Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement.

The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64-71 % of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.

Tissue metal concentrations and antioxidant enzyme activity in western north Atlantic white sharks (Carcharodon carcharias).

Anthropogenic practices have increased metal contamination in marine ecosystems. Most sharks have long lifespans, occupy an important ecological position at the top of marine food webs, and can accumulate metals. However, reference levels of metal contaminants in the tissues of sharks, particularly, apex predators such as the white shark (Carcharodon carcharias), are lacking. In this study, concentrations of copper (Cu), cadmium (Cd), nickel (Ni), lead (Pb), silver (Ag), and zinc (Zn) were measured in the muscle tissue of white (n = 42) and tiger (Galeocerdo cuvier; n = 3) sharks. Metal exposure in various species, including sharks, has been correlated with increased oxidative stress. Therefore, the main objectives of this study were to assess metal accumulation and antioxidant enzyme activity (superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx)) in the muscle tissue of the population of white sharks and tiger sharks inhabiting the Western North Atlantic. The measured parameters were qualitatively compared between species. The small sample size of tiger sharks (collected from only one site) limited statistical analyses, therefore, white sharks were the primary focus of this study. Differences in tissue metal (Cu, Cd, Ni, and Zn) concentrations and antioxidant enzyme activities were detected based on collection site, with significant positive correlations between Cd and enzymes, SOD and CAT, and Zn and enzymes, SOD and GPx in C. carcharias. Differences in Ni concentration were detected based on sex, with females having higher Ni levels. Additionally, plasma osmolality was not correlated with tissue metal concentrations; however, osmolality decreased with increasing length in C. carcharias. This study is the first to report baseline levels of Cu, Zn, Cd, Ni, Ag, and Pb in muscle of North Atlantic white sharks and provides new insights into oxidative stress responses of these sensitive species to metal contaminants.

No apparent negative tagging effects after 13 years at liberty for lemon shark, Negaprion brevirostris implanted with acoustic transmitter.

An intact and uncompromised internal acoustic transmitter was non-lethally recovered from a lemon shark Negaprion brevirostris, after 13 years at liberty. The shark, first tagged at an estimated age of 2 years old near South Bimini, Bahamas in 2004, was recaptured in 2017 with a total length of 264 cm. The tagged shark displayed typical growth rate, pregnancy, natal homing and pupping behaviour of other individuals in this population. This observation provides important evidence regarding the effects from long-term retention of implanted acoustic transmitters in a carcharhinid shark.

Risky business for a juvenile marine predator? Testing the influence of foraging strategies on size and growth rate under natural conditions.

Mechanisms driving selection of body size and growth rate in wild marine vertebrates are poorly understood, thus limiting knowledge of their fitness costs at ecological, physiological and genetic scales. Here, we indirectly tested whether selection for size-related traits of juvenile sharks that inhabit a nursery hosting two dichotomous habitats, protected mangroves (low predation risk) and exposed seagrass beds (high predation risk), is influenced by their foraging behaviour. Juvenile sharks displayed a continuum of foraging strategies between mangrove and seagrass areas, with some individuals preferentially feeding in one habitat over another. Foraging habitat was correlated with growth rate, whereby slower growing, smaller individuals fed predominantly in sheltered mangroves, whereas larger, faster growing animals fed over exposed seagrass. Concomitantly, tracked juveniles undertook variable movement behaviours across both the low and high predation risk habitat. These data provide supporting evidence for the hypothesis that directional selection favouring smaller size and slower growth rate, both heritable traits in this shark population, may be driven by variability in foraging behaviour and predation risk. Such evolutionary pathways may be critical to adaptation within predator-driven marine ecosystems.

Prior task experience and comparable stimulus exposure nullify focal and nonfocal prospective memory retrieval differences.

We explored the nature of focal versus nonfocal event-based prospective memory retrieval. In the context of a lexical decision task, people received an intention to respond to a single word (focal) in one condition and to a category label (nonfocal) for the other condition. Participants experienced both conditions, and their order was manipulated. The focal instruction condition was a single word presented multiple times. In Experiment 1, the stimuli in the nonfocal condition were different exemplars from a category, each presented once. In the nonfocal condition retrieval was poorer and reaction times were slower during the ongoing task as compared to the focal condition, replicating prior findings. In Experiment 2, the stimulus in the nonfocal condition was a single category exemplar repeated multiple times. When this single-exemplar nonfocal condition followed in time the single-item focal condition, focal versus nonfocal performance was virtually indistinguishable. These results demonstrate that people can modify their stimulus processing and expectations in event-based prospective memory tasks based on experience with the nature of prospective cues and with the ongoing task.

The reliability of criterion shifting in recognition memory is task dependent.

We explored 2 research questions: whether criterion shifts within different recognition tasks are reliable across testing sessions and whether such shifts correlate across the different tasks. In Experiment 1, we established consistent group-level criterion shifting based on expected strength of target items in the test. False-alarm rates were higher when expected strength was weak as opposed to strong, even when expected strength cues were unblocked at test. Test-retest reliabilities in this strength-cuing environment were good. In Experiment 2, we manipulated either the probability (high or low) or expected memory strength (strong or weak) of target items and had people perform both tasks on each of 2 days of testing. Varying the probability of target items consistently produced criterion shifts, as did manipulating target memory strength. Regarding individual differences, shifting in a given test context predicted shifting on a second day in that same test context. However, one's tendency to shift a decision criterion on 1 type of test context did not predict one's tendency to do so in the other. The extent to which people shifted their decision criterion in recognition memory testing was largely dependent on the type of test.

