Hybridization in birds-of-paradise: Widespread ancestral gene flow despite strong sexual selection in a lek-mating system.

Sexual selection can directly contribute to reproductive isolation and is an important mechanism that can lead to speciation. Lek-mating is one of the most extreme forms of sexual selection, but surprisingly does not seem to preclude occasional hybridization in nature. However, hybridization among lekking species may still be trivial if selection against offspring with intermediate phenotypes prohibits introgression. Here we investigate this further by sequencing the genomes of nearly all bird-of-paradise (Paradisaeidae) species and 10 museum specimens of putative hybrid origin. We find that intergeneric hybridization indeed still takes place despite extreme differentiation in form, plumage, and behavior. In parallel, the genomes of contemporary species contain widespread signatures of past introgression, demonstrating that hybridization has repeatedly resulted in shared genetic variation despite strong sexual isolation. Our study raises important questions about extrinsic factors that modulate hybridization probability and the evolutionary consequences of introgressive hybridization between lekking species.

The Influence of Fragmented Landscapes on Speciation.

In the face of unprecedented global transformations, unraveling the intricate mechanisms governing biodiversity patterns is imperative for predicting and interpreting species responses. An important element in this interplay is fragmentation and the spatial mosaic or arrangement of suitable sites within the landscape. Beyond its well-documented impact on biodiversity loss, fragmented landscapes also influence the origin of biodiversity, by influencing speciation dynamics. This research employs a model that integrates spatial configuration and dispersal abilities of individuals to investigate the impact of landscape configuration on species' evolutionary trajectories. Specifically, we propose a microevolutionary model where individuals are characterized by their dispersal ability and a genome, allowing population evolution and diversification. Space is explicitly characterized by suitable and unsuitable sites that define fragmented landscapes. Our model demonstrates how intermediate dispersal abilities enhance diversification. However, simulations of more fragmented landscapes result in a lower total number of individuals and a lower percentage of occupied sites by individuals, particularly when species have limited dispersal abilities. Furthermore, we have found that intermediate levels of fragmentation can stimulate greater species richness, while higher levels of speciation and extinction events tend to occur under higher fragmentations. Our results also show a non-monotonic dependence of richness on dispersal, supporting the intermediate dispersal hypothesis as promotor of diversification, demonstrating the synergistic effects of landscape configuration and species dispersal ability in the processes of speciation, extinction, and diversification. This impact of fragmentation poses a real challenge for biodiversity in the context of a dynamic world.

Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system.

Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.

Evolutionary approach for pollution study: The case of ionizing radiation.

Estimating the consequences of environmental changes, specifically in a global change context, is essential for conservation issues. In the case of pollutants, the interest in using an evolutionary approach to investigate their consequences has been emphasized since the 2000s, but these studies remain rare compared to the characterization of direct effects on individual features. We focused on the study case of anthropogenic ionizing radiation because, despite its potential strong impact on evolution, the scarcity of evolutionary approaches to study the biological consequences of this stressor is particularly true. In this study, by investigating some particular features of the biological effects of this stressor, and by reviewing existing studies on evolution under ionizing radiation, we suggest that evolutionary approach may help provide an integrative view on the biological consequences of ionizing radiation. We focused on three topics: (i) the mutagenic properties of ionizing radiation and its disruption of evolutionary processes, (ii) exposures at different time scales, leading to an interaction between past and contemporary evolution, and (iii) the special features of contaminated areas called exclusion zones and how evolution could match field and laboratory observed effects. This approach can contribute to answering several key issues in radioecology: to explain species differences in the sensitivity to ionizing radiation, to improve our estimation of the impacts of ionizing radiation on populations, and to help identify the environmental features impacting organisms (e.g., interaction with other pollution, migration of populations, anthropogenic environmental changes). Evolutionary approach would benefit from being integrated to the ecological risk assessment process.

Evolvability of cancer-associated genes under APOBEC3A/B selection.

Evolvability is an emergent hallmark of cancer that depends on intra-tumor heterogeneity and genetic variation. Mutations generated by APOBEC3 contribute to genetic variation and tumor evolvability. However, the influence of APOBEC3 on the evolvability of the genome and its differential impact on cancer genes versus non-cancer genes remains unclear. Analyzing over 40,000 human protein-coding transcripts, we identified distinct distribution patterns of APOBEC3A/B TC motifs between cancer and non-cancer genes, suggesting unique associations with cancer. Studying a bat species with numerous APOBEC3 genes, we found distinct motif patterns in orthologs of cancer genes compared to non-cancer genes, as in humans, suggesting APOBEC3 evolution to reduce impacts on the genome rather than the converse. Simulations confirmed that APOBEC3-induced heterogeneity enhances cancer evolution through bimodal patterns of mutations in certain classes of genes. Our results suggest the bimodal distribution of APOBEC-induced mutations can significantly increase cancer heterogeneity.

