Development and application of a machine learning algorithm for classification of elasmobranch behaviour from accelerometry data

Discerning behaviours of free-ranging animals allows for quantification of their activity budget, providing important insight into ecology. Over recent years, accelerometers have been used to unveil the cryptic lives of animals. The increased ability of accelerometers to store large quantities of high resolution data has prompted a need for automated behavioural classification. We assessed the performance of several machine learning (ML) classifiers to discern five behaviours performed by accelerometer-equipped juvenile lemon sharks (Negaprion brevirostris) at Bimini, Bahamas (25°44'N, 79°16'W). The sharks were observed to exhibit chafing, burst swimming, headshaking, resting and swimming in a semi-captive environment and these observations were used to ground-truth data for ML training and testing. ML methods included logistic regression, an artificial neural network, two random forest models, a gradient boosting model and a voting ensemble (VE) model, which combined the predictions of all other (base) models to improve classifier performance. The macro-averaged F-measure, an indicator of classifier performance, showed that the VE model improved overall classification (F-measure 0.88) above the strongest base learner model, gradient boosting (0.86). To test whether the VE model provided biologically meaningful results when applied to accelerometer data obtained from wild sharks, we investigated headshaking behaviour, as a proxy for prey capture, in relation to the variables: time of day, tidal phase and season. All variables were significant in predicting prey capture, with predations most likely to occur during early evening and less frequently during the dry season and high tides. These findings support previous hypotheses from sporadic visual observations.

Three decades of longlining in Bimini, Bahamas, reveals long-term trends in lemon shark Negaprion brevirostris (Carcharhinidae) catch per unit effort

In Bimini, Bahamas, the consistent employment of longlines, beginning in 1982, provided a rare opportunity to explore population trends for large resident sharks. This study assessed three shallow water longline survey periods at this location; 1982-1989, 1992-2002 and 2003-2014, with the aim of determining trends in annual catch per unit effort (CPUE) for an IUCN listed near-threatened species, the lemon shark Negaprion brevirostris. A general additive model (GAM) was used to analyse the non-linear annual CPUE values over the entire 32-year research period. The GAM displayed high variability of annual CPUE, with a peak value of 0·026 N. brevirostris per hook day (hooks day(-1) ) in 2000. The temporal pattern of CPUE indicated an abundance trend with a complete cycle, from trough to trough, occurring over a period of approximately 18 years. The 1982-1989 survey period saw the highest proportion of mature individuals (19·8%) and the smallest average pre-caudal length (LPC ; 124·8 cm). The 1992-2002 survey period had the highest average annual CPUE (0·018 hooks day(-1) ), while the 2003-2014 research period saw largest average LPC size (134·8 cm) and the lowest average CPUE values (0·009 hooks day(-1) ) of the entire research period. The long-term trend identified in this study provides a baseline for future assessment.

Using genetic inference to re-evaluate the minimum longevity of the lemon shark Negaprion brevirostris

A combination of mark-recapture and genetic sampling was used to extend the minimum longevity of an elasmobranch species and the life span estimate of the lemon shark Negaprion brevirostris was increased conservatively from 20·2 to 37 years. This increase in longevity means higher vulnerability and a longer recovery time from exploitation.

Occurrence and habitat use of the critically endangered smalltooth sawfish Pristis pectinata in the Bahamas

This study documents and discusses recent (2002-2015) sightings and captures of smalltooth sawfish Pristis pectinata in the Bahamas. Movement patterns and habitat preferences of five P. pectinata are examined: two tracked with acoustic telemetry in Bimini and three tagged with pop-up archival transmitting tags in Andros. Historically, P. pectinata may have been distributed throughout the Bahamas; however, since 2002 only 61 encounters were recorded including: Andros (30), Bimini (19) and a handful across other Islands (12). In Bimini, all P. pectinata were >225 cm (stretched total length, LST) suggesting that it is not used as a nursery area. Pristis pectinata in Andros ranged from c. 80 to 450 cm (LST) indicating that this island might be an important nursery and breeding habitat. Pristis pectinata tracked in both islands remained at depths <3 m, often adjacent to mangrove habitats, displaying residency from 42 days (Bimini) to 180 days (Andros). These preliminary findings confirm the Bahamas as an important habitat for P. pectinata and emphasize the urgent need for national protection and management of this population.

