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A key benefit of grouping in prey species is access to social information, including information about the presence of predators. Larger groups of prey animals respond both sooner and at greater distances from predators, increasing the likelihood that group members will successfully avoid capture. However, identifying predators in complex environments is a difficult task, and false alarms (alarm behaviours without genuine threat) appear surprisingly frequent across a range of taxa including insects, amphibians, fish, mammals, and birds. In some bird flocks, false alarms have been recorded to substantially outnumber true alarms. False alarms can be costly in terms of both the energetic costs of producing alarm behaviours as well as lost opportunity costs (e.g. abandoning a feeding patch which was in fact safe, losing sleep if an animal is resting/roosting, or losing mating opportunities). Models have shown that false alarms may be a substantial but underappreciated cost of group living, introducing an inherent risk to using social information and a vulnerability to the propagation of false information. This review will focus on false alarms, introducing a two-stage framework to categorise the different factors hypothesised to influence the propensity of animal groups to produce false alarms. A number of factors may affect false alarm rate, and this new framework splits these factors into two core processing stages: (i) individual perception and response; and (ii) group processing of predator information. In the first stage, individuals in the group monitor the environment for predator cues and respond. The factors highlighted in this stage influence the likelihood that an individual will misclassify stimuli and produce a false alarm (e.g. lower light levels can make predator identification more difficult and false alarms more common). In the second stage, alarm information from individuals is processed by the group. The factors highlighted in this stage influence the likelihood of alarm information being copied by group members and propagated through the group (e.g. some animals implement group processing mechanisms that regulate the spread of behavioural responses such as consensus decision making through the quorum response). This review follows the structure of this new framework, focussing on the causes of false alarms, factors that influence false alarm rate, the transmission of alarm information through animal groups, mechanisms to mitigate the spread of false alarms, and the consequences of false alarms. Publisher PDF

Daphne Cortese, Amelia Munson and Shaun S. Kille are supported by Natural Environment Research Council Standard Grant NE/T008334/1 awarded to Shaun S. Killen. Libor Závorka was supported by Austrian Science Fund Stand Alone Project P35515-B. While studies on fish cognition are increasing, consideration of how methodological details influence the ability to detect and measure performance is lagging. Here, in two separate experiments we compared latency to leave the start position, latency to make a decision, levels of participation and success rates (whether fish entered the rewarded chamber as first choice) across different physical designs. Experiments compared fish performance across 1) two sizes of T-mazes, large and standard, and a plus-maze, and 2) open choice arenas with either two or four doors. Fish in T-mazes with longer arms took longer to leave the start chamber and were less likely to participate in a trial than fish in T-mazes with shorter arms. The number of options, or complexity, in a maze significantly impacted success, but did not necessarily impact behavioural measures, and did not impact the number of fish that reached a chamber. Fish in the plus-maze had similar latencies to leave the start box and time to reach any chamber as fish in the same sized T-maze but exhibited lower overall success. Similarly, in an open choice arena, increasing the number of options – doors to potential reward chambers- resulted in lower probability of success. There was an influence of reward position in the choice arena, with rewarded chambers closest to the sides of the arena resulting in lower latencies to enter and higher probability of decision success. Together our results allow us to offer practical suggestions towards optimal maze design for studies of fish cognition. Publisher PDF

The present paper provides an integrative theory of actions and motor programs for skill in tool use, construction, and language. We analyze preconditions for action as well as making their effects (postconditions) explicit, emphasizing the “how” of action details as well as the “what” of motor programs, aided by conceptual analysis of several brain modeling efforts. The theory is exemplified by analysis of the subtractive construction involved in percussive tooling by capuchin monkeys and Oldowan and Acheulean stone tool by protohumans making before turning to the additive construction of hafted tools. A complementary analysis focused on the construction of bird nests explores the notion of “image” and “stage” in construction. We offer a brief comparison with birdsong before arguing for a very different relation between communication and construction in humans. Pantomime lifts manipulation from practical to communicative action in protohumans, and we consider the role of pedagogy before offering hypotheses on the emergence of human language that suggest how language may have evolved from manual skills. We note that language provides an open-ended means for devising innovations in tool use and construction, but reiterate the importance of this framework for diverse future studies in ethology and comparative psychology. Publisher PDF

Funding: This work was supported by the Vienna Science and Technology Fund (WWTF) (10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines. Publisher PDF

Funding: Systematics Research Fund 2019 to KV. John Templeton Foundation (Grant Number(s): #60501; Grant recipient(s): Kevin N Laland). 1. The size of a bird's nest can play a key role in ensuring reproductive success and is determined by a variety of factors. The primary function of the nest is to protect offspring from the environment and predators. Field studies in a number of passerine species have indicated that higher-latitude populations in colder habitats build larger nests with thicker walls compared to lower-latitude populations, but that these larger nests are more vulnerable to predation. Increases in nest size can also be driven by sexual selection, as nest size can act as a signal of parental quality and prompt differential investment in other aspects of care. It is unknown, however, how these microevolutionary patterns translate to a macroevolutionary scale. 2. Here, we investigate potential drivers of variation in the outer and inner volume of open cup nests using a large dataset of nest measurements from 1117 species of passerines breeding in a diverse range of environments. Our dataset is sourced primarily from the nest specimens at the Natural History Museum (UK), complemented with information from ornithological handbooks and online databases. 3. We use phylogenetic comparative methods to test long-standing hypotheses about potential macroevolutionary correlates of nest size, namely nest location, clutch size and variables relating to parental care, together with environmental and geographical factors such as temperature, rainfall, latitude and insularity. 4. After controlling for phylogeny and parental body size, we demonstrate that the outer volume of the nest is greater in colder climates, in island-dwelling species and in species that nest on cliffs or rocks. By contrast, the inner cup volume is associated solely with average clutch size, increasing with the number of chicks raised in the nest. We do not find evidence that nest size is related to the length of parental care for nestlings. 5. Our study reveals that the average temperature in the breeding range, along with several key life-history traits and proxies of predation threat, shapes the global interspecific variation in passerine cup nest size. We also showcase the utility of museum nest collections—a historically underused resource—for large-scale studies of trait evolution. Publisher PDF

Funding information: Austrian Science Fund, Grant/Award Number: P34524-B; Biotechnology and Biological Sciences Research Council, Grant/Award Number: BB/W000768/1; Deutsche Forschungsgemeinschaft, Grant/Award Number: HO 6201/1-1; Vienna Science and Technology Fund, Grant/Award Number: MA016-061. 1. The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly with sequence divergence across species are rare and not easily accessible to empiricists. 2. We implemented polymorphism-aware phylogenetic models (PoMos), an alternative approach for species tree estimation, in the Bayesian phylogenetic software RevBayes. PoMos naturally account for incomplete lineage sorting, which is known to cause difficulties for phylogenetic inference in species radiations, and scale well with genome-wide data. Simultaneously, PoMos can estimate mutation and selection biases. 3. We have applied our methods to resolve the complex phylogenetic relationships of a young radiation of Chorthippus grasshoppers, based on coding sequences. In addition to establishing a well-supported species tree, we found a mutation bias favouring AT alleles and selection bias promoting the fixation of GC alleles, the latter consistent with GC-biased gene conversion. The selection bias is two orders of magnitude lower than genetic drift, validating the critical role of nearly neutral evolutionary processes in species radiation. 4. PoMos offer a wide range of models to reconstruct phylogenies and can be easily combined with existing models in RevBayes—for example, relaxed clock and divergence time estimation—offering new insights into the evolutionary processes underlying molecular evolution and, ultimately, species diversification. Publisher PDF

Funding: RKH thanks the Perry Foundation and the University of St Andrews for funding. AJK is supported by the strategic research program funded by the Scottish Government’s Rural and Environment Science and Analytical Services Division. Facultative endosymbionts can induce benefits and costs to their aphid hosts. In the pea aphid, Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae), infection with the γ-proteobacterium Hamiltonella defensa Moran et al. can confer resistance against parasitoids, but may also reduce the frequency of aggressive and escape behaviours exhibited in response to predators. In potato aphids, Macrosiphum euphorbiae (Thomas) (Hemiptera: Aphididae), H. defensa does not appear to influence susceptibility to parasitism, but its impact on anti-predator behaviours remains unexplored. Here we investigated defensive behaviours in two pea aphid lines (differing in H. defensa-infection status) and four potato aphid lines (that additionally differed in genotype-associated parasitism susceptibility) when faced with foraging ladybirds – Adalia bipunctata (L.) (Coleoptera: Coccinellidae) – and lacewings Chrysoperla carnea (Stephens) (Neuroptera: Chrysopidae). In response to ladybirds, symbiont-infected pea aphids exhibited proportionately fewer evasive defences (dropping and walking away) than non-infected (cured) pea aphids, but more frequent aggressive kicking. Ladybirds provoked more evasive, aggressive, and total defensive behaviours than lacewings. For potato aphids, symbiont status, predator type, and aphid genotype (i.e., assumed parasitism susceptibility) all influenced behavioural repertoires. Overall, infected lines showed greater differentiation in behaviours in response to the two predators than the uninfected lines. The presence of the symbiont H. defensa may be a key determinant of aphid anti-predator behaviours, but the fitness consequences of this are unresolved. In our study, neither symbiont infection status nor aphid genotype affected the number of aphids consumed by predators. Publisher PDF