Cognitive constraints on vocal combinatoriality in a social bird.

A critical component of language is the ability to recombine sounds into larger structures. Although animals also reuse sound elements across call combinations to generate meaning, examples are generally limited to pairs of distinct elements, even when repertoires contain sufficient sounds to generate hundreds of combinations. This combinatoriality might be constrained by the perceptual-cognitive demands of disambiguating between complex sound sequences that share elements. We test this hypothesis by probing the capacity of chestnut-crowned babblers to process combinations of two versus three distinct acoustic elements. We found babblers responded quicker and for longer toward playbacks of recombined versus familiar bi-element sequences, but no evidence of differential responses toward playbacks of recombined versus familiar tri-element sequences, suggesting a cognitively prohibitive jump in processing demands. We propose that overcoming constraints in the ability to process increasingly complex combinatorial signals was necessary for the productive combinatoriality that is characteristic of language to emerge.

EGTtools: Evolutionary game dynamics in Python.

Evolutionary Game Theory (EGT) provides an important framework to study collective behavior. It combines ideas from evolutionary biology and population dynamics with the game theoretical modeling of strategic interactions. Its importance is highlighted by the numerous high level publications that have enriched different fields, ranging from biology to social sciences, in many decades. Nevertheless, there has been no open source library that provided easy, and efficient, access to these methods and models. Here, we introduce EGTtools, an efficient hybrid C++/Python library which provides fast implementations of both analytical and numerical EGT methods. EGTtools is able to analytically evaluate a system based on the replicator dynamics. It is also able to evaluate any EGT problem resorting to finite populations and large-scale Markov processes. Finally, it resorts to C++ and MonteCarlo simulations to estimate many important indicators, such as stationary or strategy distributions. We illustrate all these methodologies with concrete examples and analysis.

Ediacaran Corumbella has a cataphract calcareous skeleton with controlled biomineralization.

Corumbella is a terminal Ediacaran tubular, benthic fossil of debated morphology, composition, and biological affinity. Here, we show that Corumbella had a biomineralized skeleton, with a bilayered construction of imbricated calcareous plates and rings (sclerites) yielding a cataphract organization, that enhanced flexibility. Each sclerite likely possessed a laminar microfabric with consistent crystallographic orientation, within an organic matrix. Original aragonitic mineralogy is supported by relict aragonite and elevated Sr (mean = ca. 11,800 ppm in central parts of sclerites). In sum, the presence of a polarisation axis, sclerites with a laminar microfabric, and a cataphract skeletal organization reminiscent of early Cambrian taxa, are all consistent with, but not necessarily indicative of, a bilaterian affinity. A cataphract skeleton with an inferred complex microstructure confirms the presence of controlled biomineralization in metazoans by the terminal Ediacaran, and offers insights into the evolution of development and ecology at the root of the 'Cambrian radiation'.

Different Traits, Different Evolutionary Pathways: Insights from Salamandrina (Amphibia, Caudata).

Species delimitation is often based on a single or very few genetic or phenetic traits, something which leads to misinterpretations and often does not provide information about evolutionary processes. Here, we investigated the diversity pattern of multiple phenetic traits of the two extant species of Salamandrina, a genus split only after molecular traits had been studied but the two species of which are phenetically very similar. The phenetic traits we studied are size, external body shape and head colour pattern, in a model comparison framework using non-linear mixed models and unsupervised and supervised clustering. Overall, we found high levels of intra-specific variability for body size and shape, depending on population belonging and habitat, while differences between species were generally lower. The habitat the salamanders dwell in also seems important for colour pattern. Basing on our findings, from the methodological point of view, we suggest (i) to take into account the variability at population level when testing for higher level variability, and (ii) a semi-supervised learning approach to high dimensional data. We also showed that different phenotypic traits of the same organism could result from different evolutionary routes. Local adaptation is likely responsible for body size and shape variability, with selective pressures more similar across species than within them. Head colour pattern also depends on habitat, differently from ventral colour pattern (not studied in this paper) which likely evolved under genetic drift.

FishPIE: A universal phylogenetically informative exon markers set for ray-finned fishes.