Genetic structure, population demography and seasonal occurrence of blacktip shark Carcharhinus limbatus in Bimini, the Bahamas

A longline survey was conducted from 2004 to 2014 to investigate the demographic population structure and seasonal abundance of the blacktip shark Carcharhinus limbatus in the Bimini Islands, the Bahamas. All individuals sampled (n = 242) were sub-adult or adults [70·1-145·1 cm pre-caudal length (LPC) range] with no neonates or YOY recorded in Bimini. Carcharhinus limbatus abundance peaked in September, coincident with the largest ratio of female to male sharks and a peak in fresh mating wounds on females. Mitochondrial control region (mtCR) DNA sequences were obtained from C. limbatus at Bimini to test whether Bimini C. limbatus are most closely related to geographically proximate populations sampled on the south-eastern coast of the U.S.A., the closest known nursery areas for this species. Nine mtCR haplotypes were observed in 32 individuals sampled at Bimini [haplotype diversity (h) = 0·821, nucleotide diversity (π) = 0·0015]. Four haplotypes observed from Bimini matched those previously found in the northern Yucatan (Mexico)-Belize and two matched a haplotype previously found in the U.S.A. Four haplotypes were novel but were closely related to the northern Yucatan-Belizean haplotypes. Pair-wise ΦST analysis showed that Bimini was significantly differentiated from all of the populations previously sampled (U.S.A. Atlantic, U.S.A. Gulf of Mexico, northern Yucatan, Belize and Brazil). This indicates that C. limbatus sampled from Bimini are unlikely from the described, proximate U.S.A. nurseries.

The behaviour and recovery of juvenile lemon sharks Negaprion brevirostris in response to external accelerometer tag attachment

Behavioural responses of lemon sharks Negaprion brevirostris to a fin-mounted tag package (CEFAS G6A tri-axial accelerometer with epoxied Sonotronics PT4 acoustic transmitter) were measured in a controlled captive environment (n = 10, total length, LT range 80-140 cm) and in free-ranging sharks upon release (n = 7, LT range 100-160 cm). No changes were detected in behaviour (i.e. swimming speed, tailbeat frequency, time spent resting and frequency of chafing) between control and tagged captive shark trials, suggesting that the tag package itself does not alter behaviour. In the free-ranging trials, an initial period of elevated swimming activity was found in all individuals (represented by overall dynamic body acceleration). Negaprion brevirostris, however, appeared to recover quickly, returning to a steady swimming state between 2 and 35 min after release. Post-release tracking found that all sharks swim immediately for the shoreline and remain within 100 m of shore for prolonged periods. Hence, although N. brevirostris are capable of quick adaptation to stressors and demonstrate rapid recovery in terms of activity, tracking data suggest that they may modify their spatial use patterns post release. This research is important in separating deviation in behaviour due to environmental stressors from artefacts caused by experimental techniques.

Diel temperature patterns of juvenile lemon sharks Negaprion brevirostris, in a shallow-water nursery

The relatively complex pattern of temperature selection exhibited by juvenile lemon sharks Negaprion brevirostris in the North Sound differed markedly from many previously described responses of fish preferenda. Thermal data demonstrated that juvenile N. brevirostris did not attempt to behaviourally maintain a constant eccritic temperature. Rather, juveniles selected progressively warmer temperatures throughout the day until reaching the highest temperatures available, and then moved to cooler temperatures during late evening and early morning hours. It is possible that by exploiting habitat thermal heterogeneity juvenile N. brevirostris prolong activities such as feeding or digestion well into the cooler parts of the evening. The complex pattern of temperature occupation by juvenile N. brevirostris within the thermally heterogeneous North Sound nursery is probably linked to key daily activities such as prey capture, predator avoidance and digestive efficiency.

