Effective size closely approximates the census size in the heavily exploited western Atlantic population of the sandbar shark, Carcharhinus plumbeus

The sandbar shark, Carcharhinus plumbeus, is a long-lived species with low lifetime fecundity that is heavily fished in the western North Atlantic. Inshore nursery grounds increase survivorship of sandbar shark pups and the principal nurseries are in the mid-Atlantic region. We calculated effective number of breeders (N_b) and effective population size (N_e) for adults utilizing the nursery grounds of the Delaware Bay and the Eastern Shore of Virginia by genotyping 902 animals across five cohorts at eight microsatellite loci. Estimates of N_b and N_e were compared to estimates of census size (N_c) of cohorts obtained from Delaware Bay. The estimated N_e/N_c and N_b/N_c ratios were 0.45 or higher whether the Delaware Bay cohorts were considered as distinct year classes or combined. This is in contrast to estimated N_e/N_c ratios in other exploited marine fishes, which are several orders of magnitude smaller. Instead, the N_e/N_c ratio of sandbar sharks is similar to that found in marine and terrestrial mammals.     

The breeding biology of lemon sharks at a tropical nursery lagoon

Surprisingly little is known about the reproductive behaviour and breeding biology of most shark species, especially in natural populations. Here, we characterize reproductive patterns and use of a natal nursery at Bimini, Bahamas by lemon sharks, Negaprion brevirostris. We systematically and exhaustively sampled young lemon sharks at Bimini annually from 1995 to 2000 and opportunistically sampled adults over the same period. Out of the 897 young sharks sampled, 119 could be assigned to five sampled mothers using microsatellite genotyping. Reproductive females showed strong philopatry to the nursery, returning to Bimini every two years to give birth. Each of these females may rely entirely on the Bimini nursery for recruitment. The protection of known nursery grounds should therefore figure prominently in conservation efforts for large coastal shark species. The reconstruction of paternal genotypes indicates that litters are sired by multiple males, and females mate with different males nearly every breeding cycle. The ubiquitous polyandry reported here raises the possibility that genetic incompatibility and post-copulatory paternity-biasing mechanisms may operate in viviparous sharks.     

Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years

We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out‐migrating smolt and post‐spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (N_b) and the generational effective population size (N_e) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed N_e estimates, suggesting that mature male parr are significantly increasing N_b and N_e over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.     

Reconstruction of parental microsatellite genotypes reveals female polyandry and philopatry in the lemon shark, Negaprion brevirostris

Because sharks possess an unusual suite of reproductive characteristics, including internal fertilization, sperm storage, relatively low fecundity, and reproductive modes that range from oviparity to viviparity, they can provide important insight into the evolution of mating systems and sexual selection. Yet, to date, few studies have characterized behavioral and genetic mating systems in natural populations of sharks or other elasmobranchs. In this study, highly polymorphic microsatellite loci were used to examine breeding biology of a large coastal shark, the lemon shark, Negaprion brevirostris, at a tropical lagoon nursery. Over six years, 910 lemon sharks were sampled and genotyped. Young were assigned into sibling groups that were then used to reconstruct genotypes of unsampled adults. We assigned 707 of 735 young sharks to one of 45 female genotypes (96.2%), and 485 (66.0%) were assigned to a male genotype. Adult female sharks consistently returned to Bimini on a biennial cycle to give birth. Over 86% of litters had multiple sires. Such high levels of polyandry raise the possibility that polyandry evolved in viviparous sharks to reduce genetic incompatibilities between mother and embryos. We did not find a relationship between relatedness of mates and the number of offspring produced, indicating that inbreeding avoidance was probably not driving pre- or postcopulatory mate choice. Adult male sharks rarely sired more than one litter at Bimini and may mate over a broader geographic area.     

