resevol: An R package for spatially explicit models of pesticide resistance given evolving pest genomes.

The evolution of pesticide resistance is a widespread problem with potentially severe consequences for global food security. We introduce the resevol R package, which simulates individual-based models of pests with evolving genomes that produce complex, polygenic, and covarying traits affecting pest life history and pesticide resistance. Simulations are modelled on a spatially-explicit and highly customisable landscape in which crop and pesticide application and rotation can vary, making the package a highly flexible tool for both general and tactical models of pest management and resistance evolution. We present the key features of the resevol package and demonstrate its use for a simple example simulating pests with two covarying traits. The resevol R package is open source under GNU Public License. All source code and documentation are available on GitHub.

A multispecies assessment of wildlife impacts on local community livelihoods.

Conflicts between the interests of agriculture and wildlife conservation are a major threat to biodiversity and human well-being globally. Addressing such conflicts requires a thorough understanding of the impacts associated with living alongside protected wildlife. Despite this, most studies reporting on human-wildlife impacts and the strategies used to mitigate them focus on a single species, thus oversimplifying often complex systems of human-wildlife interactions. We sought to characterize the spatiotemporal patterns of impacts by multiple co-occurring species on agricultural livelihoods in the eastern Okavango Delta Panhandle in northern Botswana through the use of a database of 3264 wildlife-incident reports recorded from 2009 to 2015 by the Department of Wildlife and National Parks. Eight species (African elephants [Loxodonta africana], hippopotamuses [Hippopotamus amphibious], lions [Panthera leo], cheetah [Acinonyx jubatus], African wild dogs [Lycaon pictus], hyenas [Crocuta crocuta], leopards [Panthera pardus], and crocodiles [Crocodylus niloticus]) appeared on incident reports, of which 56.5% were attributed to elephants. Most species were associated with only 1 type of damage (i.e., either crop damage or livestock loss). Carnivores were primarily implicated in incident reports related to livestock loss, particularly toward the end of the dry season (May-October). In contrast, herbivores were associated with crop-loss incidents during the wet season (November-April). Our results illustrate how local communities can face distinct livelihood challenges from different species at different times of the year. Such a multispecies assessment has important implications for the design of conservation interventions aimed at addressing the costs of living with wildlife and thereby mitigation of the underlying conservation conflict. Our spatiotemporal, multispecies approach is widely applicable to other regions where sustainable and long-term solutions to conservation conflicts are needed for local communities and biodiversity.

Article Impact Statement: Impacts of protected wildlife on local community livelihoods can vary and overlap across species, spatial scales, and time of the year. Una Evaluación Multiespecie de los Impactos de la Fauna sobre el Sustento de la Comunidad Local Resumen Los conflictos entre los intereses de la agricultura y la conservación de fauna son una gran amenaza para la biodiversidad y el bienestar humano en todo el mundo. Para tratar estos conflictos se requiere un entendimiento exhaustivo de los impactos asociados con la convivencia con fauna protegida. A pesar de esto, la mayoría de los estudios que reportan sobre los impactos humano-fauna y las estrategias que se usan para mitigarlos se enfocan en una sola especie, lo que simplifica demasiado los complejos sistemas de interacciones humano-fauna. Buscamos caracterizar los patrones espaciotemporales de los impactos por múltiples especies coocurrentes sobre el sustento agrícola en la franja oriental del Delta del Okavango al norte de Botswana mediante el uso de una base de datos de 3,264 reportes de incidentes con fauna registrados entre 2009 y 2015 por el Departamento de Vida Silvestre y Parques Nacionales. Ocho especies (elefante africano [Loxodonta africana], hipopótamo [Hippopotamus amphibious], león [Panthera leo], chita [Acinonyx jubatus], licaón [Lycaon pictus], hiena [Crocuta crocuta], leopardo [Panthera pardus] y cocodrilo [Crocodylus niloticus]) aparecieron en los reportes de incidentes, de los cuales el 56.5% estaba atribuido a los elefantes. La mayoría de las especies estuvo asociada sólo con un tipo de daño (es decir, daño a cultivos o pérdida de ganado). Los carnívoros fueron los principales implicados en los reportes de incidentes relacionados con la pérdida de ganado, particularmente hacia el final de la temporada seca (mayo-octubre). Al contrario, los herbívoros estuvieron asociados con los incidentes de pérdida de cultivos durante la temporada de lluvias (noviembre-abril). Nuestros resultados ejemplifican cómo las comunidades locales pueden enfrentar diferentes dificultades en su sustento por parte de diferentes especies durante diferentes periodos en el año. Tal evaluación multiespecie tiene consecuencias importantes para el diseño de las intervenciones de conservación enfocadas en la resolución de los efectos de la convivencia con la fauna y por lo tanto la mitigación del conflicto de conservación subyacente. Nuestro enfoque multiespecie espaciotemporal puede aplicarse ampliamente a otras regiones en donde las comunidades y la biodiversidad local necesitan soluciones sustentables y a largo plazo para los conflictos de conservación.

