Museum genomics reveals the hybrid origin of an extinct crater lake endemic.

Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.

The effect of light during embryonic development on laterality and exploration in Western Rainbowfish.

Several factors affect the development of lateralization such as hormones and light exposure during early development. Laterality also often correlates with other behavioral traits. To examine whether there is a common mechanism underlying the development of laterality and other behaviors, we manipulated laterality by exposing embryos of the Western rainbowfish (Melatotaenia australis) to light or continuous darkness during early development and determined whether a shift in laterality was associated with a change in behavior in a novel environment test at two different ages. We found that exposing eggs to darkness led to offspring that displayed significantly less lateralized behavior in the mirror test two weeks after hatching than offspring from eggs exposed to light. Interestingly, the effects of rearing condition were lost by 3 months of age. These data suggest that exposure to light can influence laterality very early in development, but such bias can be overwritten by developmental processes post-hatch. Moreover, our manipulation of laterality apparently had no influence on exploration suggesting independent causal mechanisms. The experimental manipulation of light exposure during development could be a useful tool for enhancing individuals with a specific laterality and behavioral traits to aid future research into the causes and consequences of laterality.

Scaling of Activity Space in Marine Organisms across Latitudinal Gradients.

AbstractUnifying models have shown that the amount of space used by animals (e.g., activity space, home range) scales allometrically with body mass for terrestrial taxa; however, such relationships are far less clear for marine species. We compiled movement data from 1,596 individuals across 79 taxa collected using a continental passive acoustic telemetry network of acoustic receivers to assess allometric scaling of activity space. We found that ectothermic marine taxa do exhibit allometric scaling for activity space, with an overall scaling exponent of 0.64. However, body mass alone explained only 35% of the variation, with the remaining variation best explained by trophic position for teleosts and latitude for sharks, rays, and marine reptiles. Taxon-specific allometric relationships highlighted weaker scaling exponents among teleost fish species (0.07) than sharks (0.96), rays (0.55), and marine reptiles (0.57). The allometric scaling relationship and scaling exponents for the marine taxonomic groups examined were lower than those reported from studies that had collated both marine and terrestrial species data derived using various tracking methods. We propose that these disparities arise because previous work integrated summarized data across many studies that used differing methods for collecting and quantifying activity space, introducing considerable uncertainty into slope estimates. Our findings highlight the benefit of using large-scale, coordinated animal biotelemetry networks to address cross-taxa evolutionary and ecological questions.

Smart sharks: a review of chondrichthyan cognition.

450 million years of evolution have given chondrichthyans (sharks, rays and allies) ample time to adapt perfectly to their respective everyday life challenges and cognitive abilities have played an important part in that process. The diversity of niches that sharks and rays occupy corresponds to matching diversity in brains and behaviour, but we have only scratched the surface in terms of investigating cognition in this important group of animals. The handful of species that have been cognitively assessed in some detail over the last decade have provided enough data to safely conclude that sharks and rays are cognitively on par with most other vertebrates, including mammals and birds. Experiments in the lab as well as in the wild pose their own unique challenges, mainly due to the handling and maintenance of these animals as well as controlling environmental conditions and elimination of confounding factors. Nonetheless, significant advancements have been obtained in the fields of spatial and social cognition, discrimination learning, memory retention as well as several others. Most studies have focused on behaviour and the underlying neural substrates involved in cognitive information processing are still largely unknown. Our understanding of shark cognition has multiple practical benefits for welfare and conservation management but there are obvious gaps in our knowledge. Like most marine animals, sharks and rays face multiple threats. The effects of climate change, pollution and resulting ecosystem changes on the cognitive abilities of sharks and stingrays remain poorly investigated and we can only speculate what the likely impacts might be based on research on bony fishes. Lastly, sharks still suffer from their bad reputation as mindless killers and are heavily targeted by commercial fishing operations for their fins. This public relations issue clouds people's expectations of shark intelligence and is a serious impediment to their conservation. In the light of the fascinating results presented here, it seems obvious that the general perception of sharks and rays as well as their status as sentient, cognitive animals, needs to be urgently revisited.

Intraspecific variation in muscle growth of two distinct populations of Port Jackson sharks under projected end-of-century temperatures.