Understanding the evolutionary history of the highly diverse ray-finned fishes has been challenging, and the development of more universal primers for phylogenetic analyses may help overcoming these challenges. We developed FishPIE, a nested PCR primer set of 82 phylogenetically informative exon markers, and tested it on 203 species from 31 orders of Actinopterygii. We combined orthologous sequences of the FishPIE markers obtained from published genomes and transcriptomes and constructed the phylogeny of 710 species belonging to 190 families and 60 orders. The resulting phylogenies had topologies comparable to previous phylogenomic studies. We demonstrated that the FishPIE markers could address phylogenetic questions across broad taxonomic levels. By incorporating the newly sequenced taxa, we were able to shed new light on the phylogeny of the highly diverse Cypriniformes. Thus, FishPIE holds great promise for generating genetic data for broad taxonomic groups and accelerating our understanding of the fish tree of life.

Evolutionary analyses reveal immune cell receptor GPR84 as a conserved receptor for bacteria-derived molecules.

The G protein-coupled receptor 84 (GPR84) is found in immune cells and its expression is increased under inflammatory conditions. Activation of GPR84 by medium-chain fatty acids results in pro-inflammatory responses. Here, we screened available vertebrate genome data and found that GPR84 is present in vertebrates for more than 500 million years but absent in birds and a pseudogene in bats. Cloning and functional characterization of several mammalian GPR84 orthologs in combination with evolutionary and model-based structural analyses revealed evidence for positive selection of bear GPR84 orthologs. Naturally occurring human GPR84 variants are most frequent in Asian populations causing a loss of function. Further, we identified cis- and trans-2-decenoic acid, both known to mediate bacterial communication, as evolutionary highly conserved ligands. Our integrated set of approaches contributes to a comprehensive understanding of GPR84 in terms of evolutionary and structural aspects, highlighting GPR84 as a conserved immune cell receptor for bacteria-derived molecules.

Paving the way for precise diagnostics of antimicrobial resistant bacteria.

The antimicrobial resistance (AMR) crisis from bacterial pathogens is frequently emerging and rapidly disseminated during the sustained antimicrobial exposure in human-dominated communities, posing a compelling threat as one of the biggest challenges in humans. The frequent incidences of some common but untreatable infections unfold the public health catastrophe that antimicrobial-resistant pathogens have outpaced the available countermeasures, now explicitly amplified during the COVID-19 pandemic. Nowadays, biotechnology and machine learning advancements help create more fundamental knowledge of distinct spatiotemporal dynamics in AMR bacterial adaptation and evolutionary processes. Integrated with reliable diagnostic tools and powerful analytic approaches, a collaborative and systematic surveillance platform with high accuracy and predictability should be established and implemented, which is not just for an effective controlling strategy on AMR but also for protecting the longevity of valuable antimicrobials currently and in the future.

An exquisitely preserved in-ovo theropod dinosaur embryo sheds light on avian-like prehatching postures.

Despite the discovery of many dinosaur eggs and nests over the past 100 years, articulated in-ovo embryos are remarkably rare. Here we report an exceptionally preserved, articulated oviraptorid embryo inside an elongatoolithid egg, from the Late Cretaceous Hekou Formation of southern China. The head lies ventral to the body, with the feet on either side, and the back curled along the blunt pole of the egg, in a posture previously unrecognized in a non-avian dinosaur, but reminiscent of a late-stage modern bird embryo. Comparison to other late-stage oviraptorid embryos suggests that prehatch oviraptorids developed avian-like postures late in incubation, which in modern birds are related to coordinated embryonic movements associated with tucking - a behavior controlled by the central nervous system, critical for hatching success. We propose that such pre-hatching behavior, previously considered unique to birds, may have originated among non-avian theropods, which can be further investigated with additional discoveries of embryo fossils.

Looking across Scales in Disease Ecology and Evolution.

AbstractOver the past few decades, it has become clear that ecological and evolutionary dynamics are influenced by processes operating across spatial and temporal scales. Processes that operate on small spatial scales have the potential to influence dynamics at much larger scales; for example, a change in the physiology of a primary producer can alter primary productivity in an ecosystem. Similarly, evolution-a process that historically was thought of as occurring at longer timescales-can influence ecological dynamics and vice versa. The importance of considering multiple scales is broadly true in ecology and evolution, and it is especially important for studies of disease ecology and evolution. Yet characterizing the scales at which individual studies operate is surprisingly challenging, as we (re)discovered while trying to characterize articles published in this journal over the past three decades. However, while it is difficult to determine where one scale ends and another begins, it is also clear that work that spans across a spectrum can yield insights that could not be gleaned from a narrower focus. To demonstrate this, we highlight studies previously published in this journal that show the value of working across scales. We then introduce the six articles that comprise this Focused Topic section. Together, these articles present systems, theory, and methods that provide important insights that could not have been obtained from studying a single scale in isolation.

A worked bone assemblage from 120,000-90,000 year old deposits at Contrebandiers Cave, Atlantic Coast, Morocco.