This research would not have been possible without the generous EPSRC stipend; we are very grateful for the awarding of this studentship to Alan Scaramangas. Our understanding of aposematism (the conspicuous signalling of a defence for the deterrence of predators) has advanced notably since its first observation in the late nineteenth century. Indeed, it extends the scope of a well-established game-theoretical model of this very same process both from the analytical standpoint (by considering regimes of varying background mortality and colony size) and from the practical standpoint (by assessing its efficacy and limitations in predicting the evolution of prey traits in finite simulated populations). The nature of the manuscript at hand is more mathematical and it’s aim is two-fold: first, to determine the relationship between evolutionarily stable levels of defence and signal strength under various regimes of background mortality and colony size. Second, to compare these predictions with simulations of finite prey populations that are subject to random local mutation. We compare the roles of absolute resident fitness, mutant fitness and stochasticity in the evolution of prey traits and discuss the importance of population size in the above. Publisher PDF

Some data are collected on circular (rather than linear) scales. Often researchers are interested in comparing two samples of such circular data to test the hypothesis that they came from the same underlying population. Recently, we compared 18 statistical approaches to testing such a hypothesis, and recommended two as particularly effective. A very recent publication introduced a novel statistical approach that was claimed to outperform the methods that we had indicated were highest performing. However, the evidence base for this claim was limited. Here we perform simulation studies to offer a more detailed comparison of the new “Angular Randomisation Test” (ART) with existing tests. We expand previous evaluations in two ways: exploring small and medium sized samples, and exploring a range of different shapes for the underlying distribution(s). We find that the ART controls type I error rates at the nominal level. The ART had greater power than established methods in detecting a difference in underlying distribution caused by a shift around the circle. Its performance advantage in this case was strongest when samples where small and unbalanced in size. When the difference between underlying unimodal distributions was in shape rather than central tendency, then the ART was at least as good (and sometimes considerably more powerful) than the established methods, except when distributions samples were small and uneven in size, and the smaller sample came from a more concentrated underlying distribution. In such cases its power could be markedly inferior to established alternatives. The ART was also inferior to alternatives in dealing with axially distributed data. We conclude that under widely-encountered circumstances the ART test can be recommended for its simplicity of implementation, but researchers should be aware of situations where it cannot be recommended. Grant Number: P32586 to LL. For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. EPM receives funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 948728). EPM acknowledges the HPC facility at the Max Planck Institute for Neurobiology of Behavior—caesar.

Funding: This article is a contribution of the COVID-19 Bio-Logging Initiative, which is funded in part by the Gordon and Betty Moore Foundation (GBMF9881) and the National Geographic Society (NGS-82515R-20) (both grants to C.R.). COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals’ 1-hour 95th percentile displacements declined by 12% and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide. Postprint

Funding: This research was supported by a European Research Council Consolidator (grant no. 771387). Recent years have seen renewed interest in the role of religious systems as drivers of the evolution of cooperation in human societies. One suggestion is that a cultural tradition of ancestor worship might have evolved as a "descendant-leaving strategy" of ancestors by encouraging increased altruism particularly between distant kin. Specifically, Coe and others have suggested a mechanism of cultural transmission exploiting social learning biases, whereby ancestors have been able to establish parental manipulation of kin recognition and perceived relatedness as a traditional behavior, leading to increased altruism among co-descendants and thereby maximizing the ancestor’s long-term inclusive fitness. Here, we develop a demographically explicit model in order to quantify the resulting increase in altruism and concomitant “ancestor-descendant conflict”, and to determine the evolutionary feasibility of religiously motivated cultural norms that promote altruism among co-descendants. Our analysis reveals that such norms could indeed drive an overall increase in altruism with potential for ancestor-descendant conflict, particularly in low-dispersal settings. Moreover, we find that natural selection can favor traditions encouraging increased altruism towards co-descendants under a range of conditions, with the inclusive-fitness costs of enacting an inappropriately high level of altruism being offset by inclusive-fitness benefits derived from the cultural tradition facilitating kin recognition. Publisher PDF

This work was funded by a NERC Independent Research Fellowship (NE/K009370/1) and a Leverhulme Trust grant (RPG-2017-041 V) awarded to C.C.I. Of widespread interest in animal behavior and ecology is how animals search their environment for resources, and whether these search strategies are optimal. However, movement also affects predation risk through effects on encounter rates, the conspicuousness of prey, and the success of attacks. Here, we use predatory fish attacking a simulation of virtual prey to test whether predation risk is associated with movement behavior. Despite often being demonstrated to be a more efficient strategy for finding resources such as food, we find that prey displaying Lévy motion are twice as likely to be targeted by predators than prey utilizing Brownian motion. This can be explained by the predators, at the moment of the attack, preferentially targeting prey that were moving with straighter trajectories rather than prey that were turning more. Our results emphasize that costs of predation risk need to be considered alongside the foraging benefits when comparing different movement strategies. Publisher PDF

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Funding Information: We are especially thankful to Rob G. Bijlsma who generously shared with us his extensive dataset from the Sahel region. We are also thankful to Afan Ajang, Linn M. Bjørvik, Tamuka Chapata, Wouter van Dongen, Patrick Guay, Lenka Harmáčková, Lukasz Jankowiak, Jan van der Kamp, Lennox Kirao, Jakub Kosicki, Philista Malaki, Pretty Maoko, John Mchetto, Grayson Mwakalebe, Organisation for Tropical Studies (South Africa), Diogo Samia, Trine Hay Setsaas, Libor Vaicenbacher and Leo Zwarts for their help with data collection. MW is thankful to Allison Piper, and a Deakin University Faculty of Science, Engineering and the Built Environment National and International Research Collaboration Grant in Kenya and BEACH (Beach Ecology and Conservation Hub; Venus Bay) in Australia. In Kenya, field data collection was approved by National Commission for Science Technology and Innovation no. NACOSTI/P14/4653/660 to M.W. and P.M. and no. NACOSTI/P18/52438/25493 to MW, Kenya Wildlife Service no KWS/BRP/5001 to M.W. A Rocha Kenya and the National Museum of Kenya supported and helped conduct fieldwork in Kenya. In South Africa, the University of Cape Town Science Faculty Animal Ethics Committee (2015/V11/SC) to S.J.C., Northern Cape Department of Environment and Nature Conservation (FAUNA 1489/2015) to P.P. In Brazil, we worked on private lands where no permits were required. In Australia, research was approved by the Deakin University (B32/2012, B11/2015, B10/2018), the Charles Darwin University Animal Ethics (A11013), the Macquarie University Animal Research Committee (99021), the Queensland Parks and Wildlife Service (#FA/000379/00/SA), and the Northern Territory Parks and Wildlife (41035 and 55233). This study was financially supported by the DSI-NRF Centre of Excellence at the FitzPatrick Institute of African Ornithology, University of Cape Town (grant to S.J.C.), The Leventis Foundation through the A.P. Leventis Ornithological Research Institute, Jos Nigeria (grant to B.D.A.B.), by a fellowship of the Fulbright (Slovakia) programme to P.M. for a visit to the University of California, Los Angeles. Animal tolerance towards humans can be a key factor facilitating wildlife–human coexistence, yet traits predicting its direction and magnitude across tropical animals are poorly known. Using 10,249 observations for 842 bird species inhabiting open tropical ecosystems in Africa, South America, and Australia, we find that avian tolerance towards humans was lower (i.e., escape distance was longer) in rural rather than urban populations and in populations exposed to lower human disturbance (measured as human footprint index). In addition, larger species and species with larger clutches and enhanced flight ability are less tolerant to human approaches and escape distances increase when birds were approached during the wet season compared to the dry season and from longer starting distances. Identification of key factors affecting animal tolerance towards humans across large spatial and taxonomic scales may help us to better understand and predict the patterns of species distributions in the Anthropocene.