Evolution of Inbreeding Avoidance and Inbreeding Preference through Mate Choice among Interacting Relatives.

While extensive population genetic theory predicts conditions favoring evolution of self-fertilization versus outcrossing, there is no analogous theory that predicts conditions favoring evolution of inbreeding avoidance or inbreeding preference enacted through mate choice given obligate biparental reproduction. Multiple interacting processes complicate the dynamics of alleles underlying such inbreeding strategies, including sexual conflict, distributions of kinship, genetic drift, purging of mutation load, direct costs, and restricted kin discrimination. We incorporated these processes into an individual-based model to predict conditions where selection should increase or decrease frequencies of alleles causing inbreeding avoidance or inbreeding preference when females or males controlled mating. Selection for inbreeding avoidance occurred given strong inbreeding depression when either sex chose mates, while selection for inbreeding preference occurred given very weak inbreeding depression when females chose but never occurred when males chose. Selection for both strategies was constrained by direct costs and restricted kin discrimination. Purging was negligible, but allele frequencies were strongly affected by drift in small populations, while selection for inbreeding avoidance was weak in larger populations because inbreeding risk decreased. Therefore, while selection sometimes favored alleles underlying inbreeding avoidance or preference, evolution of such strategies may be much more restricted and stochastic than is commonly presumed.

Inbreeding parents should invest more resources in fewer offspring.

Inbreeding increases parent-offspring relatedness and commonly reduces offspring viability, shaping selection on reproductive interactions involving relatives and associated parental investment (PI). Nevertheless, theories predicting selection for inbreeding versus inbreeding avoidance and selection for optimal PI have only been considered separately, precluding prediction of optimal PI and associated reproductive strategy given inbreeding. We unify inbreeding and PI theory, demonstrating that optimal PI increases when a female's inbreeding decreases the viability of her offspring. Inbreeding females should therefore produce fewer offspring due to the fundamental trade-off between offspring number and PI. Accordingly, selection for inbreeding versus inbreeding avoidance changes when females can adjust PI with the degree that they inbreed. By contrast, optimal PI does not depend on whether a focal female is herself inbred. However, inbreeding causes optimal PI to increase given strict monogamy and associated biparental investment compared with female-only investment. Our model implies that understanding evolutionary dynamics of inbreeding strategy, inbreeding depression, and PI requires joint consideration of the expression of each in relation to the other. Overall, we demonstrate that existing PI and inbreeding theories represent special cases of a more general theory, implying that intrinsic links between inbreeding and PI affect evolution of behaviour and intrafamilial conflict.

Trade-offs and coexistence in fluctuating environments: evidence for a key dispersal-fecundity trade-off in five nonpollinating fig wasps.

