Evaluating sources of bias in pedigree-based estimates of breeding population size.

Applications of genetic-based estimates of population size are expanding, especially for species for which traditional demographic estimation methods are intractable due to the rarity of adult encounters. Estimates of breeding population size (NS ) are particularly amenable to genetic-based approaches as the parameter can be estimated using pedigrees reconstructed from genetic data gathered from discrete juvenile cohorts, therefore eliminating the need to sample adults in the population. However, a critical evaluation of how genotyping and sampling effort influence bias in pedigree reconstruction, and how these biases subsequently influence estimates of NS , is needed to evaluate the efficacy of the approach under a range of scenarios. We simulated a model system to understand the interactive effects of genotyping and sampling effort on error in genetic pedigrees reconstructed from the program COLONY. We then evaluated how errors in pedigree reconstruction influenced bias and precision in estimates of NS using three different rarefaction estimators. Results indicated that pedigree error can be minimal when adequate genetic data are available, such as when juvenile sample sizes are large and/or individuals are genotyped at many informative loci. However, even in cases for which data are limited, using results of the simulation analysis to understand the magnitude and sources of bias in reconstructed pedigrees can still be informative when estimating NS . We applied results of the simulation analysis to evaluate N ̂ $$ \hat{N} $$ S for a population of federally endangered Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) in the Delaware River, USA. Our results indicated that NS is likely to be three orders of magnitude lower compared with historic breeding population sizes, which is a considerable advancement in our understanding of the population status of Atlantic sturgeon in the Delaware River. Our analyses are broadly applicable in the design and interpretation of studies seeking to estimate NS and can help to guide conservation decisions when ecological uncertainty is high. The utility of these results is expected to grow as rapid advances in genetic technologies increase the popularity of genetic population monitoring and estimation.

Baseline Health and Nutritional Parameters of Wild Sand Tigers Sampled in Delaware Bay.

Species-specific hematological reference values are essential for diagnosis and treatment of disease and maintaining overall health of animals. This information is lacking for many species of elasmobranchs maintained in zoos and aquaria, thus reducing the effectiveness of care for these animals. Descriptive statistics and reference intervals were calculated for hematocrit and complete blood cell counts, biochemistry and protein electrophoresis parameters, trace minerals, vitamins, heavy metals, reproductive hormones, and fatty acids in the blood of 153 wild Sand Tigers Carcharias taurus of both sexes and a range of sizes caught in Delaware Bay (Delaware, USA). Mean hematocrit, total white blood cell counts, lymphocyte differentials, glucose, phosphorus, amylase, and aspartate aminotransferase levels were significantly higher in juveniles than in adults. Levels of estradiol, progesterone, testosterone, and differences in selenium and eicosapentaenoic acid (a polyunsaturated fatty acid) between males and females suggest that they are important parameters for improving Sand Tiger breeding success in managed care. Finally, blood metal levels for arsenic, cadmium, lead, and mercury suggest low levels of contaminant exposure for Sand Tigers during their summer residence in Delaware Bay. The results of this study provide baseline health parameters for wild Sand Tigers that will aid in effective maintenance of aquarium animals and contribute to a greater understanding of the biology of these sharks and efforts to accomplish sustainable management of their populations.

A satellite-based mobile warning system to reduce interactions with an endangered species.

Earth-observing satellites are a major research tool for spatially explicit ecosystem nowcasting and forecasting. However, there are practical challenges when integrating satellite data into usable real-time products for stakeholders. The need of forecast immediacy and accuracy means that forecast systems must account for missing data and data latency while delivering a timely, accurate, and actionable product to stakeholders. This is especially true for species that have legal protection. Acipenser oxyrinchus oxyrinchus (Atlantic sturgeon) were listed under the United States Endangered Species Act in 2012, which triggered immediate management action to foster population recovery and increase conservation measures. Building upon an existing research occurrence model, we developed an Atlantic sturgeon forecast system in the Delaware Bay, USA. To overcome missing satellite data due to clouds and produce a 3-d forecast of ocean conditions, we implemented data interpolating empirical orthogonal functions (DINEOF) on daily observed satellite data. We applied the Atlantic sturgeon research model to the DINEOF output and found that it correctly predicted Atlantic sturgeon telemetry occurrences over 90% of the time within a 3-d forecast. A similar framework has been utilized to forecast harmful algal blooms, but to our knowledge, this is the first time a species distribution model has been applied to DINEOF gap-filled data to produce a forecast product for fishes. To implement this product into an applied management setting, we worked with state and federal organizations to develop real-time and forecasted risk maps in the Delaware River Estuary for both state-level managers and commercial fishers. An automated system creates and distributes these risk maps to subscribers' mobile devices, highlighting areas that should be avoided to reduce interactions. Additionally, an interactive web interface allows users to plot historic, current, future, and climatological risk maps as well as the underlying model output of Atlantic sturgeon occurrence. The mobile system and web tool provide both stakeholders and managers real-time access to estimated occurrences of Atlantic sturgeon, enabling conservation planning and informing fisher behavior to reduce interactions with this endangered species while minimizing impacts to fisheries and other projects.