The emergence of Homo sapiens in Pleistocene Africa is associated with a profound reconfiguration of technology. Symbolic expression and personal ornamentation, new tool forms, and regional technological traditions are widely recognized as the earliest indicators of complex culture and cognition in humans. Here we describe a bone tool tradition from Contrebandiers Cave on the Atlantic coast of Morocco, dated between 120,000-90,000 years ago. The bone tools were produced for different activities, including likely leather and fur working, and were found in association with carnivore remains that were possibly skinned for fur. A cetacean tooth tip bears what is likely a combination of anthropogenic and non-anthropogenic modification and shows the use of a marine mammal tooth by early humans. The evidence from Contrebandiers Cave demonstrates that the pan-African emergence of complex culture included the use of multiple and diverse materials for specialized tool manufacture.

Nervous System-Systemic Crosstalk in SARS-CoV-2/COVID-19: A Unique Dyshomeostasis Syndrome.

SARS-CoV-2 infection is associated with a spectrum of acute neurological syndromes. A subset of these syndromes promotes higher in-hospital mortality than is predicted by traditional parameters defining critical care illness. This suggests that deregulation of components of the central and peripheral nervous systems compromises the interplay with systemic cellular, tissue and organ interfaces to mediate numerous atypical manifestations of COVID-19 through impairments in organismal homeostasis. This unique dyshomeostasis syndrome involves components of the ACE-2/1 lifecycles, renin-angiotensin system regulatory axes, integrated nervous system functional interactions and brain regions differentially sculpted by accelerated evolutionary processes and more primordial homeostatic functions. These biological contingencies suggest a mechanistic blueprint to define long-term neurological sequelae and systemic manifestations such as premature aging phenotypes, including organ fibrosis, tissue degeneration and cancer. Therapeutic initiatives must therefore encompass innovative combinatorial agents, including repurposing FDA-approved drugs targeting components of the autonomic nervous system and recently identified products of SARS-CoV-2-host interactions.

Coevolutionary transitions emerging from flexible molecular recognition and eco-evolutionary feedback.

Highly mutable viruses evolve to evade host immunity that exerts selective pressure and adapts to viral dynamics. Here, we provide a framework for identifying key determinants of the mode and fate of viral-immune coevolution by linking molecular recognition and eco-evolutionary dynamics. We find that conservation level and initial diversity of antigen jointly determine the timing and efficacy of narrow and broad antibody responses, which in turn control the transition between viral persistence, clearance, and rebound. In particular, clearance of structurally complex antigens relies on antibody evolution in a larger antigenic space than where selection directly acts; viral rebound manifests binding-mediated feedback between ecology and rapid evolution. Finally, immune compartmentalization can slow viral escape but also delay clearance. This work suggests that flexible molecular binding allows a plastic phenotype that exploits potentiating neutral variations outside direct contact, opening new and shorter paths toward highly adaptable states.

The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs.

In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600-3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity with that of modern dogs, but it also shared some features with the wild wolf microbiome, as a kind of transitional state between them. The dietary niche, as also inferred from the microbiome composition, was omnivorous, with evidence of consumption of starchy agricultural foods. Of interest, the Solarolo dog microbiome was particularly enriched in sequences encoding alpha-amylases and complemented a low copy number of the host amylase gene. These findings suggest that Neolithic dogs could have responded to the transition to a starch-rich diet by expanding microbial functionalities devoted to starch catabolism, thus compensating for delayed host response.

Quality Assurance and Improvement Project in Echocardiography Laboratory: The Pivotal Importance of Organizational and Managerial Processes.

Echocardiography plays a vital role in the diagnosis and management of cardiovascular conditions. Echocardiography use is progressively increasing nowadays, and this is correlated to the evolving echo indications, to the relatively new available echocardiography modes (tissue Doppler imaging, speckle tracking imaging, three-dimensional mode, etc.) and modalities (transthoracic, transesophageal, and intracardiac) along with the various available clinical approaches (point of care echo, portable echo, etc.). Quality assurance in echocardiography is correlated to appropriate use criteria, adequate equipment, standardization of performance and reporting, along with timely storage and archiving. Quality improvement plan must target strategic planning, with metrics and timeline for assessment and re-assessment of results. Improvement project aims to ensure and enhance conformity with appropriate use criteria and standardization, timely completion of exams and reports, detection of discrepancies, and continuous improvement of knowledge and skills. Strategic planning is essential in this context in order to develop organizational and managerial processes, with regular auditing for a highly professional and advanced level of echocardiography, while ensuring teamwork and standards of ethical values.

Systematic errors in orthology inference and their effects on evolutionary analyses.

The availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy-identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs that experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction that mimic expected patterns of gene evolution.