Relationships between otolith and fish size from Mediterranean and north‐eastern Atlantic species to be used in predator–prey studies

Regressions between fish length and otolith size are provided for 40 species from the north‐eastern Atlantic Ocean and 142 species from the Mediterranean Sea. Regressions were also estimated at genus level. Most of the regressions (c. 84%) explained a high percentage of the deviance (>75%).     

Feedback between size balance and consumption strongly affects the consequences of hatching phenology in size‐dependent predator–prey interactions

In many size‐dependent predator–prey systems, hatching phenology strongly affects predator–prey interaction outcomes. Early‐hatched predators can easily consume prey when they first interact because they encounter smaller prey. However, this process by itself may be insufficient to explain all predator–prey interaction outcomes over the whole interaction period because the predator–prey size balance changes dynamically throughout their ontogeny. We hypothesized that hatching phenology influences predator–prey interactions via a feedback mechanism between the predator–prey size balance and prey consumption by predators. We experimentally tested this hypothesis in an amphibian predator–prey model system. Frog tadpoles Rana pirica were exposed to a predatory salamander larva Hynobius retardatus that had hatched 5, 12, 19 or 26 days after the frog tadpoles hatched. We investigated how the salamander hatch timing affected the dynamics of prey mortality, size changes of both predator and prey, and their subsequent life history (larval period and size at metamorphosis). The predator–prey size balance favoured earlier hatched salamanders, which just after hatching could successfully consume more frog tadpoles than later hatched salamanders. The early‐hatched salamanders grew rapidly and their accelerated growth enabled them to maintain the predator‐superior size balance; thus, they continued to exert strong predation pressure on the frog tadpoles in the subsequent period. Furthermore, frog tadpoles exposed to the early‐hatched salamanders were larger at metamorphosis and had a longer larval period than other frog tadpoles. These results suggest that feedback between the predator‐superior size balance and prey consumption is a critical mechanism that strongly affects the impacts of early hatching of predators in the short‐term population dynamics and life history of the prey. Because consumption of large nutrient‐rich prey items supports the growth of predators, a similar feedback mechanism may be common and have strong impacts on phenological shifts in size‐dependent trophic relationships.     

Antagonistic species interaction drives selection for sex in a predator–prey system

The evolutionary maintenance of sexual reproduction has long challenged biologists as the majority of species reproduce sexually despite inherent costs. Providing a general explanation for the evolutionary success of sex has thus proven difficult and resulted in numerous hypotheses. A leading hypothesis suggests that antagonistic species interaction can generate conditions selecting for increased sex due to the production of rare or novel genotypes that are beneficial for rapid adaptation to recurrent environmental change brought on by antagonism. To test this ecology‐based hypothesis, we conducted experimental evolution in a predator (rotifer)–prey (algal) system by using continuous cultures to track predator–prey dynamics and in situ rates of sex in the prey over time and within replicated experimental populations. Overall, we found that predator‐mediated fluctuating selection for competitive versus defended prey resulted in higher rates of genetic mixing in the prey. More specifically, our results showed that fluctuating population sizes of predator and prey, coupled with a trade‐off in the prey, drove the sort of recurrent environmental change that could provide a benefit to sex in the prey, despite inherent costs. We end with a discussion of potential population genetic mechanisms underlying increased selection for sex in this system, based on our application of a general theoretical framework for measuring the effects of sex over time, and interpreting how these effects can lead to inferences about the conditions selecting for or against sexual reproduction in a system with antagonistic species interaction.     

Diversity and coexistence are influenced by time‐dependent species interactions in a predator–prey system

Although numerous studies show that communities are jointly influenced by predation and competitive interactions, few have resolved how temporal variability in these interactions influences community assembly and stability. Here, we addressed this challenge in experimental microbial microcosms by employing empirical dynamic modelling tools to: (1) detect causal interactions between prey species in the absence and presence of a predator; (2) quantify the time‐varying strength of these interactions and (3) explore stability in the resulting communities. Our findings show that predators boost the number of causal interactions among community members, and lead to reduced dynamic stability, but higher coexistence among prey species. These results correspond to time‐varying changes in species interactions, including emergence of morphological characteristics that appeared to reduce predation, and indirectly facilitate growth of predator‐susceptible species. Jointly, our findings suggest that careful consideration of both context and time may be necessary to predict and explain outcomes in multi‐trophic systems.     