Impact of early life stress on alcohol consumption and on the short- and long-term responses to alcohol in adolescent female rats

We examined the interaction between early life stress and vulnerability to alcohol in female rats exposed to prenatal restraint stress (PRS rats). First we studied the impact of PRS on ethanol preference during adolescence. PRS slightly increased ethanol preference per se, but abolished the effect of social isolation on ethanol preference. We then studied the impact of PRS on short- and long-term responses to ethanol focusing on behavioral and neurochemical parameters related to depression/anxiety. PRS or unstressed adolescent female rats received 10% ethanol in the drinking water for 4 weeks from PND30 to PND60. At PND60, the immobility time in the forced-swim test did not differ between PRS and unstressed rats receiving water alone. Ethanol consumption had no effect in unstressed rats, but significantly reduced the immobility time in PRS rats. In contrast, a marked increase in the immobility time was seen after 5 weeks of ethanol withdrawal only in unstressed rats. Hippocampal levels of neuropeptide Y (NPY) and mGlu1a metabotropic glutamate receptors were increased at the end of ethanol treatment only in unstressed rats. Ethanol treatment had no effect on levels of corticotropin-releasing hormone (CRH) in the hippocampus, striatum, and prefrontal cortex of both groups of rats. After ethanol withdrawal, hippocampal levels of mGlu1 receptors were higher in unstressed rats, but lower in PRS rats, whereas NPY and CRH levels were similar in the two groups of rats. These data indicate that early life stress has a strong impact on the vulnerability and responsiveness to ethanol consumption during adolescence.

Prey selection and functional response of juvenile lemon sharks Negaprion brevirostris

Prey preference of juvenile lemon sharks Negaprion brevirostris was examined in experiments conducted in field-based pens where the fish were offered meals of live teleosts: grey snapper Lutjanus griseus and yellow fin majorra Gerres cinereus in ratios of L. griseus:G. cinereus varying from 10:0 to 2:8. Relative electivity indices for each treatment showed that N. brevirostris preyed on G. cinereus rather than L. griseus. They showed a prey preference relating to density of G. cinereus (type II functional response) but not to L. griseus.

When bigger is not better: selection against large size, high condition and fast growth in juvenile lemon sharks

Selection acting on large marine vertebrates may be qualitatively different from that acting on terrestrial or freshwater organisms, but logistical constraints have thus far precluded selection estimates for the former. We overcame these constraints by exhaustively sampling and repeatedly recapturing individuals in six cohorts of juvenile lemon sharks (450 age-0 and 255 age-1 fish) at an enclosed nursery site (Bimini, Bahamas). Data on individual size, condition factor, growth rate and inter-annual survival were used to test the 'bigger is better', 'fatter is better' and 'faster is better' hypotheses of life-history theory. For age-0 sharks, selection on all measured traits was weak, and generally acted against large size and high condition. For age-1 sharks, selection was much stronger, and consistently acted against large size and fast growth. These results suggest that selective pressures at Bimini may be constraining the evolution of large size and fast growth, an observation that fits well with the observed small size and low growth rate of juveniles at this site. Our results support those of some other recent studies in suggesting that bigger/fatter/faster is not always better, and may often be worse.

Impact of an intense stress on ethanol consumption in female rats characterized by their pre-stress preference: modulation by prenatal stress

We examined the influence of prenatal stress on alcohol preference in adult female rats exposed to an intense stress. To take into account interindividual variability, the study was conducted in animals categorized as low or high alcohol preferring. After footshock, control high-preferring rats strongly reduced their alcohol consumption; in contrast, alcohol consumption was not changed in high-preferring rats that were prenatally stressed.

A pilot study of rat brain regional distribution of calcitonin, katacalcin and calcitonin gene-related peptide before and after antipsychotic treatment

In contrast to extensive determinations of calcitonin gene-related peptide (CGRP) in neural tissues, calcitonin and its carboxyl-terminal flanking peptide katacalcin (in human PDN-21) have not been systematically measured by radioimmunoassay (RIA) in discrete brain structures. Using microwave irradiation (MW), a procedure that increases the recovery of neuropeptides, we investigated by radioimmunoassay (RIA) the rat brain regional distribution of CGRP like- immunoreactivity (-LI), calcitonin-LI, and katacalcin-LI. Calcitonin-LI and katacalcin-LI were found in low concentrations in frontal cortex, occipital cortex, striatum and hippocampus. Moreover, a 4-week treatment with antipsychotic drugs altered the concentrations of the calcitonin-gene family peptides in the frontal cortex, occipital cortex, and hippocampus; the magnitude of these changes, however, was only moderate. Lastly, calcitonin-LI and katacalcin-LI baseline concentrations as well as after antipsychotic treatment were highly correlated in the frontal cortex, striatum, and hippocampus. The possible regulatory role of calcitonin gene family peptides in the central nervous system (CNS) needs to be further explored.

