Apicomplexa is a diverse protistan phylum composed almost exclusively of metazoan-infecting parasites, including the causative agents of malaria, cryptosporidiosis, and toxoplasmosis. A single apicomplexan genus, Nephromyces, was described in 2010 as a mutualist partner to its tunicate host. Here we present genomic and transcriptomic data from the parasitic sister species to this mutualist, Cardiosporidium

128 years ago, August Weismann proposed that the only source of inherited genetic variation in animals is the germline1. Julian Huxley reasoned that if this were true, it would falsify Jean-Baptiste Lamarck′s theory that acquired characteristics are heritable2. Since then, scientists have discovered that not all animals segregate germline cells from somatic cells permanently and early in development3

Species may persist through the unprecedented changes in global conditions using genetic adaptation or physiological plasticity. However, few empirical studies have revealed the relationship between adaptation and plasticity or addressed the long-standing debate on whether plasticity impedes or facilitates adaptive evolution. Here, we used experimental evolution and reciprocal transplantation of the

By altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study

Vertebrates evolved mechanisms for sodium conservation and gas exchange in conjunction with migration from aquatic to terrestrial habitats. Epithelial Na+ channel (ENaC) function is critical to systems responsible for extracellular fluid homeostasis and gas exchange. ENaC is activated by cleavage at multiple specific extracellular polybasic sites, releasing inhibitory tracts from the channel's α and

The success of antimicrobial treatment is threatened by the evolution of drug resistance. Population genetic models are an important tool in mitigating that threat. However, most such models consider resistance emergence via a single mutational step. Here, we assembled experimental evidence that drug resistance evolution follows two patterns: i) a single mutation, which provides a large MIC increase

Coronaviruses are highly pathogenic and therefore important human and veterinary pathogens viruses worldwide. Members of family Coronaviridae have previously been analysed phylogenetically, resulting in proposals of virus interrelationships. However, available Coronavirus phylogenies remain unrooted, based on limited sampling, and normally depend on a single method. The main subjects of this study

In 1995, Pleijel raised an issue on the coding of complex (multistate) characters: to find a unique coding approach satisfying both informational and semantical criteria. Following Pleijel′s work, this study aims to propose a new answer to this problematic. We proposed here to use hierarchical characters instead of classical partitional ones as hierarchy allows to deal effectively with the different

A global cross-discipline effort is ongoing to characterize the evolution of SARS-CoV-2 virus and generate reliable epidemiological models of its diffusion. To this end, phylogenomic approaches leverage accumulating genomic mutations to track the evolutionary history of the virus and benefit from the surge of sequences deposited in public databases. Yet, such methods typically rely on consensus sequences

The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying domestic species (alpaca and llama) in archaeological sites based on morphometry is challenging because of similarity with respect to their wild ancestors. In this study, we generated mitogenomes for 61 ancient camelids dated between 3,500 - 2,400 years BP (Early Formative period) from

The phylum Apicomplexa encompasses 6000 ubiquitous animal parasites, including Plasmodium, the most deadly human parasite on Earth. Anciently parasitic lineages, like apicomplexans, lose core metabolic pathways over time, as they evolve less costly scavenging mechanisms. The recent description of a mutualistic apicomplexan, Nephromyces, from deep within this parasitic group, opened the possibility

In many animal species, parents provide care for their offspring, but the parental roles of the two sexes differ considerably between and within species. Here, we use an individual-based simulation approach to investigate the evolutionary emergence and stability of parental roles. Our conclusions are in striking contrast to the results of analytical models. In the absence of initial differences between

The total strength of sexual selection on males depends on the relationship between various components of pre- and post-copulatory fitness. Misalignment between male and female interests creates inter-locus sexual conflict, where the fitness of one sex is increased at the expense of the other. Although rarely considered, mating behaviours can also be genetically correlated between males and females

Bones in the vertebrate cranial base and limb skeleton grow by endochondral ossification, under the control of growth plates. Mechanisms of endochondral ossification are conserved across growth plates, which increases covariation in size and shape among bones, and in turn may lead to correlated changes in skeletal traits not under direct selection. We used micro-CT and geometric morphometrics to characterize