Multiple spawning run contingents and population consequences in migratory striped bass Morone saxatilis.

Multiple spawning run contingents within the same population can experience varying demographic fates that stabilize populations through the portfolio effect. Multiple spawning run contingents (aka run timing groups) are reported here for the first time for striped bass, an economically important coastal species, which is well known for plastic estuarine and shelf migration behaviors. Adult Hudson River Estuary striped bass (n = 66) were tagged and tracked with acoustic transmitters from two known spawning reaches separated by 90 km. Biotelemetry recaptures for two years demonstrated that each river reach was associated with separate contingents. Time series of individual spawning phenologies were examined via nonparametric dynamic time warping and revealed two dominant time series centroids, each associated with a separate spawning reach. The lower spawning reach contingent occurred earlier than the higher reach contingent in 2017 but not in 2018. The majority (89%) of returning adults in 2018 showed the same contingent behaviors exhibited in 2017. Spawning contingents may have been cued differently by temperatures, where warming lagged 1-week at the higher reach in comparison to the lower reach. The two contingents exhibited similar Atlantic shelf migration patterns with strong summer fidelity to Massachusetts Bay and winter migrations to the southern US Mid-Atlantic Bight. Still, in 2017, differing times of departure into nearby shelf waters likely caused the early lower reach contingent to experience substantially higher mortality than the later upper reach contingent. Anecdotal evidence suggests that higher fishing effort is exerted on the early-departing individuals as they first enter shelf fisheries. Thus, as in salmon, multiple spawning units can lead to differential demographic outcomes, potentially stabilizing overall population dynamics.

Comparative migration ecology of striped bass and Atlantic sturgeon in the US Southern mid-Atlantic bight flyway.

Seasonal migrations are key to the production and persistence of marine fish populations but movements within shelf migration corridors or, "flyways", are poorly known. Atlantic sturgeon and striped bass, two critical anadromous species, are known for their extensive migrations along the US Mid-Atlantic Bight. Seasonal patterns of habitat selection have been described within spawning rivers, estuaries,and shelf foraging habitats, but information on the location and timing of key coastal migrations is limited. Using a gradient-based array of acoustic telemetry receivers, we compared the seasonal incidence and movement behavior of these species in the near-shelf region of Maryland, USA. Atlantic sturgeon incidence was highest in the spring and fall and tended to be biased toward shallow regions, while striped bass had increased presence during spring and winter months and selected deeper waters. Incidence was transient (mean = ~2 d) for both species with a pattern of increased residency (>2 d) during autumn and winter, particularly for striped bass, with many individuals exhibiting prolonged presence on the outer shelf during winter. Flyways also differed spatially between northern and southern migrations for both species and were related to temperature: striped bass were more likely to occur in cool conditions while Atlantic sturgeon preferred warmer temperatures. Observed timing and spatial distribution within the Mid-Atlantic flyway were dynamic between years and sensitive to climate variables. As shelf ecosystems come under increasing maritime development, gridded telemetry designs represent a feasible approach to provide impact responses within key marine flyways like those that occur within the US Mid-Atlantic Bight.

Differential migration in Chesapeake Bay striped bass.

