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The facial differences between recent Pan troglodytes and Homo sapiens can be used as a proxy for the reduction of facial prognathism that happened during evolutionary transition between Australopithecines and early Homo. The projecting nasal morphology of Homo has been considered both a passive consequence of anatomical reorganization related to brain and integrated craniofacial evolution as well as an adaptation related to air-conditioning during physiological and behavioral shifts in human evolution. Yet, previous research suggested impaired air-conditioning in Homo challenging respiratory adaptations based on computational fluid dynamics (CFD) and airflow simulations. Here we improved CFD model at the inflow region and also carried out three-dimensional (3D) geometric morphometrics to address the hypothesis of impaired air-conditioning in humans and species differences in airway shape. With the new CFD model we simulated pressure, velocity, and temperature changes in airflow of six adult humans and six chimpanzees and analyzed 164 semi-landmarks of 10 humans and 10 chimpanzees for 3D size and shape comparisons. Our finding shows significantly different internal 3D nasal airways. Also, species means of pressure, velocity, and temperature differed statistically significantly. However, form-related differences in temperature exchanges seem subtle and may question adaptive disadvantages. We rather support a hypothesis of craniofacial changes in the Australopithecus-Homo transition that are related to brain evolution and craniofacial integration with facial and nasal modifications that contribute to maintain respiratory adaptations related to air conditioning., This work is supported by the Ministerio de Ciencia e Innovacion of Spain (Grant No. PID2019-105097RB-I00/AEI/10.13039/501100011033; and PID2020-115854GB-I00).

Since the emergence of the first fungi some 700 million years ago, unicellular yeast-like forms have emerged multiple times in independent lineages via convergent evolution. While tens to hundreds of millions of years separate the independent evolution of these unicellular organisms, they share remarkable phenotypic and metabolic similarities, and all have streamlined genomes. Yeasts occur in every aquatic environment yet examined. Many species are aquatic; perhaps most are amphibious. How these species have evolved to thrive in aquatic habitats is fundamental to understanding functions and evolutionary mechanisms in this unique group of fungi. Here we review the state of knowledge of the physiological and ecological diversity of amphibious yeasts and their key evolutionary adaptations enabling survival in aquatic habitats. We emphasize some genera previously thought to be exclusively terrestrial. Finally, we discuss the ability of many yeasts to survive in extreme habitats and how this might lend insight into ecological plasticity, including amphibious lifestyles.

Research focused on understanding the evolutionary factors that shape parity mode evolution among vertebrates have long focused on squamate reptiles (snakes and lizards), which contain all but one of the evolutionary transitions from oviparity to viviparity among extant amniotes. While most hypotheses have focused on the role of cool temperatures in favoring viviparity in thermoregulating snakes and lizards, there is a growing appreciation in the biogeographic literature for the importance of lower oxygen concentrations at high elevations for the evolution of parity mode. However, the physiological mechanisms underlying how hypoxia might reduce fitness, and how viviparity can alleviate this fitness decrement, has not been systematically evaluated. We qualitatively evaluated previous research on reproductive and developmental physiology, and found that (1) hypoxia can negatively affect fitness of squamate embryos, (2) oxygen availability in the circulatory system of adult lizards can be similar or greater than an egg, and (3) gravid females can possess adaptive phenotypic plasticity in response to hypoxia. These findings suggest that the impact of hypoxia on the development and physiology of oviparous and viviparous squamates would be a fruitful area of research for understanding the evolution of viviparity. To that end, we propose an integrative research program for studying hypoxia and the evolution of viviparity in squamates.

International audience; The appearance of leaves with flattened laminae about 400 million years (Myr) ago had broad impacts on the Earth's ecosystem. The influential telome theory presents a model for this evolutionary transition, although it lacks plausible molecular evidence. Recently, microtubule-mediated mechanical feedback was proposed as a parsimonious alternative mechanism to explain leaf blade evolution.

The major evolutionary transitions from unicellular organisms to multicellularity resulted in a profusion of complex life forms. During the transition from single cells to multicellular life, groups of cells acquired the capacity for reproduction as discrete units; however, the selective causes and underlying mechanisms remain debated. One perspective views the evolution of multicellularity as a shift in the timescale at which natural selection primarily operates-from that of individual cells to the timescale of reproducing groups of cells. Therefore, a distinguishing feature of multicellular reproduction, as opposed to simple growth of a multicellular collective, is that the capacity for reproduction must develop over a timescale that is greater than the reproductive timescale of a single cell. Here, I suggest that the emergence of specialized reproductive cells (the germ line) was an essential first stage of the evolutionary transition to multicellularity because it imposed the necessary "delay"-allowing natural selection to operate over the longer timescale of a multicellular life cycle, ultimately resulting in the evolution of complex multicellular organisms. This perspective highlights the possibility that the ubiquity of a germ-soma distinction among complex multicellular organisms reflects the fact that such life cycles, on first emergence, had the greatest propensity to participate in Darwinian evolution.