A genetic assessment of polyandry and breeding-site fidelity in lemon sharks

We here employ 11 microsatellite markers and recently developed litter reconstruction methods to infer mating system parameters (i.e. polyandry and breeding-site fidelity) at a lemon shark nursery site in Marquesas Key, Florida. Four hundred and eight juvenile or subadult sharks were genotyped over eight complete breeding seasons. Using this information, we were able to infer family structure, as well as fully or partially reconstruct genotypes of 46 mothers and 163 fathers. Multiple litter reconstruction methods were used, and novel simulations helped define apparent bias and precision of at least some mating system parameters. For Marquesas Key, we find that adult female lemon sharks display high levels of polyandry (81% of all litters sampled) and stronger fidelity to the nursery site than do males. Indeed, few male sharks sired offspring from more than one litter during the course of the study. These findings were quite similar to previous results from another lemon shark nursery site (Bimini, Bahamas), suggesting conserved mating system parameters despite significant variation in early life-history traits (i.e. body size and growth) among sites. The finding of at least some site fidelity in females also supports the need for careful conservation of each nursery.     

Effects of large-scale anthropogenic development on juvenile lemon shark (Negaprion brevirostris) populations of Bimini, Bahamas

The waters around Bimini (25° 43.70′ N, 79° 18.00′ W) provide an ideal nursery location for juvenile lemon sharks, Negaprion brevirostris, but this habitat is threatened by the development of a large resort. Since 1999 the North Sound (NS) has been subjected to intermittent periods of dredging, the most intensive of which was in March 2001. Possible effects from the development up to June 2006 were investigated by: comparing growth rates of juvenile lemon sharks in the NS, Sharkland (SL) and South Bimini (SB) nurseries between 1995-2005 using before-after, control-impact (BACI) analysis; analyzing survival of juvenile lemon sharks in the NS and SL between 1995–2006; and by comparing habitat structures in the NS and SB nurseries in 2003 and 2005. BACI analysis detected no statistically significant difference between the growth rates of juvenile lemon sharks in the three nurseries before and after the impact date of March 2001. However, a reduction in the survival rate of juvenile lemon sharks in the NS after March 2001 was statistically significant, including a 23.5% decline in first-year survival. Habitat structure of the NS in 2003 and 2005 also varied with the mean percentage cover of the seagrass Thalassia testudinum declining by 17.7% since 2003. Our results indicate a correlation between the development thus far and a decline in the survival rates of juvenile lemon sharks and changes in the habitat structure of the NS. To elucidate further information regarding potential effects of the resort development on juvenile lemon sharks in the NS nursery, we suggest several future research directions.     

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 (∼ age 3) at a subtropical island (Bimini, Bahamas), through to the onset of sexual maturity (∼ 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 (∼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.     

EVOLUTIONARY POTENTIAL OF A LARGE MARINE VERTEBRATE: QUANTITATIVE GENETIC PARAMETERS IN A WILD POPULATION

Estimating quantitative genetic parameters ideally takes place in natural populations, but relatively few studies have overcome the inherent logistical difficulties. For this reason, no estimates currently exist for the genetic basis of life-history traits in natural populations of large marine vertebrates. And yet such estimates are likely to be important given the exposure of this taxon to changing selection pressures, and the relevance of life-history traits to population productivity. We report such estimates from a long-term (1995–2007) study of lemon sharks ( Negaprion brevirostris ) conducted at Bimini, Bahamas. We obtained these estimates by genetically reconstructing a population pedigree (117 dams, 487 sires, and 1351 offspring) and then using an "animal model" approach to estimate quantitative genetic parameters. We find significant additive genetic (co)variance, and hence moderate heritability, for juvenile length and mass. We also find substantial maternal effects for these traits at age-0, but not age-1, confirming that genotype–phenotype interactions between mother and offspring are strongest at birth; although these effects could not be parsed into their genetic and nongenetic components. Our results suggest that human-imposed selection pressures (e.g., size-selective harvesting) might impose noteworthy evolutionary change even in large marine vertebrates. We therefore use our findings to explain how maternal effects may sometimes promote maladaptive juvenile traits, and how lemon sharks at different nursery sites may show "constrained local adaptation." We also show how single-generation pedigrees, and even simple marker-based regression methods, can provide accurate estimates of quantitative genetic parameters in at least some natural systems.     

