Understanding how species will respond to rapid environmental change is a central question in conservation biology. Genome–environment association (GEA) and genomic offset analyses offer valuable tools for detecting local adaptation and assessing vulnerability to climate change. In this study, we investigate local adaptation signals and the adaptive potential to changing climates in Dendropsophus elegans, a widespread treefrog endemic to the Brazilian Atlantic Forest (AF), one of the world’s most threatened biodiversity hotspots. Using RAD-sequencing data from 29 individuals across 25 localities and a reference genome from D. ebraccatus, we identified 3,447 high-quality SNPs. We employed two GEA analyses to detect loci potentially under climatic selection across environmental gradients and estimate genetic offset related to climate change. Our analyses showed evidence of stronger genetic structuring in the northern and southern portions of the forest, and greater admixture in the central zone. Different GEA methods revealed 12 candidate loci linked to temperature seasonality and precipitation extremes suggesting populations adapted to local climatic conditions along the AF’s latitudinal gradient. Our findings suggest a potential adaptive divergence in D. elegans shaped by local climates. Under this assumption, and by quantifying genomic offset, we identified populations potentially at higher risk of maladaptation under future climate scenarios on the edges of the AF biome, particularly in the southwestern and coastal regions. These results underscore the importance of integrating adaptive genetic variation into conservation planning, particularly in rapidly changing and fragmented landscapes such as the Atlantic Forest.

A rapid drop of sea level at the Eocene-Oligocene transition (EOT; 34-33 Ma) triggered a marine mass extinction event and the turnover of terrestrial fauna, but its influence on the diversification of nearshore marine fish communities is unclear. Goby fishes (Acanthomorpha: Percomorpha: Gobiiformes) provide an ideal system to investigate the hypothesis that ecological opportunity at the EOT triggered the proliferation of coastal marine fishes. However, despite more than 30 years of molecular evolutionary research, divergence time estimates for gobies are widely variable, incomplete with respect to sampling of taxonomic families and sub-familial lineages, and far older than evident by the modest fossil record. Here we use 1,314 ultraconserved element (UCE) sequences sampled from 121 species, including all gobiiform families and sub-familial goby lineages, to infer phylogeny and node ages under species tree and relaxed molecular clock models. Our time-calibrated phylogenomic hypothesis reconciles molecular clock- and fossil-based estimates for gobiiform diversification, dating the origin of Apogonidae and Gobioidei to the uppermost Late Cretaceous, with lower to middle Paleogene divergence of the gobioid backbone and an explosion of goby lineages at the EOT. Our results support a remarkably recent evolutionary origin of goby families and stimulate new questions on the seemingly exceptional diversity of the group.

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.

Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that differ from their adult forms in morphology and ecology. Focusing disproportionately on the evolution of adult forms unnecessarily hinders our understanding of the pressures shaping evolution over time. Non-adult disparity patterns are particularly important to consider for coastal ray-finned fishes, which can have juvenile phases with distinct phenotypes. These juvenile forms are often associated with sheltered nursery environments, with phenotypic shifts between adults and juvenile stages that are readily apparent in locomotor morphology. Whether this ontogenetic variation in locomotor morphology reflects a decoupling of diversification dynamics between life stages remains unknown. Here we investigate the evolutionary dynamics of locomotor morphology between adult and juvenile triggerfishes. We integrate a time-calibrated phylogenetic framework with geometric morphometric approaches and measurement data of fin aspect ratio and incidence, and reveal a mismatch between morphospace occupancy, the evolution of morphological disparity, and the tempo of trait evolution between life stages. Collectively, our results illuminate how the heterogeneity of morpho-functional adaptations can decouple the mode and tempo of morphological diversification between ontogenetic stages.