Sea urchins and their relatives are grouped together taxonomically in the class Echinoidea (phylum Echinodermata). Echinoids exhibit remarkable variation in their pentaradially symmetric body shape phenotypes, from spheroid tests (skeletons) in sea urchins to discoid tests in sand dollars. Researchers have speculated on the morphological evolutionary transitions among these phenotypes without reaching consensus. We designed and performed an experiment in which sea urchins grew under a geometric constraint manifested through restricted vertical spatial dimension physically limiting growth in height. Individuals in this treatment group became flatter relative to individuals in a control group after 8 weeks. These findings may be considered as instantiating phenotypic accommodation, an underappreciated phenomenon that may constitute the first step in novel phenotype evolution. We present preliminary speculations relating phenotypically accommodated changes in shape and morphological evolutionary relationships among echinoids. By demonstrating a plausible initiating mechanism in a morphological transition, we hope to contribute to theoretical discussions about phenotypic evolution, emphasizing the role that physical factors play in changing complex biological systems.

The evolutionary history of many organisms is characterized by major changes in morphology and distribution. Specifically, alterations of body mass and geographic distribution may profoundly influence organismal life-history traits. Here, we reconstructed the evolutionary history of flight-feather molt strategy using data from 1,808 Neornithes species. Our analysis suggests that the ancestral molt strategy of first-year birds was partial or entirely absent, and that complete wing flight-feather molt in first-year birds first evolved in the late Eocene and Oligocene (25–40 Ma), at least 30 Myr after birds first evolved. Complete flight-feather molt occurred mainly at equatorial latitudes and in relatively low body mass species, following a diversification of body mass within the lineage. We conclude that both body mass and geographic distribution shaped the evolution of molt strategies and propose that the evolutionary transition towards complete juvenile molt in the Neornithes is a novel, relatively late adaptation.

In prebiotic evolution, self-replicating molecules are believed to have evolved into complex living systems by expanding their information and functions open-endedly. Theoretically, such evolutionary complexification could occur through successive appearance of novel replicators that interact with one another to form replication networks. Here we performed long-term evolution experiments using an RNA that replicates by a self-encoded RNA replicase. The RNA diversified into multiple coexisting host and parasite lineages, whose frequencies in the population initially fluctuated and gradually stabilized. The final population, comprising five RNA lineages, forms a replicator network with diverse interactions, including cooperation to help the replication of all other members. These results support the capability of molecular replicators to spontaneously develop complexity through Darwinian evolution, a critical step for the emergence of life.

Evolutionary transitions among ecological interactions are widely known, although their detailed dynamics remain absent for most population models. Adaptive dynamics has been used to illustrate how the parameters of population models might shift through evolution, but within an ecological regime. Here we use adaptive dynamics combined with a generalised logistic model of population dynamics to show that transitions of ecological interactions might appear as a consequence of evolution. To this purpose we introduce a two-microbial toy model in which population parameters are determined by a bookkeeping of resources taken from (and excreted to) the environment, as well as from the byproducts of the other species. Despite its simplicity, this model exhibits all sorts of ecological transitions, some of which resemble those found in nature. Overall, the model shows a clear trend toward the emergence of mutualism.

The evolution of large insect societies is a major evolutionary transition that occurred in the long-extinct ancestors of termites, ants, corbiculate bees, and vespid wasps. Researchers have long used 'social ladder thinking': assuming progressive stepwise phenotypic evolution and asserting that extant species with simple societies (e.g. some halictid bees) represent the ancestors of species with complex societies, and thus provide insight into general early steps of eusocial evolution. We discuss how this is inconsistent with data and modern evolutionary 'tree thinking'. Phylogenetic comparative methods with broad sampling provide the best means to make rigorous inferences about ancestral traits and evolutionary transitions that occurred within each lineage, and to determine whether consistent phenotypic and genomic changes occurred across independent lineages.

Multicellular organisms appeared on Earth through several independent major evolutionary transitions. Are such transitions reversible? Addressing this fundamental question entails understanding the benefits and costs of multicellularity versus unicellularity. For example, some wild yeast strains form multicellular clumps, which might be beneficial in stressful conditions, but this has been untested. Here, we show that unicellular yeast evolve from clump‐forming ancestors by propagating samples from suspension after larger clumps have settled. Unicellular yeast strains differed from their clumping ancestors mainly by mutations in the AMN1 (Antagonist of Mitotic exit Network) gene. Ancestral yeast clumps were more resistant to freeze/thaw, hydrogen peroxide, and ethanol stressors than their unicellular counterparts, but they grew slower without stress. These findings suggest disadvantages and benefits to multicellularity and unicellularity that may have impacted the emergence of multicellular life forms.