INTERMITTENT BREEDING AND CONSTRAINTS ON LITTER SIZE: CONSEQUENCES FOR EFFECTIVE POPULATION SIZE PER GENERATION (Ne) AND PER REPRODUCTIVE CYCLE (Nb)

In iteroparous species, it is easier to estimate N_b (effective number of breeders in one reproductive cycle) than N_e (effective population size per generation). N_b can be used as a proxy for N_e and also can provide crucial insights into eco‐evolutionary processes that occur during reproduction. We used analytical and numerical methods to evaluate effects of intermittent breeding and litter/clutch size on inbreeding N_b and N_e. Fixed or random litter sizes ≥ 3 have little effect on either effective‐size parameter; however, in species (e.g., many large mammals) in which females can produce only one offspring per cycle, female N_b = ∞ and overall N_b = 4N_b(male). Intermittent breeding reduces the pool of female breeders, which reduces both female and overall N_b; reductions are larger in high‐fecundity species with high juvenile mortality and increase when multiple reproductive cycles are skipped. Simulated data for six model species showed that both intermittent breeding and litter‐size constraints increase N_e, but only slightly. We show how to quantitatively account for these effects, which are important to consider when (1) using N_b to estimate N_e, or (2) drawing inferences about male reproductive success based on estimates of female N_b.     

Homing ability of young lemon sharks, <Emphasis Type="Italic">Negaprion brevirostris</Emphasis>

Synopsis We carried out the first experimental study testing an elasmobranchs ability to return home. We displaced juvenile lemon sharks,Negaprion brevirostris, 4–16 km from their observed home ranges at Bimini Islands, Bahamas during daylight and at night. We tracked all sharks except one back to the Bimini Islands and most returned to their home ranges observed before displacement. Even sharks displaced to a site closer to another island with suitable habitat for young lemon sharks returned to their home ranges at Bimini Islands. Sharks displayed a preferred compass direction (PCD) toward the east as their first swimming direction after release, suggesting an innate sense of direction. This bearing was followed shortly afterwards by a home-oriented direction. Swimming speeds prior to reaching shore were approximately twice as fast than the usual cruising speed reported for juvenile lemon sharks. The return of young (0–2 years), inexperienced sharks to their original home range indicate high site fidelity and an ability to home.     

salmonnb: a program for computing cohort‐specific effective population sizes (Nb) in Pacific salmon and other semelparous species using the temporal method

We describe a new method and a computer program salmonn b to calculate the effective number of breeders (N_b) per year in semelparous species with variable age at maturity. The existing temporal method for the ‘salmon’ life history produces an estimate of the harmonic mean N_b in the two sampled years. salmonn b reads genotypic data in standard formats and computes yearly N_b values by combining information from pairwise comparisons of samples taken in 3 or more years. Simulations show that the new method produces unbiased estimates of yearly N_b, and precision is inversely proportional to true effective size.     

A comparison of single‐sample effective size estimators using empirical toad (Bufo calamita) population data: genetic compensation and population size‐genetic diversity correlations

The accuracy and precision of four single‐sample estimators of effective population size, N_e (heterozygote excess, linkage disequilibrium, Bayesian partial likelihood and sibship analysis) were compared using empirical data (microsatellite genotypes) from multiple natterjack toad (Bufo calamita) populations in Britain (n = 16) and elsewhere in Europe (n = 10). Census size data were available for the British populations. Because toads have overlapping generations, all of these methods estimated the number of effective breeders N_b rather than N_e. The heterozygote excess method only provided results, without confidence limits, for nine of the British populations. Linkage disequilibrium gave estimates for 10 British populations, but only six had finite confidence limits. The Bayesian and sibship methods both produced estimates with finite confidence limits for all the populations. Although the Bayesian method was the most precise, on most criteria (insensitivity to locus number, correlation with other effective and census size estimates and correlation with genetic diversity) the sibship method performed best. The results also provided evidence of genetic compensation in natterjack toads, and highlighted how the relationship between effective size and genetic diversity can vary as a function of geographical scale.     

