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International audience; While the exploitation of aquatic fauna and flora has been documented in several primate species to date, the evolutionary contexts and mechanisms behind the emergence of this behavior in both human and non-human primates remain largely overlooked. Yet, this issue is particularly important for our understanding of human evolution, as hominins represent not only the primate group with the highest degree of adaptedness to aquatic environments, but also the only group in which true coastal and maritime adaptations have evolved. As such, in the present study we review the available literature on primate foraging strategies related to the exploitation of aquatic resources and their putative associated cognitive operations. We propose that aquatic resource consumption in extant primates can be interpreted as a highly site-specific behavioral expression of a generic adaptive foraging decision-making process, emerging in sites at which the local cost-benefit trade-offs contextually favor aquatic over terrestrial foods. Within this framework, we discuss the potential impacts that the unique intensification of this behavior in hominins may have had on the evolution of the human brain and spatial ecology.

International audience; The COVID-19 pandemic has led to a resurgence of the debate on whether host-parasite interactions should evolve towards avirulence. In this review, we first show that SARS-CoV-2 virulence is evolving, before explaining why some expect the mortality caused by the epidemic to converge towards that of human seasonal alphacoronaviruses. Leaning on existing theory, we then include viral evolution into the picture and discuss hypotheses explaining why the virulence has increased since the beginning of the pandemic. Finally, we mention some potential scenarios for the future.

The collection of animal position data via GPS tracking devices has increased in quality and usage in recent years. Animal position and movement, although measured discretely, follows the same principles of kinematic motion, and as such, the process is inherently continuous and differentiable. I demonstrate the functionality and visual elegance of smoothing spline models. I discuss the challenges and benefits of implementing such an approach, and I provide an analysis of movement and social interaction of seven jaguars inhabiting the Taiamã Ecological Station, Pantanal, Brazil, a region with the highest known density of jaguars. In the analysis, I derive measures for pairwise distance, cooccurrence, and spatiotemporal association between jaguars, borrowing ideas from density estimation and information theory. These measures are feasible as a result of spline model estimation, and they provide a critical tool for a deeper investigation of cooccurrence duration, frequency, and localized spatio‐temporal relationships between animals. In this work, I characterize a variety of interactive relationships between pairs of jaguars, and I particularly emphasize the relationships in movement of two male–female and two male–male jaguar pairs exhibiting highly associative relationships., I propose the use of smoothing spline models to explore animal movement and social interaction. I propose temporal‐state density estimation and localized mutual information measures to characterize behavior and strength of association between jaguars on a refined and unified time grid. I provide further characterization of time‐dependent male–male and female–male relationships in this region, an important step in determining conservation policy for an endangered neotropical predator.

International audience; Oropouche fever is a zoonotic dengue-like syndrome caused by Oropouche virus. In August–September 2020, dengue-like syndrome developed in 41 patients in a remote rainforest village in French Guiana. By PCR or microneutralization, 23 (82.1%) of 28 tested patients were positive for Oropouche virus, documenting its emergence in French Guiana.

International audience; An outbreak of severe acute respiratory syndrome coronavirus 2 caused by the Gamma variant of concern infected 24/44 (55%) employees of a gold mine in French Guiana (87% symptomatic, no severe forms). The attack rate was 60% (15/25) among fully vaccinated miners and 75% (3/4) among unvaccinated miners without a history of infection.

Hermetia illucens, the black soldier fly, is a dipteran of the family Stratiomyidae. This detritivorous insect is increasingly used in mass production to reduce bio-waste and produce food for aquaculture and poultry farms. It originates from the north of Latin America and has spread over much of the planet. For the last ten years, many companies have been breeding and processing larvae from a circular economy perspective. This CIFRE thesis aims to improve genetic and genomic knowledge on the black soldier fly for performance improvement and selection. We focused, in a first step, on obtaining and analyzing a reference genome for the species using hybrid sequencing. We also worked on the genetic diversity and invasive history of BSF. We did this through global sampling using the CO1 gene and assembling about 60 complete mitochondrial genomes. We have shown the complexity of the black soldier fly's invasion scenarios combining an ancient process of natural dispersal on the American continent and the importance of human introductions, notably due to industrial breeding. Finally, we also looked at the structural variations of the genomes induced by transposable elements in natural populations of Hermetia illucens to determine the most active elements in the genomes and their evolutionary dynamics. This work revealed the species' surprising and unexpected genetic and genomic diversity. It opens new perspectives towards selection and improvement experiments on the black soldier fly for the entomoculture industry., Hermetia illucens, la mouche soldat noire, est un diptère de la famille des Stratiomyidae. Cet insecte détritivore est de plus en plus utilisé en élevage de masse pour réduire les biodéchets et produire de la nourriture à destination des élevages aquacoles et avicoles. Elle est originaire du nord de l'Amérique Latine et s'est répandue sur une grande partie de la planète. Depuis une dizaine d'années, un nombre croissant d'entreprises élèvent et transforment des larves dans une optique d'économie circulaire. Cette thèse CIFRE a pour but d'améliorer les connaissances génétiques et génomiques sur la mouche soldat noire pour l'amélioration des performances et de la sélection. Nous nous sommes concentrés, dans un premier temps, sur l'obtention et l'analyse d'un génome de référence, pour l'espèce en utilisant du séquençage hybride. Nous avons également travaillé sur la diversité génétique et l'histoire invasive de la BSF. Nous l'avons fait au moyen d'un échantillonnage mondial en utilisant à la fois le gène CO1 et l'assemblage d'une soixantaine de génomes mitochondriaux complets. Nous avons montré la complexité des scénarios d'invasion de la mouche soldat noire combinant à la fois un processus ancien de dispersion naturelle sur le continent Américain ainsi que, l'importance des introductions humaines, notamment en raison des élevages industriels. Enfin nous nous sommes également intéressés aux variations structurales des génomes, induites par les éléments transposables dans les populations naturelles d'Hermetia illucens, afin de déterminer les éléments les plus actifs dans les génomes ainsi que leurs dynamiques évolutives. Ce travail a révélé une étonnante et inattendue diversité génétique et génomique au sein de l'espèce. Il ouvre de nouvelles perspectives vers des expérimentations de sélection et d'amélioration sur la mouche soldat noire pour l'industrie entomocole.

