During their long evolutionary history, land plants have evolved a range of adaptations to different abiotic stressors. These help explain present-day diversity and distribution patterns, as well as the potential resilience of natural and agricultural systems to a changing climate. Most previous research has focused on adaptation to individual stressors and much less is known about how plants deal with exposure to multiple abiotic stressors. Consequently, the evolutionary processes leading to abiotic stress polyresistance (i.e. resistance to multiple abiotic stressors) remain poorly understood. Here, we showcase plants in hot and cold deserts as a compelling system for studying evolution of polyresistance. We focus on three abiotic stressors with substantial physiological overlap - drought, frost and salinity - and present six plant groups that occur in both hot and cold deserts, thus being exposed to these stressors in at least parts of their ranges: Gnetales, Amaranthaceae sensu lato, Nitrariaceae, Poaceae, Tamaricaceae-Frankeniaceae and Zygophyllaceae. We examine key questions regarding the sequence and mechanisms underlying abiotic stress polyresistance evolution and summarize the diverse adaptive strategies that allow persistence under multiple environmental pressures. In doing so, we highlight how trade-offs and facilitation among abiotic stress responses may have influenced the evolutionary pathways that lead to present-day polyresistance. Despite limited evidence, broad patterns emerge for the plant groups examined here, with facilitation appearing especially important, at least during early stages of polyresistance evolution. However, fundamental knowledge gaps remain. Macroevolutionary and macroecological approaches, coupled with historical biogeography and palaeoclimatic and palaeoecological reconstructions, can be used to advance understanding of abiotic stress polyresistance evolution in plants. This will pave the way for applied trait-based research to support climate change mitigation, conservation and sustainable crop improvement in a rapidly changing world.
Carrion is a ubiquitous resource in both terrestrial and aquatic ecosystems, yet it has long been overlooked in ecological research. Over the past two decades, studies on carrion and the many organisms that exploit it have flourished, revealing not only wide-ranging ecological functions but also significance far beyond ecology. This growing body of knowledge underscores the need for the formal recognition and consolidation of carrion ecology as a distinct ecological discipline. In this review, we begin by outlining the ecological features that make carrion a unique resource, provide practical definitions of scavenger and scavenging to reduce persistent ambiguities, describe carcass decomposition by linking stages with insect succession, and position carrion within a broader scientific context. Building on this foundation, we then pursue three main goals. First, we show how incorporating carrion ecology enriches ecological concepts and paradigms across levels of biological organisation, from individuals to ecosystems. Second, we emphasise how expanding knowledge of carrion ecology informs many disciplines beyond ecology. Third, we present a conceptual framework that integrates the diverse ecological functions of carrion across eco-evolutionary timescales and addresses the structured and dynamic connections among the multiple disciplines concerned with carrion. By underscoring the ecological and interdisciplinary relevance of this resource, our framework not only clarifies the components and flows of the carrion system but also highlights opportunities for novel cross-disciplinary collaborations. As carrion ecology continues to mature as a scientific field, we expect that this review and synthesis will consolidate current knowledge, stimulate innovative research across disciplines, and firmly position carrion ecology within the broader ecological and scientific landscape.
Billions of animals worldwide live in captivity across diverse settings, with the vast majority being inherently social species whose welfare fundamentally depends on appropriate social interactions with conspecifics. This review examines the critical role of social environments in captive animal welfare across laboratory, zoo, farm, and companion animal contexts. We first demonstrate how inappropriate group sizes and compositions negatively impacts animal welfare through multiple pathways: impaired physical health and cognitive development, compromised emotional states and altered behavioural expression. Next, we analyse whether current legislative frameworks account sufficiently for social needs. Although regulations acknowledge the danger of overcrowding and the importance of a partner, they predominantly emphasise density requirements without adequately addressing species-specific social structures. Finally, to address these shortcomings, we propose that observations of natural groups are needed to inform a wide variety of sociality characteristics. This should be guided by an established sociality framework to provide a benchmark for social needs in captivity. These should then be refined by preference tests and integrated in flexible management practices. Much progress has been made to improve the physical environment of captive animals yet advances in addressing their social environment have not kept pace. Bridging this gap will be essential if we want to ensure animals in human care can experience lives that meet their needs.