The extent of (in)equality is highly diverse across species of social mammals, but we have a poor understanding of the factors that produce or inhibit equitable social organizations. Here, we adopt a comparative evolutionary perspective to test whether the evolution of social dominance hierarchies, a measure of social inequality in animals, exhibits phylogenetic conservatism and whether interspecific variation in these traits can be explained by sex, age or captivity. We find that hierarchy steepness and directional consistency evolve rapidly without any apparent constraint from evolutionary history. Given this extraordinary variability, we next consider multiple factors that have evolved to mitigate social inequality. Social networks, coalitionary support and knowledge transfer advantage to privilege some individuals over others. Nutritional access and prenatal stressors can impact the development of offspring, generating health disparities with intergenerational consequences. Intergenerational transfer of material resources (e.g. stone tools, food stashes, territories) advantage those who receive. Nonetheless, many of the same social species that experience unequal access to food (survival) and mates (reproduction) engage in levelling mechanisms such as food sharing, adoption, revolutionary coalitions, forgiveness and inequity aversion. Taken together, mammals rely upon a suite of mechanisms of (in)equality to balance the costs and benefits of group living. This article is part of the theme issue ‘Evolutionary ecology of inequality’.

Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction site-associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.[Andes; ddRADSeq; introgression; lizards; mtDNA; reptiles; SNPs.].

Rampant structural inequality exists across human societies, exerting a powerful influence on the health of individuals around the globe. Differential access to – and variation in – material wealth contributes greatly to this imbalance. Intergenerational transfer of material wealth can advantage some individuals over less fortunate individuals, shaping divergent destinies and creating a hierarchy of privilege. This concept is familiar within the context of human economic and social systems, but we argue that privilege is not a uniquely human phenomenon. Rather, privilege has evolved multiple times and its phylogenetic reach may be startlingly widespread across the Tree of Life, raising the provocative possibility that comparative study of privilege may offer insights leading to effective strategies countering inequality in human societies.

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies and patterns from the fossil record explain this dominance by correlating the origin of major acanthomorph lineages with the Cretaceous–Palaeogene mass extinction. Here we infer a time-calibrated phylogeny using ultraconserved elements that samples 91.4% of all acanthomorph families and investigate patterns of body shape disparity. Our results show that acanthomorph lineages steadily accumulated throughout the Cenozoic and underwent a significant expansion of among-clade morphological disparity several million years after the end-Cretaceous. These acanthomorph lineages radiated into and diversified within distinct regions of morphospace that characterize iconic lineages, including fast-swimming open-ocean predators, laterally compressed reef fishes, bottom-dwelling flatfishes, seahorses and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of multiple species-rich and phenotypically disparate lineages independently diversifying across the globe under a wide range of ecological conditions. The authors construct a time-calibrated phylogeny spanning >90% of spiny-rayed fishes to explore patterns of body shape disparity within acanthomorphs. They find a trend of steady accumulation of lineages from the Cenozoic, with an increase in morphological disparity following the Cretaceous–Palaeogene event, facilitating the radiation of diverse morphotypes that characterize acanthomorphs’ widespread ecological success today.

The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211 genera, and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 Ma during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity. [Biodiversity; Characiformes; macroevolution; Neotropics; phylogenomics; ultraconserved elements.].

Boxfish (Ostraciidae) have peculiar body shapes, with conspicuous keels formed by their bony carapaces. Previous studies have proposed various hydrodynamic roles for these keels, including reducing drag during swimming, contributing to passive stabilization of the swimming course, or providing resistance against roll rotations. Here, we tested these hypotheses using computational fluid dynamics simulations of five species of Ostraciidae with a range of carapace shapes. The hydrodynamic performance of the original carapace surface models, obtained from laser scanning of museum specimens, was compared with models where the keels had been digitally reduced. The original carapaces showed no reduced drag or increased passive stability against pitch and yaw compared to the reduced-keel carapaces. However, consistently for all studied species, a strong increase in roll drag and roll-added mass was observed for the original carapaces compared to the reduced-keel carapaces, despite the relatively small differences in keel height. In particular, the damping of roll movement by resistive drag torques increased considerably by the presence of keels. Our results suggest that the shape of the boxfish carapace is important in enabling the observed roll-free forward swimming of boxfish and may facilitate the control of manoeuvres.

