Age Structure Response of Principal Groundfish to Marine Protected Areas in New England

Atlantic cod (Gadus morhua), yellowtail flounder (Limanda ferruginea), and haddock (Melanogrammus aeglefinnus) were once dominant species in the New England fisheries economy, together accounting for over half of the landings value of groundfish. Over the last several decades, all three species have experienced dramatic shifts in spawning stock biomass (SSB) with current estimates for cod stocks at 3% and 7% of target biomass (Gulf of Maine and Georges Bank stocks, respectively), a strong contrast to haddock stocks that are nearly fully recovered (NEFSC 2014, 2017). As principally demersal species, they are easily targeted by trawl and gillnet, the former representing the majority of landings in New England waters. Now considered a choke species for the entire groundfish fleet, the current state of cod may signal the demise of other fish stocks if management measures are not adjusted. Despite a 2010 shift from input controls to a mixture of input controls (i.e., year-round closures) and output controls (i.e., hard quotas), along with yield-based stock assessment reference points, the outcomes for these key groundfish have been confounding. Some suggest that the failure to account for age structure of populations in management may underplay the value of old fish, those which are generally removed by commercial fishing (Le Bris 2013, Secor 2015, Stige et al. 2017). Age truncation, vulnerability to overoptimistic assessment, and increasing amplitude of climate oscillations all put the recovery of certain species at risk (Berkeley 2004, Pershing et al. 2015). One of the key management changes enacted with the Sustainable Fisheries Act of 1996, was the implementation of year-round closures throughout New England waters. Heralded as a backstop to uncertainty, these temporary Marine Protected Areas impart a conservative management approach with the simple goal of reducing overall mortality. Nearly 25 years after the first areas were closed to fishing, research has been inconclusive about the effects on the groundfish species that they were designed to protect (Murawski et al 2005, Kerr et al 2012). Until now, no study has investigated the effects of these closures on the age structure of these three species. To measure change, I applied three age metrics: mean age, age diversity, and catch-per-unit-effort of age 5+ fish. Together, these three metrics provide measures of change across large spatial and temporal scales. In Chapter 1 of this thesis, I employ a Before-After Control-Impact (BACI) analysis to five year-round fisheries closures in New England. Data was drawn from over 35 years of the New England Fisheries Science Center’s bottom-trawl survey. Using stratified-random and distance-based controls, I employed generalized linear models (GLMs) and hurdle models to define significant changes to groundfish age structure. Further investigations describe the temporal response to closed areas and discuss the different ways that closure effects on age structure can manifest. Results show that in several cases, these closures function to improve age metrics in the species they were designed to protect. Discussion of the magnitude of change and confounding management factors lead to future considerations of spatial management of groundfish. In Chapter 2 of this thesis, I focus on Cashes Ledge Closed Area (CL). Designed to reduce groundfish mortality, its effects on the age structure recovery on Atlantic cod are unclear. Previous work here has shown that in areas where older fish range, adjacent to Essential Fish Habitat (EFH), catch inside closures can produce up to 8 times more old cod (age 5+) than surrounding open areas (Sherwood & Grabowski 2016). While the benefits of protected areas assigned EFH status seem obvious, it is unclear how age structure of the cod population in this area responds across distance and varying habitat. Results on cod from Chapter 1 show limited sampling throughout the closure, particularly over complex bottom that is difficult to trawl. With a survey designed to measure the same age metrics as Chapter 1, I sampled sites using alternate gear types (gillnet and handline) across the entire closure and adjacent fishing grounds to the Northwest. Results showing a significant positive closure effect support those of previous work (Sherwood & Grabowski 2016), but the subtle magnitude of change and results of habitat modeling, reveal that nearly 15 years after the closure was implemented, depth is the major driver of these measured age structure metrics. Highest age structure metrics manifest over habitat characterized by shallow and complex bottom, which serve as havens for a species under serious threat from fishing mortality and climate change. Chapter 1 provides a broad perspective of change over large scales of space and time. Samples are grouped over the entire closures and before-after periods include as many as 25 years of data. Chapter 2 provides a detailed investigation of a single closure over two summer/fall sampling seasons, 15 years after closure. Together these chapters provide perspective on what age structure health looks like and its lasting implications on the future of the groundfish fishery in New England

Advancing acoustic studies of pelagic fish and zooplankton at the western Atlantic-Arctic gateway

