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.

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.

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.

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.

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.

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.

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\'.

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.

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.

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.