Integrity and trust in that integrity are fundamental to academic research. However, procedures for monitoring the trustworthiness of research, and for investigating cases where concern about possible data fraud have been raised are not well established. Here we suggest a practical approach for the investigation of work suspected of fraudulent data manipulation using Benford’s Law. This should be of value to both individual peer-reviewers and academic institutions and journals. In this, we draw inspiration from well-established practices of financial auditing. We provide synthesis of the literature on tests of adherence to Benford’s Law, culminating in advice of a single initial test for digits in each position of numerical strings within a dataset. We also recommend further tests which may prove useful in the event that specific hypotheses regarding the nature of data manipulation can be justified. Importantly, our advice differs from the most common current implementations of tests of Benford’s Law. Furthermore, we apply the approach to previously-published data, highlighting the efficacy of these tests in detecting known irregularities. Finally, we discuss the results of these tests, with reference to their strengths and limitations.

Funding: This work was supported by the University of St Andrews. Artificial light at night (ALAN) has been implicated in the global decline of insect populations. Causal mechanisms contributing to declines remain unclear, however. Here we examine causal factors which could link some declining terrestrial insect populations with ALAN. To do so, we defined the closest and furthest halves of individual bushes according to the nearest source of artificial light. We sampled leaves and invertebrates from both sides to determine herbivory and abundance. First, we observed that, within bushes, leaves were significantly more likely to display herbivory at closer distances to established streetlighting. This may be due to the phenomenon of positive phototaxis in insects (flight to light). Further, insects within bushes were significantly more abundant on the side closest to streetlighting at midnight, but not at midday, when lights are unilluminated. Consequently, we argue that ALAN creates bottom-up trophic effects, driven by insect light attraction behaviours even at the scale of single plants. Publisher PDF

MBM is supported by a Royal Society (London) University Research Fellowship. Log-linear models are widely used for assessing determinants of fitness in empirical studies, for example, in determining how reproductive output depends on trait values or environmental conditions. Similarly, theoretical works of fitness and natural selection employ log-linear models, often with a negative quadratic term, generating Gaussian fitness functions. However, in the specific application of regression-based analysis of natural selection, such models are rarely employed. Rather, OLS regression is the predominant means of assessing the form of natural selection. OLS regressions allow specific evolutionary quantitative parameters, selection gradients, to be estimated, and benefit from the fact that the associated statistical models are easily applied. We examine whether selection gradients can be directly expressed in terms of the coefficients of models using exponential fitness functions with linear or quadratic arguments. Such models can be easily fitted with generalised linear models (GLMs). The expressions we obtain coincide with those for Gaussian functions, but relax the major constraint that the (log) fitness function is concave (downwardly curved). Additionally these results lead to univariate and multivariate analyses of both linear and quadratic selection that potentially incorporate pragmatic and interpretable models of fitness functions, where the parameters can be related analytically to selection gradients, and that can be operationalised using widely-available statistical tools. Publisher PDF

Social learning is widespread in the animal kingdom and is involved in behaviours from navigation and predator avoidance to mate choice and foraging. While social learning has been extensively studied in group-living species, this article presents a literature review demonstrating that social learning is also seen in a range of non-grouping animals, including arthropods, fishes and tetrapod groups, and in a variety of behavioural contexts. We should not be surprised by this pattern, since non-grouping animals are not necessarily non-social, and stand to benefit from attending to and responding to social information in the same ways that group-living species do. The article goes on to ask what non-grouping species can tell us about the evolution and development of social learning. First, while social learning may be based on the same cognitive processes as other kinds of learning, albeit with social stimuli, sensory organs and brain regions associated with detection and motivation to respond to social information may be under selection. Non-grouping species may provide useful comparison taxa in phylogenetic analyses investigating if and how the social environment drives selection on these input channels. Second, non-grouping species may be ideal candidates for exploring how ontogenetic experience of social cues shapes the development of social learning, allowing researchers to avoid some of the negative welfare implications associated with raising group-living animals under restricted social conditions. Finally, while non-grouping species may be capable of learning socially under experimental conditions, there is a need to consider how non-grouping restricts access to learning opportunities under natural conditions and whether this places a functional constraint on what non-grouping animals actually learn socially in the wild. Publisher PDF

Scleractinian corals are colonial animals with a range of life history strategies, making up diverse species assemblages that define coral reefs. We tagged and tracked approximately 30 colonies from each of 11 species during seven trips spanning six years (2009-2015) in order to measure their vital rates and competitive interactions on the reef crest at Trimodal Reef, Lizard Island, Australia. Pairs of species were chosen from five growth forms where one species of the pair was locally rare (R) and the other common (C). The sampled growth forms were massive [Goniastrea pectinata (R) and G. retiformis (C)], digitate [Acropora humilis (R) and A. cf. digitifera (C)], corymbose [A. millepora (R) and A. nasuta (C)], tabular [A. cytherea (R) and A. hyacinthus (C)] and arborescent [A. robusta (R) and A. intermedia (C)]. An extra corymbose species with intermediate abundance, A. spathulata was included when it became apparent that A. millepora was too rare on the reef crest, making the 11 species in total. The tagged colonies were visited each year in the weeks prior to spawning. During visits, two or more observers each took 2-3 photographs of each tagged colony from directly above and on the horizontal plane with a scale plate to track planar area. Dead or missing colonies were recorded and new colonies tagged in order to maintain approximately 30 colonies per species throughout the six years of the study. In addition to tracking tagged corals, 30 fragments were collected from neighboring untagged colonies of each species for counting numbers of eggs per polyp (fecundity); and fragments of untagged colonies were brought into the laboratory where spawned eggs were collected for biomass and energy measurements. We also conducted surveys at the study site to generate size structure data for each species in several of the years. Each tagged colony photograph was digitized by at least two people. Therefore, we could examine sources of error in planar area for both photographers and outliners. Competitive interactions were recorded for a subset of species by measuring the margins of tagged colony outlines interacting with neighboring corals. The study was abruptly ended by Tropical Cyclone Nathan (Category 4) that killed all but nine of the over 300 tagged colonies in early 2015. Nonetheless, these data will be of use to other researchers interested in coral demography and coexistence, functional ecology, and parametrizing population, community and ecosystem models. The data set is not copyright restricted, and users should cite this paper when using the data. Publisher PDF

Funding: W.B.X., S.A.B., J.M.C., R.v.K., and D.M. were supported by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, funded by the German Research Foundation (DFG FZT-118, 20254881); B.J.M. was supported by NSF EPSCOR Track II 201947 and USDA Hatch grant (MAFES #1011538); N.J.G was supported by NSF EPSCOR Track II 201947; I.S.M. was supported by the European Union’s Horizon 2020 research and innovation program under Marie Sklodowska -Curie grant (no. 894644); H.S. was supported by Japan Society for the Promotion of Science (JP19K21569 and JP21H03402); A.E.M. and M.D. were supported by Leverhulme Trust (RPG-2019-402). A.F.E acknowledges the Fisheries Society of the British Isles Studentship. BioTIME used here was supported by ERC AdG 250189 and PoC 727440 (to A.E.M.), and Leverhulme Trust Research Centre–the Leverhulme Centre for Anthropocene Biodiversity (to M.D.). While human activities are known to elicit rapid turnover in species composition through time, the properties of the species that increase or decrease their spatial occupancy underlying this turnover are less clear. Here, we used an extensive dataset of 238 metacommunity time series of multiple taxa spread across the globe to evaluate whether species that are more widespread (large-ranged species) differed in how they changed their site occupancy over the 10–90 years the metacommunities were monitored relative to species that are more narrowly distributed (small-ranged species). We found that on average, large-ranged species tended to increase in occupancy through time, whereas small-ranged species tended to decrease. These relationships were stronger in marine than in terrestrial and freshwater realms. However, in terrestrial regions, the directional changes in occupancy were less extreme in protected areas. Our findings provide evidence for systematic decreases in occupancy of small-ranged species, and that habitat protection could mitigate these losses in the face of environmental change. Publisher PDF

Funding: A.E.M. thanks the Leverhulme Trust (RPG-2019–402) for support. Recent research has uncovered rapid compositional and structural reorganization of ecological assemblages, with these changes particularly evident in marine ecosystems. However, the extent to which these ongoing changes in taxonomic diversity are a proxy for change in functional diversity is not well understood. Here we focus on trends in rarity to ask how taxonomic rarity and functional rarity covary over time. Our analysis, drawing on 30 years of scientific trawl data, reveals that the direction of temporal shifts in taxonomic rarity in two Scottish marine ecosystems is consistent with a null model of change in assemblage size (i.e. change in numbers of species and/or individuals). In both cases, however, functional rarity increases, as assemblages become larger, rather than showing the expected decrease. These results underline the importance of measuring both taxonomic and functional dimensions of diversity when assessing and interpreting biodiversity change. Publisher PDF