Drilini are soft-bodied predatory click-beetles (Elateridae: Agrypninae) with incompletely metamorphosed females. Due to divergent morphology, their classification has been contentious. We present the first densely sampled molecular phylogeny of Drilini based on nuclear and mitochondrial markers. Altogether, 44 species, representing all genera, were analysed using maximum likelihood and the Bayesian approach. Molecular analyses recovered five major clades that were also well supported by morphology. Afrotropical lineages mark deep splits. Most Palearctic species belong to a terminal clade. A few species of the predominantly Afrotropical Selasia are distributed from Arabia up to the Himalayas and Thailand. The origin of Drilini is dated to the Late Eocene (~35.5 Mya) and rapid radiation is identified from the Eocene/Oligocene to the Middle Miocene. We describe the gradual transformation of male morphological traits, e.g. the level of sclerotization, structure of mouthparts, loss of the thoracic interlocking mechanism, shortened elytra and expanded larviform abdomen. Five new genera, Austroselasia, Habeshaselasia, Illubaboria, Malacodrilus and Mashaselasia are proposed. Latoselasia, previously a subgenus of Wittmerselasia, is elevated to the genus rank. Five new species, Habeshaselasia nekemtensis, H. illubaborensis, Illubaboria bicolor, Malacodrilus hajeki and Mashaselasia aethiopica are described.

The Major Transitions in evolution include events and processes that result in the emergence of new levels of biological individuality. For collectives to undergo Darwinian evolution, their traits must be heritable, but the emergence of higher-level heritability is poorly understood and has long been considered a stumbling block for nascent evolutionary transitions. A change in the means by which genetic information is utilized and transmitted has been presumed necessary. Using analytical models, synthetic biology, and biologicallyinformed simulations, we explored the emergence of trait heritability during the evolution of multicellularity. Contrary to existing theory, we show that no additional layer of genetic regulation is necessary for traits of nascent multicellular organisms to become heritable; rather, heritability and the capacity to respond to natural selection on multicellular-level traits can arise “for free.” In fact, we find that a key emergent multicellular trait, organism size at reproduction, is usually more heritable than the underlying cell-level trait upon which it is based, given reasonable assumptions.

Transitions between sexual and unisexual reproductive modes have significant consequences for the evolutionary trajectories of species. These transitions have occurred numerous times in vertebrates and are frequently mediated by hybridization events. Triploid unisexual vertebrates are thought to arise through hybridization between individuals of a diploid unisexual lineage and a sexual species, although additional evidence that confirms this mechanism is needed in numerous groups. North American whiptail lizards (Aspidoscelis) are notable for being one of the largest radiations of unisexual vertebrates, and the most diverse group of Aspidoscelis includes numerous triploid lineages that have no known diploid unisexual ancestors. This pattern of "missing" ancestors may result from the short evolutionary life span of unisexual lineages or the selective advantages of polyploidy, or it could suggest that alternative mechanisms of triploid formation are operating in nature. We leverage genomic, morphological, and karyotypic data to describe a new diploid unisexual whiptail and show that it is likely the unisexual progenitor of an extant triploid lineage, A. opatae. We also resolve patterns of polyploidization within the A. sexlineatus species group and test predictions about the phenotypic outcomes of hybridization.

It has been suggested that the human species may be undergoing an evolutionary transition in individuality (ETI). But there is disagreement about how to apply the ETI framework to our species, and whether culture is implicated as either cause or consequence. Long-term gene–culture coevolution (GCC) is also poorly understood. Some have argued that culture steers human evolution, while others proposed that genes hold culture on a leash. We review the literature and evidence on long-term GCC in humans and find a set of common themes. First, culture appears to hold greater adaptive potential than genetic inheritance and is probably driving human evolution. The evolutionary impact of culture occurs mainly through culturally organized groups, which have come to dominate human affairs in recent millennia. Second, the role of culture appears to be growing, increasingly bypassing genetic evolution and weakening genetic adaptive potential. Taken together, these findings suggest that human long-term GCC is characterized by an evolutionary transition in inheritance (from genes to culture) which entails a transition in individuality (from genetic individual to cultural group). Thus, research on GCC should focus on the possibility of an ongoing transition in the human inheritance system.

Life-history traits represent organisms' strategies to navigate the fitness trade-offs between survival and reproduction. Eric Charnov developed three dimensionless metrics to quantify fundamental life-history trade-offs. Lifetime reproductive effort (LRE), relative reproductive lifespan (RRL) and relative offspring size (ROS), together with body mass can be used to classify life-history strategies across the four major classes of tetrapods: amphibians, reptiles, mammals and birds. First, we investigate how the metrics have evolved in concert with body mass within tetrapod lineages. In most cases, we find evidence for correlated evolution among body mass and the three dimensionless metrics. Second, we compare life-history strategies across the four classes of tetrapods and find that LRE, RRL and ROS delineate a space in which the major tetrapod classes occupy mostly unique subspaces. These distinct combinations of life-history strategies provide us with a framework to understand the impact of major evolutionary transitions in energetics, physiology and ecology.