The environmental conditions organisms experience during early development can have powerful and sustained effects on morphology, physiology, behaviour, and performance. Such developmental effects can influence reproductive success, survival, and life-history strategies and can be transmitted across generations (i.e. trans and intergenerational effects). In this way, developmental effects can be powerful drivers of evolutionary change. Given the developmental environment affects a range of phenotypic traits, it has been proposed that physiological responses to developmental conditions are modulated through cellular mechanisms that are shared across cell and tissue types, such as mitochondrial function. Mitochondrial respiratory function is highly sensitive to environmental conditions and exposure to adverse conditions during development can have sustained effects on different aspects of aerobic respiration in mitochondria. However, it is currently unknown if these effects are widespread across taxonomic groups and which components of mitochondrial respiratory function are most likely to be affected by the environment during development. We compiled data from 86 studies to examine the effects of developmental stressors (nutritional imbalance, glucocorticoid hormone exposure, parental care deprivation, and psychological disturbance) on mitochondrial respiratory function using meta-analysis. We sought to uncover whether there are general effects of developmental stressors on different aspects of mitochondrial respiratory function (antioxidants, metabolic capacity, oxidative damage, oxidative stress, and aerobic respiration). We tested how the type of developmental stressor, together with timing of exposure (prenatal versus postnatal), and sex and taxon of the test subjects influenced the magnitude, direction, and duration of effects on mitochondrial respiratory function. Finally, we tested which aspects of mitochondrial respiratory function were most impacted by developmental stressors. We found that exposure to glucocorticoids, parental care deprivation, and psychological disturbances during development generally decreased mitochondrial respiratory function. Generally, these developmental stressors increased the production of reactive oxygen species and oxidative damage and reduced aerobic respiration, metabolic capacity, and antioxidant levels. Nutritional imbalances during development (including both restricted and excessive nutrition) had a slight negative effect on mitochondrial respiratory function, but this effect may be influenced by publication bias. Overall, our results show that exposure to stressors during development negatively affects mitochondrial respiratory function, suggesting that changes in cellular metabolism may link developmental stressors to variation in whole animal traits and individual fitness.
The emergence of eukaryotes marks a monumental juncture in the 4.6-billion-year evolutionary odyssey of our planet. Despite decades of research, the origin of eukaryotic life remains unresolved, with many of its nuances still veiled in the mists of time. While the progenitors of modern eukaryotes have roots that extend deep into the ancient past, the age of the last common ancestor to all modern eukaryotes - whether this was ancient or relatively recent - continues to spark debates. This review does not seek to settle this controversy but instead synthesizes competing perspectives from paleontology, lipid biology, molecular dating, phylogenetics, and geochemistry, emphasizing the necessity for critical evaluation of conflicting evidence across disciplines. We aim to offer a critically informed, cross-disciplinary synthesis for one of the most significant evolutionary transitions in Earth's history.