Although pervasive, the effects of climate change vary regionally, possibly resulting in differential behavioral, physiological, and/or phenotypic responses among populations within broadly distributed species. Juvenile Port Jackson sharks (Heterodontus portusjacksoni) from eastern and southern Australia were reared at their current (17.6 °C Adelaide, South Australia [SA]; 20.6 °C Jervis Bay, New South Wales [NSW]) or projected end-of-century (EOC) temperatures (20.6 °C Adelaide, SA; 23.6 °C Jervis Bay, NSW) and assessed for morphological features of skeletal muscle tissue. Nearly all skeletal muscle properties including cellularity, fiber size, myonuclear domain, and satellite cell density did not differ between locations and thermal regimes. However, capillary density was significantly influenced by thermal treatment, where Adelaide sharks raised at current temperatures had a lower capillarity than Jervis Bay sharks raised at ambient or projected EOC temperatures. This may indicate higher metabolic costs at elevated temperatures. However, our results suggest that regardless of the population, juvenile Port Jackson sharks may have limited acclimatory potential to alter muscle metabolic features under a temperature increase, which may make this species vulnerable to climate change.

Diving into the diet of provisioned smooth stingrays using stable isotope analysis.

Recreational fishing waste, produced from processing catches at shore-based fish cleaning facilities and discarded into adjacent waters, is foraged by various aquatic species. However, the potential alterations to the diet of consumers of these resources are poorly studied. Smooth stingrays (Bathytoshia brevicaudata) are a large demersal mesopredatory ray species and common scavenger of recreational fishing discards around southern Australia. Due to their attraction to fish cleaning sites, they are also common targets of unregulated 'stingray feeding' tourism where they are fed commercially produced baits (e.g., pilchards). This study provides a preliminary assessment of the diet of smooth stingrays provisioned recreational fishing discards and baits at two sites in southern New South Wales, Australia (Discard Site: recreational fishing discards only; Provisioning Site: recreational fishing discards and commercial baits) using stable isotope analysis of carbon (δ13 C) and nitrogen (δ15 N), and Bayesian stable isotope mixing models. Our results indicate that at both sites invertebrates, considered a main part of the natural diet of smooth stingrays, made a limited contribution to the diets of provisioned stingrays, while a benthic teleost fish that is a common recreational catch was the dominant contributor. As the assessed teleost is potentially a natural prey item for smooth stingrays, it remains unclear whether the contribution came from recreational fishing discards or natural foraging. However, due to smooth stingrays' typically opportunistic foraging strategy, we expected a greater mixture of resources from low to high trophic level prey than was observed. These results suggest that smooth stingrays have either lower reliance on invertebrates as a result of utilizing provisioned resources or higher reliance on teleost fishes than previously thought. Commercial bait products fed to stingrays at the Provisioning Site were not a major contributor to the diets of smooth stingrays, suggesting this activity has a low impact on their nutrition.

Preliminary observations on the movement ecology of a crested horn shark (Heterodontus galeatus).

The residency and movements of a single acoustically tagged female crested horn shark (Heterodontus galeatus) were monitored in Jervis Bay, Australia. The individual was intermittently detected by receivers throughout the 8-year study period and showed preference for particular rocky reefs in terms of its residency indices and duration of residency events. This individual exhibited lower residency and dissimilar movement patterns to that of the well-studied and sympatric Port Jackson shark (Heterodontus portusjacksoni), highlighting the need for research into the basic life history and movement ecology of H. galeatus.

Population variation in the thermal response to climate change reveals differing sensitivity in a benthic shark.

Many species with broad distributions are exposed to different thermal regimes which often select for varied phenotypes. This intraspecific variation is often overlooked but may be critical in dictating the vulnerability of different populations to environmental change. We reared Port Jackson shark (Heterodontus portusjacksoni) eggs from two thermally discrete populations (i.e. Jervis Bay and Adelaide) under each location's present-day mean temperatures, predicted end-of-century temperatures and under reciprocal-cross conditions to establish intraspecific thermal sensitivity. Rearing temperatures strongly influenced MO2 Max and critical thermal limits, regardless of population, indicative of acclimation processes. However, there were significant population-level effects, such that Jervis Bay sharks, regardless of rearing temperature, did not exhibit differences in MO2 Rest , but under elevated temperatures exhibited reduced maximum swimming activity with step-wise increases in temperature. In contrast, Adelaide sharks reared under elevated temperatures doubled their MO2 Rest , relative to their present-day temperature counterparts; however, maximum swimming activity was not influenced. With respect to reciprocal-cross comparisons, few differences were detected between Jervis Bay and Adelaide sharks reared under ambient Jervis Bay temperatures. Similarly, juveniles (from both populations) reared under Adelaide conditions had similar thermal limits and swimming activity (maximum volitional velocity and distance) to each other, indicative of conserved acclimation capacity. However, under Adelaide temperatures, the MO2 Rest of Jervis Bay sharks was greater than that of Adelaide sharks. This indicates that the energetics of cooler water population (Adelaide) is likely more thermally sensitive than that of the warmer population (Jervis Bay). While unique to elasmobranchs, these data provide further support that by treating species as static, homogeneous populations, we ignore the impacts of thermal history and intraspecific variation on thermal sensitivity. With climate change, intraspecific variation will manifest as populations move, demographics change or extirpations occur, starting with the most sensitive populations.