The molecular basis of venom resistance in a rattlesnake‐squirrel predator‐prey system

Understanding how interspecific interactions mould the molecular basis of adaptations in coevolving species is a long‐sought goal of evolutionary biology. Venom in predators and venom resistance proteins in prey are coevolving molecular phenotypes, and while venoms are highly complex mixtures it is unclear if prey respond with equally complex resistance traits. Here, we use a novel molecular methodology based on protein affinity columns to capture and identify candidate blood serum resistance proteins (“venom interactive proteins” [VIPs]) in California Ground Squirrels (Otospermophilus beecheyi) that interact with venom proteins from their main predator, Northern Pacific Rattlesnakes (Crotalus o. oreganus). This assay showed that serum‐based resistance is both population‐ and species‐specific, with serum proteins from ground squirrels showing higher binding affinities for venom proteins of local snakes compared to allopatric individuals. Venom protein specificity assays identified numerous and diverse candidate prey resistance VIPs but also potential targets of venom in prey tissues. Many specific VIPs bind to multiple snake venom proteins and, conversely, single venom proteins bind multiple VIPs, demonstrating that a portion of the squirrel blood serum “resistome” involves broad‐based inhibition of nonself proteins and suggests that resistance involves a toxin scavenging mechanism. Analyses of rates of evolution of VIP protein homologues in related mammals show that most of these proteins evolve under purifying selection possibly due to molecular constraints that limit the evolutionary responses of prey to rapidly evolving snake venom proteins. Our method represents a general approach to identify specific proteins involved in co‐evolutionary interactions between species at the molecular level.     

Consistent size‐independent harvest selection on fish body shape in two recreationally exploited marine species

Harvesting wild animals may exert size‐independent selection pressures on a range of morphological, life history, and behavioral traits. Most work so far has focused on selection pressures on life history traits and body size as morphological trait. We studied here how recreational fishing selects for morphological traits related to body shape, which may correlate with underlying swimming behavior. Using landmark‐based geometric morphometrics, we found consistent recreational fishing‐induced selection pressures on body shape in two recreationally exploited marine fish species. We show that individuals with larger‐sized mouths and more streamlined and elongated bodies were more vulnerable to passively operated hook‐and‐line fishing independent of the individual's body size or condition. While the greater vulnerability of individuals with larger mouth gapes can be explained by the direct physical interaction with hooks, selection against streamlined and elongated individuals could either involve a specific foraging mode or relate to underlying elevated swimming behavior. Harvesting using passive gear is common around the globe, and thus, size‐independent selection on body shape is expected to be widespread potentially leaving behind individuals with smaller oral gapes and more compact bodies. This might have repercussions for food webs by altering foraging and predation.     

Using the otolith sulcus to aid in prey identification and improve estimates of prey size in diet studies of a piscivorous predator