Funding: M.G.F. acknowledges funding from St Andrews’ School of Biology. J.P. acknowledges IAST funding from the French National Research Agency (ANR) under the Investments for the Future (Investissements d’Avenir) program, grant ANR-17-EURE-0010. Eusociality, where largely unreproductive offspring help their mothers reproduce, is a major form of social organization. An increasingly documented feature of eusociality is that mothers induce their offspring to help by means of hormones, pheromones or behavioural displays, with evidence often indicating that offspring help voluntarily. The co-occurrence of maternal influence and offspring voluntary help may be explained by what we call the converted helping hypothesis, whereby maternally manipulated helping subsequently becomes voluntary. Such hypothesis requires that parent-offspring conflict is eventually dissolved—for instance, if the benefit of helping increases sufficiently over evolutionary time. We show that help provided by maternally manipulated offspring can enable the mother to sufficiently increase her fertility to transform parent-offspring conflict into parent-offspring agreement. This conflict-dissolution mechanism requires that helpers alleviate maternal life-history trade-offs, and results in reproductive division of labour, high queen fertility and honest queen signalling suppressing worker reproduction—thus exceptionally recovering diverse features of eusociality. As such trade-off alleviation seemingly holds widely across eusocial taxa, this mechanism offers a potentially general explanation for the origin of eusociality, the prevalence of maternal influence, and the offspring’s willingness to help. Overall, our results explain how a major evolutionary transition can happen from ancestral conflict. Publisher PDF

How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell–cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years., This work was supported by a European Research Council Consolidator Grant (ERC-2012-Co -616960), and grants (BFU2017-90114-P) from Ministerio de Economía y Competitividad (MINECO), Agencia Estatal de Investigación (AEI), and Fondo Europeo de Desarrollo Regional (FEDER) to I.R.-T. We also acknowledge ‘la Caixa’ Grant for Doctoral Studies from ‘la Caixa’ Banking Foundation (ID 100010434) (Spain) to A.P.-P. (LCF/BQ/ES16/11570008), and a Marie Skłodowska-Curie Individual Fellowship under the EU Framework Programme for Research and Innovation Horizon 2020 (project ID 747789) and an Ayuda Juan de la Cierva-Incorporación (IJC2018-036657-I) to M.M.L.

Viviparity, an innovation enhancing maternal control over developing embryos, has evolved >150 times in vertebrates, and has been proposed as an adaptation to inhabit cold habitats. Yet, the behavioral, physiological, morphological, and life history features associated with live-bearing remain unclear. Here, we capitalize on repeated origins of viviparity in phrynosomatid lizards to tease apart the phenotypic patterns associated with this innovation. Using data from 125 species and phylogenetic approaches, we find that viviparous phrynosomatids repeatedly evolved a more cool-adjusted thermal physiology than their oviparous relatives. Through precise thermoregulatory behavior viviparous phrynosomatids are cool-adjusted even in warm environments, and oviparous phrynosomatids warm-adjusted even in cool environments. Convergent behavioral shifts in viviparous species reduce energetic demand during activity, which may help offset the costs of protracted gestation. Whereas dam and offspring body size are similar among both parity modes, annual fecundity repeatedly decreases in viviparous lineages. Thus, viviparity is associated with a lower energetic allocation into production. Together, our results indicate that oviparity and viviparity are on opposing ends of the fast-slow life history continuum in both warm and cool environments. In this sense, the ‘cold climate hypothesis’ fits into a broader range of energetic/life history trade-offs that influence transitions to viviparity.

It is of fundamental importance for the field of evolutionary biology to understand when and why major evolutionary transitions occur. Live-bearing young (viviparity) is a major evolutionary change and has evolved from egg-laying (oviparity) independently in many vertebrate lineages and most abundantly in lizards and snakes. Although contemporary viviparous squamate species generally occupy cold climatic regions across the globe, it is not known whether viviparity evolved as a response to cold climate in the first place. Here, we used available published time-calibrated squamate phylogenies and parity data on 3,498 taxa. We compared the accumulation of transitions from oviparity to viviparity relative to background diversification and a simulated binary trait. Extracting the date of each transition in the phylogenies and informed by 65 my of global palaeoclimatic data, we tested the nonexclusive hypotheses that viviparity evolved under the following: (a) cold, (b) long-term stable climatic conditions and (c) with background diversification rate. We show that stable and long-lasting cold climatic conditions are correlated with transitions to viviparity across squamates. This correlation of parity mode and palaeoclimate is mirrored by background diversification in squamates, and simulations of a binary trait also showed a similar association with palaeoclimate, meaning that trait evolution cannot be separated from squamate lineage diversification. We suggest that parity mode transitions depend on environmental and intrinsic effects and that background diversification rate may be a factor in trait diversification more generally.