Understanding fish cognition: a review and appraisal of current practices.

With over 30,000 recognized species, fishes exhibit an extraordinary variety of morphological, behavioural, and life-history traits. The field of fish cognition has grown markedly with numerous studies on fish spatial navigation, numeracy, learning, decision-making, and even theory of mind. However, most cognitive research on fishes takes place in a highly controlled laboratory environment and it can therefore be difficult to determine whether findings generalize to the ecology of wild fishes. Here, we summarize four prominent research areas in fish cognition, highlighting some of the recent advances and key findings. Next, we survey the literature, targeting these four areas, and quantify the nearly ubiquitous use of captive-bred individuals and a heavy reliance on lab-based research. We then discuss common practices that occur prior to experimentation and within experiments that could hinder our ability to make more general conclusions about fish cognition, and suggest possible solutions. By complementing ecologically relevant laboratory-based studies with in situ cognitive tests, we will gain further inroads toward unraveling how fishes learn and make decisions about food, mates, and territories.

Residency and movement patterns of adult Port Jackson sharks (Heterodontus portusjacksoni) at a breeding aggregation site.

Examining the movement ecology of mesopredators is fundamental to developing an understanding of their biology, ecology and behaviour, as well as the communities and ecosystems they influence. The limited research on the residency and movements of benthic marine mesopredators has primarily used visual tags, which do not allow for the efficient and accurate monitoring of individual space use. In this study, the authors investigated the residency and movement patterns of Port Jackson sharks Heterodontus portusjacksoni (Meyer 1793) at a breeding aggregation site in Jervis Bay, south-eastern Australia, using passive acoustic telemetry to further our understanding of the movement ecology of these important mesopredators. Between 2012 and 2014, individuals were tagged with acoustic transmitters, and their residency and movements within the bay were monitored for up to 4 years. H. portusjacksoni showed strong preferences for particular reefs within and between breeding seasons. Males had significantly higher residency indices at their favoured sites relative to females, suggesting that males may be engaging in territorial behaviour. Conversely, female H. portusjacksoni exhibited higher roaming indices relative to males indicating that females may move between sites to assess males. Finally, H. portusjacksoni showed temporal variation in movements between reefs with individuals typically visiting more reefs at night relative to the day, dusk and dawn corresponding with their nocturnal habits.

Seasonal variation of sexually dimorphic spatial learning implicates mating system in the intertidal Cocos Frillgoby (Bathygobius cocosensis).

Spatial learning is an important cognitive function found across a multitude of species. Natural selection can enhance specific cognitive abilities depending on species ecology but, under certain conditions, spatial learning is also known to vary between sexes according to reproductive status. Despite abundant studies on spatial learning across animal taxa, those focusing on sexually dimorphic spatial learning have been largely limited to rodents. Here, we found that spatial cognition varies between the sexes in an intertidal goby, and this difference fluctuates across seasons. Males and females demonstrated similar cognitive abilities when solving a simple maze during all seasons except spring, when males were significantly less successful than females. Spring marks the beginning of the breeding season for this species, when females move between nests to choose a suitable mate, while males guard their nest and forego foraging excursions. We suggest that the reduction in male cognitive ability reduces metabolic costs at a time of reduced need. This study presents the first evidence for sexually dimorphic spatial learning in fish driven by differences in reproductive behaviour as dictated by the mating system.

Effects of reward magnitude and training frequency on the learning rates and memory retention of the Port Jackson shark Heterodontus portusjacksoni.