Dopamine receptor antagonists prevent the d-amphetamine-induced increase in calcitonin gene-related peptide levels in ventral striatum

Microdialysis in conjunction with radioimmunoassay (RIA) were used to study the effects of acute d-amphetamine or dopamine (DA) receptor antagonists administration on extracellular concentrations of calcitonin gene-related peptide (CGRP) in the ventral striatum of the rat. One hour after the subcutaneous (s.c.) injection of saline, the DA-D(1) receptor antagonist SCH 23390 (0.3 mg/kg) or the DA-D(2/3) receptor antagonist raclopride (1.0 mg/kg), one additional s.c. injection of saline or d-amphetamine (1.5 mg/kg) was given. The dialysates were collected at 60-min intervals; CGRP-like immunoreactivities (-LI) were determined by RIA. d-Amphetamine significantly increased extracellular CGRP-LI concentrations compared to the control animals. Administration of either SCH 23390 or raclopride did not significantly affect CGRP-LI concentrations. Pretreatment with either SCH 23390 or raclopride abolished the stimulatory effect of d-amphetamine on CGRP-LI levels. The results show that d-amphetamine administration results in an increase in extracellular concentrations of CGRP in the ventral striatum through a mechanism that appears to involve stimulation of either DA-D(1) or DA-D(2/3) receptors. The results also indicate that changes in dopaminergic neurotransmission affect CGRP outflow in the ventral striatum in a phasic but not tonic manner.

Neuropeptide Y (NPY) mRNA in rat brain tissue: effects of decapitation and high-energy microwave irradiation on post mortem stability

mRNA recovery from brain tissue is affected by time-interval from death to inactivation of tissue, and may depend on sacrificial method. Sacrifice by high-energy microwave irradiation increases recovery of intact neuropeptides and proteins, and it has been suggested that this may be valid also for neuropeptide mRNAs. We therefore compared post-mortem NPY mRNA recovery following decapitation or microwave irradiation. Total RNA yield was significantly higher in tissue from decapitated rats. A decline in NPY mRNA (amol/mg tissue) over time, presumably reflecting degradation, was found in frontal cortex, hippocampus and striatum. Following high-energy microwaves, NPY message levels were higher in occipital cortex, lower in the hypothalamus, and unaltered in the other brain regions examined. These results show that post-mortem processes contribute to estimates of NPY mRNA levels obtained using standard methods for obtaining brain tissue from experimental animals and raise the question whether different pools of NPY mRNA might be differentially affected by post-mortem degradation. A general protective effect of high-energy radiation against degradation is not supported.

Population genetic structure of the lemon shark (Negaprion brevirostris) in the western Atlantic: DNA microsatellite variation

DNA microsatellite markers were used to characterize the population genetic structure of the lemon shark, Negaprion brevirostris, in the western Atlantic. This study demonstrates for the first time the usefulness of microsatellites to study population genetic structure and mating systems in the Chondricthyes. Lemon sharks (mostly juveniles) were sampled non-destructively from four locations, Gullivan Bay and Marquesas Key in Florida, Bimini, Bahamas, and Atol das Rocas, Brazil. At least 545 individuals were genotyped at each of four dinucleotide loci. The number of alleles per locus ranged from 19 to 43, and expected heterozygosities ranged from 0.69 to 0.90. Relatively little genetic structure was found in the western Atlantic, with small but significant values for estimators of F(ST) and R(ST) among populations, theta (0.016) and rho (0.026), respectively. No sharp discontinuities were found between the Caribbean sites and Brazil, and most alleles were found at all four sites, indicating that gene flow occurs throughout the western Atlantic with no evidence for distinct stocks.