These files contain code and data used in this study., This work was funded by Leverhulme Trust grant RPG-2019-402, 'Darwin, Wallace, Bates and biodiversity change in the Anthropocene', awarded to Anne Magurran and Maria Dornelas, {"references":["Blowes, S. A., Supp, S. R., Antão, L. H., Bates, A., Bruelheide, H., Chase, J. M., … Dornelas, M. (2019). The geography of biodiversity change in marine and terrestrial assemblages. Science, 366(6463), 339–345. https://doi.org/10.1126/science.aaw1620","USGS Patuxent Wildlife Research Center (2014) North American Breeding Bird Survey ftp data set, version 2014.0. US Breeding Birds Survey. Available at: https://www.pwrc.usgs.gov/BBS/RawData/ (Accessed:2013).","DATRAS (2010) Fish trawl survey: ICES North Sea International Bottom Trawl Survey for commercial fish species. ICES Database of trawl surveys (DATRAS). The International Council for the Exploration of the Sea, Copenhagen. Available at: http://www.emodnet-biology.eu/data-catalog?%3Fmodule=dataset&dasid=2763, accessed 2013."]}

Funding: This study was funded by a Natural Environment Research Council Independent Research Fellowship (grant no. NE/K009524/1) and a European Research Council Consolidator Grant (no. 771387). Conflicts of interest abound not only in human affairs but also in the biological realm. Evolutionary conflict occurs over multiple scales of biological organization, from genetic outlawry within genomes, to sibling rivalry within nuclear families, to collective-action disputes within societies. However, achieving a general understanding of the dynamics and consequences of evolutionary conflict remains an outstanding challenge. Here, we show that a development of R. A. Fisher's classic ‘geometric model’ of adaptation yields novel and surprising insights into the dynamics of evolutionary conflict and resulting maladaptation, including the discoveries that: (i) conflict can drive evolving traits arbitrarily far away from all parties' optima and, indeed, if all mutations are equally likely then contested traits are more often than not driven outwith the zone of actual conflict (hyper-maladaptation); (ii) evolutionary conflicts drive persistent maladaptation of orthogonal, non-contested traits (para-maladaptation); and (iii) modular design greatly ameliorates conflict-driven maladaptation, thereby facilitating major transitions in individuality. Publisher PDF

Funding: ELC was supported by a Rutherford Discovery Fellowship from the Royal Society of New Zealand Te Apārangi and EG was supported by a University Research Fellowship from the Royal Society of London. The identification of patterns in trait evolution is essential to understand the interaction of evolutionary forces, and provides useful information for species management. Cetaceans are a phylogenetically well-resolved infraorder that exhibit distinct trait variation across behavioural, molecular and life history dimensions, yet few researchers have applied a meta-analytic or comparative approach to these traits. To understand cetacean trait evolution, we used a phylogenetic generalised least squares approach to examine the cognitive buffer hypothesis (CBH). A large brain should buffer individuals against environmental challenges through increasing survival rates, and a longer lifespan should buffer individuals against the cost of extended development for larger brains according to the CBH, leading to an expected positive correlation between brain size and lifespan. In contrast to this expectation, previously observed in taxa including primates, we found a negative correlation between brain size and lifespan in cetaceans. This suggests cetaceans experience selective pressures different from most other mammals in these traits but may be more similar to some social mammalian carnivores that display alloparenting. We also provide a comprehensive dataset to explore additional aspects of trait evolution but which would greatly benefit from studies on behavioural ecology across cetaceans and increased focus on data deficient species. Publisher PDF

Funding: This work was funded by an ERC Consolidator Grant to A. Gardner (grant no. 771387), by the School of Biology of the University of St Andrews, and by a John Templeton Foundation grant to K.N. Laland and T. Uller (grant ID 60501). Natural selection acts on developmentally constructed phenotypes, but how does development affect evolution? This question prompts a simultaneous consideration of development and evolution. However, there has been a lack of general mathematical frameworks mechanistically integrating the two, which may have inhibited progress on the question. Here, we use a new mathematical framework that mechanistically integrates development into evolution to analyse how development affects evolution. We show that, while selection pushes genotypic and phenotypic evolution up the fitness landscape, development determines the admissible evolutionary pathway, such that evolutionary outcomes occur at path peaks rather than landscape peaks. Changes in development can generate path peaks, triggering genotypic or phenotypic diversification, even on constant, single-peak landscapes. Phenotypic plasticity, niche construction, extra-genetic inheritance, and developmental bias alter the evolutionary path and hence the outcome. Thus, extra-genetic inheritance can have permanent evolutionary effects by changing the developmental constraints, even if extra-genetically acquired elements are not transmitted to future generations. Selective development, whereby phenotype construction points in the adaptive direction, may induce adaptive or maladaptive evolution depending on the developmental constraints. Moreover, developmental propagation of phenotypic effects over age enables the evolution of negative senescence. Overall, we find that development plays a major evolutionary role. Publisher PDF

Funding: We are grateful for support from the Natural Environment Research Council to NWB (NE/L011255/1 and NE/T000619/1). The effects of within-generation plasticity vs. transgenerational plasticity on trait expression are poorly understood, but important for evaluating plasticity's evolutionary consequences. We tested how genetics, within-generation plasticity, and transgenerational plasticity jointly shape traits influencing rapid evolution in the field cricket Teleogryllus oceanicus. In Hawaiian populations attacked by acoustically orienting parasitoid flies, a protective, X-linked variant ("flatwing") eliminates male acoustic sexual signals. Silent males rapidly spread to fixation, dramatically changing the acoustic environment. First, we found evidence supporting flatwing-associated pleiotropy in juveniles: pure-breeding flatwing males and females exhibit greater locomotion than those with normal-wing genotypes. Second, within-generation plasticity caused homozygous-flatwing females developing in silence, which mimics all-flatwing populations, to attain lower adult body condition and reproductive investment than those experimentally exposed to song. Third, maternal song exposure caused transgenerational plasticity in offspring, affecting adult, but not juvenile, size, condition, and reproductive investment. This contrasted with behavioral traits, which were only influenced by within-generation plasticity. Fourth, we matched and mismatched maternal and offspring social environments and found that transgenerational plasticity sometimes interacted with within-generation plasticity and sometimes opposed it. Our findings stress the importance of evaluating plasticity of different traits and stages across generations when evaluating its fitness consequences and role in adaptation. Publisher PDF

Funding: C.F., U.B. and D.J.R. acknowledge COST Action ‘European Soil-Biology Data Warehouse for Soil Protection’ (EUdaphobase), CA18237, supported by COST (European Cooperation in Science and Technology). AEM thanks the Leverhulme Trust (RPG-2019-401). D.B.B. was supported by an NSF Postdoc Research Fellowship in Biology (NSF 000733206), S.M.R. was supported by an NSERC Discovery Grant Author Contributions, A.V.S. was supported by NSF 1755336, C.S.M was supported by NSF 1398620 and N.J.G was supported by NSF 2019470. 1. Dated, geo-referenced museum specimens are a rich data source for reconstructing species' distribution and abundance patterns. However, museum records are potentially biased towards over-representation of rare species, and it is unclear whether museum records can be used to estimate relative abundance in the field. 2. We assembled 17 coupled field and museum datasets to quantitatively compare relative abundance estimates with the Dirichlet distribution. Collectively, these datasets comprise 73,039 museum records and 1,405,316 field observations of 2,240 species. 3. Although museum records of rare species overestimated relative abundance by 1-fold to over 100-fold (median study = 9.0), the relative abundance of species estimated from museum occurrence records was strongly correlated with relative abundance estimated from standardized field surveys (r2 range of 0.10-0.91, median study = 0.43). 4. These analyses provide a justification for estimating species relative abundance with carefully curated museum occurrence records, which may allow for the detection of temporal or spatial shifts in the rank ordering of common and rare species. Publisher PDF

This work was supported by the Queen Sirikit Scholarship and the European Research Council (grant no. 771387). A classic result of sex-allocation theory is that the sex ratio is predicted to be invariant with respect to the rate of dispersal. However, a recent mathematical analysis has suggested that if individuals are able to adjust their probability of dispersal according to the local density of their neighbourhood, then a lower rate of dispersal will be associated with greater female-bias. Here, we perform a computer simulation test of this prediction. Our simulation data provide strong qualitative support for the prediction, and a Monte Carlo randomization test of significance allows us to reject the null hypothesis of the invariance relationship. Publisher PDF