Empathy is the glue that holds societies together and yet several fundamental questions about empathy persist. What is empathy (the definitional question)? Is it uniquely human and, if not, which nonhuman animals possess empathy (the distribution question)? Which type or quality of empathy is realized in different species (the quality question)? To tackle these three questions, we developed a species-sensitive, multidimensional profile account of empathy. The main function of this account is to enable cross-species comparisons and to capture the rich variety of typical empathetic phenomena. Therefore, we aim to characterize behaviour-based cognitive profiles of empathy which are built on multifactorial characterizations of the dimensions of empathy and of the features realizing these dimensions. The distribution question can be answered by assessing family resemblances of profiles of empathy to paradigmatic cases of empathy. Answers to the quality question can be provided with reference to the relevant empathy profile, which allows us to describe and predict associated behaviours. To gain an initial understanding of the feasibility of this framework for interspecies comparisons, we applied it to four groups of animals: rodents, apes, canids and corvids. Comparing these groups, we demonstrate that each species has a specific empathy profile which has a predictive power: in complex situations requiring empathy, distinct profiles will result in more distinct behavioural responses whereas similar profiles will result in more similar responses, even among phylogenetically distinct groups. This new multidimensional profile account enables fine-grained comparisons within and between species instead of the prevailing all or nothing perspectives of empathy. Furthermore, it offers the integration of phylogenetic and ontogenetic perspectives thereby providing a crucial tool to explicate the notion of empathy to humans and other animals in a species-sensitive way. We demonstrate this framework by applying it specifically to empathy, and the framework's advantages invite it to be generalized to all rich and flexible cognitive abilities in nonhuman animals.
Tumour cell dormancy is a reversible, non-proliferative state in which cancer cells arrest in the G0 phase of the cell cycle. Increasingly recognized as a critical survival strategy, dormancy enables cancer cells to withstand therapeutic insult, escape immune surveillance, and endure hostile microenvironments. Clinically, dormant cells underlie extended asymptomatic intervals following primary treatment and are notably implicated in estrogen receptor-positive (ER+) breast cancer, prostate cancer, and clear cell renal cell carcinoma. In this review, we synthesize recent insights into hypoxia-mediated dormancy and, using breast cancer bone metastasis as an archetypal model, delineate how spatiotemporally heterogeneous hypoxia shapes the metastatic cascade. Specifically, we show that graded hypoxia in the primary tumour initiates dormancy traits, while persistent hypoxia within metastatic niches - such as the bone marrow - reinforces and deepens quiescence. These transitions are orchestrated by stage-specific activation of hypoxia-inducible factor 1α (HIF-1α) and its dynamic transcriptional outputs. We further argue that a mechanistic understanding of dormancy requires integrative frameworks that bridge single-cell level regulatory programs - including cell-cycle arrest, translational inhibition, and metabolic reprogramming - with systems-level networks capturing the dynamic, multistage nature of metastasis. Such integration may uncover actionable vulnerabilities within dormant cell populations and guide the development of precision therapies targeting minimal residual disease.
Following the discovery of identity discrimination, particularly self and kin discrimination amongst plant competitors, research on interplant interactions has advanced significantly within plant physiology and evolutionary ecology. This review synthesizes current knowledge on how both self and kin discrimination influence plant growth, resource allocation, defence, and reproduction. I highlight their ecological and evolutionary consequences for population dynamics, community structure, and multi-trophic interactions. A key insight is that, under some circumstances, identity discrimination may shape the maintenance or erosion of genetic diversity by modulating competitive interactions and spatial genetic structure within populations. Finally, I present several open questions, such as how identity discrimination operates across gradients of plant competition and trophic levels, and propose a few testable hypotheses and experimental approaches regarding the role of competitive identity discrimination under natural settings.