Differential migration-increased migration propensity with increasing individual size-is common in migratory species. Like other forms of partial migration, it provides spatial buffering against regional differences in habitat quality and sources of mortality. We investigated differential migration and its consequences to survival and reproductive patterns in striped bass, a species with well-known plasticity in migration behaviors. A size-stratified sample of Potomac River (Chesapeake Bay) Morone saxatilis striped bass was implanted with acoustic transmitters and their subsequent coastal shelf migrations recorded over a 4-yr period by telemetry receivers throughout the Mid-Atlantic Bight and Southern New England. A generalized linear mixed model predicted that ≥ 50% of both males and females depart the Chesapeake Bay at large sizes >80 cm total length. Egressing striped bass exited through both the Chesapeake Bay mouth and Delaware Bay (via the Chesapeake and Delaware Canal), favoring the former. All large fish migrated to Massachusetts shelf waters and in subsequent years repeatedly returned to regions within Massachusetts and Cape Cod Bays. Within this dominant behavior, minority behaviors included straying, skipped spawning, and residency by large individuals (those expected to migrate). Analysis of the last day of transmission indicated that small resident striped bass experienced nearly 2-fold higher loss rates (70% yr-1) than coastal shelf emigrants (37% yr-1). The study confirmed expectations for a threshold size at emigration and different mortality levels between Chesapeake Bay (resident) and ocean (migratory) population contingents; and supported the central premise of the current assessment and management framework of a two-contingent population: smaller Chesapeake Bay residents and a larger ocean contingent. An improved understanding of differential migration thus affords an opportunity to specify stock assessments according to different population sub-components, and tailor reference points and control rules between regions and fishing stakeholder groups.

Social Network Analysis Reveals Potential Fission-Fusion Behavior in a Shark.

Complex social networks and behaviors are difficult to observe for free-living marine species, especially those that move great distances. Using implanted acoustic transceivers to study the inter- and intraspecific interactions of sand tiger sharks Carcharias taurus, we observed group behavior that has historically been associated with higher order mammals. We found evidence strongly suggestive of fission-fusion behavior, or changes in group size and composition of sand tigers, related to five behavioral modes (summering, south migration, community bottleneck, dispersal, north migration). Our study shows sexually dimorphic behavior during migration, in addition to presenting evidence of a potential solitary phase for these typically gregarious sharks. Sand tigers spent up to 95 consecutive and 335 cumulative hours together, with the strongest relationships occurring between males. Species that exhibit fission-fusion group dynamics pose a particularly challenging issue for conservation and management because changes in group size and composition affect population estimates and amplify anthropogenic impacts.

Implantation and Recovery of Long-Term Archival Transceivers in a Migratory Shark with High Site Fidelity.

We developed a long-term tagging method that can be used to understand species assemblages and social groupings associated with large marine fishes such as the Sand Tiger shark Carcharias taurus. We deployed internally implanted archival VEMCO Mobile Transceivers (VMTs; VEMCO Ltd. Nova Scotia, Canada) in 20 adult Sand Tigers, of which two tags were successfully recovered (10%). The recovered VMTs recorded 29,646 and 44,210 detections of telemetered animals respectively. To our knowledge, this is the first study to demonstrate a method for long-term (~ 1 year) archival acoustic transceiver tag implantation, retention, and recovery in a highly migratory marine fish. Results show low presumed mortality (n = 1, 5%), high VMT retention, and that non-lethal recovery after almost a year at liberty can be achieved for archival acoustic transceivers. This method can be applied to study the social interactions and behavioral ecology of large marine fishes.

Shifting distributions of adult Atlantic sturgeon amidst post-industrialization and future impacts in the Delaware River: a maximum entropy approach.

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) experienced severe declines due to habitat destruction and overfishing beginning in the late 19(th) century. Subsequent to the boom and bust period of exploitation, there has been minimal fishing pressure and improving habitats. However, lack of recovery led to the 2012 listing of Atlantic sturgeon under the Endangered Species Act. Although habitats may be improving, the availability of high quality spawning habitat, essential for the survival and development of eggs and larvae may still be a limiting factor in the recovery of Atlantic sturgeon. To estimate adult Atlantic sturgeon spatial distributions during riverine occupancy in the Delaware River, we utilized a maximum entropy (MaxEnt) approach along with passive biotelemetry during the likely spawning season. We found that substrate composition and distance from the salt front significantly influenced the locations of adult Atlantic sturgeon in the Delaware River. To broaden the scope of this study we projected our model onto four scenarios depicting varying locations of the salt front in the Delaware River: the contemporary location of the salt front during the likely spawning season, the location of the salt front during the historic fishery in the late 19(th) century, an estimated shift in the salt front by the year 2100 due to climate change, and an extreme drought scenario, similar to that which occurred in the 1960's. The movement of the salt front upstream as a result of dredging and climate change likely eliminated historic spawning habitats and currently threatens areas where Atlantic sturgeon spawning may be taking place. Identifying where suitable spawning substrate and water chemistry intersect with the likely occurrence of adult Atlantic sturgeon in the Delaware River highlights essential spawning habitats, enhancing recovery prospects for this imperiled species.