Funding: J.D.B. was supported by a Royal Society University Research Fellowship. H.M.R., G.D.R. and M.P.S. were supported by NERC (NE/D010 667/1) during data collection, and H.M.R. was supported by a Junior Research Fellowship from Churchill College, Cambridge and the Max Planck Society during data analysis and manuscript preparation. In a variety of aposematic species, the conspicuousness of an individual's warning signal and the quantity of its chemical defence are positively correlated. This apparent honest signalling is predicted by resource competition models which assume that the production and maintenance of aposematic defences compete for access to antioxidant molecules that have dual functions as pigments and in protecting against oxidative damage. To test for such trade-offs, we raised monarch butterflies (Danaus plexippus) on different species of their milkweed host plants (Apocynaceae) that vary in quantities of cardenolides to test whether (i) the sequestration of cardenolides as a secondary defence is associated with costs in the form of oxidative lipid damage and reduced antioxidant defences; and (ii) lower oxidative state is associated with a reduced capacity to produce aposematic displays. In male monarchs conspicuousness was explained by an interaction between oxidative damage and sequestration: males with high levels of oxidative damage became less conspicuous with increased sequestration of cardenolides, whereas those with low oxidative damage became more conspicuous with increased levels of cardenolides. There was no significant effect of oxidative damage or concentration of sequestered cardenolides on female conspicuousness. Our results demonstrate a physiological linkage between the production of coloration and oxidative state, and differential costs of sequestration and signalling in monarch butterflies. Publisher PDF

We thank the A.P. Leventis Conservation Foundation for supporting this work. One possible hypothesis for the function of post-fledging dispersal is to locate a suitable future breeding area. This post-fledging period may be particularly important in migratory species because they have a limited period to gather information prior to autumn migration, and in protandrous species, males must quickly acquire a territory after returning from spring migration to maximize their fitness. Here we use color-ring resightings to investigate how the post-fledging dispersal movements of the Cyprus wheatear Oenanthe cypriaca, a small migratory passerine, relate to their first breeding territory the following year when they return from migration. We found that males established first breeding territories that were significantly closer to their post-fledging location than to their natal sites or to post-fledging locations of other conspecifics, but these patterns were not apparent in females. Our findings suggest that familiarity with potential breeding sites may be important for juveniles of migratory species, particularly for the sex that acquires and advertises breeding territories. Exploratory dispersal prior to a migrant’s first autumn migration may contribute toward its breeding success the following year, further highlighting the importance of early seasonal breeding on fitness and population dynamics more generally. Publisher PDF

A forager searching for food can cue on a distant feeding group to infer the location of a food patch it could share. This behavior, known as local enhancement, reduces variance in time between meals, but its effect on long-term uptake rate is less resolved. An influential simulation study concluded that benefits through reduced variance would be mitigated by reduced long-term uptake rate. This cost comes about through spatial clumping of foragers, leading to overlapping search paths and, thus, reduced aggregate patch finding. Here, we revise the previous model and submit it to more extensive investigation. Our simulations reveal that local enhancement can increase mean uptake rates but only when food patches are scarce in the environment. Contrary to previous speculations, we do not find that high-value patches or strong heterogeneity in patch quality strengthens this potential added benefit to local enhancement. As such, our simulations delineate situations where selection pressures based on maximizing long-term uptake rate act antagonistically or synergistically with starvation-avoidance through reduced temporal variance in feeding. Publisher PDF

Funding was provided by the Australian Research Council (DE130100688) and Isobel Bennett Marine Biology Fellowship from the Lizard Island Reef Research Foundation to ASH. CFYC was supported by funding granted to MD by the Leverhulme Centre. MD is supported by a National Science Foundation–Natural Environment Research Council Biological Oceanography grant (1948946), the Leverhulme Trust Research Centre–the Leverhulme Centre for Anthropocene Biodiversity and a Leverhulme Research Grant (RPG-2019-402). Herbivory is a core ecosystem function that is delivered heterogeneously across space. Disentangling the drivers of foraging patterns is key to understanding the functional impact of herbivores. Because intrinsic drivers of foraging like metabolism, nutritional requirements, and movement costs scale allometrically, foraging movement patterns in terrestrial herbivores have been shown to also scale positively with body size. However, spatial patterns of herbivory can also be explained by orthogonal factors such as trophic position, competition, and functional groupings. Here, we investigate body size and species traits as drivers of the spatial scaling of foraging patterns in herbivorous coral reef fishes. We quantified foraging patterns of 119 individuals from nine common herbivorous species using focal individual surveys. Body size, species identity, feeding substrata, social grouping, and functional group were tested as predictors of three foraging metrics: foraging area, inter-foray distance, and tortuosity. Our resulting model revealed that species identity overshadowed body size as a predictor in models for all foraging metrics. While foraging area was explained best by species only, the resulting tortuosity and mean inter-foray distance models included a small effect of body size that explained within-species variation. We do not find strong support for size-scaling of foraging patterns in our study species. These findings indicate that foraging allometry based on Optimal Foraging Theory cannot be generally applied to reef fish assemblages due to a diversity of foraging strategies, such as spatial partitioning and territoriality. Our work reveals the importance of behavioural ecology and taxonomic diversity in understanding herbivory, especially given the functional differences across species. With coral reefs under threat across the world, this is an important step to disentangling the spatial delivery of a core ecosystem function. Publisher PDF

Funders: U.S. National Science Foundation (Grant Number(s): 1855962), China Scholarship Council (Grant Number(s): 201703780018), Natural Environment Research Council (Grant Number(s): IAPETUS2 PhD studentship (A.D.), NE/T0006191/1, NW/L011255/1). There is tantalizing evidence that phenotypic plasticity can buffer novel, adaptive genetic variants long enough to permit their evolutionary spread, and this process is often invoked in explanations for rapid adaptive evolution. However, the strength and generality of evidence for it is controversial. We identify a conceptual problem affecting this debate: recombination, segregation, and independent assortment are expected to quickly sever associations between genes controlling novel adaptations and genes contributing to trait plasticity that facilitates the novel adaptations by reducing their indirect fitness costs. To make clearer predictions about this role of plasticity in facilitating genetic adaptation, we describe a testable genetic mechanism that resolves the problem: genetic covariance between new adaptive variants and trait plasticity that facilitates their persistence within populations. We identify genetic architectures that might lead to such a covariance, including genetic coupling via physical linkage and pleiotropy, and illustrate the consequences for adaptation rates using numerical simulations. Such genetic covariances may also arise from the social environment, and we suggest the indirect genetic effects that result could further accentuate the process of adaptation. We call the latter mechanism of adaptation social drive, and identify methods to test it. We suggest that genetic coupling of plasticity and adaptations could promote unusually rapid ‘runaway’ evolution of novel adaptations. The resultant dynamics could facilitate evolutionary rescue, adaptive radiations, the origin of novelties, and other commonly studied processes. Publisher PDF

Funding: The authors acknowledge the Research/Scientific Computing teams at The James Hutton Institute and NIAB for providing computational resources and technical support for the “UK’s Crop Diversity Bioinformatics HPC” (BBSRC grant BB/S019669/1), use of which has contributed to the results reported within this paper. Access to this was provided via the University of St Andrews Bioinformatics Unit which is funded by a Wellcome Trust ISSF award (grant 105621/Z/14/Z and 204821/Z/16/Z). XK was supported by a World-Leading PhD Scholarship from St Leonard’s Postgraduate School of the University of St Andrews. VAS and KK were partially supported by HATUA, The Holistic Approach to Unravel Antibacterial Resistance in East Africa, a three-year Global Context Consortia Award (MR/S004785/1) funded by the National Institute for Health Research, Medical Research Council and the Department of Health and Social Care. KK is supported by the Academy of Medical Sciences, the Wellcome Trust, the Government Department of Business, Energy and Industrial Strategy, the British Heart Foundation Diabetes UK, and the Global Challenges Research Fund [Grant number SBF004\1093]. KK is additionally supported by the Economic and Social Research Council HIGHLIGHT CPC- Connecting Generations Centre [Grant number ES/W002116/1]. Background Availability of linked biomedical and social science data has risen dramatically in past decades, facilitating holistic and systems-based analyses. Among these, Bayesian networks have great potential to tackle complex interdisciplinary problems, because they can easily model inter-relations between variables. They work by encoding conditional independence relationships discovered via advanced inference algorithms. One challenge is dealing with missing data, ubiquitous in survey or biomedical datasets. Missing data is rarely addressed in an advanced way in Bayesian networks; the most common approach is to discard all samples containing missing measurements. This can lead to biased estimates. Here, we examine how Bayesian network structure learning can incorporate missing data. Methods We use a simulation approach to compare a commonly used method in frequentist statistics, multiple imputation by chained equations (MICE), with one specific for Bayesian network learning, structural expectation-maximization (SEM). We simulate multiple incomplete categorical (discrete) data sets with different missingness mechanisms, variable numbers, data amount, and missingness proportions. We evaluate performance of MICE and SEM in capturing network structure. We then apply SEM combined with community analysis to a real-world dataset of linked biomedical and social data to investigate associations between socio-demographic factors and multiple chronic conditions in the US elderly population. Results We find that applying either method (MICE or SEM) provides better structure recovery than doing nothing, and SEM in general outperforms MICE. This finding is robust across missingness mechanisms, variable numbers, data amount and missingness proportions. We also find that imputed data from SEM is more accurate than from MICE. Our real-world application recovers known inter-relationships among socio-demographic factors and common multimorbidities. This network analysis also highlights potential areas of investigation, such as links between cancer and cognitive impairment and disconnect between self-assessed memory decline and standard cognitive impairment measurement. Conclusion Our simulation results suggest taking advantage of the additional information provided by network structure during SEM improves the performance of Bayesian networks; this might be especially useful for social science and other interdisciplinary analyses. Our case study show that comorbidities of different diseases interact with each other and are closely associated with socio-demographic factors. Postprint Publisher PDF