Reef-building corals are foundational species in coral reef ecosystems and are threatened by many stressors including rising ocean temperatures. In 2015/16 and 2016/17, corals around the world experienced consecutive bleaching events and most coral populations are projected to experience temperatures above their current bleaching thresholds annually by 2050. Adaptation to higher temperatures is therefore

Dating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. This is the case for instance for horizontal gene transfer events and ancient coevolutionary relationships

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their own network in the genomes, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific gene, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates

Assessing the phylogenetic compatibility between individual gene families is a crucial and often computationally demanding step in many phylogenomics analyses. Here we describe the Evolutionary Similarity Index (IES) to assess shared evolution between gene families using a weighted Orthogonal Distance Regression applied to sequence distances. This approach allows for straightforward pairing of paralogs

Populations of European honeybee subspecies, Apis mellifera , have the ability to adapt naturally to the ectoparasitic mite, Varroa destructor . It is possible that a tolerance to mite-vectored viruses may contribute to colony survival. If this is the case, surviving populations should show lower virus titers and prevalence compared to susceptible populations. Here, we investigated the prevalence and

The Himalayan uplift, a tectonic event of global importance, seemingly disseminated aquatic biodiversity broadly across Asia. But surprisingly, this hypothesis has yet to be tested. We do so herein by sequencing 1,140 base-pair of mtDNA cytochrome-b for 72 tetraploid Nepalese/Bhutanese Snowtrout (Schizothorax spp.), combining those data with 67 GENBANK sequences (59 ingroup/8 outgroup), then reconstructing

Hosts with high immune sensitivity benefit from rapid recovery but suffer multiple costs thereof. We distinguish between immunopathological costs due to collateral damage and autoimmune costs due to false positives against self. Selection on sensitivity follows different trajectories depending on the cost nature and the overlap degree between host- and parasitic molecular signatures. Increased parasite

Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh

Stereum is a globally widespread genus of basidiomycete fungi with conspicuous shelf-like fruiting bodies. Several species have been extensively studied due to their economic importance, but broader Stereum taxonomy has been stymied by pervasive morphological crypsis in the genus. Here, we provide a preliminary investigation into species boundaries among some North American Stereum. The nominal species

Early-life conditions have profound effects on many life-history traits. In particular, early-life diet affects both juvenile development, and adult survival and reproduction. Early-life diet also has consequences for the ability of adults to withstand stressors such as starvation, temperature and desiccation. However, it is less well known how early-life diet influences the ability of adults to respond

Inbreeding depression is a key factor in the evolution of mating strategies and breeding systems across the eukaryotic tree of life. Yet its potential impact in partially asexual species has only received little attention. We studied inbreeding depression in the cyclical parthenogen Daphnia magna by following mixtures of inbred and outbred genotypes from an early embryonic stage through hatching to

Understanding impacts on species diversification is fundamental to our understanding of the evolutionary processes underlying biodiversity. The 'behavioural drive hypothesis' posits that behavioural innovation, coupled with the social transmission of innovative behaviours, can increase rates of evolution and diversification, as novel behaviours expose individuals to new selection regimes. We test this

The central-marginal hypothesis (CMH) predicts high genetic diversity at the species' geographic centre and low genetic diversity at the species' geographic margins. However, most studies examining the CMH have neglected potential effect of past climate. Here, we test six hypotheses, representing effects of past climate and contemporary range position, for their ability to explain the spatial patterns

Theory shows how sexual selection can exaggerate male traits beyond naturally selected optima and also how natural selection can ultimately halt trait elaboration. Empirical evidence supports this theory, but to date, there have been no experimental evolution studies directly testing this logic, and little examination of possible associated effects on female fitness. Here we used experimental evolution

The effectiveness of selection varies among species. It is often estimated by means of an 'effective population size' based on neutral polymorphism, but this is confounded in complex ways with demography. The strength of codon bias more directly pertains to how well adaptation at many sites can be maintained in the face of deleterious mutations, but past metrics that compare codon bias across species

As habitat loss is a major driver of amphibian population declines, protected areas (PAs) can play a crucial role in amphibian conservation. Documenting how well the global PA network captures the evolutionary history of amphibians can inform conservation prioritisation and action. We conducted a phylogenetic gap analysis to assess the extent to which amphibian phylogenetic diversity (PD) is unprotected