Microbes form the majority of life on Earth, but have been systematically underrepresented in historical research. The sequencing revolutions of the last two decades have completely changed the way we can study microbial genomic information, giving us the means to probe ever deeper into their evolution. In a first study, we developed a new approach to screen large short-read datasets for the presence of lineages and genes of interest. By using gene-centric assembly and phylogenetic placement, we integrate the strengths of reference-based with phylogenetic screening methods to efficiently reconstruct gene sequences and label them taxonomically. This will enable researchers to more efficiently select datasets which are likely to contain desired lineages and genes. In the second study, we recover five metagenome-assembled genomes from the previously uncharacterized Hikarchaeia. We infer them to be the closest relatives of haloarchaea and study the evolution of genome content since the last common ancestor of these two aerobic groups with anaerobic methanogens. We detect patterns of gradual evolutionary transition, including the early loss of methanogenesis-related genes and the acquisition of the genetic basis for aerobic respiration. Furthermore, genomes of haloarchaea underwent significant expansion, mostly through transfers from diverse groups of bacteria, whereas Hikarchaeia display genome streamlining typical of marine prokaryotes. In a third study, we reconstructed two new bacterial families, Mitibacteraceae and Athabascaceae, that branch as sister clades to all previously known Rickettsiales. Their genomes lack the characteristic reduction of rickettsial bacteria but resemble free-living alphaproteobacteria. However, they contain several conserved features, such as the rvh type 4 secretion system. We reconstructed the last common ancestor of all Rickettsiales and inferred it as a free-living organism associated with marine biofilms. Further, we propose a model for the transition towards host-association found in all classical Rickettsiales. The fourth study explores the diversity and evolution of the eukaryotic orphan lineage Picozoa. With the help of 43 new single amplified genomes, Picozoa are placed within the supergroup Archaeplastida, in a clade together with red algae and the predatory rhodelphids. In contrast to other archaeplastids, picozoan genomes show no sign of a (cryptic) plastid or plastid-associated gene transfers. This suggests that Picozoa completely lost the primary plastid early in their evolution, or that in fact they never possessed it. These findings raise further questions about the acquisition of the plastid in the archaeplastidal ancestor and the frequency of plastid loss. In summary, this thesis explores several important evolutionary transitions across the tree of life using environmental genome reconstruction, phylogenomics and ancestral state reconstruction approaches.

Major evolutionary transitions describe how biological complexity arises; e.g. in evolution of complex multicellular bodies, and superorganismal insect societies. Such transitions involve the evolution of division of labour, e.g. as queen and worker castes in insect societies. Castes across different evolutionary lineages are thought to be regulated by a conserved genetic toolkit. However, this hypothesis has not been tested thoroughly across the complexity spectrum of the major transition. Here we reveal, using machine learning analyses of brain transcription, evidence of a shared genetic toolkit across the spectrum of social complexity in Vespid wasps. Whilst molecular processes underpinning the simpler societies (which likely represent the origins of social living) are conserved throughout the major transition, additional processes appear to come into play in more complex societies. Such fundamental shifts in regulatory processes with complexity may typify other major evolutionary transitions, such as the evolution of multicellularity.

Summary New hydrodynamic analyses demonstrate that Palaeozoic jawless vertebrates, laden with heavy bony armour, were active, capable swimmers. This challenges previous hypotheses suggesting they were bottom feeders and impacts our understanding of the evolutionary transition from jawless to jawed vertebrates.

Major evolutionary transitions can be triggered by behavioural novelty, and are often associated with ‘adaptive suites’, which involve shifts in multiple co-adapted traits subject to complex interactions.Heliconiusbutterflies represent one such example, actively feeding on pollen, a behaviour unique among butterflies. Pollen feeding permits a prolonged reproductive lifespan, and co-occurs with a constellation of behavioural, neuroanatomical, life history, morphological and physiological traits that are absent in closely related, non-pollen-feeding genera. As a highly tractable system, supported by considerable ecological and genomic data,Heliconiusare an excellent model for investigating how behavioural innovation can trigger a cascade of adaptive shifts in multiple diverse, but interrelated, traits. Here, we synthesize current knowledge of pollen feeding inHeliconius, and explore potential interactions between associated, putatively adaptive, traits. Currently, no physiological, morphological or molecular innovation has been explicitly linked to the origin of pollen feeding, and several hypothesized links between different aspects ofHeliconiusbiology remain poorly tested. However, resolving these uncertainties will contribute to our understanding of how behavioural innovations evolve and subsequently alter the evolutionary trajectories of diverse traits impacting resource acquisition, life history, senescence and cognition.

The long-term accumulation of biodiversity has been punctuated by remarkable evolutionary transitions that allowed organisms to exploit new ecological opportunities. Mesozoic flying reptiles (the pterosaurs), which dominated the skies for more than 150 million years, were the product of one such transition. The ancestors of pterosaurs were small and probably bipedal early archosaurs1, which were certainly well-adapted to terrestrial locomotion. Pterosaurs diverged from dinosaur ancestors in the Early Triassic epoch (around 245 million years ago); however, the first fossils of pterosaurs are dated to 25 million years later, in the Late Triassic epoch. Therefore, in the absence of proto-pterosaur fossils, it is difficult to study how flight first evolved in this group. Here we describe the evolutionary dynamics of the adaptation of pterosaurs to a new method of locomotion. The earliest known pterosaurs took flight and subsequently appear to have become capable and efficient flyers. However, it seems clear that transitioning between forms of locomotion2,3—from terrestrial to volant—challenged early pterosaurs by imposing a high energetic burden, thus requiring flight to provide some offsetting fitness benefits. Using phylogenetic statistical methods and biophysical models combined with information from the fossil record, we detect an evolutionary signal of natural selection that acted to increase flight efficiency over millions of years. Our results show that there was still considerable room for improvement in terms of efficiency after the appearance of flight. However, in the Azhdarchoidea4, a clade that exhibits gigantism, we test the hypothesis that there was a decreased reliance on flight5–7 and find evidence for reduced selection on flight efficiency in this clade. Our approach offers a blueprint to objectively study functional and energetic changes through geological time at a more nuanced level than has previously been possible. Phylogenetic statistical analyses, biophysical models and information from the fossil record show that an evolutionary signal of natural selection acted to increase the flight efficiency of pterosaurs over millions of years.