The patterns of distribution among fish and zooplankton in the Arctic and their deep ocean habitats remain poorly described. Climatic disruptions to natural variability in temperature, light, and nutrient supply can modify species distributions, impacting the ecosystem at various levels. Across spatial and vertical domains, these environmental factors form complex relationships with species assemblages, which are challenging to measure with conventional sampling methods. Hydroacoustics is a promising approach to studying the distribution of organisms in hard-to-reach ecosystems. This thesis aims to advance new hydroacoustic methodologies for the study of pelagic fish and zooplankton and identify the structural drivers of their communities and distribution along the boundaries of Arctic-Atlantic modulated ecosystems. In my thesis, I used several emerging technologies, including lowered acoustic probes and broadband acoustic measurements, to assess the distributional patterns of pelagic fish and zooplankton at meter-level to ocean basin scales. I found that measurements of lanternfish inhabiting deep-scattering layers require detailed analysis that includes the identification and removal of anomalous signals, which can arise from a combination of physical and biological processes. To deal with this, I introduced a machine learning approach that helps identify anomalous signals and improves the precision of acoustic density measurements. When examining similar lanternfish dominated communities at the basin scale, I report that temperature-driven water mass boundaries act as a barrier to the dispersal of mesopelagic communities at high-latitudes, in both the northern and southern hemispheres. Furthermore, this same boundary appears to impact the vertical distribution of pelagic life, with likely impacts the vertical transport of nutrients and carbon. In the high Arctic, I report mixing processes in glacial fjord ecosystems can impact the vertical distribution of copepods and the morphological patterns of marine snow. This work highlights contrasting conditions outside of two adjacent marine terminating glaciers, which each offer a glimpse of what future Arctic conditions may bring. Overall, my work contributes to a greater understanding of the structural drivers of Arctic pelagic communities and can be used to understand their sensitivities to future change

Evidence of temperature control on mesopelagic fish and zooplankton communities at high latitudes

Across temperate and equatorial oceans, a diverse community of fish and zooplankton occupies the mesopelagic zone, where they are detectable as sound-scattering layers. At high latitudes, extreme day-night light cycles may limit the range of some species, while at lower latitudes communities are structured by dynamic ocean processes, such as temperature. Using acoustic and oceanographic measurements, we demonstrate that latitudinal changes in mesopelagic communities align with polar boundaries defined by deep ocean temperature gradients. At the transition to cold polar water masses we observe abrupt weakening and vertical dispersion of acoustic backscatter of mesopelagic organisms, thereby altering the structure of the mesopelagic zone. In the Canadian Arctic, we used biological sampling to show that this boundary is associated with a significant change in the pelagic fish community structure. Rapid ocean warming projected at mesopelagic depths could shift these boundaries with far-reaching effects on ecosystem function and biogeochemical cycles

Comparing eDNA metabarcoding and conventional pelagic netting to inform biodiversity monitoring in deep ocean environments

The performance of environmental DNA (eDNA) metabarcoding has rarely been evaluated against conventional sampling methods in deep ocean mesopelagic environments. We assessed the biodiversity patterns generated with eDNA and two co-located conventional methods, oblique midwater trawls and vertical multinets, to compare regional and sample-level diversity. We then assessed the concordance of ecological patterns across water column habitats and evaluated how DNA markers and the level of sampling effort influenced the inferred community. We found eDNA metabarcoding characterized regional diversity well, detecting more taxa while identifying similar ecological patterns as conventional samples. Within sampling locations, eDNA metabarcoding rarely detected taxa across more than one replicate. While more taxa were found in eDNA than oblique midwater trawls within sample stations, fewer were found compared to vertical multinets. Our simulations show greater eDNA sampling effort would improve concordance with conventional methods. We also observed that using taxonomic data from multiple markers generated ecological patterns most similar to those observed with conventional methods. Patterns observed with Exact Sequence Variants were more stable across markers suggesting they are more powerful for detecting change. eDNA metabarcoding is a valuable tool for identifying and monitoring biological hotspots but some methodological adjustments are recommended for deep ocean environments

Ecosystem mapping in the Central Arctic Ocean (CAO) during the SAS-Oden expedition

As a result of global warming, the marine ecosystem around the North Pole, the Central Arctic Ocean (CAO), is in fast transition from a permanently to a seasonally ice-covered ocean. The sea-ice loss is expected to enable summer access to the CAO for non-icebreaking ships, including fishery vessels, in the near future1. However, the lack of knowledge on the CAO ecosystem impedes any assessment of the sustainability of potential future fisheries in the CAO. Taking a precautionary approach, the EU and nine countries in October 2018 signed the Agreement to Prevent Unregulated High Seas Fisheries in the Central Arctic Ocean. This agreement entered into force in June 2021 and a.o. requires the establishment of a joint scientific program to improve the understanding of the CAO ecosystem, including mapping and monitoring. To reduce the existing lack of knowledge, 12 scientists from the EFICA Consortium participated, together with 26 other on-board scientists, in sampling and data collection of ecosystem data during the Swedish SAS-Oden expedition in summer 2021. This report describes the field work performed by the EFICA scientists using water-column acoustics, deep-sea optical observations, and fish, zooplankton, sediment otolith and eDNA sampling for targeting fish, zooplankton and mammals. Further ecosystem data (physical, chemical and biological) were collected by the EFICA scientists in collaboration with other scientists on-board. Together with this report, a metadata database containing lists of all collected samples and data that are relevant for future fish-stock modelling and assessment studies was delivered to the European Commission