The complexity of food webs and how it depends on environmental variables is a long-standing question in ecology. Food-chain length depends on many factors, such as productive space, disturbance and spatial processes. It is not clear though how food-chain length should vary with adaptive evolutionary changes of the constitutive species. Assuming that each trophic level is subject to a competition-colonization trade-off, we model the adaptive evolution of their colonization rates and its consequences on equilibrium occupancies and food-chain length. When colonization rates are allowed to evolve, longer food chains can persist. Extinction, perturbation and habitat loss all affect the evolutionary-stable colonization rates, but trade-off strength (costs of dispersal) has a major role: weaker trade-offs yield longer chains. Our results suggest a strong link between within-trophic level competition, spatial occupancies and food-chain length. Although these eco-evo dynamics partly alleviate the constraint on food-chain length in metacommunities, we show it is no magic bullet: the highest, most vulnerable, trophic levels are also those that least benefit from evolution. Our model generates qualitative predictions regarding how trait evolution affects the response of communities to disturbance and habitat loss. This highlights the importance of eco-evolutionary dynamics at metacommunity level in determining food-chain length.

International audience; We present a unifying, tractable approach for studying the spread of viruses causing complex diseases that require to be modeled using a large number of types (e.g., infective stage, clinical state, risk factor class). We show that recording each infected individual's infection age, i.e., the time elapsed since infection, 1. The age distribution $n(t, a)$ of the population at time $t$ can be described by means of a first-order, one-dimensional partial differential equation (PDE) known as the McKendrick-von Foerster equation. 2. The frequency of type $i$ at time $t$ is simply obtained by integrating the probability $p(a, i)$ of being in state $i$ at age a against the age distribution $n(t, a)$. The advantage of this approach is three-fold. First, regardless of the number of types, macroscopic observables (e.g., incidence or prevalence of each type) only rely on a one-dimensional PDE "decorated" with types. This representation induces a simple methodology based on the McKendrick-von Foerster PDE with Poisson sampling to infer and forecast the epidemic. We illustrate this technique using a French data from the COVID-19 epidemic. Second, our approach generalizes and simplifies standard compartmental models using high-dimensional systems of ordinary differential equations (ODEs) to account for disease complexity. We show that such models can always be rewritten in our framework, thus, providing a low-dimensional yet equivalent representation of these complex models. Third, beyond the simplicity of the approach, we show that our population model naturally appears as a universal scaling limit of a large class of fully stochastic individual-based epidemic models, here the initial condition of the PDE emerges as the limiting age structure of an exponentially growing population starting from a single individual.

Antibiotic resistance is rapidly spreading by horizontal transfer of resistance genes in mobile genetic elements. While plasmids are key drivers of this process, very few integrative phages encode antibiotic resistance genes. Here, we find that phage-plasmids, elements that are both phages and plasmids, often carry antibiotic resistance genes. We found 60 phage-plasmids with 184 antibiotic resistance genes, including broad-spectrum-cephalosporins, carbapenems, aminoglycosides, fluoroquinolones and colistin. These genes are in a few hotspots, seem to have been co-translocated with transposable elements, and are often in class I integrons, which had not been previously found in phages. We tried to induce six phage-plasmids with resistance genes (including four with resistance integrons) and succeeded in five cases. Other phage-plasmids and integrative prophages were co-induced in these experiments. As a proof of principle, we focused on a P1-like element encoding an extended spectrum β-lactamase, blaCTX-M-55. After induction, we confirmed that it’s capable to infect and convert four other E. coli strains. Its re-induction led to further conversion of a sensitive strain, confirming it’s a fully functional phage. This study shows that phage-plasmids carry a large diversity of clinically relevant antibiotic resistance genes that they transfer across bacteria. As plasmids, these elements seem very plastic and capable of acquiring genes from other plasmids. As phages, they may provide novel paths of transfer for resistance genes, because they can infect bacteria distant in time and space from the original host. As a matter of alarm, they may also eventually mediate transfer to other types of phages.ImportanceDissemination of antimicrobial resistances is a major threat to global health. Here, we show that a group of temperate bacterial viruses (=phages), termed phage-plasmids, commonly encode different and multiple types of resistance genes of high clinical importance, often in integrons. This is unexpected since phages typically do not carry resistance genes and, hence, do not confer their hosts with resistance upon infection and genome integration. Our experiments with phage-plasmids isolated from clinical settings confirmed they infect sensitive strains, rendering them antibiotic resistant. The spread of antibiotic resistance genes by phage-plasmids is worrisome because it dispenses cell-to-cell contact, necessary for the canonical plasmid transfer (=conjugation). Furthermore, their integrons are now genetic platforms for the acquisition of novel resistance genes.

The cecal appendix had been considered as a useless vestige since Darwin's work, but recent research questioned this idea demonstrating that the cecal appendix appeared among the mammals at least 80 million years ago and has made multiple and independent appearances without any obvious correlation with diet, social life, ecology, or size of the cecum. However, functions and probable selective advantage conferred by this anatomical structure still remain enigmatic. We found, through analyses of data on 258 mammalian species, that cecal appendix presence is correlated with increased maximal observed longevity. This is the first demonstration of a correlation between cecal appendix presence and life history. Interestingly, the classical evolutionary theory of aging that predicts an increased longevity when the extrinsic mortality is reduced has been questioned several times, but recent comparative studies asserted its validity in the taxa, which experience age‐dependent and density‐dependent mortality, as in mammals. Thus, the cecal appendix may contribute to the increase in longevity through a reduction of extrinsic mortality. A lower risk of fatal infectious diarrhea is one of the most plausible hypotheses that could explain it. However, several hypotheses coexist about the possible functions of the cecal appendix, and our results provide new insights about this much‐disputed question. In addition, we show that the cecal appendix arose at least 16 times and was lost only once during the evolutionary history of the considered mammals, an asymmetry that supports the existence of a positive selective of this structure., Most people think about the appendix as a useless and even harmful structure that is removed on emergency in case of appendicitis. This belief harks as far back as Darwin, but it has been questioned by recent works that suggests that the cecal appendix does have a function. In this study, we found that the presence of an appendix is correlated with greater longevity in mammals, even when controlling for the strong positive size effects and for the phylogeny.