Mussels and oysters are important ecosystem engineers which modify the physical and chemical characteristics of the environment and create habitats that support highly diverse associated communities. In the Mediterranean Sea, the native Mediterranean mussel Mytilus galloprovincialis and the European flat oyster Ostrea edulis, together the introduced Pacific cupped oyster Magallana gigas, are among the most important habitat builders and farmed molluscs. The widespread disappearance of natural beds of mussels and flat oysters, driven by multiple anthropogenic disturbances, disease outbreaks, and harmful invasive species, has led to the loss of the diverse communities they support. Moreover, the proliferation of harmful invasive species is exacerbated by mollusc aquaculture, which represents one of the main vectors for the introduction and spread of non-native species (NNS) in the Mediterranean. The aim of this review is to compile the first comprehensive database of macrofauna associated with wild and farmed M. galloprovincialis, O. edulis and M. gigas in the Mediterranean Sea, based on an extensive literature review. Specifically, we aimed to identify differences in the diversity of associated fauna among the three mollusc species, assess variability of the fauna between wild and farmed systems, highlight associated non-native species, reveal knowledge gaps, and provide directions for future research. Overall, we recorded 782 taxa, with polychaetes, molluscs, arthropods, and ascidians representing the most species-rich groups. Fauna associated with mussels is the most extensively studied and consequently the most diverse, with a considerably higher number of taxa reported from wild mussel habitats (647) than from mussel farms (204), likely reflecting higher environmental heterogeneity in natural contexts. By contrast, the higher diversity of fauna reported from farmed European oysters (163 taxa) compared to wild ones (50 taxa), is consistent with greater research effort focused on aquaculture systems. Fauna associated with naturalized populations of Pacific oysters (M. gigas) remains severely understudied, with only a few species reported to date. Information on fauna associated with molluscs is particularly lacking along much of the African coastline. Future research should therefore prioritize these understudied habitats and regions. To date, a total of 52 non-native species have been reported from mussel and oyster habitats, with arthropods, molluscs and ascidians comprising the majority. Mussels host the highest number of NNS. Reports of NNS from mollusc habitats are increasing, particularly in mussel and oyster farms, suggesting that research efforts should focus on the detection and monitoring of NNS in Mediterranean aquaculture systems. Particular attention should be given to key groups such as non-native ascidians and shell-boring polychaetes, which are known pests and parasites of molluscs. This review provides a baseline for monitoring changes in communities associated with mussels and oysters in the Mediterranean. It may also serve as a reference point for the implementation of management strategies aimed at conserving and restoring mollusc habitats, as well as limiting the spread of non-native and pest species in aquaculture systems.
Fire regimes are changing worldwide, with increases in the frequency, extent, and severity of fires posing growing risks to biodiversity. Fire severity - the degree of habitat alteration following fire - strongly influences both immediate survival and long-term recovery of fauna. Yet species' responses to severe fire are highly variable, shaped by traits, time since fire, and ecosystem context. We conducted a global systematic review of studies quantifying terrestrial vertebrate responses across fire-severity gradients. Using ordinal logistic regression, we assessed the predictive value of functional traits, time since fire, taxonomy, and ecosystem type for species' abundance and occurrence after fire. Across all severity comparisons, most species showed neutral responses; however, high severity fires elicited both more negative and more positive responses than low severity fires. Species with weak shelter, canopy-foraging habits, and preferences for closed canopies were more likely to decline after high severity fire. Negative responses diminished with increasing time since fire, highlighting opportunities for population recovery. Our findings identify functional traits that confer vulnerability to severe fire and provide a basis for predicting species' responses in unstudied taxa or regions. Targeted management, particularly within the first few years post-fire, will be critical to safeguard susceptible species as high severity fires become more frequent.
Numerous studies have revealed the importance of research on the communities capable of colonizing animal surfaces (epibionts) and the animals on which they live (basibionts). Very few studies have considered epizoic diatoms, and there are gaps and biases in our knowledge, including the choice of basibionts, the methods used, and the habitats in which they live. This literature review aims to (i) identify the main basibionts that host diatom communities and the diatom taxa associated with them, in both marine and freshwater environments; (ii) explore the key ecological factors shaping these diatom assemblages; and (iii) reassess critically the commonly applied concept of commensalism in epibiont-host relationships. Our literature review revealed that most research has been focused on charismatic basibiont groups, especially Chordata (notably Testudines and Cetacea), followed by Arthropoda and Mollusca, while taxa such as Bryozoa, Porifera, Cnidaria, Echinodermata, and Annelida have received far less attention. Most studies were carried out in marine settings, particularly in the Americas, and the number of publications has increased since the early 2000s. Taxonomic data on diatom communities shows that the genera Navicula, Nitzschia, Cocconeis and Amphora are the most frequently found as epizoic diatoms. In some cases, highly host-specific diatoms have been documented, for example Pseudohimantidium pacificum, Protoraphis atlantica, Falcula hyalina, and Sceptronema orientale on copepods. From a functional point of view, 'motile' diatoms were dominant on Chordata, Mollusca, and Arthropoda, followed by the 'high-profile' ecological guild. This dominance suggests active interaction between the organisms, supporting the development of well-structured communities on the hosts. There are several types of interaction, depending on the host and epibiont considered. We propose the concepts of triggers and drivers as a framework to describe the initial diversity and development of the epibiont community on the host, and we interpret the nature of these relationships as falling along a continuum from commensalism to parasitism and mutualism. Although diatoms are considered valuable tools for environmental monitoring, we suggest that host displacement and interactions with substrates may be considered as limiting factors for the use of epizoic diatoms in environmental monitoring. However, they may provide useful insights into host ecology, such as the range of host displacement and habits, feeding behaviour, and ecological traits, helping to clarify the trophic and behavioural interactions among basibionts and epibionts. This integrative perspective enhances our understanding of both diatom dispersal and their ecological tolerance and adaptability across diverse environmental contexts.