Digitized specimens are an indispensable resource for rapidly acquiring big datasets and typically must be pre‐processed prior to conducting analyses. One crucial image pre‐processing step in any image analysis workflow is image segmentation, or the ability to clearly contrast the foreground target from the background noise in an image. This procedure is typically done manually, creating a potential bottleneck for efforts to quantify biodiversity from image databases. Image segmentation meta‐algorithms using deep learning provide an opportunity to relax this bottleneck. However, the most accessible pre‐trained convolutional neural networks (CNNs) have been trained on a small fraction of biodiversity, thus limiting their utility. We trained a deep learning model to automatically segment target fish from images with both standardized and complex, noisy backgrounds. We then assessed the performance of our deep learning model using qualitative visual inspection and quantitative image segmentation metrics of pixel overlap between reference segmentation masks generated manually by experts and those automatically predicted by our model. Visual inspection revealed that our model segmented fishes with high precision and relatively few artifacts. These results suggest that the meta‐algorithm (Mask R‐CNN), in which our current fish segmentation model relies on, is well suited for generating high‐fidelity segmented specimen images across a variety of background contexts at rapid pace. We present Sashimi , a user‐friendly command line toolkit to facilitate rapid, automated high‐throughput image segmentation of digitized organisms. Sashimi is accessible to non‐programmers and does not require experience with deep learning to use. The flexibility of Mask R‐CNN allows users to generate a segmentation model for use on diverse animal and plant images using transfer learning with training datasets as small as a few hundred images. To help grow the taxonomic scope of images that can be recognized, Sashimi also includes a central database for sharing and distributing custom‐trained segmentation models of other unrepresented organisms. Lastly, Sashimi includes both auxiliary image pre‐processing functions useful for some popular downstream color pattern analysis workflows, as well as a simple script to aid users in qualitatively and quantitatively assessing segmentation model performance for complementary sets of automatically and manually segmented images.

Current phylogenetic comparative methods modeling quantitative trait evolution generally assume that, during speciation, phenotypes are inherited identically between the two daughter species. This, however, neglects the fact that species consist of a set of individuals, each bearing its own trait value. Indeed, because descendent populations after speciation are samples of a parent population, we can expect their mean phenotypes to randomly differ from one another potentially generating a “jump” of mean phenotypes due to asymmetrical trait inheritance at cladogenesis. Here, we aim to clarify the effect of asymmetrical trait inheritance at speciation on macroevolutionary analyses, focusing on model testing and parameter estimation using some of the most common models of quantitative trait evolution. We developed an individual-based simulation framework in which the evolution of phenotypes is determined by trait changes at the individual level accumulating across generations, and cladogenesis occurs then by separation of subsets of the individuals into new lineages. Through simulations, we assess the magnitude of phenotypic jumps at cladogenesis under different modes of trait inheritance at speciation. We show that even small jumps can strongly alter both the results of model selection and parameter estimations, potentially affecting the biological interpretation of the estimated mode of evolution of a trait. Our results call for caution when interpreting analyses of trait evolution, while highlighting the importance of testing a wide range of alternative models. In the light of our findings, we propose that future methodological advances in comparative methods should more explicitly model the intraspecific variability around species mean phenotypes and how it is inherited at speciation.

Ecological and evolutionary processes govern the fitness, propagation, and interactions of organisms through space and time, and viruses are no exception. While coronavirus disease 2019 (COVID-19) research has primarily emphasized virological, clinical, and epidemiological perspectives, crucial aspects of the pandemic are fundamentally ecological or evolutionary. Here, we highlight five conceptual domains of ecology and evolution - invasion, consumer-resource interactions, spatial ecology, diversity, and adaptation - that illuminate (sometimes unexpectedly) the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We describe the applications of these concepts across levels of biological organization and spatial scales, including within individual hosts, host populations, and multispecies communities. Together, these perspectives illustrate the integrative power of ecological and evolutionary ideas and highlight the benefits of interdisciplinary thinking for understanding emerging viruses.