This chapter compares two sexual systems: hermaphroditism (each individual can produce gametes of either sex) and gonochorism (each individual produces gametes of only one of the two distinct sexes) in crustaceans. These two main sexual systems contain a variety of alternative modes of reproduction, which are of great interest from applied and theoretical perspectives. The chapter focuses on the description, prevalence, analysis, and interpretation of these sexual systems, centering on their evolutionary transitions. The ecological correlates of each reproductive system are also explored. In particular, the prevalence of “unusual” (non-gonochoristic) reproductive strategies has been identified under low population densities and in unpredictable/unstable environments, often linked to specific habitats or lifestyles (such as parasitism) and in colonizing species. Finally, population-level consequences of some sexual systems are considered, especially in terms of sex ratios. The chapter aims to provide a broad and extensive overview of the evolution, adaptation, ecological constraints, and implications of the various reproductive modes in this extraordinarily successful group of organisms.

Rubisco sustains the biosphere through the fixation of CO2 into biomass. In plants and cyanobacteria, Form I Rubisco is structurally comprised of large and small subunits, whereas all other Rubisco Forms lack small subunits. Thus, the rise of the Form I complex through the innovation of small subunits represents a key, yet poorly understood, transition in Rubisco’s evolution. Through metagenomic analyses, we discovered a previously uncharacterized clade sister to Form I Rubisco that evolved without small subunits. This clade diverged prior to the evolution of cyanobacteria and the origin of the small subunit; thus, it provides a unique reference point to advance our understanding of Form I Rubisco evolution. Structural and kinetic data presented here reveal how a proto-Form I Rubisco assembled and functioned without the structural stability imparted from small subunits. Our findings provide insight into a key evolutionary transition of the most abundant enzyme on Earth and the predominant entry point for nearly all global organic carbon.

Significance Army ants form some of the largest insect societies on the planet and famously forage in mass raids, in which many thousands of ants stream out of the nest in search of live prey. Here we show that this complex collective behavior has evolved from group raiding, which is practiced by relatives of army ants with smaller colonies. Through laboratory experiments, we discovered that group raids and mass raids follow similar organizational principles and that mass raids emerge from group raids when colony size is artificially increased. This suggests that ancient expansions in colony size, rather than changes in individual behavioral rules, led to the evolution of mass raids in the first army ants., The mass raids of army ants are an iconic collective phenomenon, in which many thousands of ants spontaneously leave their nest to hunt for food, mostly other arthropods. While the structure and ecology of these raids have been relatively well studied, how army ants evolved such complex cooperative behavior is not understood. Here, we show that army ant mass raiding has evolved from a different form of cooperative hunting called group raiding, in which a scout directs a small group of ants to a specific target through chemical communication. We describe the structure of group raids in the clonal raider ant, a close relative of army ants in the subfamily Dorylinae. We find evidence that the coarse structure of group raids and mass raids is highly conserved and that all doryline ants likely follow similar behavioral rules for raiding. We also find that the evolution of army ant mass raiding occurred concurrently with expansions in colony size. By experimentally increasing colony size in the clonal raider ant, we show that mass raiding gradually emerges from group raiding without altering individual behavioral rules. This suggests that increasing colony size can explain the evolution of army ant mass raids and supports the idea that complex social behaviors may evolve via mechanisms that need not alter the behavioral interaction rules that immediately underlie the collective behavior of interest.

The diversification of life-histories is mediated by cooperation, innovations of biological information, modularity, and heterochrony in developmental processes. These processes are defined, contextualized, and exemplified, studying the evolution of coloniality (i.e. life-history involving modularization of the multicellular individual) in the family of benthic tunicates Styelidae. This study proposes that in these colonial tunicates there is an inter-generational division of labor, where one generation is feeding, a second is developing by morphogenetic processes, and a third is aging by programmed cell death and phagocytosis. The communication system developed in these colonies is mediated, by changes in proportion, location, and gene expression of specialized blood cells. Colonial life-history in animals is related to the reduction of individual size; development of extra-corporeal tissues to interconnect zooids; the inter-generational division of labor; and the reduction of zooid’s individuality. Processes analogous with the widely accepted major evolutionary transitions (METs), suggesting that coloniality could be studied as a MET. The understanding of colonial life-histories could provide information about key mechanisms for life diversification.

Unlike all other archaeal lineages, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaea are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here we reconstructed the genomic content and growth temperature of the ancestor of all AOA as well as the ancestors of the marine and soil lineages based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (I) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (II) an expansion of regulatory capacities in transcription and central metabolic functions and (III) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.