Biotic resistance, the reduction in invasion success caused by native communities, plays an important role in the long-term dynamics of biological invasions. A large body of empirical research on biotic resistance has accumulated since the last comprehensive review on the subject 20 years ago, enabling us to achieve a refined understanding of biotic resistance and its dynamics. Here, we aim to reshape research on biotic resistance to alien plant invasions by (i) synthesizing existing evidence on biotic resistance and (ii) exploring the so far rarely considered interplay between biotic resistance mechanisms (i.e. competition, aboveground and belowground antagonisms, and diversity-invasibility effects) and the potential eco-evolutionary changes in biotic resistance over time. To address the first aspect, we conducted a global meta-analysis of 240 experimental studies to assess the mechanisms by which and the extent to which biotic resistance of native communities affects the performance of alien plant species. We show that competition with native plant species, aboveground antagonism (e.g. herbivores) and diversity-invasibility effects significantly reduced alien plant performance, whereas there was no evidence for consistent effects of belowground antagonism (e.g. soil pathogens). Competition exerted the strongest biotic resistance, followed by aboveground antagonism. However, the strength of biotic resistance also depended on the alien plant performance measure considered (vegetative performance, survival, reproductive performance, or population growth). From the small set of studies that considered more than one biotic resistance mechanism, we did not detect an overall synergistic effect of combined mechanisms. The meta-analysis results also revealed that biotic resistance first decreased with the residence time of the alien plant species but increased again after approximately 200 years. In a subset of studies directly comparing species of different origin, we did not detect a difference in biotic resistance to alien versus native species. To address the second aspect, we expanded the limited empirical evidence on temporal dynamics by presenting a conceptual causal network and an accompanying mathematical model to explore the eco-evolutionary dynamics of biotic resistance mechanisms. Our conceptual and mathematical models highlight that biotic resistance is determined by both the attributes of the alien species (i.e. invasiveness) and of the recipient community (i.e. invasibility). Both factors can change over time as inter- and/or intraspecific selection cause changes in the composition and overall density of the native community and the alien species. As invaders evolve and the successful ones persist, biotic resistance initially decreases, then increases again due to intra- and interspecific adaptation of the native community. Using the findings from the comprehensive synthesis of empirical studies and our modelling approach, we highlight research avenues to better understand the temporal dynamics of biotic resistance to plant invasions, including how biotic resistance depends on multiple mechanisms and performance measures, how it may differently affect alien versus native species and crucially, how it changes over time.