The ecological principle of competitive exclusion states that species competing for identical resources cannot coexist, but this principle is paradoxical because ecologically similar competitors are regularly observed. Coexistence is possible under some conditions if a fluctuating environment changes the competitive dominance of species. This change in competitive dominance implies the existence of trade-offs underlying species' competitive abilities in different environments. Theory shows that fluctuating distance between resource patches can facilitate coexistence in ephemeral patch competitors, given a functional trade-off between species dispersal ability and fecundity. We find evidence supporting this trade-off in a guild of five ecologically similar nonpollinating fig wasps and subsequently predict local among-patch species densities. We also introduce a novel colonization index to estimate relative dispersal ability among ephemeral patch competitors. We suggest that a dispersal ability-fecundity trade-off and spatiotemporally fluctuating resource availability commonly co-occur to drive population dynamics and facilitate coexistence in ephemeral patch communities.

Demographic mechanisms of inbreeding adjustment through extra-pair reproduction.

One hypothesis explaining extra-pair reproduction is that socially monogamous females mate with extra-pair males to adjust the coefficient of inbreeding (f) of extra-pair offspring (EPO) relative to that of within-pair offspring (WPO) they would produce with their socially paired male. Such adjustment of offspring f requires non-random extra-pair reproduction with respect to relatedness, which is in turn often assumed to require some mechanism of explicit pre-copulatory or post-copulatory kin discrimination. We propose three demographic processes that could potentially cause mean f to differ between individual females' EPO and WPO given random extra-pair reproduction with available males without necessarily requiring explicit kin discrimination. Specifically, such a difference could arise if social pairings formed non-randomly with respect to relatedness or persisted non-randomly with respect to relatedness, or if the distribution of relatedness between females and their sets of potential mates changed during the period through which social pairings persisted. We used comprehensive pedigree and pairing data from free-living song sparrows (Melospiza melodia) to quantify these three processes and hence investigate how individual females could adjust mean offspring f through instantaneously random extra-pair reproduction. Female song sparrows tended to form social pairings with unrelated or distantly related males slightly less frequently than expected given random pairing within the defined set of available males. Furthermore, social pairings between more closely related mates tended to be more likely to persist across years than social pairings between less closely related mates. However, these effects were small and the mean relatedness between females and their sets of potential extra-pair males did not change substantially across the years through which social pairings persisted. Our framework and analyses illustrate how demographic and social structuring within populations might allow females to adjust mean f of offspring through random extra-pair reproduction without necessarily requiring explicit kin discrimination, implying that adjustment of offspring f might be an inevitable consequence of extra-pair reproduction. New theoretical and empirical studies are required to explore the general magnitude of such effects and quantify the degree to which they could facilitate or constrain long-term evolution of extra-pair reproduction.

Trade-offs and coexistence: a lottery model applied to fig wasp communities.

Ecological communities in which organisms complete their life cycles on discrete ephemeral patches are common and often support an unusually large number of species. Explaining this diversity is challenging for communities of ecologically similar species undergoing preemptive competition, where classic coexistence mechanisms may not readily apply. We use nonpollinating fig wasps as a model community characterized by high diversity and preemptive competition to show how subadditive population growth and a trade-off between competitor fecundity and dispersal ability can lead to coexistence. Because nonpollinator species are often closely related, have similar life histories, and compete for the same discrete resources, understanding their coexistence is challenging given competitive exclusion is expected. Empirical observations suggest that nonpollinating fig wasp species may face a trade-off between egg loads and dispersal abilities. We model a lottery in which a species' competitive ability is determined by a trade-off between fecundity and dispersal ability. Variation in interpatch distance between figs generates temporal variability in the relative benefit of fecundity versus dispersal. We show that the temporal storage effect leads to coexistence for a range of biologically realistic parameter values. We further use individual-based modeling to show that when species' traits evolve, coexistence is less likely but trait divergence can result. We discuss the implications of this coexistence mechanism for ephemeral patch systems wherein competition is strongly preemptive.

A global systematic review of frugivorous animal tracking studies and the estimation of seed dispersal distances.