The effects of study order and backward associative strength on illusory recollection: A source-strength effect does not always occur.

We investigated illusory recollection by dividing lists of associated words into three subsets (high, medium and low) based on their backward associative strength (BAS) to an unstudied theme. Participants studied these subsets at different visual locations on a computer screen and afterwards were given a source memory test. In Experiment 1, we varied the order in which high- and medium-BAS subsets were studied. In Experiment 2, we again manipulated study order as well as the associative strength of the medium-BAS subsets (strong or weak). Across both experiments, illusory recollection was constrained by both study order and BAS. Source attributions to the high-BAS location were more likely (a source-strength effect) when high-BAS items were studied first or studied following items of relatively low associative strength. However, attributions to the strong medium-BAS studied location were more likely when these items were studied before high-BAS items. These findings are interpreted as resulting from misbinding of source details at encoding which can be explained by the activation-monitoring theory of illusory recollection.

Regional-scale migrations and habitat use of juvenile lemon sharks (Negaprion brevirostris) in the US South Atlantic.

Resolving the geographic extent and timing of coastal shark migrations, as well as their environmental cues, is essential for refining shark management strategies in anticipation of increasing anthropogenic stressors to coastal ecosystems. We employed a regional-scale passive acoustic telemetry array encompassing 300 km of the east Florida coast to assess what factors influence site fidelity of juvenile lemon sharks (Negaprion brevirostris) to an exposed coastal nursery at Cape Canaveral, and to document the timing and rate of their seasonal migrations. Movements of 54 juvenile lemon sharks were monitored for three years with individuals tracked for up to 751 days. While most sharks demonstrated site fidelity to the Cape Canaveral region December through February under typical winter water temperatures, historically extreme declines in ocean temperature were accompanied by rapid and often temporary, southward displacements of up to 190 km along the Florida east coast. From late February through April each year, most sharks initiated a northward migration at speeds of up to 64 km day(-1) with several individuals then detected in compatible estuarine telemetry arrays in Georgia and South Carolina up to 472 km from release locations. Nineteen sharks returned for a second or even third consecutive winter, thus demonstrating strong seasonal philopatry to the Cape Canaveral region. The long distance movements and habitat associations of immature lemon sharks along the US southeast coast contrast sharply with the natal site fidelity observed in this species at other sites in the western Atlantic Ocean. These findings validate the existing multi-state management strategies now in place. Results also affirm the value of collaborative passive arrays for resolving seasonal movements and habitat preferences of migratory coastal shark species not easily studied with other tagging techniques.

Long-term natal site-fidelity by immature lemon sharks (Negaprion brevirostris) at a subtropical island.

Although many sharks begin their life confined in nursery habitats, it is unknown how rapidly they disperse away from their natal area once they leave the nursery. We examine this issue in immature lemon sharks (Negaprion brevirostris) from the time they leave the nursery (approximately age 3) at a subtropical island (Bimini, Bahamas), through to the onset of sexual maturity (approximately age 12). From 1995 to 2007 we tagged and genotyped a large fraction of the nursery-bound sharks at this location (0-3 years of age, N = 1776 individuals). From 2003 to 2007 we sampled immature sharks aged from 3 to 11 years (N = 150) living around the island and used physical/genetic tag recaptures coupled with kinship analysis to determine whether or not each of these 'large immature sharks' was locally born. We show that many island-born lemon sharks remain close to their natal area for long periods (years) after leaving the nursery; more than half of the sampled sharks up to 135 cm total length ( approximately 6 years old) were locally born. The fraction of locally born sharks gradually declined with increasing shark size, indicating that dispersal is relatively slow and does not primarily occur after sharks reach a threshold size. Local conservation measures (e.g. localized fishery closures, marine protected areas) can therefore help protect island-born lemon sharks even after they leave the nursery habitat.

Biotic and abiotic factors affect the nest environment of embryonic leatherback turtles, Dermochelys coriacea.

Clutches of leatherback turtles, Dermochelys coriacea, have lower hatching success than those of other sea turtles, but causes of high embryonic mortality are unknown. We measured characteristics of clutches along with spatial and temporal changes in PO(2) and temperature during incubation to determine the extent to which they affected the developmental environment of leatherback embryos. Minimum PO(2) in nests decreased as both the total number and mass of metabolizing embryos increased. Increases in both the number and mass of metabolizing embryos caused an increase in maximum nest temperature. However, neither PO(2) nor temperature was correlated with hatching success. Our measurements of relatively high nest PO(2) (lowest 17.1 kPa or 16.9% O(2)) indicate that hypoxia apparently does not cause the low hatching success of leatherback clutches. Oxygen partial pressure increased and temperature decreased from the center toward the periphery of leatherback nests. We inferred from these measurements that positions of eggs within nests vary in quality and potentially affect overall developmental success of entire clutches. The large metabolic mass of leatherback clutches and limits to gas flux imposed by the sand create a situation in which leatherback embryos collectively affect their own environment.