Diet studies are fundamental for understanding trophic connections in marine ecosystems. In the southeastern US, the common bottlenose dolphin Tursiops truncatus is the predominant marine mammal in coastal waters, but its role as a top predator has received little attention. Diet studies of piscivorous predators, like bottlenose dolphins, start with assessing prey otoliths recovered from stomachs or feces, but digestive erosion hampers species identification and underestimates fish weight (FW). To compensate, FW is often estimated from the least affected otoliths and scaled to other otoliths, which also introduces bias. The sulcus, an otolith surface feature, has a species‐specific shape of its ostium and caudal extents, which is within the otolith edge for some species. We explored whether the sulcus could improve species identification and estimation of prey size using a case study of four sciaenid species targeted by fisheries and bottlenose dolphins in North Carolina. Methods were assessed first on otoliths from a reference collection (n = 421) and applied to prey otoliths (n = 5,308) recovered from 120 stomachs of dead stranded dolphins. We demonstrated in reference‐collection otoliths that cauda to sulcus length (CL:SL) could discriminate between spotted seatrout (Cynoscion nebulosus) and weakfish (Cynoscion regalis) (classification accuracy = 0.98). This method confirmed for the first time predation of spotted seatrout by bottlenose dolphins in North Carolina. Using predictive models developed from reference‐collection otoliths, we provided evidence that digestion affects otolith length more than sulcus or cauda length, making the latter better predictors. Lastly, we explored scenarios of calculating total consumed biomass across degrees of digestion. A suggested approach was for the least digested otoliths to be scaled to other otoliths iteratively from within the same stomach, month, or season as samples allow. Using the otolith sulcus helped overcome challenges of species identification and fish size estimation, indicating their potential use in other diet studies.     

The possible role of predator–prey dynamics as an influence on early hominin use of burned landscapes

Foraging in burned areas has been suggested to represent the earliest stage in the use and control of fire by early hominins. Recently burned areas offer immediate foraging benefits including increased search efficiency for high‐ranked food items and decreased hunting opportunities for ambush predators. As such, they provide a triple‐bonus (reduced risk from ambush, ease of terrestrial travel and higher foraging returns) for some primates. However, previous studies have not yet accounted for other types of predators e.g., coursing (endurance predators that can pursue prey over long distances) which were sympatric with hominins and may also have exploited these environments. Behavioral ecology studies on the use of burned landscapes by extant carnivores demonstrate that while some ambush predators avoid recently burned areas, coursing predators do take advantage of their immediate hunting opportunities. Research examining habitat selection by animals under the simultaneous threat of multiple predator species with different modes of hunting, and the diversity of Plio‐Pleistocene carnivore guild is suggestive of two possible evolutionary scenarios in which hominins could either have selected or avoided burned areas (3–2 mya), based on whether ambush or coursing predators were perceived as presenting the greatest risk.     

Systematic deviations from linear size spectra of lake fish communities are correlated with predator–prey interactions and lake‐use intensity

Size structure of organisms at logarithmic scale (i.e. size spectrum) can often be described by a linear function with a negative slope; however, substantial deviations from linearity have often been found in natural systems. Theoretical studies suggest that greater nonlinearity in community size spectrum is associated with high predator–prey size ratios but low predator–prey abundance ratios; however, empirical evaluation of the effects of predator–prey interactions on nonlinear structures remains scarce. Here, we aim to empirically explore the pattern of the size‐specific residuals (i.e. deviations from the linear regression between the logarithmic fish abundance and the logarithmic mean fish size) by using size spectra of fish communities in 74 German lakes. We found that nonlinearity was strong in lakes with high predator–prey abundance ratios but at low predator–prey size ratios. More specifically, our results suggest that only large predators, even if occurring in low abundances, can control the density of prey fishes in a broad range of size classes in a community and thus promote linearity in the size spectrum. In turn, the lack of large predator fishes may cause high abundances of fish in intermediate size classes, resulting in nonlinear size spectra in these lakes. Moreover, these lakes were characterized by a more intense human use including high fishing pressure and high total phosphorus concentrations, which have negative impacts on the abundance of large, predatory fish. Our findings indicate that nonlinear size spectra may reflect dynamical processes potentially caused by predator–prey interactions. This opens a new perspective in the research on size spectrum, and can be relevant to further quantify the efficiency of energy transfer in aquatic food webs.     