The development of adaptive responses to novel situations via learning has been demonstrated in a wide variety of animal taxa. However, knowledge on the learning abilities of one of the oldest extant vertebrate groups, Chondrichthyes, remains limited. With the increasing interest in global wildlife tourism and shark feeding operations, it is important to understand the capacities of these animals to form associations between human activities and food. We used an operant conditioning regime with a simple spatial cognitive task to investigate the effects of reinforcement frequency and reward magnitude on the learning performance and memory retention of Port Jackson sharks (Heterodontus portusjacksoni). Twenty-four Port Jackson sharks were assigned one of four treatments differing in reward magnitude and reinforcement frequency (large magnitude-high frequency; large magnitude-low frequency; small magnitude-high frequency; small magnitude-low frequency). The sharks were trained over a 21-day period to compare the number of days that it took to learn to pass an assigned door to feed. Sharks trained at a high reinforcement frequency demonstrated faster learning rates and a higher number of passes through the correct door at the end of the trials, while reward magnitude had limited effects on learning rate. This suggests that a reduction in reinforcement frequency during tourism-related feeding operations is likely to be more effective in reducing the risk of sharks making associations with food than limiting the amount of food provided.

Correction to: Effects of reward magnitude and training frequency on the learning rates and memory retention of the Port Jackson shark Heterodontus portusjacksoni.

In the original publication of the article, the Fig. 4 was erroneously published.

Assessment of Machine Learning Models to Identify Port Jackson Shark Behaviours Using Tri-Axial Accelerometers.

Movement ecology has traditionally focused on the movements of animals over large time scales, but, with advancements in sensor technology, the focus can become increasingly fine scale. Accelerometers are commonly applied to quantify animal behaviours and can elucidate fine-scale (<2 s) behaviours. Machine learning methods are commonly applied to animal accelerometry data; however, they require the trial of multiple methods to find an ideal solution. We used tri-axial accelerometers (10 Hz) to quantify four behaviours in Port Jackson sharks (Heterodontus portusjacksoni): two fine-scale behaviours (<2 s)-(1) vertical swimming and (2) chewing as proxy for foraging, and two broad-scale behaviours (>2 s-mins)-(3) resting and (4) swimming. We used validated data to calculate 66 summary statistics from tri-axial accelerometry and assessed the most important features that allowed for differentiation between the behaviours. One and two second epoch testing sets were created consisting of 10 and 20 samples from each behaviour event, respectively. We developed eight machine learning models to assess their overall accuracy and behaviour-specific accuracy (one classification tree, five ensemble learners and two neural networks). The support vector machine model classified the four behaviours better when using the longer 2 s time epoch (F-measure 89%; macro-averaged F-measure: 90%). Here, we show that this support vector machine (SVM) model can reliably classify both fine- and broad-scale behaviours in Port Jackson sharks.

Seasonal and developmental diet shifts in sympatric and allopatric intertidal gobies determined by stomach content and stable isotope analysis.

Resource partitioning facilitates the coexistence of sympatric species through spatial, temporal and/or trophic strategies. Fishes living in the intertidal zone demonstrate highly adaptive plastic behaviour, including resource partitioning, through spatial and temporal shifts in diet and microhabitat. Although intertidal fish assemblages are influenced by inter- and intraspecific competition, few studies have compared the extent of resource partitioning between sympatric species in the context of trophic niche plasticity. Here we used complementary approaches, stomach content and stable isotope (δ13 C and δ15 N) analyses, to evaluate seasonal and developmental shifts in trophic niche position in two sympatric (Favonigobius lentiginosus and Bathygobius krefftii) and one allopatric (Bathygobius cocosensis) species of intertidal goby. The results indicate that resource partitioning in the two sympatric species varied with season, with almost no trophic niche overlap in summer to about ~30% overlap in winter. Also, evidence of dietary changes was found in B. cocosensis, which is likely associated with a shift in microhabitat and intraspecific competition. The findings highlight the temporal range of behavioural plasticity in trophic niche position of intertidal gobies, which likely has high adaptive value in the dynamic intertidal zone.

Environmental enrichment influences spatial learning ability in captive-reared intertidal gobies (Bathygobius cocosensis).

Behavioural plasticity is an advantageous trait for animals living in dynamic environments, and can be induced through learning. While some behavioural traits are innate, others are framed by experience and learning during an individual's lifetime. Many studies have investigated cognitive abilities in fish species from contrasting environments, but the relative contribution of natural selection versus behavioural plasticity in cognitive variability remains equivocal. Furthermore, rearing conditions in laboratories are often mundane, failing to encourage natural behaviour in the species used in these studies. Here, we captured juvenile gobies (Bathygobius cocosensis) from intertidal rockpools, and raised them in captivity under varied environmental enrichment treatments that mimic variation observed in coastal habitats. When tested in a simple spatial learning task, individuals from complex rearing treatments (rock or oyster substrate) reached learning criteria faster than those reared in less complex (seagrass) and homogenous environments (sand substrate). Interestingly, gobies reared in complex environments demonstrated longer latencies to start the task than gobies in homogeneous treatments. Our results indicate that cognitive ability is strongly shaped by individual experience during ontogeny, and exposure to reduced environmental complexity in early life leads to reduced cognitive abilities in intertidal gobies.