Tracking genetic changes of populations through time allows a more direct study of the evolutionary processes acting on the population than a single contemporary sample. Several statistical methods have been developed to characterize the demography and selection from temporal population genetic data. However, these methods are usually developed under the assumption of outcrossing reproduction and might

Mating systems have profound effects on genetic diversity and compatibility. The convergent evolution of self-fertilization in three Caenorhabditis species provides a powerful lens to examine causes and consequences of mating system transitions. Among the selfers, C. tropicalis is the least genetically diverse and most afflicted by outbreeding depression. We generated a chromosomal-scale genome for

In many yeast species the three genes at the center of the galactose catabolism pathway, GAL1, GAL10 and GAL7, are neighbors in the genome and form a metabolic gene cluster. We report here that some yeast strains in the genus Torulaspora have much larger GAL clusters that include genes for melibiase (MEL1), galactose permease (GAL2), glucose transporter (HGT1), phosphoglucomutase (PGM1), and the transcription

Contemporary high-throughput mutagenesis experiments are providing an increasingly detailed view of the complex patterns of genetic interaction that occur between multiple mutations within a single protein or regulatory element. By simultaneously measuring the effects of thousands of combinations of mutations, these experiments have revealed that the genotype-phenotype relationship typically reflects

Studying how novel phenotypes originate and evolve is fundamental to the field of evolutionary biology as it allows us to understand how organismal diversity is generated and maintained. However, determining the basis of novel phenotypes is challenging as it involves orchestrated changes at multiple biological levels. Here, we aim to overcome this challenge by using a comparative species framework

The concept that complex ancestral traits can never be re-acquired after their loss has grown popular since its initial formulation and is often referred to as Dollo's law. Nonetheless, several macroevolutionary evidences - along with molecular ones - suggest instances where complex phenotypes could have been lost throughout a clade evolutionary history and subsequently reverted to their former state

Hybridization and polyploidization are powerful mechanisms of speciation. Hybrid speciation often coincides with whole-genome duplication (WGD) in eukaryotes. This suggests that WGD allows hybrids to thrive by restoring fertility and/or increasing access to adaptive mutations. Alternatively, it has been suggested that hybridization itself may trigger WGD. Testing these models requires quantifying the

Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express phylogenetic problems. Here we show that universal probabilistic programming languages

Species delimitation, the process of deciding how to group a set of organisms into units called species, is one of the most challenging problems in evolutionary computational biology. While many methods exist for species delimitation, most based on the coalescent theory, few are scalable to very large datasets and those methods that scale tend to be not very accurate. Species delimitation is closely

Humans reached the Mariana Islands in the western Pacific by ~3500 years ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2000 years later. Yet, the settlement of Polynesia has received far more attention than the settlement of the

Nephridiophagids are unicellular eukaryotes that parasitize the Malpighian tubules of numerous insects. Their life cycle comprises multinucleate vegetative plasmodia that divide into oligonucleate and uninucleate cells, and sporogonial plasmodia that form uninucleate spores. Nephridiophagids are poor in morphological characteristics, and although they have been tentatively identified as early-branching

During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four extant genera, each of which contains only a single species. These species include the bone-cracking spotted, striped, and brown hyenas, and the specialised insectivorous aardwolf. Previous genome studies have analysed the evolutionary histories of the spotted and brown hyenas, but little

Studying the development of fitness related traits in hybrids from populations diverging in sympatry is a fundamental approach to understand the processes of speciation. However, such traits are often affected by covariance structures that complicate the comprehension of these processes, especially because the interactive relationships between traits of different nature (e.g. morphology, behaviour

The complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million-tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome. Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed

Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here

The wealth of high-quality genomes for numerous species has motivated many investigations into the genetic underpinnings of phenotypes. Comparative genomics methods approach this task by identifying convergent shifts at the genetic level that are associated with traits evolving convergently across independent lineages. However, these methods have complex statistical behaviors that are influenced by

Understanding whether and how temperature increases alter the effects of mutations on protein stability is crucial for understanding the limits to thermal adaptation by organisms. Currently, it is generally assumed that the stability effects of mutations are independent of temperature. Yet, mutations should become increasingly destabilizing as temperature rises due to the increase in the energy of