International audience; Human papillomaviruses (HPVs), the most oncogenic virus known to humans, are often associated with Herpes Simplex Virus-2 (HSV-2) infections. The involvement of the latter in cervical cancer is controversial but its longterm infections might modulate the mucosal microenvironment in a way that favors carcinogenesis. We know little about coinfections between HSV-2 and HPVs, and studying the immunological and microbiological dynamics in the early stages of these infections may help identify or rule out potential interactions. We report two cases of concomitant productive, although asymptomatic, HSV-2 and HPV infections in young women (aged 20 and 25). The women were followed up for approximately a year, with clinical visits every two months and weekly self-samples. We performed quantitative analyses of their HSV-2 and HPV viral loads, immunological responses (IgG and IgM antibodies and local cytokines expression profiles), vaginal microbiota composition, as well as demographic and behavior data. We detect interactions between virus loads, immune response, and the vaginal microbiota, which improve our understanding of HSV-2 and HPVs' coinfections and calls for further investigation with larger cohorts.

International audience; Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available on github.com/evolbioinfo/phylodeep.

We analyzed 324,734 SARS-CoV-2 variant screening tests from France enriched with 16,973 whole-genome sequences sampled during September 1, 2021-February 28, 2022. Results showed the estimated growth advantage of the Omicron variant over the Delta variant to be 105% (95% CI 96%-114%) and that of the BA.2 lineage over the BA.1 lineage to be 49% (95% CI 44%-52%). Quantitative PCR cycle threshold values were consistent with an increased ability of Omicron to generate breakthrough infections. Epidemiologic modeling shows that, in spite of its decreased virulence, the Omicron variant can generate important critical COVID-19 activity in hospitals in France. The magnitude of the BA.2 wave in hospitals depends on the level of relaxing of control measures but remains lower than that of BA.1 in median scenarios.

New gene formation is one of the major sources of evolutionary innovations for organisms. Beyond their mutational effects, transposable elements can be source of new genes. During my thesis, I have studied Harbinger DNA transposons, which I have characterized in teleost fish genomes. Moreover, I have identified four new genes derived from Harbinger transposons in vertebrates by bioinformatical screening. Three of them were formed at the base of jawed vertebrates around 500 million years ago, and another at the base of sarcopterygians around 430 million years ago. Using the zebrafish model, we have observed that these genes are expressed during early development and in adult tissues, with a co-expression in male brain. They are also activated in human brain, particularly during fetal development. In order to study Harbinger-derived genes function, their inactivation was performed using CRISPR/Cas9 and morpholino antisense oligonucleotide techniques. The inactivation of MSANTD2 gene, which has been associated with neurodevelopmental diseases such as autism spectrum disorder and schizophrenia, produced embryos with delayed development as well as tail and nervous system malformations, specifically with brain ventricles and neuronal pattern defects. Thus, this thesis has highlighted the recurrent and concomitant molecular domestications of Harbinger transposons, which have led to a new gene family in vertebrates. The study of one its member, MSANTD2, contributes to a better understanding of genetic innovations having driven the evolution of the nervous system in vertebrates., La formation de nouveaux gènes est une source majeure d’innovation pour les organismes. Au-delà de leurs effets mutagènes, les éléments transposables peuvent être source de nouveaux gènes. Lors de cette thèse, j’ai étudié les transposons à ADN Harbinger, que j’ai pu caractériser chez les poissons téléostéens. J’ai de plus identifié chez les vertébrés par criblage bioinformatique quatre nouveaux gènes dérivés de transposons Harbinger, trois formés à la base des vertébrés à mâchoires il y a environ 500 millions d’années et un chez les sarcoptérygiens il y a environ 430 millions d’années. Chez le poisson-zèbre, ces gènes sont exprimés pendant le développement précoce et dans les tissus adultes, avec une co-expression dans le cerveau mâle. Ils sont également activés dans le cerveau humain, en particulier pendant le développement fœtal. Afin d’étudier la fonction des gènes dérivés de transposons Harbinger, leur inactivation a été réalisée par CRISPR/Cas9 et oligonucléotides antisense de type morpholino. L’inactivation du gène MSANTD2, qui a été associé à des maladies neurodéveloppementales comme les troubles du spectre de l’autisme et la schizophrénie, produit des embryons présentant des retards de développement et des malformations de la queue et du système nerveux, en particulier des défauts de formation des ventricules du cerveau et de patterns neuronaux. Ainsi, cette thèse a permis de mettre en évidence des domestications moléculaires récurrentes de transposons Harbinger qui ont abouti à la formation d’une nouvelle famille de gènes chez les vertébrés. L’étude d’un des membres, MSANTD2, contribue à une meilleure compréhension des innovations génétiques qui ont déterminé l’évolution précoce du système nerveux des vertébrés.

International audience; Infectious disease transmission patterns in some outbreaks can be more heterogeneous than in others, with striking effects on the way epidemics unfold. Some studies show that the biological sources of heterogeneity may matter, but they tend to do so without controlling for the overall heterogeneity in the number of secondary cases caused by an infection. Here, we control for this important bias to explore the role of individual variation in infection duration and transmission rate on parasite emergence and spread. We simulate outbreaks using a stochastic SIR model, with and without parasite evolution. Consistently with existing studies, we show that the variance in the number of secondary infections has the strongest effect on outbreak emergence probability but has little effect on the epidemic dynamic once emergence is certain. The origin of heterogeneity also affects the probability of emergence, but its more striking effects are about properties of epidemics that do emerge. In particular, assuming more realistic variances in infection duration distributions lead to faster outbreaks and a higher peak of incidence. When the parasite requires evolutionary changes to be able to spread, the impact of heterogeneity depends on the underlying evolutionary model. If the parasite evolves within the host, decreasing the infection duration variance decreases the probability of emergence. These results show that using realistic distributions for infection duration is necessary to accurately capture the effect of individual heterogeneity on epidemiological dynamics, which has implications for the monitoring and control of infectious diseases, as well as data collection.