The evolutionary transition to multicellularity has occurred on numerous occasions, but transitions to complex life forms are rare. While the reasons are unclear, relevant factors include the intensity of within-versus between-group selection that are likely to have shaped the course of life cycle evolution. A highly structured environment eliminates the possibility of mixing between evolving lineages, thus ensuring strong competition between groups. Less structure intensifies competition within groups, decreasing opportunity for group-level evolution. Here, using populations of the bacteriumPseudomonas fluorescens,we report the results of experiments that explore the effect of lineage mixing on the evolution of nascent multicellular groups. Groups were propagated under regimes requiring reproduction via a life cycle replete with developmental and dispersal (propagule) phases, but in one treatment lineages never mixed, whereas in a second treatment, cells from different lineages experienced intense competition during the dispersal phase. The latter treatment favoured traits promoting cell growth at the expense of traits underlying group fitness – a finding that is supported by results from a mathematical model. Together our results show that the transition to multicellularity benefits from ecological conditions that maintain discreteness not just of the group (soma) phase, but also of the dispersal (germline) phase.

Cellular differentiation is one of the hallmarks of complex multicellularity, allowing individual organisms to capitalize on among-cell functional diversity. The evolution of multicellularity is a major evolutionary transition that allowed for the increase of organismal complexity in multiple lineages, a process that relies on the functional integration of cell-types within an individual. Multiple hypotheses have been proposed to explain the origins of cellular differentiation, but we lack a general understanding of what makes one cell-type distinct from others, and how such differentiation arises. Here, we describe how the use of Boolean networks (BNs) can aid in placing empirical findings into a coherent conceptual framework, and we emphasize some of the standing problems when interpreting data and model behaviors.

Shewanella strains are characterized by versatile metabolic capabilities, resulting in their wide distribution in the ocean at different depths. Considering that particle sedimentation is an important dynamic process in the ocean, we hypothesized that hadal Shewanella species evolved from the upper ocean. In this study, we isolated three novel Shewanella strains from deep-sea sediments in the Southwest Indian Ocean. Genome sequencing indicated that strains YLB-06 and YLB-08 represent two novel species in the genus Shewanella. Through phylogenomic analysis, we showed that speciation and genomic changes in marine Shewanella strains are related to water depth. We further confirmed the aforementioned hypothesis and revealed a two-stage process of the evolutionary transition of Shewanella from the upper ocean to the hadal zone by comparative genomics and gene gain/loss analysis. Finally, the transcriptomic analysis demonstrated that recently obtained genes are strictly repressed and may thus play a minor role in the response to environmental changes.

Dramatic evolutionary transitions in morphology are often assumed to be adaptive in a new habitat. However, these assumptions are rarely tested because such tests require intermediate forms, which are often extinct. In vertebrates, the evolution of an elongate, limbless body is generally hypothesized to facilitate locomotion in fossorial and/or cluttered habitats. However, these hypotheses remain untested because few studies examine the locomotion of species ranging in body form from tetrapod to snake-like. Here, we address these functional hypotheses by testing whether trade-offs exist between locomotion in surface, fossorial and cluttered habitats in Australian Lerista lizards, which include multiple intermediate forms. We found that snake-like species penetrated sand substrates faster than more lizard-like species, representing the first direct support of the adaptation to fossoriality hypothesis. By contrast, body form did not affect surface locomotion or locomotion through cluttered leaf litter. Furthermore, all species with hindlimbs used them during both fossorial and surface locomotion. We found no evidence of a trade-off between fossorial and surface locomotion. This may be either because Lerista employed kinematic strategies that took advantage of both axial- and limb-based propulsion. This may have led to the differential occupation of their habitat, facilitating diversification of intermediate forms.

Evolutionary transitions in individuality (hereafter, ETIs), such as the transition to multi-cellularity and the transition to social colonies, have been at the centre of evolutionary research, but only few attempts were made to systematically operationalize this concept. Here, we devise a set of four indicators intended to assess the change in complexity during ETIs: system size, inseparability, reproductive specialization and non-reproductive specialization. We then conduct a quantitative comparison across multiple taxa and ETIs. Our analysis reveals that inseparability has a crucial role in the process; it seems irreversible and may mark the point where a group of individuals becomes a new individual at a higher hierarchical level. Interestingly, we find that disparate groups demonstrate a similar pattern of progression along ETIs.

Symbiotic interactions between organisms have aided major evolutionary transitions. The interaction between two microorganisms has parallels with the evolution of mitochondria — key organelles in eukaryotic cells. Symbiosis between two microorganisms sheds light on organelle evolution.