Funding: UK National Institute for Health Research, UK Medical Research Council, and the Department of Health and Social Care. Background Poverty is a proposed driver of antimicrobial resistance, influencing inappropriate antibiotic use in low-income and middle-income countries (LMICs). However, at subnational levels, studies investigating multidimensional poverty and antibiotic misuse are sparse, and the results are inconsistent. We aimed to investigate the relationship between multidimensional poverty and antibiotic use in patient populations in Kenya, Tanzania, and Uganda. Methods In this mixed-methods study, the Holistic Approach to Unravelling Antimicrobial Resistance (HATUA) Consortium collected data from 6827 outpatients (aged 18 years and older, or aged 14–18 years and pregnant) with urinary tract infection (UTI) symptoms in health-care facilities in Kenya, Tanzania, and Uganda. We used Bayesian hierarchical modelling to investigate the association between multidimensional poverty and self-reported antibiotic self-medication and non-adherence (ie, skipping a dose and not completing the course). We analysed linked qualitative in-depth patient interviews and unlinked focus-group discussions with community members. Findings Between Feb 10, 2019, and Sept 10, 2020, we collected data on 6827 outpatients, of whom 6345 patients had complete data; most individuals were female (5034 [79·2%]), younger than 35 years (3840 [60·5%]), worked in informal employment (2621 [41·3%]), and had primary-level education (2488 [39·2%]). Antibiotic misuse was more common among those least deprived, and lowest among those living in severe multidimensional poverty. Regardless of poverty status, difficulties in affording health care, and more familiarity with antibiotics, were related to more antibiotic misuse. Qualitative data from linked qualitative in-depth patient interviews (n=82) and unlinked focus-group discussions with community members (n=44 groups) suggested that self-medication and treatment non-adherence were driven by perceived inconvenience of the health-care system, financial barriers, and ease of unregulated antibiotic access. Interpretation We should not assume that higher deprivation drives antibiotic misuse. Structural barriers such as inefficiencies in public health care, combined with time and financial constraints, fuel alternative antibiotic access points and treatment non-adherence across all levels of deprivation. In designing interventions to reduce antibiotic misuse and address antimicrobial resistance, greater attention is required to these structural barriers that discourage optimal antibiotic use at all levels of the socioeconomic hierarchy in LMICs. Publisher PDF

How important are sampling and experimental design decisions in shaping test subject behaviour under laboratory conditions? We examined the effects of circatidal rhythm, time held in captivity, sampling location (open or covered areas of habitat), acclimation period and water depth on activity and emergence latency in hermit crabs (Pagurus bernhardus). We found that subjects held in captivity for 1 month and those collected from the open were faster to emerge from their shells after disturbance compared, respectively, to those tested after 1 day in captivity or collected from beneath cover. We also found that subjects tested after shorter acclimation periods were more active than those tested following longer acclimation periods. Our findings reveal that sampling and study design decisions can have pronounced influences on subject behaviour measured under otherwise common conditions, with potentially important implications for interpretation and reproducibility of findings. As researchers we should take care to explicitly consider how sampling biases and effects arising from our experimental protocols might affect the behavioural responses of test subjects. Doing so can help us make more reasonable generalizations beyond our subject pool, draw better-informed comparisons between studies and achieve greater reproducibility of findings. Publisher PDF

Funding: This work was supported by the University of St Andrews. Artificial light at night (ALAN) is thought to be detrimental for terrestrial insect populations. While there exists evidence for lower abundance under ALAN, underlying mechanisms remain unclear. One mechanism by which ALAN may contribute to insect declines may be through facilitating increased predation. We investigated this by experimentally manipulating insect-substitute abundance under differential levels of light. We used insect-containing birdfeed placed at varying distances from streetlights as a proxy for terrestrial insects, inspecting the rate of predation before and after dusk (when streetlights are, respectively, off and on). We found that there was a significantly greater effect of increasing distance on predation after dusk, suggesting that predation was actually reduced by greater levels of artificial light. This may occur because ALAN also increases the vulnerability of insectivores to their own predators. Implications for foraging behaviour and alternative explanations are discussed. Publisher PDF

Funding: This research would not have been possible without support from our partners: CARIMAM and the University of the West Indies, and funders: the National Geographic Society (NGS-62320R-19-2), the AGOA Sanctuary, the Natural Sciences and Engineering Research Council of Canada (NSERC), and the Animal Behavior Society. Environmental variables are often the primary drivers of species' distributions as they define their niche. However, individuals, or groups of individuals, may sometimes adopt a limited range within this larger suitable habitat as a result of social and cultural processes. This is the case for Eastern Caribbean sperm whales. While environmental variables are reasonably successful in describing the general distribution of sperm whales in the region, individuals from different cultural groups have distinct distributions around the Lesser Antilles islands. Using data collected over 2 years of dedicated surveys in the Eastern Caribbean, we conducted habitat modeling and habitat suitability analyses to investigate the mechanisms responsible for such fine‐scale distribution patterns. Vocal clan‐specific models were dramatically more successful at predicting distribution than general species models, showing how a failure to incorporate social factors can impede accurate predictions. Habitat variation between islands did not explain vocal clan distributions, suggesting that cultural group segregation in the Eastern Caribbean sperm whale is driven by traditions of site/island fidelity (most likely maintained through conformism and homophily) rather than habitat type specialization. Our results provide evidence for the key role of cultural knowledge in shaping habitat use of sperm whales within suitable environmental conditions and highlight the importance of cultural factors in shaping sperm whale ecology. We recommend that social and cultural information be incorporated into conservation and management as culture can segregate populations on fine spatial scales in the absence of environmental variability. Publisher PDF

Funding: Funding was awarded to WC from the A.P. Leventis Conservation Foundation. First time migrants (juveniles hereafter) of many species migrate without specific knowledge of non-breeding locations, but experience may aid adults in timing and route decisions because they can migrate more efficiently to their previous non-breeding sites. Consequently, we expect a transition to more efficient migratory behaviour with age, but when and how this happens is little known. We used light-level geolocator data from Cyprus wheatears Oenanthe cypriaca to compare migration timing and route directness between juveniles and adults, and repeatability of their timing and non-breeding locations. We predicted that juveniles would depart and arrive later than adults for both autumn and spring migration; that duration of migration would be greater for juveniles; that routes taken by juveniles would be less direct than those for adults; and that autumn and spring departure timing, and non-breeding locations, would be more repeatable for adults between two years than for juveniles between their first and subsequent migration. We found that juveniles departed significantly later than adults in autumn but there was no difference in arrival timing, and although spring departure timings did not differ, juveniles arrived on the breeding grounds later than adults. Nevertheless, we found no significant age-related difference in the duration of migration in autumn or spring. Yet, juvenile migrations were less direct than those of adults in autumn, but not spring. We found evidence that spring departure timing and non-breeding locations were repeatable for adults but not juveniles. Our findings show that age-related changes in migratory behaviour begin to occur during the first annual cycle demonstrating the potential for early adaptation to environmental variability within an individual’s life. Publisher PDF