The use of otolith shape analysis for ageing juvenile red snapper, Lutjanus campechanus

Morphological changes in otolith shape with age, of young (<age 3) red snapper were examined through shape analysis and tested as an objective method for age determination. Otoliths from two collections of juvenile fish (hatchery and wild) were used in the study. First, shape analysis was applied to a series of known-age otoliths from hatchery-reared age 0, 1 and 2 fish. Multidimensional scaling and non-parametric analysis of similarities showed significant shape differences among the three age classes of fish. Discriminant function analysis and cross-validation classification showed 65.6% correct age classification based on shape variables alone, and 86.7% correct age classification with inclusion of otolith weight in the discriminant function (n?=?90). Subsequently, the method was applied to otoliths from a series of age 0, 1 and 2 wild caught red snapper. Otoliths from wild fish showed a similar age classification success rate of 68.9% based on shape variables alone and 86.7% correct age classification with the inclusion of otolith weight in the discriminant function (n?=?90). Ageing of juvenile red snapper through otolith increment counts has been difficult in past studies and this study provides an alternative, objective method of otolith shape analysis for ageing young fish of this species.     

Influence of intra‐ and interspecific variation in predator–prey body size ratios on trophic interaction strengths

1. Predation is a pervasive force that structures food webs and directly influences ecosystem functioning. The relative body sizes of predators and prey may be an important determinant of interaction strengths. However, studies quantifying the combined influence of intra‐ and interspecific variation in predator–prey body size ratios are lacking.
2. We use a comparative functional response approach to examine interaction strengths between three size classes of invasive bluegill and largemouth bass toward three scaled size classes of their tilapia prey. We then quantify the influence of intra‐ and interspecific predator–prey body mass ratios on the scaling of attack rates and handling times.
3. Type II functional responses were displayed by both predators across all predator and prey size classes. Largemouth bass consumed more than bluegill at small and intermediate predator size classes, while large predators of both species were more similar. Small prey were most vulnerable overall; however, differential attack rates among prey were emergent across predator sizes. For both bluegill and largemouth bass, small predators exhibited higher attack rates toward small and intermediate prey sizes, while larger predators exhibited greater attack rates toward large prey. Conversely, handling times increased with prey size, with small bluegill exhibiting particularly low feeding rates toward medium–large prey types. Attack rates for both predators peaked unimodally at intermediate predator–prey body mass ratios, while handling times generally shortened across increasing body mass ratios.
4. We thus demonstrate effects of body size ratios on predator–prey interaction strengths between key fish species, with attack rates and handling times dependent on the relative sizes of predator–prey participants.
5. Considerations for intra‐ and interspecific body size ratio effects are critical for predicting the strengths of interactions within ecosystems and may drive differential ecological impacts among invasive species as size ratios shift.

     

Enhanced understanding of predator–prey relationships using molecular methods to identify predator species,individual and sex

Predator species identification is an important step in understanding predator‐prey interactions, but predator identifications using kill site observations are often unreliable. We used molecular tools to analyse predator saliva, scat and hair from caribou calf kills in Newfoundland, Canada to identify the predator species, individual and sex. We sampled DNA from 32 carcasses using cotton swabs to collect predator saliva. We used fragment length analysis and sequencing of mitochondrial DNA to distinguish between coyote, black bear, Canada lynx and red fox and used nuclear DNA microsatellite analysis to identify individuals. We compared predator species detected using molecular tools to those assigned via field observations at each kill. We identified a predator species at 94% of carcasses using molecular methods, while observational methods assigned a predator species to 62.5% of kills. Molecular methods attributed 66.7% of kills to coyote and 33.3% to black bear, while observations assigned 40%, 45%, 10% and 5% to coyote, bear, lynx and fox, respectively. Individual identification was successful at 70% of kills where a predator species was identified. Only one individual was identified at each kill, but some individuals were found at multiple kills. Predator sex was predominantly male. We demonstrate the first large‐scale evaluation of predator species, individual and sex identification using molecular techniques to extract DNA from swabs of wild prey carcasses. Our results indicate that kill site swabs (i) can be highly successful in identifying the predator species and individual responsible; and (ii) serve to inform and complement traditional methods.     