Beta-defensins are an essential group of cysteine-rich host-defence peptides involved in vertebrate innate immunity and are generally monodomain. Among bird defensins, the avian β-defensin 11 (AvBD11) is unique because of its peculiar structure composed of two β-defensin domains. The reasons for the appearance of such ‘polydefensins’ during the evolution of several, but not all branches of vertebrates, still remain an open question. In this study, we aimed at exploring the origin and evolution of the bird AvBD11 using a phylogenetic approach. Although they are homologous, the N- and C-terminal domains of AvBD11 share low protein sequence similarity and possess different cysteine spacing patterns. Interestingly, strong variations in charge properties can be observed on the C-terminal domain depending on bird species but, despite this feature, no positive selection was detected on the AvBD11 gene (neither on site nor on branches). The comparison of AvBD11 protein sequences in different bird species, however, suggests that some amino acid residues may have undergone convergent evolution. The phylogenetic tree of avian defensins revealed that each domain of AvBD11 is distant from ovodefensins (OvoDs) and may have arisen from different ancestral defensins. Strikingly, our phylogenetic analysis demonstrated that each domain of AvBD11 has common ancestors with different putative monodomain β-defensins from crocodiles and turtles and are even more closely related with these reptilian defensins than with their avian paralogs. Our findings support that AvBD11′s domains, which differ in their cysteine spacing and charge distribution, do not result from a recent internal duplication but most likely originate from a fusion of two different ancestral genes or from an ancestral double-defensin arisen before the Testudines-Archosauria split.

For the past century, scientists have debated whether or not ageing is directly selected by evolution. Because ageing occurs, by definition, late in life - that is, after the organism’s development is complete - many people believe that it cannot be actively selected for as a process. Furthermore, because it reduces an individual’s fitness, it is thought unlikely to be selected for. In agreement with this viewpoint, numerous theories have been proposed in the last 75 years to explain the observation of its widespread presence in the realm of life. The bd model of ageing is based on a simple life-history trait model that we recently introduced.Our model suggests that senescence can be positively selected through evolution due to the increased evolvability it confers on organisms, not through a specific mechanism but through a ‘function ageing’, limiting organismal maintenance and reproduction. It confirms the substrate for mutation accumulation and antagonistic pleiotropy theories while providing an elegant explanation for the apparent tradeoff between longevity and fertility that led to the disposable soma theory without requiring an energy tradeoff. Furthermore, it predicts that the Lansing effect will be present in organisms that exhibit rapid post-reproductive senescence. This formal and numerical modeling of the evolution of ageing also provides new hints for testing the validity of existing theories.

International audience; Ionotropic glutamate receptors (iGluRs) are a major class of ligand-gated ion channels that are widespread in the living kingdom. Their critical role in excitatory neurotransmission and brain function of vertebrates has made them a compelling subject of interest for neurophysiologists and pharmacologists. This is particularly true for NMDA receptor (NMDARs), a subclass of iGluRs that act as central drivers of synaptic plasticity in the CNS. How and when the unique properties of NMDARs arose during evolution, and how they relate to the evolution of the nervous system, remain open questions. Recent years have witnessed a boom in both genomic and structural data, such that it is now possible to analyse the evolution of iGluR genes on an unprecedented scale and within a solid molecular framework. In this review, combining insights from phylogeny, atomic structure and physiological and mechanistic data, we discuss how evolution of NMDAR motifs and sequences shaped their architecture and functionalities. We trace differences and commonalities between NMDARs and other iGluRs, emphasizing a few distinctive properties of the former regarding ligand binding and gating, permeation, allosteric modulation and intracellular signalling. Finally, we speculate on how specific molecular properties of iGuRs arose to supply new functions to the evolving structure of the nervous system, from early metazoan to present mammals.

International audience; A 1-year population-based prospective study was launched in Seychelles, a country with one of the highest human incidence of leptospirosis worldwide, to describe the characteristic features of the epidemiology of the disease and highlight the most prominent risk factors. Diagnosis was based on the IgM enzyme-linked immunosorbent assay, microscopic agglutination test, and real-time PCR. A standardized questionnaire was administered to 219 patients aged ³ 13 years consulting for acute febrile illness. The high incidence of leptospirosis in Seychelles was confirmed. The disease was particularly severe, as the case fatality rate was 11.8%. Leptospirosis was positively associated in univariate analysis with socio-professional and clinical variables including gardening/farming, oliguria, jaundice, conjunctivitis, history of hepatitis C virus infection, anemia, thrombocytopenia, and/or biological renal failure. Epidemiological analyses of the questionnaires highlighted a link of the disease with living in houses (versus apartment), the presence of animals around and in houses, gardening, and misuse of personal protective equipment. Multivariate analyses indicated that being a farmer/landscaper and having cattle and cats around the home are the most significant drivers of leptospirosis. Biological features most associated with leptospirosis were thrombocytopenia, leukocytosis, high values for renal function tests, and elevated total bilirubin. We report changes in behavior and exposure compared with data collected on leptospirosis 25 years ago, with indication that healthcare development has lowered case fatality. Continuous health education campaigns are recommended as well as further studies to clarify the epidemiology of human leptospirosis, especially the role of domestic animals.

When environmental conditions are unpredictable, expressing alternative phenotypes spreads the risk of failure, a mixed strategy called bet-hedging. In the southern part of its range, the Parsley frog Pelodytes punctatus breeds from autumn to spring. Our aim was to study the breeding phenology and reproductive success associated with the use of those two seasonal niches to understand how this breeding strategy can be maintained. Field surveys revealed that breeding phenology was typically bimodal with a higher breeding effort in autumn. More importantly, in spring, the survival rate of offspring was severely reduced by the presence of autumn tadpoles, indicating a clear priority effect. However, the autumn cohort often failed to survive over winter, in which case spring cohorts were often successful. Based on those results, we constructed a model in which females can allocate a variable portion of eggs to each season and added a priority effect. We conclude that the existence of the two breeding seasons may indeed constitute a bet-hedging strategy.

High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve., This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900). S.R. was funded by the MICINN/FSE/AEI (PRE2018-084755) and VH was funded by the Generalitat de Catalunya (FI2017_B00468). DrosEU is funded by an ESEB Special Topic Network award.