Bridging the data gaps in the epidemiology of hepatitis C virus infection in Malaysia using multi-parameter evidence synthesis

BACKGROUND: Collecting adequate information on key epidemiological indicators is a prerequisite to informing a public health response to reduce the impact of hepatitis C virus (HCV) infection in Malaysia. Our goal was to overcome the acute data shortage typical of low/middle income countries using statistical modelling to estimate the national HCV prevalence and the distribution over transmission pathways as of the end of 2009. METHODS: Multi-parameter evidence synthesis methods were applied to combine all available relevant data sources - both direct and indirect - that inform the epidemiological parameters of interest. RESULTS: An estimated 454,000 (95% credible interval [CrI]: 392,000 to 535,000) HCV antibody-positive individuals were living in Malaysia in 2009; this represents 2.5% (95% CrI: 2.2-3.0%) of the population aged 15-64 years. Among males of Malay ethnicity, for 77% (95% CrI: 69-85%) the route of probable transmission was active or a previous history of injecting drugs. The corresponding proportions were smaller for male Chinese and Indian/other ethnic groups (40% and 71%, respectively). The estimated prevalence in females of all ethnicities was 1% (95% CrI: 0.6 to 1.4%); 92% (95% CrI: 88 to 95%) of infections were attributable to non-drug injecting routes of transmission. CONCLUSIONS: The prevalent number of persons living with HCV infection in Malaysia is estimated to be very high. Low/middle income countries often lack a comprehensive evidence base; however, evidence synthesis methods can assist in filling the data gaps required for the development of effective policy to address the future public health and economic burden due to HCV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12879-014-0564-6) contains supplementary material, which is available to authorized users

Patient Satisfaction with Primary Care Office-Based Buprenorphine/Naloxone Treatment

BACKGROUND: Factors associated with satisfaction among patients receiving primary care–based buprenorphine/naloxone are unknown. OBJECTIVE: To identify factors related to patient satisfaction in patients receiving primary care–based buprenorphine/naloxone that varied in counseling intensity (20 vs 45 minutes) and office visit frequency (weekly vs thrice weekly). DESIGN AND PARTICIPANTS: One hundred and forty-two opioid-dependent subjects. MEASUREMENTS: Demographics, drug treatment history, and substance use status at baseline and during treatment were collected. The primary outcome was patient satisfaction at 12 weeks. RESULTS: Patients’ mean overall satisfaction score was 4.4 (out of 5). Patients were most satisfied with the medication and ancillary services and indicated strong willingness to refer a substance-abusing friend for the same treatment. Patients were least satisfied with their interactions with other opioid-dependent patients, referrals to Narcotics Anonymous, and the inconvenience of the treatment location. Female gender (β = .17, P = .04) and non-White ethnicity/race (β = .17, P = .04) independently predicted patient satisfaction. Patients who received briefer counseling and buprenorphine/naloxone dispensed weekly had greater satisfaction than those whose medication was dispensed thrice weekly (mean difference 4.9, 95% confidence interval 0.08 to 9.80, P = .03). CONCLUSIONS: Patients are satisfied with primary care office-based buprenorphine/naloxone. Providers should consider the identified barriers to patient satisfaction

Primary Care Office-based Buprenorphine Treatment: Comparison of Heroin and Prescription Opioid Dependent Patients

BACKGROUND: Prescription opioid dependence is increasing, but treatment outcomes with office-based buprenorphine/naloxone among these patients have not been described. METHODS: We compared demographic, clinical characteristics and treatment outcomes among 200 patients evaluated for entry into a trial of primary care office-based buprenorphine/naloxone treatment stratifying on those who reported exclusive heroin use (n = 124), heroin and prescription opioid use (n = 47), or only prescription opioid use (n = 29). RESULTS: Compared to heroin-only patients, prescription-opioid-only patients were younger, had fewer years of opioid use, and less drug treatment history. They were also more likely to be white, earned more income, and were less likely to have Hepatitis C antibodies. Prescription-opioid-only patients were more likely to complete treatment (59% vs. 30%), remained in treatment longer (21.0 vs. 14.2 weeks), and had a higher percent of opioid-negative urine samples than heroin only patients (56.3% vs. 39.8%), all p values < .05. Patients who used both heroin and prescription opioids had outcomes that were intermediate between heroin-only and prescription-opioid-only patients. CONCLUSIONS: Individuals dependent on prescription opioids have an improved treatment response to buprenorphine/naloxone maintenance in an office-based setting compared to those who exclusively or episodically use heroin