Ontogenetic diet shifts and prey selection in nursery bound lemon sharks, Negaprion brevirostris, indicate a flexible foraging tactic

Ontogenetic variations in shark diet are often qualitatively inferred from dietary analysis and hindered by high levels of unidentified prey or small sample sizes. This study focused on nursery bound lemon sharks (Negaprion brevirostris, n?=?396), enabling some control over the confounding variables of prey choice associated with ontogeny. Nursery bound lemon sharks exhibited weak ontogenetic variation in dietary composition with high levels of dietary overlap. Variation in prey preference of lemon sharks with ontogeny was complex, but revealed a continuous shift from predominantly opportunistic benthic foraging as neonates to more selective piscivory with increasing shark size while in the nursery. Lemon sharks demonstrated a discrete ontogenetic shift in the number of prey consumed and stomach content weight (Kruskal-Wallis tests p?<?0.01), as well as prey size (ANOVA, p?<?0.001). All sizes of sharks exhibited positive size selection of prey (Mann?CWhitney U tests, p?<?0.01). However, the lack of size preference by all but the largest lemon sharks for their major prey (yellowfin mojarra, Gerres cinereus), suggests neonate sharks, while capable of occasionally foraging on large prey, are relatively inept opportunistic foragers. This was evident in high diet breadth, low diversity of consumed prey and lower trophic level than larger sharks. This study represents the first quantitative analysis of ontogenetic variation in prey preference and size selection in sharks, indicating a flexible foraging tactic in lemon sharks and the importance of hunting ability and predator size in prey choice.     

Genetic substructure and admixture as important factors in linkage disequilibrium‐based estimation of effective number of breeders in recovering wildlife populations

The number of effective breeders (N_b) and effective population size (N_e) are population parameters reflective of evolutionary potential, susceptibility to stochasticity, and viability. We have estimated these parameters using the linkage disequilibrium‐based approach with LDNE through the latest phase of population recovery of the brown bears (Ursus arctos) in Finland (1993–2010; N = 621). This phase of the recovery was recently documented to be associated with major changes in genetic composition. In particular, differentiation between the northern and the southern genetic cluster declined rapidly within 1.5 generations. Based on this, we have studied effects of the changing genetic structure on N_b and N_e, by comparing estimates for whole Finland with the estimates for the two genetic clusters. We expected a potentially strong relationship between estimate sizes and genetic differentiation, which should disappear as the population recovers and clusters merge. Consistent with this, our estimates for whole Finland were lower than the sum of the estimates of the two genetic clusters and both approaches produced similar estimates in the end. Notably, we also found that admixed genotypes strongly increased the estimates. In all analyses, our estimates for N_e were larger than N_b and likely reflective for brown bears of the larger region of Finland and northwestern Russia. Conclusively, we find that neglecting genetic substructure may lead to a massive underestimation of N_b and N_e. Our results also suggest the need for further empirical analysis focusing on individuals with admixed genotypes and their potential high influence on N_b and N_e.     

Review of Elasmobranch Behavioral Studies Using Ultrasonic Telemetry with Special Reference to the Lemon Shark, Negaprion Brevirostris, Around Bimini Islands, Bahamas