Significance The origin of mitochondria is a challenging and intensely debated issue. Mitochondria are ancestrally present in eukaryotes, and their endosymbiotic inclusion was an extremely important step during the transition from prokaryotes to eukaryotes. However, because of the unknown order of eukaryotic inventions (e.g., cytoskeleton, phagocytosis, and endomembranes), it is unknown whether they led to or followed the acquisition of mitochondria. According to the farming hypothesis, the mitochondrial ancestor was captured by a phagocytotic host, but the advantage was not direct metabolic help provided by the symbiont; rather, it was provisioning captured prey to farmers in poor times, like humans farm pigs. Our analytical and computational models prove that farming could lead to stable endosymbiosis without any further benefit assumed between partners., The origin of mitochondria was a major evolutionary transition leading to eukaryotes, and is a hotly debated issue. It is unknown whether mitochondria were acquired early or late, and whether it was captured via phagocytosis or syntrophic integration. We present dynamical models to directly simulate the emergence of mitochondria in an ecoevolutionary context. Our results show that regulated farming of prey bacteria and delayed digestion can facilitate the establishment of stable endosymbiosis if prey-rich and prey-poor periods alternate. Stable endosymbiosis emerges without assuming any initial metabolic benefit provided by the engulfed partner, in a wide range of parameters, despite that during good periods farming is costly. Our approach lends support to the appearance of mitochondria before any metabolic coupling has emerged, but after the evolution of primitive phagocytosis by the urkaryote.

Imperfect knowledge of ancestral behaviour often hampers tracing behavioural evolution. This limitation is reduced in orb weaving spiders, because spider orb web construction behaviour and the cues used by modern orb-weavers are well-studied and highly conserved. Several species in orb-weaving families build non-orb webs that are clearly derived from orbs, allowing transitions from ancestral to modern behaviours to be described with high confidence. Three major patterns of general evolutionary significance were found in 69 phylogenetically independent transitions in 15 groups in 8 families: ancestral traits were often maintained as units; the most frequent of the eight different types of ancestral trait change was transfer of an ancestral behaviour to a new context; and ‘new’ traits that had no clear homology with ancestral traits were also common. Changes occurred in all major stages of orb construction. This may be the most extensive summary of evolutionary transitions in behaviour yet compiled.

Understanding the evolutionary forces that influence sexual dimorphism is a fundamental goal in biology. Here, we focus on one particularly extreme example of sexual dimorphism. Many mammal species possess a bone in their penis called a baculum. The female equivalent of this bone is called the baubellum and occurs in the clitoris, which is developmentally homologous to the male penis. To understand the potential linkage between these two structures, we scored baculum/baubellum presence/absence across 163 species and analyzed their distribution in a phylogenetic framework. The majority of species (N = 134) shared the same state in males and females (both baculum and baubellum present or absent). However, the baubellum has experienced significantly more transitions, and more recent transitions, so that the remaining 29 species have a baculum but not a well‐developed baubellum. Even in species where both bones are present, the baubellum shows more ontogenetic variability and harbors more morphological variation than the baculum. Our study demonstrates that the baculum and baubellum are generally correlated across mammals, but that the baubellum is more evolutionarily and developmentally labile than the baculum. The accumulation of more evolutionary transitions, especially losses in the baubellum, as well as noisier developmental patterns, suggests that the baubellum may be nonfunctional, and lost over time.

Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes, and in those creating a new pair. In fact, substitution rates are biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of “drift-induced selection” operating at every point along the equilibrium paths: stochastic jumps off the paths return with, on average, a directional bias in favor of the dominant segregating sex chromosome. Our results offer a novel explanation for the observed preponderance of dominant sex determining genes, and hint that drift-induced selection may be a common force in standard population genetic systems.

The evolutionary transition from single-celled to multicellular growth is a classic and intriguing problem in biology. Saccharomyces cerevisiae is a useful model to study questions regarding cell aggregation, heterogeneity and cooperation. In this review, we discuss scenarios of group formation and how this promotes facultative multicellularity in S. cerevisiae. We first describe proximate mechanisms leading to aggregation. These mechanisms include staying together and coming together, and can lead to group heterogeneity. Heterogeneity is promoted by nutrient limitation, structured environments and aging. We then characterize the evolutionary benefits and costs of facultative multicellularity in yeast. We summarize current knowledge and focus on the newest state-of-the-art discoveries that will fuel future research programmes aiming to understand facultative microbial multicellularity.

The evolution and diversification of animal reproductive modes have been pivotal questions in behavioral ecology. Amphibians present the highest diversity of reproductive modes among vertebrates, involving various behavioral, physiological and morphological traits. One of such features is the amplexus, the clasp or embrace of males on females during reproduction, which is almost universal to anurans. Hypotheses about the origin amplexus are limited and have not been thoroughly tested, nor had they taken into account evolutionary relationships in most comparative studies. However, these considerations are crucial to understand the evolution of reproductive modes. Here, using an evolutionary framework, we reconstruct the ancestral state of amplexus in 686 anuran species; investigate whether the amplexus type is a conserved trait; and test whether sexual size dimorphism (SSD) could have influenced the amplexus type or male performance while clasping females. Overall, we found evidence of at least 35 evolutionary transitions in amplexus type across anurans. We also found that amplexus exhibits a high phylogenetic signal (it is conserved across Anura evolutionary history) and the amplexus type does not evolve in association with SSD. We discuss the implications of our findings on the diversity of amplexus types across anurans.