prior to the policy change. RESULTS: The concentrated attention by the media given to the suffering of children with epilepsy appears to have prompted the rapid change in policy by the UK government. A variety of strategies were used to develop a highly emotive response to garner support for reform. Media stories emphasized the injustice of two extremely sick children being unable to access the medicine they apparently needed to enable them to have a 'normal' childhood. Three groups of 'claim-makers' were identified as important in influencing public opinion: families, high-profile individuals and campaigning groups. CONCLUSIONS: The case of medicinal cannabis in the United Kingdom suggests that policy reform can occur when a scandal is successfully manufactured. We must be cautious, however, about over-emphasizing the role of scandal as a driver of policy change in this context: only a limited set of circumstances will permit a prescription for cannabis-based medicine to be issued in the United Kingdom.

Symbiogenesis as a driving force of evolution: The legacy of Boris Kozo-Polyansky.

We analyze evolutionary views of Boris Kozo-Polyansky (1890-1957) who was the first who formulated the symbiotic theory of evolution as a concept in his book, Symbiogenesis: A New Principle of Evolution (1924). Later, starting from 1967, Lynn Margulis independently formulated and further developed the concept of symbiogenesis. Although the ideas on the symbiotic origin of chloroplasts and mitochondria appeared earlier, the book of Kozo-Polyansky presented symbiogenesis as the main factor of complexification in the course of evolution, not only in relation to the origin of eukaryotic cell. Kozo-Polyansky incorporated the ideas of symbiogenesis into a broader paradigm that anticipated the important concepts of the modern Extended Evolutionary Synthesis such as the idea of net of life, the evolutionary role of apoptosis, the ideas of punctuated equilibrium, and the concept of metasystem transition.

The efficient Lamarckian spread of life in the cosmos.

In this Chapter we discuss the various mechanisms that are available for the possible transfer of cosmic microbial living systems from one cosmic habitat to another. With the 100 or so habitable planets that are now known to exist in our galaxy alone transfers of cometary dust carrying life including fragments of icy planetoids/asteroids would be expected to occur on a routine basis. It is thus easy to view the galaxy as a single connected "biosphere" of which our planet Earth is a minor component. The Hoyle-Wickramasinghe Panspermia paradigm provides a cogent biological rationale for the actual widespread existence of Lamarckian modes of inheritance in terrestrial systems (which we review here). Thus the Panspermia paradigm provides the raison d'etre for Lamarckian Inheritance. Under a terrestrially confined neoDarwinian viewpoint such an association may have been thought spurious in the past. Our aim here is to outline the main evidence for rapid terrestrial-based Lamarckian-based evolutionary hypermutation processes dependent on reverse transcription-coupled mechanisms among others. Such rapid adaptation mechanisms would be consistent with the effective cosmic spread of living systems. For example, a viable, or cryo-preserved, living system traveling through space in a protective matrix will of necessity need to adapt rapidly and proliferate on landing in a new cosmic niche. Lamarckian mechanisms thus come to the fore and supersede the slow (blind and random) genetic processes expected under neoDarwinian Earth centred theories.

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.

The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements.

Theories of the genetics underlying punctuated equilibrium (PE) have been vague to date. Here the developmental gene hypothesis is proposed, which states that: 1) developmental regulatory (DevReg) genes are responsible for the orchestration of metazoan morphogenesis and their extreme conservation and mutation intolerance generates the equilibrium or stasis present throughout much of the fossil record and 2) the accumulation of regulatory elements and recombination within these same genes-often derived from transposable elements-drives punctuated bursts of morphological divergence and speciation across metazoa. This two-part hypothesis helps to explain the features that characterize PE, providing a theoretical genetic basis for the once-controversial theory. Also see the video abstract here https://youtu.be/C-fu-ks5yDs.

Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts.

Phylogenetic comparative methods (PCMs) have been used to study the evolution of quantitative traits in various groups of organisms, ranging from micro-organisms to animal and plant species. A common approach has been to assume a Gaussian phylogenetic model for the trait evolution along the tree, such as a branching Brownian motion (BM) or an Ornstein-Uhlenbeck (OU) process. Then, the parameters of the process have been inferred based on a given tree and trait data for the sampled species. At the heart of this inference lie multiple calculations of the model likelihood, that is, the probability density of the observed trait data, conditional on the model parameters and the tree. With the increasing availability of big phylogenetic trees, spanning hundreds to several thousand sampled species, this approach is facing a two-fold challenge. First, the assumption of a single Gaussian process governing the entire tree is not adequate in the presence of heterogeneous evolutionary forces acting in different parts of the tree. Second, big trees present a computational challenge, due to the time and memory complexity of the model likelihood calculation. Here, we explore a sub-family, denoted GLInv, of the Gaussian phylogenetic models, with the transition density exhibiting the properties that the expectation depends Linearly on the ancestral trait value and the variance is Invariant with respect to the ancestral value. We show that GLInv contains the vast majority of Gaussian models currently used in PCMs, while supporting an efficient (linear in the number of nodes) algorithm for the likelihood calculation. The algorithm supports scenarios with missing data, as well as different types of trees, including trees with polytomies and non-ultrametric trees. To account for the heterogeneity in the evolutionary forces, the algorithm supports models with "shifts" occurring at specific points in the tree. Such shifts can include changes in some or all parameters, as well as the type of the model, provided that the model remains within the GLInv family. This contrasts with most of the current implementations where, due to slow likelihood calculation, the shifts are restricted to specific parameters in a single type of model, such as the long-term selection optima of an OU process, assuming that all of its other parameters, such as evolutionary rate and selection strength, are global for the entire tree. We provide an implementation of this likelihood calculation algorithm in an accompanying R-package called PCMBase. The package has been designed as a generic library that can be integrated with existing or novel maximum likelihood or Bayesian inference tools.