A review of past behavioral ultrasonic telemetry studies of sharks and rays is presented together with previously unpublished material on the behavior of the lemon shark, Negaprion brevirostris, around the Bimini Islands, Bahamas. The review, focusing on movement behaviors of 20 shark and three ray species, reveals that elasmobranchs exhibit a variety of temporal and spatial patterns in terms of rates-of-movement and vertical as well as horizontal migrations. The lack of an apparent pattern in a few species is probably attributable to the scarcity of tracking data. Movements are probably governed by several factors, some still not studied, but data show that food, water temperature, bottom type, and magnetic gradient play major roles in a shark's decision of where and when to swim. A few species exhibit differences in behavior between groups of sharks within the same geographical area. This interesting finding warrants further research to evaluate the causes of these apparent differences and whether these groups constitute different subpopulations of the same species. The lack of telemetry data on batoids and some orders of sharks must be addressed before we can gain a more comprehensive understanding of the behavior of elasmobranch fishes. Previously unpublished data from 47 smaller and 38 larger juvenile lemon sharks, collected over the decade 1988–1998, provide new results on movement patterns, habitat selection, activity rhythms, swimming speed, rate-of-movement, and homing behavior. From these results we conclude that the lemon shark is an active predator with a strong, apparently innate homing mechanism. This species shows ontogenetic differences in habitat selection and behavior, as well as differences in movements between groups of individuals within the same area. We suggest three hypotheses for future research on related topics that will help to understand the enigmatic behavior of sharks.     

Evoked Potential Audiograms of the Nurse Shark (Ginglymostoma cirratum) and the Yellow Stingray (Urobatis jamaicensis)

The hearing thresholds of the nurse shark, Ginglymostoma cirratum, and the yellow stingray, Urobatis jamaicensis, were measured using auditory evoked potentials (AEP). Stimuli were calibrated using a pressure-velocity probe so that the acoustic field could be completely characterized. The results show similar hearing thresholds for both species and similar hearing thresholds to previously measured audiograms for the lemon shark, Negaprion brevirostris, and the horn shark, Heterodontis francisi. All of these audiograms suggest poor hearing abilities, raising questions about field studies showing attraction of sharks to acoustic signals. By extrapolating the particle acceleration thresholds into estimates of their equivalent far-field sound pressure levels, it appears that these sharks cannot likely detect most of the sounds that have attracted sharks in the field.     

Spatial ecology of juvenile lemon sharks (<Emphasis Type="Italic">Negaprion brevirostris</Emphasis>) in tidal creeks and coastal waters of Eleuthera,The Bahamas

Fisheries exploitation and habitat alteration are threatening lemon shark (Negaprion bevirostris) populations because they use nearshore regions as nursery sites. As such, there is a need for information on the spatial ecology of juvenile lemon sharks to identify critical habitats that require protection, as well as to understand their basic ecology. The purpose of this study was to determine the habitat preferences and movement patterns of juvenile lemon sharks along a sub-section of coastline characterized by coastal flats and tidal creeks of Eleuthera, The Bahamas. Eleven juvenile lemon sharks (766 ± 127 mm total length; mean±SD) were captured from various tidal creeks within the 23 km study area and were surgically implanted with acoustic transmitters. A series of 27 hydrophone receivers acted as a passive monitoring array to detect tagged individuals as they moved among habitats. Findings suggest that juvenile lemon sharks tagged in this study prefer shallow water habitats within tidal creeks, and typically display high site fidelity with occasional forays to alternate habitats or creeks. In fact, more than 90% of tagged lemon sharks had the greatest percentage of detections located at a receiver at or close to the location where they were tagged. There was no evidence of differences in diel or seasonal movement and habitat use. Knowledge gained from this study will be useful for directing future conservation and management strategies including coastal development plans and marine protected areas.     

Interannual variation in effective number of breeders and estimation of effective population size in long‐lived iteroparous lake sturgeon (Acipenser fulvescens)