It is assumed that host genetic variability for susceptibility to infection will necessarily condition the evolution of viruses, either by driving them to diversification into strains that track the different host defense alleles (e.g., antigenic diversity), or by canalization to infect only the most susceptible genotypes. Associated to these processes, virulence may or may not increase. To tackle

With rising antibiotic resistance, alternative treatments for communicable diseases are increasingly relevant. One possible alternative for some types of infections is honey, used in wound care since before 2000 BCE and more recently in licensed, medical-grade products. However, it is unclear whether medical application of honey results in the evolution of bacterial honey resistance, and whether this

Cobalamin is a cofactor present in essential metabolic pathways in animals and one of the water-soluble vitamins. It is a complex compound synthesized solely by prokaryotes. Cobalamin dependence is scattered across the tree of life. In particular, fungi and plants were deemed devoid of cobalamin. We demonstrate that cobalamin is utilized by all fungal lineages, except for Dikarya. This observation

How an organisms sensory system functions is central to how it navigates its environment and meets the behavioural challenges associated with survival and reproduction. Comparing sensory systems across species can reveal how facets of behaviour and ecology promote adaptive shifts in the relative importance of certain environmental cues. The insect olfactory system is prominent model for investigating

Lateral gene transfer (LGT) has been documented in a broad range of prokaryotes and eukaryotes, and it can promote adaptation. LGT of functional nuclear genes has been reported among some plants, but systematic studies are needed to assess the frequency and facilitators of LGT in the group. We scan the genomes of a diverse set of 17 grass species that span more than 50 million years of divergence and

Evolutionary theory predicts that vertically transmitted symbionts are selected for low virulence, as their fitness is directly correlated to that of their host. In contrast with this prediction, the Wolbachia strain wMelPop drastically reduces its Drosophila melanogaster host lifespan at high rearing temperatures. It is generally assumed that this feature is maintained because the D. melanogaster-wMelPop

Biodiversity in southwestern North America has a complex biogeographic history involving tectonism interspersed with climatic fluctuations. This yields a contemporary pattern replete with historic idiosyncrasies often difficult to interpret when viewed from through the lens of modern ecology. The Aspidoscelis tigris (Tiger Whiptail) complex (Squamata: Teiidae) is one such group in which potential taxonomic

Symbiotic relationships between bioluminescent bacteria and fishes have evolved multiple times across hundreds of fish taxa, but relatively little is known about the specificity of these associations and how conserved they have been through time. This study describes the degree of specificity of a bioluminescent symbiosis between cardinalfishes in the genus Siphamia and luminous bacteria in the Vibrio

Human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most closely related, by average genetic distance, to two coronaviruses isolated from bats, RaTG13 and RmYN02. However, there is a segment of high amino acid similarity between human SARS-CoV-2 and a pangolin isolated strain, GD410721, in the receptor binding domain (RBD) of the spike protein, a pattern that can be caused by either

Management of agricultural pests requires an understanding of pest species diversity, their interactions with beneficial insects and spatial-temporal patterns of pest abundance. Invasive and agriculturally important insect pests can build up very high populations, especially in cropping landscapes. Traditionally, sampling effort for species identification involves small sample sizes and is labour intensive

Lake Malawi cichlid fishes exhibit extensive divergence in form and function among closely related species separated by a relatively small number of genetic changes. During the past million years, hundreds of species have diversified along an ecological axis in rock vs. sand habitats. We compared the genomes of rock- and sand-dwelling species and asked which genetic variants in which genes differed

Unsupervised AI (artificial intelligence) can obtain novel knowledge from big data without particular models or prior knowledge and is highly desirable for unveiling hidden features in big data. SARS-CoV-2 poses a serious threat to public health and one important issue in characterizing this fast-evolving virus is to elucidate various aspects of their genome sequence changes. We previously established

Adaptation to the local environment is a major driver of speciation. Yet, it remains largely unknown whether natural selection directly causes intrinsic reproductive isolation (hybrid sterility or inviability) between locally adapted populations. Here, we show that adaptive divergence in shoot gravitropism, the ability of a plants shoot to bend upwards in response to the downward pull of gravity, contributes