Seed dispersal is one of the most important ecosystem functions globally. It shapes plant populations, enhances forest succession, and has multiple, indirect benefits for humans, yet it is one of the most threatened processes in plant regeneration, worldwide. Seed dispersal distances are determined by the diets, seed retention times and movements of frugivorous animals. Hence, understanding how we can most effectively describe frugivore movement and behaviour with rapidly developing animal tracking technology is key to quantifying seed dispersal. To assess the current use of animal tracking in frugivory studies and to provide a baseline for future studies, we provide a comprehensive review and synthesis on the existing primary literature of global tracking studies that monitor movement of frugivorous animals. Specifically, we identify studies that estimate dispersal distances and how they vary with body mass and environmental traits. We show that over the last two decades there has been a large increase in frugivore tracking studies that determine seed dispersal distances. However, some taxa (e.g. reptiles) and geographic locations (e.g. Africa and Central Asia) are poorly studied. Furthermore, we found that certain morphological and environmental traits can be used to predict seed dispersal distances. We demonstrate that flight ability and increased body mass both significantly increase estimated seed dispersal mean and maximum distances. Our results also suggest that protected areas have a positive effect on mean seed dispersal distances when compared to unprotected areas. We anticipate that this review will act as a reference for future frugivore tracking studies, specifically to target current taxonomic and geographic data gaps, and to further explore how seed dispersal relates to key frugivore and fruit traits.

Achieving international biodiversity targets: Learning from local norms, values and actions regarding migratory waterfowl management in Kazakhstan.

Migratory species are protected under international legislation; their seasonal movements across international borders may therefore present opportunities for understanding how global conservation policies translate to local-level actions across different socio-ecological contexts. Moreover, local-level management of migratory species can reveal how culture and governance affects progress towards achieving global targets. Here, we investigate potential misalignment in the two-way relationship between global-level conservation policies (i.e. hunting bans and quotas) and local-level norms, values and actions (i.e. legal and illegal hunting) in the context of waterfowl hunting in northern Kazakhstan as a case-study.Northern Kazakhstan is globally important for waterfowl and a key staging area for arctic-breeding species. Hunting is managed through licences, quotas and seasonal bans under UN-AEWA intergovernmental agreements. To better understand the local socio-ecological context of waterfowl hunting, we take a mixed-methods approach using socio-ecological surveys, informal discussions and population modelling of a focal migratory goose species to: (a) investigate motivations for hunting in relation to socio-economic factors; (b) assess knowledge of species' protection status; and (c) predict the population size of Lesser White-fronted Geese (LWfG; Anser erythropus; IUCN Vulnerable) under different scenarios of survival rates and hunting offtake, to understand how goose population demographics interact with the local socio-ecological context.Model results showed no evidence that waterfowl hunting is motivated by financial gain; social and cultural importance were stronger factors. The majority of hunters are knowledgeable about species' protection status; however, 11% did not know LWfG are protected, highlighting a key area for increased stakeholder engagement.Simulations of LWfG population growth over a 20-year period showed LWfG are highly vulnerable to hunting pressure even when survival rates are high. This potential impact of hunting highlights the need for effective regulation along the entire flyway; our survey results show that hunters were generally compliant with newly introduced hunting regulations, showing that effective regulation is possible on a local level. Synthesis and applications. Here, we investigate how global conservation policy and local norms interact to affect the management of a threatened migratory species, which is particularly important for the protection and sustainable management of wildlife that crosses international borders where local contexts may differ. Our study highlights that to be effective and sustainable in the long-term, global conservation policies must fully integrate local socio-economic, cultural, governance and environmental contexts, to ensure interventions are equitable across entire species' ranges. This approach is relevant and adaptable for different contexts involving the conservation of wide-ranging and migratory species, including the 255 migratory waterfowl covered by UN-AEWA (United Nations Agreement on the Conservation of African-Eurasian Migratory Waterbirds).

Component response rate variation underlies the stability of highly complex finite systems.