Animal survival in the wild is largely dependent on their ability to locate food sources, find mates, and avoid predators - tasks which are all heavily reliant on their sense of smell. However, to be adept at these behaviours, animals must navigate a complex odour landscape where odour can be released in many forms, including odour trails and airborne odour plumes. Odour plumes result when an odour is carried by ambient wind, where its structure changes with distance from the odour source, providing potential navigational cues to searching animals. Odour plumes adopt a variety of structures depending on the odour landscape, such as pulled odour filaments that are interleaved with pockets of air in a turbulent environment. Due to advancements in fluid dynamics technology allowing for the detailed measurement of airborne odour plumes, recent studies have begun to explore how odour plume properties affect olfactory search behaviour in mammals. For example, our own studies have demonstrated that intermittency is an odour plume property that can inform olfactory search, is encoded in early stages of olfactory processing within the olfactory bulb, and is subject to changes in representation based on active sampling strategies. This review summarizes how mammalian odour-based navigation depends on and can be guided by odour plume properties.
Insects are the most abundant and ecologically important animal migrants. Yet, we know relatively little about the patterns and processes underlying insect migration. Dragonflies (Anisoptera) and damselflies (Zygoptera) comprise the ancient insect order Odonata, whose ancestors were the first organisms to fly on Earth. Several members of Odonata are known to migrate long distances and have considerable impacts on ecosystems through biomass and nutrient transfer, pest control and species interactions. However, most aspects of odonate migration remain unknown and available data have not been fully reviewed from a global perspective in over two decades. This lack of consensus has repercussions on species monitoring, specialised conservation efforts and scientific progress. Here, we review odonate migration ecology, addressing: (i) what odonate migration is; (ii) why odonates migrate; and (iii) which odonate species migrate. We define two types of odonate migration: multi-generational migration, where back-and-forth migratory journeys are completed over several generations, and single-generational migration, where the same individuals leave and return to the original reproductive habitat. We conclude that within single-generational migration, altitudinal migration is currently the only known strategy, and we present the first complete list of species observed to perform this type of migration, where refuge is temporarily sought at high-altitude sites away from the reproductive habitat. In addition, we generate an exhaustive global list of 85 dragonfly and 15 damselfly species for which migration has been confirmed (total = 100 species) and a list of 85 possible migrants (22 damselfly species; 63 dragonfly species). Consideration of phylogeny suggests that migration has evolved multiple times within Odonata, and is present in four extant dragonfly families and two extant damselfly families. Approximately 1.5% of all odonate species are migratory, with the proportion rising to approximately 2.9% if species deemed to be possible migrants are also included. Thus, overall, migration is a relatively uncommon strategy in Odonata. Among dragonflies, the vast majority (73%) of migratory species occur in the Libellulidae with 62 confirmed migratory species, equating to 5.9% of all libellulids, whereas in damselflies, migrants are divided almost equally between Coenagrionidae (N = 8) and Lestidae (N = 7), with the genus Ischnura in Coenagrionidae having the most migrants of all damselfly genera (N = 5). Biogeographically, the proportion of migratory species is highest in the Palearctic (10.8%), followed by the Nearctic (6.8%), results that may reflect research bias or indicate that migration is an adaptation favoured at high latitudes. Interestingly, most odonate migrants appear to be species of 'Least Concern' according to the IUCN Red List and are potentially resilient to environmental change because of adaptations associated with their migratory strategy, such as opportunism, generalism and long-distance mobility.
The apolipoprotein E ε4 (APOE4) allele is a risk factor for cardiovascular disease and for multiple neurodegenerative diseases, most notably Alzheimer's disease (AD). However, in healthy infants to adults, the encoded apolipoprotein E protein plays a role in many physiological functions, in both the periphery and in the brain, which can help us understand the biological contribution of this protein to disease. This review aims to describe the role of APOE genotype in a wide range of human physiological processes in healthy young/middle-aged individuals, including reproduction, cardiovascular health, inflammation, lipid metabolism, cognition, and brain structure/function, as well as how APOE genotype mediates the effects of external factors in these individuals, such as traumatic brain injury, pollution, lifestyle factors, and viral infections. The research covered in this review demonstrates that a person's APOE genotype affects a wide array of human physiological processes, from infancy to adulthood, with important differences observed in male and female study participants. We also discuss the evolutionary involvement and the 'antagonistic pleiotropy' hypothesis of APOE4. Understanding the biology and the mechanisms that are affected by APOE genotype in healthy young/middle-aged individuals is vital for understanding how this common allele contributes to the development of cardiovascular and neurodegenerative diseases, and how these diseases can be prevented.