Behavioral and immunotoxic effects of Prograf® (tacrolimus) in the male Siamese fighting fish.

Siamese fighting fish (Betta splendens) has been extensively exploited in the behavioral and physiological toxicology studies of drugs. Tacrolimus is an immunosuppressant drug largely used in liver and renal transplantations. Here we found that a 7-day exposure of male B. splendens to concentrations of 0.05 and 0.1 µg/mL Prograf® (tacrolimus) caused alterations in aggression and immunity indexes. Tacrolimus exposed fish presented lower opercular display in a mirror test which is indicative of reduced aggression. In addition, serum levels of lysozyme, IgM, alternative complement, and bactericidal activity of subjects exposed to 0.1 µg/mL tacrolimus were lower than those from the control treatment. These results showed the behavioral impairment and immunotoxic impacts of tacrolimus in a model of aquatic toxicology. The results suggest fishes provide a possible model for better understanding of the drug action in vertebrates, and possible consequences for the environment via its effects on non-target organisms in an ecotoxicology context.

Lack of social preference between unfamiliar and familiar juvenile Port Jackson sharks Heterodontus portusjacksoni.

This study investigated whether captive-reared juvenile Port Jackson sharks Heterodontus portusjacksoni choose to aggregate and if familiarity is one of the mechanisms driving social preference. In a controlled binary-choice experiment, juvenile sharks were given the option to associate or not with unfamiliar conspecifics, or to associate or not with familiar conspecifics. In neither group did juvenile H. portusjacksoni actively choose to associate with conspecifics, but familiarity decreased the proportion of time spent near a conspecific only during the initial phase of the experiment. Treatment (1 or 3 shoal mates), sex and size had no effect on aggregation behaviour. These findings suggest that familiarity is not a driver of social preferences in juvenile H. portusjacksoni, contrary to results in another shark species. Additionally, adult H. portusjacksoni form large aggregations during the breeding season and actively associate with familiar sex and size-matched individuals, thus our results suggest the species undergoes an ontogenetic shift in social behaviour.

Food approach conditioning and discrimination learning using sound cues in benthic sharks.

The marine environment is filled with biotic and abiotic sounds. Some of these sounds predict important events that influence fitness while others are unimportant. Individuals can learn specific sound cues and 'soundscapes' and use them for vital activities such as foraging, predator avoidance, communication and orientation. Most research with sounds in elasmobranchs has focused on hearing thresholds and attractiveness to sound sources, but very little is known about their abilities to learn about sounds, especially in benthic species. Here we investigated if juvenile Port Jackson sharks could learn to associate a musical stimulus with a food reward, discriminate between two distinct musical stimuli, and whether individual personality traits were linked to cognitive performance. Five out of eight sharks were successfully conditioned to associate a jazz song with a food reward delivered in a specific corner of the tank. We observed repeatable individual differences in activity and boldness in all eight sharks, but these personality traits were not linked to the learning performance assays we examined. These sharks were later trained in a discrimination task, where they had to distinguish between the same jazz and a novel classical music song, and swim to opposite corners of the tank according to the stimulus played. The sharks' performance to the jazz stimulus declined to chance levels in the discrimination task. Interestingly, some sharks developed a strong side bias to the right, which in some cases was not the correct side for the jazz stimulus.

Learning and robustness to catch-and-release fishing in a shark social network.

Individuals can play different roles in maintaining connectivity and social cohesion in animal populations and thereby influence population robustness to perturbations. We performed a social network analysis in a reef shark population to assess the vulnerability of the global network to node removal under different scenarios. We found that the network was generally robust to the removal of nodes with high centrality. The network appeared also highly robust to experimental fishing. Individual shark catchability decreased as a function of experience, as revealed by comparing capture frequency and site presence. Altogether, these features suggest that individuals learnt to avoid capture, which ultimately increased network robustness to experimental catch-and-release. Our results also suggest that some caution must be taken when using capture-recapture models often used to assess population size as assumptions (such as equal probabilities of capture and recapture) may be violated by individual learning to escape recapture.