Effects of typical and atypical antipsychotics on neuropeptide Y in rat brain tissue and microdialysates from ventral striatum

The main goal of this study was to investigate effects of typical (haloperidol) and atypical (risperidone) antipsychotic drugs on brain regional neuropeptide Y (NPY)-like immunoreactivity (-LI) tissue concentrations and on release of NPY-LI in freely moving rats. An additional aim was to explore the effect of d-amphetamine on NPY-LI release following pretreatment with typical and atypical antipsychotics. During a 4-week period, male Wistar rats were fed chow to which vehicle, risperidone (1.15 mg/100 g food or 2.3 mg/100 g food), or haloperidol (1.15 mg/100 g food) were added. In one series of experiments, the animals were sacrificed on day 30 with focused microwave irradiation, the brain regions dissected and extracted for radioimmunoassay of NPY-LI. In another experimental series, probes were inserted into the ventral striatum. The perfusates were collected at 60-min intervals; NPY-LI was determined by radioimmunoassay. Haloperidol significantly increased NPY-LI in hypothalamus and the occipital cortex. In contrast, haloperidol decreased tissue levels of NPY-LI in striatum. Moreover, haloperidol and risperidone also significantly decreased extracellular NPY-LI concentrations in the ventral striatum. d-amphetamine (1.5 mg/kg) significantly increased extracellular NPY-LI in the vehicle group. Both haloperidol and risperidone pretreatments abolished the effect of d-amphetamine. The results show that d-amphetamine as well as haloperidol and risperidone selectively and specifically affect NPY-LI concentrations in brain tissue and microdialysates and that the effect of d-amphetamine is abolished by both typical and atypical antipsychotics.

Induction and duration of tonic immobility in the lemon shark, Negaprion brevirostris

Tonic immobility (TI) is an unlearned behavioral response characterized by a state of immobility and torpor. Effect of inter-trial interval on duration of tonic immobility was assessed in thirty, juvenile lemon sharks (Negaprion brevirostris). Regression analyses showed that massed trials of 12 per session increased the average duration of tonic immobility by 475 sec compared to spaced trials of 1 per session. Each experiment was composed of 24 trials. TI is stable and durations much longer in the lemon shark than for other sharks. These findings have enabled us to develop a quantitative bioassay for use in testing chemical shark repellents.

Rod and cone pigments of the Atlantic guitarfish, Rhinobatos lentiginosus Garman

Using both extraction- and micro-spectrophotometric (MSP) methods the visual pigment(s) from the rods and cones of the Atlantic guitarfish, Rhinobatos lentiginosus, were shown to be spectrally similar, if not identical (lambda max = 498-499 nm). Color vision, therefore, is unlikely unless mediated via colored oil droplets in the inner segments. The identical lambda max for the rod and cone pigments suggest that vision in both dim and bright light may correlate with the underwater spectrum over the depths and the times of day that guitarfish are active. The primary advantage of the blue-green sensitive visual pigments, we suggest, is to enhance the contrast of targets silhouetted against the background spacelight.

Shark repellent lipophilic constituents in the defense secretion of the Moses sole (Pardachirus marmoratus)

The defense secretion of Moses sole (Pardachirus marmoratus), the fish known to repel sharks, contains lipophilic ichthyotoxins in addition to pardaxin, a peptidic ichthyotoxin. Pardaxin has previously been regarded as the only factor responsible for the shark repellency of the secretion. On the basis of the shark repellent activity observed with the lipophile, it is considered to participate in the repellency of the secretion. Further separation of the toxic lipophile yielded five steroid monoglycosides, named mosesins. Their structures have been elucidated by nuclear magnetic resonance spectroscopy and corroborated by correlating them spectroscopically or chemically to cholic acid or to pavoninins, the related glycosides isolated from the secretion of the congeneric peacock sole, P. pavoninus.

Synthetic surfactants: a new approach to the development of shark repellents

The toxic and shark repellent secretion of Pardachirus marmoratus (PMC) and a series of 15 surfactants and industrial detergents were assayed for their lethality to fish, termination of shark's tonic immobility and feeding inhibition of aggressive, hungry lemon sharks. Sodium and lithium lauryl sulfate salts were more potent than PMC in all three bioassays. Graduated activity, from mildly repellent to inactive, was demonstrated by several other surfactants. The abundance, versatility, chemical stability, modifiability, and low price of detergents justify their use in further development of effective shark repellents.

Sharks: Attraction by Low-Frequency Sounds

Large sharks (Carcharhinidae, Sphyrnidae), in their natural environment, were attracted to low-frequency (predominantly 20 to 60 cy/sec) pulsed sounds, but apparently not to higher frequency (400 to 600 cy/sec) pulsed sounds, or to low-frequency continuous sounds. The sharks apparently detected and oriented to the sounds in the acoustic far field.