The stability of a complex system generally decreases with increasing system size and interconnectivity, a counterintuitive result of widespread importance across the physical, life, and social sciences. Despite recent interest in the relationship between system properties and stability, the effect of variation in response rate across system components remains unconsidered. Here I vary the component response rates (γ) of randomly generated complex systems. I use numerical simulations to show that when component response rates vary, the potential for system stability increases. These results are robust to common network structures, including small-world and scale-free networks, and cascade food webs. Variation in γ is especially important for stability in highly complex systems, in which the probability of stability would otherwise be negligible. At such extremes of simulated system complexity, the largest stable complex systems would be unstable if not for variation in γ. My results therefore reveal a previously unconsidered aspect of system stability that is likely to be pervasive across all realistic complex systems.

Games as Tools to Address Conservation Conflicts.

Conservation conflicts represent complex multilayered problems that are challenging to study. We explore the utility of theoretical, experimental, and constructivist approaches to games to help to understand and manage these challenges. We show how these approaches can help to develop theory, understand patterns in conflict, and highlight potentially effective management solutions. The choice of approach should be guided by the research question and by whether the focus is on testing hypotheses, predicting behaviour, or engaging stakeholders. Games provide an exciting opportunity to help to unravel the complexity in conflicts, while researchers need an awareness of the limitations and ethical constraints involved. Given the opportunities, this field will benefit from greater investment and development.

When does female multiple mating evolve to adjust inbreeding? Effects of inbreeding depression, direct costs, mating constraints, and polyandry as a threshold trait.

Polyandry is often hypothesized to evolve to allow females to adjust the degree to which they inbreed. Multiple factors might affect such evolution, including inbreeding depression, direct costs, constraints on male availability, and the nature of polyandry as a threshold trait. Complex models are required to evaluate when evolution of polyandry to adjust inbreeding is predicted to arise. We used a genetically explicit individual-based model to track the joint evolution of inbreeding strategy and polyandry defined as a polygenic threshold trait. Evolution of polyandry to avoid inbreeding only occurred given strong inbreeding depression, low direct costs, and severe restrictions on initial versus additional male availability. Evolution of polyandry to prefer inbreeding only occurred given zero inbreeding depression and direct costs, and given similarly severe restrictions on male availability. However, due to its threshold nature, phenotypic polyandry was frequently expressed even when strongly selected against and hence maladaptive. Further, the degree to which females adjusted inbreeding through polyandry was typically very small, and often reflected constraints on male availability rather than adaptive reproductive strategy. Evolution of polyandry solely to adjust inbreeding might consequently be highly restricted in nature, and such evolution cannot necessarily be directly inferred from observed magnitudes of inbreeding adjustment.

Variation in parent-offspring kinship in socially monogamous systems with extra-pair reproduction and inbreeding.

Female extra-pair reproduction in socially monogamous systems is predicted to cause cuckolded socially-paired males to conditionally reduce paternal care, causing selection against extra-pair reproduction and underlying polyandry. However, existing models and empirical studies have not explicitly considered that cuckolded males might be related to their socially-paired female and/or to her extra-pair mate, and therefore be related to extra-pair offspring that they did not sire but could rear. Selection against paternal care, and hence against extra-pair reproduction, might then be weakened. We derive metrics that quantify allele-sharing between within-pair and extra-pair offspring and their mother and her socially-paired male in terms of coefficients of kinship and inbreeding. We use song sparrow (Melospiza melodia) paternity and pedigree data to quantify these metrics, and thereby quantify the joint effects of extra-pair reproduction and inbreeding on a brood's total allelic value to its socially-paired parents. Cuckolded male song sparrows were almost always detectably related to extra-pair offspring they reared. Consequently, although brood allelic value decreased substantially following female extra-pair reproduction, this decrease was reduced by within-pair and extra-pair reproduction among relatives. Such complex variation in kinship within nuclear families should be incorporated into models considering coevolutionary dynamics of extra-pair reproduction, parental care, and inbreeding.

What happens after inbreeding avoidance? Inbreeding by rejected relatives and the inclusive fitness benefit of inbreeding avoidance.