This study was funded by the Carnegie Trust (#RIG008238 to CS) and John Templeton Foundation (#60501 to KNL). Aim Our aim was to evaluate the role of ecological and life-history factors in shaping global variation in offspring size in a marine clade with a diverse range of parental care behaviours. Location Global. Time period Data sourced from literature published from 1953 until 2019. Major taxa studied Marine teleost fishes. Methods We compiled a species-level dataset of egg and hatch size for 1,639 species of marine fish across 45 orders. We used Bayesian phylogenetic mixed models to evaluate the relationship between offspring size and environmental factors (i.e., mean temperature, chlorophyll-a and dissolved oxygen content together with their annual variation), as well as latitude, reproductive strategy, parental body size and fecundity. We also tested long-standing hypotheses about the co-evolution of offspring size and the presence of parental care in BayesTraits. Results After controlling for parental body size and phylogenetic history, we find that increased egg size is associated with colder and oxygen-rich waters, while hatch size further depends on food supply and the reproductive strategy exhibited by the species. Irrespective of the initial investment in egg size, species with parental care or demersal egg development yield larger hatchlings compared to pelagic spawners. We also demonstrate that hatch size has co-evolved with advanced forms of care in association with parental body but fail to find a relationship with other types of care. Main conclusions Our study shows that parental care behaviours, together with environmental context, influence the evolution of classic life-history trade-offs on a global scale. While the initial investment in eggs is driven primarily by temperature and oxygen content, hatch size also reflects the impact of care an offspring has received throughout development. In support of the 'offspring-first' hypothesis, we find that an increase in hatch size drives the evolution of advanced care provision. Postprint

Human disturbances may constitute a significant stressor for wildlife, especially where human recreational activities overlap with fitness-enhancing activities such as feeding. Disturbances cause an animal to flee from the perceived predation risk, using energy, rather than remaining and gaining energy. Such reactions are, however, context-dependent, as predicted by optimal escape theory: animals should only flee when the perceived risk of predation of remaining exceeds the risk of starvation of leaving. Animals may also learn that humans do not generally represent a predation risk after repeated false alarms and then learn to only respond when approached deliberately and closely. We tested the Flight Initiation Distance (FID; distance at which an approached animal begins escape) of feeding or roosting Eurasian Oystercatchers Haematopus ostralegus (oystercatchers) to a human (as a simulated predator) in areas with or without humans on beaches in south-east Scotland. We predicted roosting oystercatchers to respond earlier (greater FID) than feeding birds because the risk of starvation will be lower, and earlier on beaches where there were no humans at the start of the experiment because a human will then represent a more novel predator signal. As predicted, oystercatchers escaped at greater distances away from the perceived threat when feeding and in areas with humans. We found that escape distances decreased (greater tolerance of the perceived threat) as the number of people in an area increased, but people being present or not explained more of the variation in the data. The results show that oystercatchers habituate on a short timescale to non-lethal human presence and generally respond to perceived predation risk in accordance with the predictions of optimal escape theory. Postprint

Funding: This work is jointly supported by the Natural Environment Research Council, UK (NE/T004487/1 for AM and MD) and the Taiwan Ministry of Science and Technology under Contracts NERC-MOST 108-2923-M-007-003 (for AC and CC). AM and MD also acknowledge support from the Leverhulme Trust (RPG-2019-401). 1. Biodiversity is a multifaceted concept covering different levels of organisation from genes to ecosystems. Biodiversity has at least three dimensions: (i) Taxonomic diversity (TD): a measure that is sensitive to the number and abundances of species. (ii) Phylogenetic diversity (PD): a measure that incorporates not only species abundances but also species evolutionary histories. (iii) Functional diversity (FD): a measure that considers not only species abundances but also species? traits. 2. We integrate the three dimensions of diversity under a unified framework of Hill numbers and their generalizations. Our TD quantifies the effective number of equally-abundant species, PD quantifies the effective total branch length, mean-PD (PD divided by tree depth) quantifies the effective number of equally-divergent lineages, and FD quantifies the effective number of equally-distinct virtual functional groups (or functional ?species?). Thus, TD, mean-PD and FD are all in the same units of species/lineage equivalents and can be meaningfully compared. 3. Like species richness, empirical TD, PD and FD based on sampling data, depend on sampling effort and sample completeness. For TD (Hill numbers), the iNEXT (interpolation and extrapolation) standardization was developed for standardizing sample size or sample completeness (as measured by sample coverage, the fraction of individuals that belong to the observed species) to make objective comparisons across studies. This paper extends the iNEXT method to the iNEXT.3D standardization to encompass all three dimensions of diversity via sample-size- and sample-coverage-based rarefaction and extrapolation under the unified framework. The asymptotic diversity estimates (i.e., sample size tends to infinity and sample coverage tends to unity) are also derived. In addition to individual-based abundance data, the proposed iNEXT.3D standardization is adapted to deal with incidence-based occurrence data. 4. We apply the integrative framework and the proposed iNEXT.3D standardization to measure temporal alpha-diversity changes for estuarine fish assemblage data spanning four decades. The influence of environmental drivers on diversity change are also assessed. Our analysis informs a mechanistic interpretation of biodiversity change in the three dimensions of diversity. The accompanying freeware, iNEXT.3D, developed during this project, facilitates all computation and graphics. Postprint

Sexual selection is a key component of evolutionary biology. However, from the very formulation of sexual selection by Darwin, the nature and extent of sexual selection have been controversial. Recently, such controversy has led back to the fundamental question of just what sexual selection is. This has included how we incorporate female-female reproductive competition into sexual or natural selection. In this review, we do four things. First, we examine what we want a definition to do. Second, we define sexual selection: sexual selection is any selection that arises from fitness differences associated with nonrandom success in the competition for access to gametes for fertilization. An important outcome of this is that as mates often also offer access to resources, when those resources are the targets of the competition, rather than their gametes, the process should be considered natural rather than sexual selection. We believe this definition encapsulates both much of Darwin’s original thinking about sexual selection, and much of how contemporary biologists use the concept of sexual selection. Third, we address alternative definitions, focusing in some detail on the role of female reproductive competition. Fourth, we challenge our definition with a number of scenarios, for instance where natural and sexual selection may align (as in some forms of endurance rivalry), or where differential allocation means teasing apart how fecundity and access to gametes influence fitness. In conclusion, we emphasize that whilst the ecological realities of sexual selection are likely to be complex, the definition of sexual selection is rather simple., Sexual selection is a crucial component of evolutionary biology yet debate over what forms of selection do or don’t comprise sexual selection have re-surfaced over the last couple of decades. Here we provide and justify a definition of sexual selection, that is focused on competition for access to gametes, and challenge that definition with ecologically complex scenarios. We hope this will allow the field to move forward, building on a firm conceptual basis.

Funding: This work was supported by the National Council for Science and Technology (CONACyT, Mexico, https://conacyt.mx) through scholarship number 472286 to CTH, and the AP Leventis Conservation Foundation (https://www.leventisfoundation.org/). Understanding general migration characteristics and how breeding and non-breeding sites are connected is crucial for predicting the response of long-distance migratory bird populations to environmental changes. We use data collected from six geolocators to describe migratory routes and identify breeding and non-breeding locations, migratory behaviour and differences between spring and autumn migration of Common Whitethroats Curruca communis, an Afro-Palearctic migrant, wintering in Nigeria. Most individuals departed on spring migration in April, following a north-easterly direction, arriving at their breeding grounds across central-eastern Europe (~425,000 km2) in May. Departures from breeding grounds took place between July and August in a south-westerly direction. During spring migration individuals travelled longer distances at faster rates making its overall duration shorter than autumn migration. We suggest that, while Whitethroats can cross the Sahara Desert and Mediterranean Sea in a single flight, they are likely to refuel before and after crossing. Results indicate that Whitethroats undertook loop migration and visited two wintering sites: first in the Sahel, then in Nigeria, where they remained until spring migration. Geolocator results and data from the European Union for Bird Migration’s (EURING) ringing database suggest that Whitethroats have a relatively high migratory spread—individuals from a single non-breeding site breed across a wide area of Europe. Our research is the first to track and describe the complete annual cycle of Whitethroats and one of the few studies to do so for any Afro-Palearctic migrant from non-breeding grounds. We identified the Sahel as an important refuelling and first wintering site indicating its conservation, alongside other stopover sites, is crucial for the species. We believe that changes in this region will have severe effects on a subset of individuals of specific European breeding populations, but these effects will greatly depend on the severity of the changes and at what spatial scale they occur. Publisher PDF