Cephalopod beaks provide critical information in understanding cephalopod biology, their ecology and their role in marine ecosystems. Although mandible shape has been shown to be adaptive in many vertebrate taxa, coleoid beak shape and its possible relationships with trophic ecology and habitat use has never been investigated. This is partly due to the consensus that the diet of coleoids is not diversified enough for the beaks to reflect dietary adaptations. More recently, studies have proposed that the beaks of paralarvae of octopods, argonauts, and some squid show features that may facilitate prey ingestion, and that the diet varies during the life cycle, ranging from detritivory in paralarvae to carnivory in adults in some ommastrephid species. This suggests that the debate on the possible adaptive signal in cephalopod beaks should be revisited. Here, we investigated whether variation in cephalopod beak shape reflects ecology and/or, is driven by phylogenetic relatedness. We imaged 101 lower and 108 upper beaks in 3D belonging to 75 species of octopods and squids. Morphometric analysis shows that there is a significant but only moderate phylogenetic signal. Comparative, phylogenetically informed, analyses demonstrate that beak shape is also driven by ecology. We detected significant differences in beak shape between species inhabiting different habitats (pelagic, benthic, or demersal) and of different trophic levels. These results provide new insights into the drivers of beak shape diversity in coleoids and suggest that beak shape has evolved adaptively in relation to diet and habitat use.

International audience; Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting cooccurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site. bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.

International audience; Commentaire du livre d'Adam Kucharski.

À l’origine de la diversité du vivant, l’évolution biologique est le phénomène par lequel les espèces naissent, se transforment ou disparaissent au cours du temps. Son étude fait intervenir des méthodes d’analyse sophistiquées qui reposent à la fois sur la modélisation mathématique des processus biologiques qui interviennent et sur la conception d’algorithmes efficaces pour ajuster ces modèles aux données génétiques et morphologiques.Modèles et méthodes pour l’évolution biologique expose les principales méthodes utilisées pour étudier l’évolution et offre un large panorama illustrant la variété des approches formelles mises en oeuvre notamment dans l’optimisation combinatoire, les modèles stochastiques, l’inférence statistique, l’échantillonnage par Monte-Carlo.Certaines des applications marquantes de ces méthodes y sont détaillées. Elles concernent, par exemple, l’étude d’événements migratoires des anciennes populations humaines ou la progression des épidémies.

Report and scientific justification of the project: al-Ula DPA Project : Ethnographic, genetic, and morphometric analyses of the date palm agrobiodiversity in al-‘Ulā oasis.Annual Report to AFALULA (Agence française pour le développement d'al-Ula) & RCU (Royal Commission for AlUla)., Rapport et justification scientifique du projet: al-Ula DPA Project : Ethnographic, genetic, and morphometric analyses of the date palm agrobiodiversity in al-‘Ulā oasis.Rapport annuel à AFALULA (Agence française pour le développement d'al-Ula) & RCU (Royal Commission for al-‘Ulā).

This version of the article has been peer-reviewed and recommended by Peer Community in Evolutionary Biology (https://peercommunityjournal.org/item/10.24072/pcjournal.190.pdf).Raw mapping files (BAM files) and metadata have been uploaded to the Short Read Archive (SRA, NCBI) under the bioproject ID PRJNA603262 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA603262/).Custom scripts produced for data analysis are deposited in Zenodo (https://doi.org/10.5281/zenodo.7225771).; Deciphering the genetic bases of behavioural traits is essential to understanding how they evolve and contribute to adaptation and biological diversification, but it remains a substantial challenge, especially for behavioural traits with polygenic architectures. In this study, we developed a population genomics approach coupled with functional predictions to address the evolution and genetic basis of olfactory-based assortative mate preferences in the house mouse, suspected tohave evolved as a response to selection against hybridisation. We used whole genome resequencing data and the C2 statistic of the program BAYPASS, which contrasts allele frequencies corrected for population structure, to characterize genetic differentiation between sets of populations with strong contrast in behaviour (expressing or not assortative mate preferences) and we identified some regions of the genome showing the expected significant and consistentassociation with behavioural divergence. A series of Olfactory and Vomeronasal Receptor genes, among the most differentiated genomic regions and in line with functional predictions, stand out as the prime candidates underlying this olfactory-based behavioural divergence. These genes form large gene clusters in the genome, with two main candidate clusters extending up to 1.8 Mb. Variant analyses indicate a potential dual role of regulatory and protein-coding changes in theevolution of choosiness. This study shows that combining expectations on the genomic patterns of divergence with functional expectations represents a promising route to unravelling the genetic architecture of complex trait variation and provides novel insights into the role of olfactory and vomeronasal receptors in mammal adaptation and speciation.