Quantifying interannual variation in effective adult breeding number (N_b) and relationships between N_b, effective population size (N_e), adult census size (N) and population demographic characteristics are important to predict genetic changes in populations of conservation concern. Such relationships are rarely available for long‐lived iteroparous species like lake sturgeon (Acipenser fulvescens). We estimated annual N_b and generational N_e using genotypes from 12 microsatellite loci for lake sturgeon adults (n = 796) captured during ten spawning seasons and offspring (n = 3925) collected during larval dispersal in a closed population over 8 years. Inbreeding and variance N_b estimated using mean and variance in individual reproductive success derived from genetically identified parentage and using linkage disequilibrium (LD) were similar within and among years (interannual range of N_b across estimators: 41–205). Variance in reproductive success and unequal sex ratios reduced N_b relative to N on average 36.8% and 16.3%, respectively. Interannual variation in N_b/N ratios (0.27–0.86) resulted from stable N and low standardized variance in reproductive success due to high proportions of adults breeding and the species' polygamous mating system, despite a 40‐fold difference in annual larval production across years (437–16 417). Results indicated environmental conditions and features of the species' reproductive ecology interact to affect demographic parameters and N_b/N. Estimates of N_e based on three single‐sample estimators, including LD, approximate Bayesian computation and sibship assignment, were similar to annual estimates of N_b. Findings have important implications concerning applications of genetic monitoring in conservation planning for lake sturgeon and other species with similar life histories and mating systems.     

Spatial and ontogenetic variation in growth of nursery-bound juvenile lemon sharks, <Emphasis Type="Italic">Negaprion brevirostris</Emphasis>: a comparison of two age-assigning techniques

Synopsis We compared growth rates of the lemon shark, Negaprion brevirostris, from Bimini, Bahamas and the Marquesas Keys (MK), Florida using data obtained in a multi-year annual census. We marked new neonate and juvenile sharks with unique electronic identity tags in Bimini and in the MK we tagged neonate and juvenile sharks. Sharks were tagged with tiny, subcutaneous transponders, a type of tagging thought to cause little, if any disruption to normal growth patterns when compared to conventional external tagging. Within the first 2 years of this project, no age data were recorded for sharks caught for the first time in Bimini. Therefore, we applied and tested two methods of age analysis: (1) a modified minimum convex polygon method and (2) a new age-assigning method, the cut-off technique. The cut-off technique proved to be the more suitable one, enabling us to identify the age of 134 of the 642 previously unknown aged sharks. This maximised the usable growth data included in our analysis. Annual absolute growth rates of juvenile, nursery-bound lemon sharks were almost constant for the two Bimini nurseries and can be best described by a simple linear model (growth data was only available for age-0 sharks in the MK). Annual absolute growth for age-0 sharks was much greater in the MK than in either the North Sound (NS) and Shark Land (SL) at Bimini. Growth of SL sharks was significantly faster during the first 2 years of life than of the sharks in the NS population. However, in MK, only growth in the first year was considered to be reliably estimated due to low recapture rates. Analyses indicated no significant differences in growth rates between males and females for any area.This revised version was published online in April 2005 with corrections to the fourth authors email address and affiliation.     

Population genetics of the American eel (Anguilla rostrata): FST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species

We performed population genetic analyses on the American eel (Anguilla rostrata) with three main objectives. First, we conducted the most comprehensive analysis of neutral genetic population structure to date to revisit the null hypothesis of panmixia in this species. Second, we used this data to provide the first estimates of contemporary effective population size (N_e) and to document temporal variation in effective number of breeders (N_b) in American eel. Third, we tested for statistical associations between temporal variation in the North Atlantic Oscillation (NAO), the effective number of breeders and two indices of recruit abundance. A total of 2142 eels from 32 sampling locations were genotyped with 18 microsatellite loci. All measures of differentiation were essentially zero, and no evidence for significant spatial or temporal genetic differentiation was found. The panmixia hypothesis should thus be accepted for this species. N_b estimates varied by a factor of 23 among 12 cohorts, from 473 to 10 999. The effective population size N_e was estimated at 10 532 (95% CI, 9312–11 752). This study also showed that genetically based demographic indices, namely N_b and allelic richness (Ar), can be used as surrogates for the abundance of breeders and recruits, which were both shown to be positively influenced by variation during high (positive) NAO phases. Thus, long‐term genetic monitoring of American glass eels at several sites along the North American Atlantic coast would represent a powerful and efficient complement to census monitoring to track demographic fluctuations and better understand their causes.