Retroviruses constitute a unique group of RNA viruses that have profoundly influenced both evolutionary trajectories and biomedical research. Their ability to reverse transcribe and integrate into host genomes has shaped genomic architecture across species and contributed to our understanding of oncogenes, gene regulation, and RNA biology. This review provides an in-depth examination of retroviral molecular biology, beginning with the intricacies of their genome organization. We present an in-depth discussion of the complex interplay of cis- and trans-acting RNA elements during retrovirus replication, ending with a focus on genomic RNA packaging as the basis of infectious virion production. Emphasis is placed on how, among the various viral proteins, it is the retroviral Gag (Group-specific antigen) that selectively orchestrates the packaging of the unspliced RNA amid a background of cellular and spliced viral RNAs. This is followed by our current understanding of how this process is affected by the retroviral Gag/Pol (Polymerase) and Gag/Pro (Protease)/Pol precursor proteins in the context to which the actual virion assembly takes place. Next, the review outlines emerging concepts regarding the structural basis of RNA recognition, the pivotal role of unpaired purines and long-range intragenomic interactions (LRIs), in guiding genome selection. It discusses the dynamic processes of RNA dimerization and how it is not just intricately linked but is a pre-requisite for genomic RNA encapsidation. Special attention is given to the new findings on transcription start site heterogeneity, cap sequestration, and epitranscriptomic modifications in shaping the fate of retroviral RNAs between translation and packaging since both these processes are critical for a successful viral life cycle. The review also addresses the involvement of assembly intermediates, and liquid-liquid phase separation in orchestrating efficient genome packaging and virus maturation. By integrating classical discoveries with recent findings, the review underscores the sophistication of retrovirus replication and proposes new avenues of research for therapeutic targeting of genome packaging and steps of viral assembly.
Recent methodological development in phylogenetic inference has focused predominantly on molecular data. However, renewed interest in other data types, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. However, attention has largely focused on the improvement of models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference. We present a systematic review of 164 phylogenetic analyses conducted over the last 35 years and focused on a diverse group of extinct arthropods: trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Not surprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data are missing for many tips, providing support against the exclusion of characters because of missing data. In consideration of this, as well as advances in the study of developmental biology and variational complexity, we identify several avenues for increasing the quality and quantity of morphological data going forward.
Agriculture must ensure food production without further compromising the ecosystem functions upon which it depends. Agricultural practices should therefore avoid harming farmland biodiversity, especially of taxa that supply the key ecosystem services (e.g. pollination, pest control and nutrient uptake) that ultimately support crop production. Orchards are among the largest permanent plantations worldwide and are increasingly characterised by the spread of plastic nets used to protect fruits/nuts from either abiotic (anti-hail, anti-rain, shade nets) or biotic (exclusion nets) hazards. Despite having received little attention to date, these nets may impact natural communities, acting both as physical barriers and as drivers of habitat changes to which biota must respond. Species-level responses to netting depend on the organism's ability to enter the netted environment and successfully exploit available resources. Net-mediated ecological filtering and plastic behavioural responses may alter species interactions, leading to cascading ecological impacts that may create species-poorer 'netted communities' with simplified ecological networks. Such changes may erode biological control potential, other ecosystem functions, and overall system stability. We conducted a systematic review on the effects of protection nets on biota, and reported novel empirical evidence on anti-hail nets' impacts on communities of orchard-dwelling birds, flower-visiting insects, and rodents. In total, we identified 48 studies from the literature, however this literature was strongly biased towards apple orchards, western countries, and pest taxa. Net deployment was highly effective in deterring target pest species, in some cases regardless of their original function, as even weather-protection nets limited pest populations. Side effects on non-target taxa were also often reported, such as decreases in pollinators and natural enemies, and/or increases in secondary pests or microbial diseases. However, most assessments largely disregarded non-pest taxa and the broader ecological consequences of netting. The few studies that addressed the effects of nets at the guild/community level, including our empirical study, confirmed that orchard netting resulted in species-poor assemblages, with possible ecosystem-level consequences. We propose that future assessments should pay more attention to the indirect effects of netting on non-target taxa, and on the supply of crop-supporting ecosystem services mediated by wild species occurring in agroecosystems. Due to the trade-offs between these services and net-mediated crop protection, integrated alternatives should be tested to improve the environmental sustainability of food production and biodiversity conservation in farmed landscapes.