Avoiding inbreeding, and therefore avoiding inbreeding depression in offspring fitness, is widely assumed to be adaptive in systems with biparental reproduction. However, inbreeding can also confer an inclusive fitness benefit stemming from increased relatedness between parents and inbred offspring. Whether or not inbreeding or avoiding inbreeding is adaptive therefore depends on a balance between inbreeding depression and increased parent-offspring relatedness. Existing models of biparental inbreeding predict threshold values of inbreeding depression above which males and females should avoid inbreeding, and predict sexual conflict over inbreeding because these thresholds diverge. However, these models implicitly assume that if a focal individual avoids inbreeding, then both it and its rejected relative will subsequently outbreed. We show that relaxing this assumption of reciprocal outbreeding, and the assumption that focal individuals are themselves outbred, can substantially alter the predicted thresholds for inbreeding avoidance for focal males. Specifically, the magnitude of inbreeding depression below which inbreeding increases a focal male's inclusive fitness increases with increasing depression in the offspring of a focal female and her alternative mate, and it decreases with increasing relatedness between a focal male and a focal female's alternative mate, thereby altering the predicted zone of sexual conflict. Furthermore, a focal male's inclusive fitness gain from avoiding inbreeding is reduced by indirect opportunity costs if his rejected relative breeds with another relative of his. By demonstrating that variation in relatedness and inbreeding can affect intra- and inter-sexual conflict over inbreeding, our models lead to novel predictions for family dynamics. Specifically, parent-offspring conflict over inbreeding might depend on the alternative mates of rejected relatives, and male-male competition over inbreeding might lead to mixed inbreeding strategies. Making testable quantitative predictions regarding inbreeding strategies occurring in nature will therefore require new models that explicitly capture variation in relatedness and inbreeding among interacting population members.

Resolving the conundrum of inbreeding depression but no inbreeding avoidance: Estimating sex-specific selection on inbreeding by song sparrows (Melospiza melodia).

Inbreeding avoidance among interacting females and males is not always observed despite inbreeding depression in offspring fitness, creating an apparent "inbreeding paradox." This paradox could be resolved if selection against inbreeding was in fact weak, despite inbreeding depression. However, the net magnitude and direction of selection on the degree to which females and males inbreed by pairing with relatives has not been explicitly estimated. We used long-term pedigree data to estimate phenotypic selection gradients on the degree of inbreeding that female and male song sparrows (Melospiza melodia) expressed by forming socially persistent breeding pairs with relatives. Fitness was measured as the total numbers of offspring and grand offspring contributed to the population, and as corresponding expected numbers of identical-by-descent allele copies, thereby accounting for variation in offspring survival, reproduction, and relatedness associated with variation in parental inbreeding. Estimated selection gradients on the degree to which individuals paired with relatives were weakly positive in females, but negative in males that formed at least one socially persistent pairing. However, males that paired had higher mean fitness than males that remained socially unpaired. These analyses suggest that net selection against inbreeding may be weak in both sexes despite strong inbreeding depression, thereby resolving the "inbreeding paradox."

Quantifying inbreeding avoidance through extra-pair reproduction.

Extra-pair reproduction is widely hypothesized to allow females to avoid inbreeding with related socially paired males. Consequently, numerous field studies have tested the key predictions that extra-pair offspring are less inbred than females' alternative within-pair offspring, and that the probability of extra-pair reproduction increases with a female's relatedness to her socially paired male. However, such studies rarely measure inbreeding or relatedness sufficiently precisely to detect subtle effects, or consider biases stemming from failure to observe inbred offspring that die during early development. Analyses of multigenerational song sparrow (Melospiza melodia) pedigree data showed that most females had opportunity to increase or decrease the coefficient of inbreeding of their offspring through extra-pair reproduction with neighboring males. In practice, observed extra-pair offspring had lower inbreeding coefficients than females' within-pair offspring on average, while the probability of extra-pair reproduction increased substantially with the coefficient of kinship between a female and her socially paired male. However, simulations showed that such effects could simply reflect bias stemming from inbreeding depression in early offspring survival. The null hypothesis that extra-pair reproduction is random with respect to kinship therefore cannot be definitively rejected in song sparrows, and existing general evidence that females avoid inbreeding through extra-pair reproduction requires reevaluation given such biases.