The underestimated role of temperature–oxygen relationship in large‐scale studies on size‐to‐temperature response

The observation that ectotherm size decreases with increasing temperature (temperature‐size rule; TSR) has been widely supported. This phenomenon intrigues researchers because neither its adaptive role nor the conditions under which it is realized are well defined. In light of recent theoretical and empirical studies, oxygen availability is an important candidate for understanding the adaptive role behind TSR. However, this hypothesis is still undervalued in TSR studies at the geographical level. We reanalyzed previously published data about the TSR pattern in diatoms sampled from Icelandic geothermal streams, which concluded that diatoms were an exception to the TSR. Our goal was to incorporate oxygen as a factor in the analysis and to examine whether this approach would change the results. Specifically, we expected that the strength of size response to cold temperatures would be different than the strength of response to hot temperatures, where the oxygen limitation is strongest. By conducting a regression analysis for size response at the community level, we found that diatoms from cold, well‐oxygenated streams showed no size‐to‐temperature response, those from intermediate temperature and oxygen conditions showed reverse TSR, and diatoms from warm, poorly oxygenated streams showed significant TSR. We also distinguished the roles of oxygen and nutrition in TSR. Oxygen is a driving factor, while nutrition is an important factor that should be controlled for. Our results show that if the geographical or global patterns of TSR are to be understood, oxygen should be included in the studies. This argument is important especially for predicting the size response of ectotherms facing climate warming.     

The dicey dinner dilemma: Asymmetry in predator–prey risk‐taking,a broadly applicable alternative to the life‐dinner principle

Forty years ago, the ‘life‐dinner principle’ was proposed as an example of an asymmetry that may lead prey species to experience stronger selection than their predators, thus accounting for the high frequency with which prey escape alive from interaction with a predator. This principle remains an influential concept in the scientific literature, despite several works suggesting that the concept relies on many under‐appreciated assumptions and does not apply as generally as was initially proposed. Here, we present a novel model describing a very different asymmetry to that proposed in the life‐dinner principle, but one that could apply broadly. We argue that asymmetries between the relative costs and benefits to predators and prey of selecting a risky behaviour during an extended predator–prey encounter could lead to an enhanced likelihood of escape for the prey. Any resulting advantage to prey depends upon there being a behaviour or choice that introduces some inherent danger to both predator and prey if they adopt it, but which if the prey adopts the predator must match in order to have a chance of successful predation. We suggest that the circumstances indicated by our model could apply broadly across diverse taxa, including both risky spatial or behavioural choices.     

Rapid and accurate species identification for ecological studies and monitoring using CRISPR‐based SHERLOCK

One of the most fundamental aspects of ecological research and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype‐based identification. The CRISPR‐Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently developed CRISPR‐Cas13a platform SHERLOCK (Specific High‐sensitivity Enzymatic Reporter unLOCKing) enables highly accurate taxonomic identification and has all the characteristics needed to transition to ecological and environmental disciplines. Here we conducted a series of “proof of principle” experiments to characterize SHERLOCK’s ability to accurately, sensitively and rapidly distinguish three fish species of management interest co‐occurring in the San Francisco Estuary that are easily misidentified in the field. We improved SHERLOCK’s ease of field deployment by combining the previously demonstrated rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction‐free DNA collection protocol, as well as the option of instrument‐free lateral flow detection. This approach opens the door for redefining how, where and by whom genetic identifications occur in the future.     

Effects of warming on predator–prey interactions – a resource‐based approach and a theoretical synthesis

We theoretically explore consequences of warming for predator–prey dynamics, broadening previous approaches in three ways: we include beyond‐optimal temperatures, predators may have a type III functional response, and prey carrying capacity depends on explicitly modelled resources. Several robust patterns arise. The relationship between prey carrying capacity and temperature can range from near‐independence to monotonically declining/increasing to hump‐shaped. Predators persist in a U‐shaped region in resource supply (=enrichment)‐temperature space. Type II responses yield stable persistence in a U‐shaped band inside this region, giving way to limit cycles with enrichment at all temperatures. In contrast, type III responses convey stability at intermediate temperatures and confine cycles to low and high temperatures. Warming‐induced state shifts can be predicted from system trajectories crossing stability and persistence boundaries in enrichment‐temperature space. Results of earlier studies with more restricted assumptions map onto this graph as special cases. Our approach thus provides a unifying framework for understanding warming effects on trophic dynamics.     