Funding: A.P. Leventis Conservation Foundation, Consejo Nacional de Ciencia y Tecnología (CONACyT). Grant Number: 472286. The nonbreeding period represents a significant part of an Afro-Palearctic migratory bird's annual cycle. Decisions such as whether to remain at a single site and whether to return to it across years have important effects on aspects such as survival, future breeding success, migratory connectivity, and conservation. During this study, we color-ringed 337 common Whitethroats Curruca communis and undertook daily resightings to understand site persistence and the degree of site fidelity throughout three nonbreeding periods (November-April) in Nigeria. The probability of detecting a color-ringed Whitethroat when it was present was 0.33. Site persistence varied widely across individuals (1-165 days) and did not differ significantly with sex or year, though first-year birds remained for significantly shorter periods than adults. We believe that shorter residencies are likely due to the use of multiple stationary nonbreeding sites rather than low winter survival. A minimum of 19% of individuals returned to the study site the following year and shifted, on average, 300 m, suggesting that Whitethroats have a relatively high degree of between-years site fidelity at a very fine scale. An individual's previous residency duration did not seem to determine its residency duration the following year. We suggest that spatial fidelity is high and constant through years, but temporal fidelity is not, and individual residency patterns vary, probably according to yearly and seasonal conditions. Our results highlight the complexity of the annual cycle of a single species and the importance of carrying out in situ, fine-scale research throughout a migrant's annual cycle over several years. Publisher PDF

Culture, a pillar of the remarkable ecological success of humans, is increasingly recognized as a powerful force structuring nonhuman animal populations. A key gap between these two types of culture is quantitative evidence of symbolic markers—seemingly arbitrary traits that function as reliable indicators of cultural group membership to conspecifics. Using acoustic data collected from 23 Pacific Ocean locations, we provide quantitative evidence that certain sperm whale acoustic signals exhibit spatial patterns consistent with a symbolic marker function. Culture segments sperm whale populations into behaviorally distinct clans, which are defined based on dialects of stereotyped click patterns (codas). We classified 23,429 codas into types using contaminated mixture models and hierarchically clustered coda repertoires into seven clans based on similarities in coda usage; then we evaluated whether coda usage varied with geographic distance within clans or with spatial overlap between clans. Similarities in within-clan usage of both “identity codas” (coda types diagnostic of clan identity) and “nonidentity codas” (coda types used by multiple clans) decrease as space between repertoire recording locations increases. However, between-clan similarity in identity, but not nonidentity, coda usage decreases as clan spatial overlap increases. This matches expectations if sympatry is related to a measurable pressure to diversify to make cultural divisions sharper, thereby providing evidence that identity codas function as symbolic markers of clan identity. Our study provides quantitative evidence of arbitrary traits, resembling human ethnic markers, conveying cultural identity outside of humans, and highlights remarkable similarities in the distributions of human ethnolinguistic groups and sperm whale clans. Publisher PDF

Funding: European Research Council - 771387 (AG); Natural Environment Research Council - NE/K009524/1 (AG). A surprising result emerging from the theory of sex allocation is that the optimal sex ratio is predicted to be completely independent of the rate of dispersal. This striking invariance result has stimulated a huge amount of theoretical and empirical attention in the social evolution literature. However, this sex-allocation invariant has been derived under the assumption that an individual's dispersal behaviour is not modulated by population density. Here, we investigate how density-dependent dispersal shapes patterns of sex allocation in a viscous-population setting. Specifically, we find that if individuals are able to adjust their dispersal behaviour according to local population density, then they are favoured to do so, and this drives the evolution of female-biased sex allocation. This result obtains because, whereas under density-independent dispersal, population viscosity is associated not only with higher relatedness—which promotes female bias—but also with higher kin competition—which inhibits female bias—under density-dependent dispersal, the kin-competition consequences of a female-biased sex ratio are entirely abolished. We derive analytical results for the full range of group sizes and costs of dispersal, under haploid, diploid and haplodiploid modes of inheritance. These results show that population viscosity promotes female-biased sex ratios in the context of density-dependent dispersal. Publisher PDF

Funding: This work was partially supported by the UK Engineering and Physical Sciences Research Council under grant number EP/N007565/1 (Science of Sensor Systems Software). In this paper we examine the structure of random networks that have undergone bond percolation an arbitrary, but finite, number of times. We define two types of sequential branching processes: a competitive branching process - in which each iteration performs bond percolation on the residual graph (RG) resulting from previous generations; and, collaborative branching process - where percolation is performed on the giant connected component (GCC) instead. We investigate the behaviour of these models, including the expected size of the GCC for a given generation, the critical percolation probability and other topological properties of the resulting graph structures using the analytically exact method of generating functions. We explore this model for Erds-Renyi and scale free random graphs. This model can be interpreted as a seasonal n-strain model of disease spreading. Publisher PDF

This is paper no. 208 from the A.P. Leventis Ornithological Research Institute (APLORI). Almost no systematic monitoring of bird population trends occurs in West Africa, despite rapid human population increase, habitat change, and climate change, making conservation planning problematic. We monitored bird population trends using constant-effort mist netting, in a newly protected area (Amurum Forest Reserve) on the outskirts of Jos, central Nigeria, from 2002 to 2019. We modelled the 18-year changes in trends of 10 Palearctic migrant and 41 common resident bird species and related this to any changes in annual environmental site quality using NDVI and rainfall data. The populations of most bird species were stable; 30% of migrants and 7% of residents increased, while 10% of migrants and 29% of residents declined moderately. Primary productivity, measured by NDVI, increased, and rainfall pattern was stable, suggesting that environmental conditions at the site improved slightly during the period. However, only a few species showed significant correlations of population trends with NDVI and rainfall. Overall, our results suggest that population changes were locally similar for both the Afro-Palearctic and resident bird species, being reasonably stable or increasing—although perhaps this reflected the fact that the monitoring was done within a newly protected area, which at present represents the best habitat in the wider locality. Those species that declined were mostly associated with open, grassland areas, which will have decreased as anthropogenic influences were reduced at the study site. Though we only monitored one site, the results are encouraging in that simple protection of a small habitat fragment (∼300 ha) in Nigeria yielded generally positive population benefits for both resident and Palearctic migrant species. Publisher PDF

Comparative genomics has contributed to the growing evidence that sexual selection is an important component of evolutionary divergence and speciation. Divergence by sexual selection is implicated in faster rates of divergence of the X chromosome and of genes thought to underlie sexually selected traits, including genes that are sex-biased in expression. However, accurately inferring the relative importance of complex and interacting forms of natural selection, demography and neutral processes which occurred in the evolutionary past is challenging. Experimental evolution provides an opportunity to apply controlled treatments for multiple generations and examine the consequent genomic divergence. Here we altered sexual selection intensity, elevating sexual selection in polyandrous lines and eliminating it in monogamous lines, and examined patterns of divergence in the genome ofDrosophila pseudoobscuraafter more than 160 generations of experimental evolution. Divergence is not uniform across the genome but concentrated in “islands”, many of which contain candidate genes implicated in mating behaviours and other sexually selected phenotypes. These are more often seen on the X chromosome, which shows divergence greater than neutral expectations. There are characteristic signatures of selection seen in these regions, with lower diversity and greaterFSTon the X chromosome than the autosomes, and differences in diversity on the autosomes between selection regimes. Reduced Tajima’s D implies that selective sweeps have occurred within some of the divergent regions, despite considerable recombination. These changes are associated with both differential gene expression between the lines and sex-biased gene expression within the lines. Our results are very similar to those thought to implicate sexual selection in divergence in natural populations, and hence provide experimental support for the likely role of sexual selection in driving such types of genetic divergence, but also illustrate how variable outcomes can be for different genomic regions.Impact SummaryHow does sexual selection contribute to the divergence of genomes? It is often thought that sexual selection is a potent force in evolutionary divergence, but finding ‘signatures’ of sexual selection in the genome is not straight-forward, and has been quite controversial recently. Here we used experimental evolution to allow replicate populations of fruit fly to evolve under relaxed or strengthened sexual selection for over 160 generations, then sequenced their genomes to see how they had diverged. The features we find are very similar to those reported in populations of natural species thought to be under strong sexual selection. We found that genomic divergence was concentrated in small patches of the genome rather than widespread. These are more often seen on the X chromosome, which overall shows especially elevated divergence. There are also characteristic signatures of selection seen in these regions, with lower genetic diversity suggesting that selection was strong in these regions. The changes are associated with both differential gene expression between the lines and sex-biased gene expression within the lines. Many of the patches of divergence also contain candidate genes implicated in mating behaviours and other sexually selected phenotypes. Our results provide experimental support for the likely role of sexual selection in driving such types of genetic divergence.