Language has long been considered uniquely complex in the animal kingdom; however, animal research over the last decade has begun to challenge some long-standing premises about exactly which language capacities are uniquely human. The task of resolving why and how complex communication systems evolve, particularly human language, has manifested in a rich multi-disciplinary field, which relies on accurate empirical and comparative assessment of natural animal communicative capacities. For example, comparative models of relevant gene and brain functions will remain limited without cracking the animal communication code. To achieve this, empirical research needs an updated, quantitative and comparative framework that distinguishes combinatorial systems from simpler ones. We offer such a framework by integrating new work, demonstrating diverse meaning-bearing combinatorial signalling strategies in natural animal communication, into cross-disciplinary theoretical frameworks. We detail four major mechanistic transitions which we argue offer both evolutionary and ontogenetic routes from non-combinatorial communicators, that mainly rely on single signal utterances, to generative combinatorial signal users, that mainly rely on combinatorial, meaning-based utterances. These transitions are measurable and predictable: (i) signal combination versatility; (ii) signal combination learning and conventionalization; (iii) message expansion through combinatorial mechanism diversity and versatility; and (iv) message expansion through syntax involving linear or hierarchical rules. We offer testable hypotheses for each transition and propose that species demonstrating combinatorial Transitions (i) and (ii) will be prime candidates for testing Transitions (iii) and (iv), where generativity can emerge. We also point to future methodological tools to assess the meaning of signals and their combinations in signal utterance-to-context mapping analyses. Critically, we argue that simply having research on different species is not enough - testing evolution of language theories requires comparative research across species and ontogeny, based on relatable, quantitative measures. To date, only humans demonstrate meaning-based, generative communication. However, recent discoveries, particularly of combinatorial versatility in chimpanzee (Pan troglodytes) and bonobo (Pan paniscus) vocal sequences, open the possibility of generative communication in other species. Whether such traits are human-unique can no longer be assumed but must be tested.
Recent advances in data collection technologies (e.g. automated sensor networks, satellite remote sensing, and high-throughput sequencing) have greatly expanded the availability of ecological time series, enabling new opportunities for causal analyses in dynamic ecosystems. Granger causality (GC) and convergent cross mapping (CCM), two prominent dynamical causal discovery methods, have gained attention in ecological studies for uncovering causal relationships in nonlinear systems. GC traces its roots to economics and was later extended through the information-theoretic framework of transfer entropy (TE). On the other hand, CCM was developed from studies of chaotic time series. Both methods have provided critical insights into the dynamics of complex systems. In this review, we synthesize foundational concepts and recent developments in GC and CCM, exploring their respective strengths and limitations, while clarifying their interrelationship. We also review recent advances in temporal causal discovery methods, originally developed within the framework of statistical causal inference for non-temporal data, and highlight their applicability to ecological data sets. Despite these advances, such approaches remain largely unfamiliar to ecologists. We argue that a rigorous framework of time-series-based causal inference, together with an appreciation of their diverse methodological developments to date, will not only raise awareness of unresolved challenges but also create new research opportunities in ecology. By offering an integrated perspective, we encourage the application and development of cutting-edge methods in ecology to help foster a deeper understanding of ecosystem dynamics.