The use of stable isotope ratios in whitebait otolith carbonate to identify the source of prey for Western Australian penguins

A methodology has been developed and used to investigate a direct link between juvenile whitebait (Hyperlophus vittatus), the key prey species sampled from the stomachs of Little Penguins (Eudyptula minor), and the specific nursery area of that prey. A unique application of existing methodology initially involved the measurement of the stable isotopes of oxygen (δ¹⁸O:δ¹⁶O) and carbon (δ¹³C:δ¹²C) in sagittal otolith carbonate, using standard mass spectrometric techniques. The results indicated that the inshore distribution of juvenile (0+ year old) whitebait between Cockburn Sound and Koombana Bay, Western Australia consisted of a number of separate assemblages. Measured differences in stable oxygen isotope ratios were attributed to variations in freshwater input to the embayments that provided the whitebait habitats. In contrast, the measured stable carbon isotope ratios probably resulted from the different isotopic compositions of the food webs in the various habitats. Secondly, a comparison of the average value of carbon and oxygen isotope signatures of pooled otoliths from samples of whitebait from a number of different nearshore coastal sites (assemblages), with that of whitebait obtained from the stomachs of penguins at their main breeding site (Penguin Island) indicated that the values from the penguins resemble most closely those of the average otolith values obtained from whitebait from only one site (Becher Point). Assuming that the whitebait sampled were representative of the whitebait in the nearshore habitats and the diets of the penguins, then these results imply that at the time of sampling the penguins were feeding on whitebait from only one site.     

The dynamics of a Lotka–Volterra predator–prey model with state dependent impulsive harvest for predator

According to the economic and biological aspects of renewable resources management, we propose a Lotka–Volterra predator–prey model with state dependent impulsive harvest. By using the Poincaré map, some conditions for the existence and stability of positive periodic solution are obtained. Moreover, we show that there is no periodic solution with order larger than or equal to three under some conditions. Numerical results are carried out to illustrate the feasibility of our main results. The bifurcation diagrams of periodic solutions are obtained by using the numerical simulations, and it is shown that a chaotic solution is generated via a cascade of period-doubling bifurcations, which implies that the presence of pulses makes the dynamic behavior more complex.     

The use of xenoantigenic antisera for the identification of tilapiine species: comparative laboratory and field studies

Rapid and reliable identification of tilapiine taxa and strains is essential for selective breeding purposes and the conservation of natural genetic resources. There is evidence that antisera‐mediated erythrocyte agglutination assays can fit these requirements. We evaluated the applicability of agglutination tests by studying the capacity of species characteristic antisera to recognize erythrocytes from individuals of 10 natural Ghanaian populations of Oreochromis niloticus and Sarotherodon melanotheron. The vast majority of the 218 tested individuals could be identified based on antisera‐mediated erythrocyte recognition. Controls indicated the specificity of these reactions. Still, erythrocytes from 16% of all tested specimens did not respond to any antiserum (zero responders), indicating the possible existence of blood group properties in tilapias. We discuss the specificity of the antisera, the relevance of zero responses and the applicability of these tests in aquaculture and field studies.     

Application of otolith mass and shape for discriminating scabbardfishes Aphanopus spp. in the north‐eastern Atlantic Ocean

The otolith was used to investigate the variability between Aphanopus carbo and Aphanopus intermedius inhabiting the north‐eastern Atlantic Ocean. The results indicate a high degree of morphological affinity between species and areas; a noticeable metabolic change in the otolith shape was noted in the specimens of A. carbo, which may be related to migrations of individuals from shallow water (closer to the continental coast) to deeper water (archipelagos of Madeira and the Canary Islands). The results suggest a single population for both species in the north‐eastern Atlantic Ocean, although not conclusively.