Quorum sensing systems (QSSs) are genetic systems supporting cell-cell or bacteriophage-bacteriophage communication via the production and the detection of a signal molecule, the extracellular concentration of which reflects the density of the QSS-encoding population. QSSs have a prime importance in the regulation of key biological processes such as virulence, sporulation or biofilm formation in bacteria, conjugation in plasmids or lysogeny in temperate bacteriophages. However, the genetic diversity of QSSs remains largely underexplored and the same holds for the diversity of organisms, plasmids and viruses encoding these systems. Hence, many bacterial and viral density-dependent behaviors likely await to be discovered, some of which could perhaps transform our views of microbial adaptation and of the co-evolution between bacteria and their mobile genetic elements. Specifically, this PhD in evolutionary bioinformatics explores the phylogenetic and functional diversity of quorum sensing using genome and network analysis methods applied to genetic elements traditionally neglected by this research field: genomes of poorly known lineages such as CPRs and DPANNs, environmental metagenomes, viral genomes or plasmids. In particular, this thesis lays the theoretical foundations for the inference of communication networks within environmental microbial communities and includes the development of a new method allowing the identification of QSSs of the RRNPP type (Rap-Rgg-NprR-PlcR-PrgX) that are non-homologous to already known QSSs. This work notably reveals the first bilingual bacteriophages, i.e. encoding two QSSs belonging to different genetic families, as well as the first bacteriophages predicted to manipulate in a density-dependent manner the biology of their bacterial host., Les systèmes de « Quorum Sensing » (QSSs) sont des systèmes génétiques permettant la communication entre cellules ou entre bactériophages. Cette communication est réalisée par l’émission et la détection d’une molécule signal dont la concentration extracellulaire reflète la densité de la population codant le QSS. Les QSSs ont une importance capitale dans la régulation densité-dépendante de processus biologiques clés tels que la virulence, la sporulation ou la formation de biofilms chez les bactéries, la conjugaison chez les plasmides, ou la lysogénie chez les bactériophages tempérés. Néanmoins, la diversité des QSSs demeure largement sous-explorée et il en va de même pour celle des organismes, plasmides et virus codant ces systèmes. Ainsi, beaucoup de comportements microbiens/viraux régulés de façon densité-dépendante restent probablement à découvrir, dont certains pourraient peut-être révolutionner notre vision de l’adaptation microbienne et de la coévolution entre bactéries et leurs éléments génétiques mobiles. Précisément, cette thèse de bioinformatique évolutive explore les diversités phylogénétique et fonctionnelle du processus de détection du quorum par des méthodes d’analyses de génomes et de réseaux appliquées à des éléments génétiques traditionnellement délaissés par ce champ de recherche : génomes de lignées méconnues comme les CPRs et les DPANNs, métagénomes environnementaux, génomes viraux ou encore plasmides. En particulier, cette thèse pose les bases théoriques de l’inférence de réseaux de communication au sein de communautés microbiennes environnementales et inclut le développement d’une nouvelle méthode permettant l’identification de QSSs de type RRNPP (Rap-Rgg-NprR-PlcR-PrgX) non homologues à des QSSs déjà connus. Ce travail révèle notamment les premiers bactériophages bilingues, c’est-à-dire codant deux QSSs appartenant à des familles génétiques différentes ainsi que les premiers bactériophages prédits pour manipuler de façon densité-dépendante la biologie de leur hôte bactérien.

Climate change, urbanisation, chemical pollution and disruption of ecosystems, including biodiversity loss, affect our health and wellbeing. Research is crucial to be able to respond to the current and future challenges that are often complex and interconnected by nature. The HERA Agenda, summarised in this commentary, identifies six thematic research goals in the environment, climate and health fields. These include research to 1) reduce the effects of climate change and biodiversity loss on health and environment, 2) promote healthy lives in cities and communities, 3) eliminate harmful chemical exposures, 4) improve health impact assessment and implementation research, 5) develop infrastructures, technologies and human resources and 6) promote research on transformational change towards sustainability. Numerous specific recommendations for research topics, i.e., specific research goals, are presented under each major research goal. Several methods were used to define the priorities, including web-based surveys targeting researchers and stakeholder groups as well as a series of online and face-to-face workshops, involving hundreds of researchers and other stakeholders. The results call for an unprecedented effort to support a better understanding of the causes, interlinkages and impacts of environmental stressors on health and the environment. This will require breakdown of silos within policies, research, actors as well as in our institutional arrangements in order to enable more holistic approaches and solutions to emerge. The HERA project has developed a unique and exciting opportunity in Europe to consensuate priorities in research and strengthen research that has direct societal impact. The HERA project was funded from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 825417.

Travail du groupe de modélisation de l'équipe ETE

Continuously during their development, flowering plants produce a basic developmental unit:the phytomer. Canonical phytomers are composed of an internode and an axillary meristemsubtended by a leaf. The abrupt transition from vegetative to reproductive state remodels thecomposition of the phytomers. In most Brassicaceæ, including the model plant Arabidopsisthaliana, the reproductive phytomer looses its leaf, also called bract, producing a bractlesslateral floral meristem. However, production of flowers subtended by bracts have been reportedin specific environmental conditions, but only on the basal flowers of the inflorescence, producedduring floral transition. We show that in some natural accessions of Arabidopsis thaliana, suchbasal bract-flowers are common, yet not in the reference Col-0. Notably, in Tsu-0, bract-flowers are frequent regardless of environmental conditions. Moreover, contrary to what havebeen historically proposed, bract-flowers in Tsu-0 do not result from a conversion of branchesinto flowers. A transcriptomic analysis of shoot apices over floral transition in Tsu-0 andCol-0 reveals interesting heterochronies in the dynamic of gene expressions, although theirpotential link with bract production are still under investigation. To our knowledge, this studyfirst exposes the natural variations of transcriptomes from vegetative to flowering stages in A.thaliana. Notably, we show that gene expressions diverge the most precisely at the time offloral transition, recapitulating what have been previously described at an inter-species level.We also tried to map the genetic variations controlling bracts in Tsu-0 with both bulked F2segregant populations and Recombinants Inbred Lines. The genetic determinism of this trait iscomplex and we identified two major loci located in chromosome 1. We then crossed evidencefrom our genomic and transcriptomic data (including bract mutants) to propose some plausiblecandidate genes. From a particular case of natural variation, this study revisits the mechanismsthat control bract formation in A. thaliana and their links with floral transition. By extension,our results could also enlighten the evolutionary origin of bract loss in Brassicaceæ., Le phytomère constitue l’élément de base du développement des plantes. Il se compose d’un entre-noeud, et d’un méristème sous-tendu par une feuille. Le passage du stade végétatif au stade reproductif entraine un remodelage du phytomère. Chez les Brassicaceæ, dont la plante modèle Arabidopsis thaliana, cela s’illustre notamment par la perte de la feuille, appelée bractée. Cependant, de précédentes études ont rapporté la présence de bractées à l’aisselle des premières fleurs de certaines accessions naturelles de A. thaliana, lorsqu’elles sont cultivées dans des conditions environnementales spécifiques. Au cours de ma thèse, nous montrons que la présence de bractées au niveau des premières fleurs est fréquente chez certaines accessions naturelles d’A. thaliana, mais pas chez l’accession de référence Col-0. Chez Tsu-0, la présence de ces bractées ne dépend pas des conditions environnementales, et ne résultent pas d’une conversion de branches en fleurs, contrairement à ce qui avait été proposé. L’analyse transcriptomique de méristèmes apicaux caulinaires au cours de la transition florale chez ces deux accessions naturelles révèle des hétérochronies dans la dynamique d’expression des gènes. Le lien éventuel entre ces hétérochronies et la présence de bractées reste à établir. Cette étude décrit pour la première fois les différences de dynamique d’expression de gènes au cours de la transition florale à l’échelle de la population. Nous avons pu montrer que la différence d’expression des gènes entre deux accessions est à son apogée au moment précis de la transition florale, faisant echo à ce qui avait été montré à l’échelle de l’espèce. De plus, nous avons cartographié les variants génétiques responsables de la présence de bractées chez Tsu-0 en utilisant deux approches indépendantes, l’analyse génétique d’individus F2 segrégants en masse et l’utilisation de lignées recombinantes ségrégantes. Nous avons ainsi pu identifier deux régions situées dans le chromosome 1 et associées au phénotype. Le recoupement entre les analyses génétiques et transcriptomiques permet de proposer de potentiels gènes candidats. Ainsi, cette thèse revisite l’étude des mécanismes qui contrôlent l’inhibition de la bractée au moment de la transition florale chez A. thaliana, en se basant sur une comparaison entre deux populations naturelles. Par conséquent, ces résultats nous permettront de mieux comprendre l’origine évolutive de la perte des bractées chez les Brassicaceæ.

Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level functions of interest. These experiments typically involve selection acting on populations of communities, each of which is composed of multiple species. If numerical simulations started to explore the evolutionary dynamics of this complex, multi-scale system, a comprehensive theoretical understanding of the process of artificial selection of communities is still lacking. Here, we propose a general model for the evolutionary dynamics of communities composed of a large number of interacting species, described by disordered generalised Lotka-Volterra equations. Our analytical and numerical results reveal that selection for scalar community functions leads to the emergence, along an evolutionary trajectory, of a low-dimensional structure in an initially featureless interaction matrix. Such structure reflects the combination of the properties of the ancestral community and of the selective pressure. Our analysis determines how the speed of adaptation scales with the system parameters and the abundance distribution of the evolved communities. Artificial selection for larger total abundance is thus shown to drive increased levels of mutualism and interaction diversity. Inference of the interaction matrix is proposed as a method to assess the emergence of structured interactions from experimentally accessible measures.

Sex-ratio distorters based on X-chromosome shredding are more efficient than sterile male releases for population suppression. X-shredding is a form of sex distortion that skews spermatogenesis of XY males towards the preferential transmission of Y-bearing gametes, resulting in a higher fraction of sons than daughters. Strains harboring X-shredders on autosomes were first developed in the malaria mosquito Anopheles gambiae, resulting in strong sex-ratio distortion. Since autosomal X-shredders are transmitted in a Mendelian fashion and can be selected against, their frequency in the population declines once releases are halted. However, unintended transfer of X-shredders to the Y-chromosome could produce an invasive meiotic drive element, that benefits from its biased transmission to the predominant male-biased offspring and its effective shielding from female negative selection. Indeed, linkage to the Y-chromosome of an active X-shredder instigated the development of the nuclease-based X-shredding system. Here, we analyze mechanisms whereby an autosomal X-shredder could become unintentionally Y-linked after release by evaluating the stability of an established X-shredder strain that is being considered for release, exploring its potential for remobilization in laboratory and wild-type genomes of An. gambiae and provide data regarding expression on the mosquito Y-chromosome. Our data suggest that an invasive X-shredder resulting from a post-release movement of such autosomal transgenes onto the Y-chromosome is unlikely.

In evolution, it is widely believed that phenotypic changes root in developmental changes and phenotype conservation, in developmental conservation. Seeming phenotype conservation may however hide evolutionary changes in the underlying developmental mechanisms by which a trait is produced. This cryptic evolution is also called Developmental System Drift, and the extent of this phenomenon unclear. We used a well-characterized evo-devo model system, rodent molars, to test the correlation between phenotypic and developmental evolution. Between mouse and hamster, the morphology of the lower molars has much less diverged than the morphology of the upper molars. Is development accordingly more conserved? We compared molar crown formation with a standard approach, and with a tight transcriptome time-series to get a quantitative molecular profiling of developmental states. Our data identify common trends in the development of all molars. Upper and lower molars have their specificities since the early steps of morphogenesis, at the levels of the pattern of cusp formation, cellular composition and biased gene expression. The extent of difference in lower vs. upper molar development within one species does correlate with the extent of difference in final morphology. However, the specificity of lower vs. upper molar development is drowned among the rapid evolution of development, which is highly species-specific in term of expression levels and temporal profiles. Divergence in developmental systems is almost as high for lower as it is for upper molar, despite much lesser morphological changes in lower molar crown. Hence, our results point an extensive drift in this developmental system. Because serial organs are largely sharing gene networks, it supports previous theoretical work that suggest a causal link between pleiotropy and DSD.

Biotectonics is an approach to historical biogeography based on the analysis of independently derived biological and tectonic data, which we demonstrate using the island of Sulawesi as an example. We describe the tectonic development of Sulawesi and discuss the relationship between tectonic models and phylogenetic hypotheses. We outline the problem of interpreting areagrams based on single phylogenies and stress the importance of combining all available data into a general areagram. We analysed the distributions of Sulawesi area of endemism endemics (AEEs) using 30 published phylogenies, which were converted into paralogy-free taxon-area cladograms using the programme LisBeth (Zaragüeta-Bagalis et al. 2012) from which Adam’s consensus trees were constructed using PAUP (Swofford 2002). The results of our analyses show that the relationship between the areas of endemism is congruent with the terrane history of the island. A further 79 phylogenies of Sulawesi species with extralimital distributions were analysed to determine area relationships of Sulawesi within the broader Indo-Pacific region. We demonstrate the utility of data partitioning when dealing with areas that are geologically and biologically composite by showing that analysing Asian and Australasian elements of the Sulawesi biota separately produced general areagrams that avoid artifice and are interpretable in the light of current tectonic models.

Streptococcus iniae is an emerging zoonotic pathogen of increasing concern for aquaculture and has caused several epizootics in reef fishes from the Caribbean, the Red Sea and the Indian Ocean. To study the population structure, introduction pathways and evolution of S. iniae over recurring epizootics on Reunion Island, we developed and validated a Multi Locus Sequence Typing (MLST) panel using genomic data obtained from 89 isolates sampled during epizootics occurring over the past 40years in Australia, Asia, the United States, Israel and Reunion Island. We selected eight housekeeping loci, which resulted in the greatest variation across the main S. iniae phylogenetic clades highlighted by the whole genomic dataset. We then applied the developed MLST to investigate the origin of S. iniae responsible for four epizootics on Reunion Island, first in inland aquaculture and then on the reefs from 1996 to 2014. Results suggest at least two independent S. iniae emergence events occurred on the island. Molecular data support that the first epizootic resulted from an introduction, with inland freshwater aquaculture facilities acting as a stepping-stone. Such an event may have been facilitated by the ecological flexibility of S. iniae, able to survive in both fresh and marine waters and the ability of the pathogen to infect multiple host species. By contrast, the second epizootic was associated with a distinct ST of cosmopolitan distribution that may have emerged as a result of environment disturbance. This novel tool will be effective at investigating recurrent epizootics occurring within a given environment or country that is despite the fact that S. iniae appears to have low genetic diversity within its lineage.

Highly pathogenic avian influenza viruses (HPAIVs) evolve from low pathogenic avian influenza viruses (LPAIVs) of the H5 and H7 subtypes. This evolution is characterized by the acquisition of a multi-basic cleavage site (MBCS) motif in the hemagglutinin (HA) that leads to an extended viral tropism and severe disease in poultry. One key unanswered question is whether the risk of transition to HPAIVs is similar for all LPAIVs H5 or H7 strains, or whether specific determinants in the HA sequence of some H5 or H7 LPAIV strains correlate with a higher risk of transition to HPAIVs. Here, we determined if specific features of the conserved RNA stem-loop located at the HA cleavage site-encoding region could be detected along the LPAIV to HPAIV evolutionary pathway. Analysis of the thermodynamic stability of the predicted RNA structures showed no specific patterns common to HA sequences leading to HPAIVs and distinct from those remaining LPAIVs. However, RNA structure clustering analysis revealed that most of the American lineage ancestors leading to H7 emergences via recombination shared the same viral RNA (vRNA) structure topology at the HA1/HA2 boundary region. Our study thus identified predicted secondary RNA structures present in the HA of H7 viruses, which could promote genetic recombination and acquisition of a multibasic cleavage site motif (MBCS).

The rhesus macaque provides a unique model of acquired immunity against schistosomes, which afflict >200 million people worldwide. By monitoring bloodstream levels of parasite-gut-derived antigen, we show that from week 10 onwards an established infection with Schistosoma mansoni is cleared in an exponential manner, eliciting resistance to reinfection. Secondary challenge at week 42 demonstrates that protection is strong in all animals and complete in some. Antibody profiles suggest that antigens mediating protection are the released products of developing schistosomula. In culture they are killed by addition of rhesus plasma, collected from week 8 post-infection onwards, and even more efficiently with post-challenge plasma. Furthermore, cultured schistosomula lose chromatin activating marks at the transcription start site of genes related to worm development and show decreased expression of genes related to lysosomes and lytic vacuoles involved with autophagy. Overall, our results indicate that enhanced antibody responses against the challenge migrating larvae mediate the naturally acquired protective immunity and will inform the route to an effective vaccine., To date there is only one single drug with modest efficacy and no vaccine available to protect from schistosomiasis. Here, Amaral et al. characterize the self-cure process of rhesus macaques following primary infection and secondary challenge with Schistosoma mansoni to inform future vaccine development studies.

Toxoplasma gondii is a cyst-forming apicomplexan parasite of virtually all warm-blooded species, with all true cats (Felidae) as definitive hosts. It is the etiologic agent of toxoplasmosis, a disease causing substantial public health burden worldwide. Few intercontinental clonal lineages represent the large majority of isolates worldwide. Little is known about the evolutionary forces driving the success of these lineages, the timing and the mechanisms of their global dispersal. In this study, we analyse a set of 156 genomes and we provide estimates of T. gondii mutation rate and generation time. We elucidate how the evolution of T. gondii populations is intimately linked to the major events that have punctuated the recent history of cats. We show that a unique haplotype, whose length represents only 0.16% of the whole T. gondii genome, is common to all intercontinental lineages and hybrid populations derived from these lineages. This haplotype has accompanied wildcats (Felis silvestris) during their emergence from the wild to domestic settlements, their dispersal in the Old World, and their expansion in the last five centuries to the Americas. The selection of this haplotype is most parsimoniously explained by its role in sexual reproduction of T. gondii in domestic cats.

International audience; A lot of what we know about past speciation and extinction dynamics is based on statistically fitting birth–death processes to phylogenies of extant species. Despite their wide use, the reliability of these tools is regularly questioned. It was recently demonstrated that vast ‘congruent’ sets of alternative diversification histories cannot be distinguished (i.e., are not identifiable) using extant phylogenies alone, reanimating the debate about the limits of phylogenetic diversification analysis. Here, we summarize what we know about the identifiability of the birth–death process and how identifiability issues can be addressed. We conclude that extant phylogenies, when combined with appropriate prior hypotheses and regularization techniques, can still tell us a lot about past diversification dynamics.

The evolution of mutualism between hosts and initially parasitic symbionts represents a major transition in evolution. Although vertical transmission of symbionts during host reproduction and partner control both favour the stability of mutualism, these mechanisms require specifically evolved features that may be absent in the first place. Therefore, the first steps of the transition from parasitism to mutualism may suffer from the cost of mutualism at the organismic level. We hypothesize that spatial structure can lead to the formation of higher selection levels favouring mutualism. This resembles the evolution of altruism, with the additional requirement that the offspring of mutualistic hosts and symbionts must co-occur often enough. Using a spatially explicit agent-based model we demonstrate that, starting from a parasitic system with global dispersal, the joint evolution of mutualistic effort and local dispersal of hosts and symbionts leads to a stable coexistence between parasites and mutualists. The evolution of local dispersal mimics vertical transmission and triggers the formation of mutualistic clusters, counteracting the organismic selection level of parasites that maintain global dispersal. The transition occurs when mutualistic symbionts increase the density of hosts, which strengthens competition between hosts and disfavours hosts inhabiting areas dominated by parasitic symbionts: mutualists construct the ecological conditions that allow their own spread. Therefore, the transition to mutualism may come from an eco-evolutionary feedback loop involving spatially structured population dynamics.

International audience