Spatio-Temporal Dynamics of Atlantic Cod Bycatch in the Maine Lobster Fishery and Its Impacts on Stock Assessment

Of the most iconic fish species in the world, the Atlantic cod (Gadus morhua, hereafter, cod) has been a mainstay in the North Atlantic for centuries. While many global fish stocks have received increased pressure with the advent of new, more efficient fishing technology in the mid-20th century, exceptional pressure has been placed on this prized gadoid. Bycatch, or the unintended catch of organisms, is one of the biggest global fisheries issues. Directly resulting from the failed recovery of cod in the GoM, attention has been placed as to possible sources of unaccounted catch. Among the most prominent is that of the GoM American lobster (Homarus americanus) trap fishery. My dissertation research contributes to solving these problems by making progress in five areas: Evaluating cod discard survivability, characterizing lobster effort, estimating cod bycatch, incorporating various bycatch scenarios into the current stock assessment framework, and providing an in-depth policy analysis for management to move forward. This dissertation proceeds as follows: Chapter 1 will briefly introduce regional fishing history, and the study species. Chapter 2 a will provide a preliminary habitat analysis and field project with the object of understanding when and where cod are caught as bycatch, and their subsequent survivability post-release. Chapter 3 develops a quasi-stationary bootstrapped Generalized Additive Model method to estimate Maine’s effective lobster effort spanning 2006-2013. Chapter 4 builds on the same methodologies to estimate Atlantic cod bycatch rates on the congruent spatiotemporal scale, then incorporates uncertainties from both lobster effort and bycatch rates to estimate spatiotemporal cod bycatch. Chapter 5 uses estimates from the previous chapter alongside available federal cod data to estimate historic age-structure and magnitude of cod bycatch from 1982-2016. Then, multiple scenarios are evaluated in the current assessment framework and I report on updated assessment model diagnostics and a novel approach to retrospective analysis. Chapter 6 will conclude with a detailed policy analysis of the state of fisheries in the GoM, and how cod bycatch from the lobster fishery may be equitably incorporated as to ensure productive fisheries across groundfish and lobster sectors while minimizing conflicts

Effects of climate change and variability on large pelagic fish in the Northwest Atlantic Ocean: implications for improving climate resilient management for pelagic longline fisheries

Climate change influences marine environmental conditions and is projected to increase future environmental variability. In the North Atlantic, such changes will affect the behavior and spatiotemporal distributions of large pelagic fish species (i.e., tunas, billfishes, and sharks). Generally, studies on these species have focused on specific climate-induced changes in abiotic factors separately (e.g., water temperature) and on the projection of shifts in species abundance and distribution based on these changes. In this review, we consider the latest research on spatiotemporal effects of climate-induced environmental changes to HMS’ life history, ecology, physiology, distribution, and habitat selection, and describe how the complex interplay between climate-induced changes in biotic and abiotic factors, including fishing, drives changes in species productivity and distribution in the Northwest Atlantic. This information is used to provide a baseline for investigating implications for management of pelagic longline fisheries and to identify knowledge gaps in this region. Warmer, less oxygenated waters may result in higher post-release mortality in bycatch species. Changes in climate variability will likely continue to alter the dynamics of oceanographic processes regulating species behavior and distribution, as well as fishery dynamics, creating challenges for fishery management. Stock assessments need to account for climate-induced changes in species abundance through the integration of species-specific responses to climate variability. Climate-induced changes will likely result in misalignment between current spatial and temporal management measures and the spatiotemporal distribution of these species. Finally, changes in species interactions with fisheries will require focused research to develop best practices for adaptive fisheries management and species recovery

Observing low elevation sky and the CMB Cold Spot with BICEP3 at the South Pole

BICEP3 is a 520 mm aperture on-axis refracting telescope at the South Pole, which observes the polarization of the cosmic microwave background (CMB) at 95 GHz to search for the B-mode signal from inflationary gravitational waves. In addition to this main target, we have developed a low-elevation observation strategy to extend coverage of the Southern sky at the South Pole, where BICEP3 can quickly achieve degree-scale E-mode measurements over a large area. An interesting E-mode measurement is probing a potential polarization anomaly around the CMB Cold Spot. During the austral summer seasons of 2018-19 and 2019-20, BICEP3 observed the sky with a flat mirror to redirect the beams to various low elevation ranges. The preliminary data analysis shows degree-scale E-modes measured with high signal-to-noise ratio

Analysis of Temperature-to-Polarization Leakage in BICEP3 and Keck CMB Data from 2016 to 2018

The Bicep/Keck Array experiment is a series of small-aperture refracting telescopes observing degree-scale Cosmic Microwave Background polarization from the South Pole in search of a primordial B-mode signature. As a pair differencing experiment, an important systematic that must be controlled is the differential beam response between the co-located, orthogonally polarized detectors. We use high-fidelity, in-situ measurements of the beam response to estimate the temperature-to-polarization (T → P) leakage in our latest data including observations from 2016 through 2018. This includes three years of Bicep3 observing at 95 GHz, and multifrequency data from Keck Array. Here we present band-averaged far-field beam maps, differential beam mismatch, and residual beam power (after filtering out the leading difference modes via deprojection) for these receivers. We show preliminary results of "beam map simulations," which use these beam maps to observe a simulated temperature (no Q/U) sky to estimate T → P leakage in our real data

Polarization calibration of the BICEP3 CMB polarimeter at the South Pole

The BICEP3 CMB Polarimeter is a small-aperture refracting telescope located at the South Pole and is specifically designed to search for the possible signature of inflationary gravitational waves in the Cosmic Microwave Background (CMB). The experiment measures polarization on the sky by differencing the signal of co-located, orthogonally polarized antennas coupled to Transition Edge Sensor (TES) detectors. We present precise measurements of the absolute polarization response angles and polarization efficiencies for nearly all of BICEP3's ~800 functioning polarization-sensitive detector pairs from calibration data taken in January 2018. Using a Rotating Polarized Source (RPS), we mapped polarization response for each detector over a full 360 degrees of source rotation and at multiple telescope boresight rotations from which per-pair polarization properties were estimated. In future work, these results will be used to constrain signals predicted by exotic physical models such as Cosmic Birefringence

Analysis of Temperature-to-Polarization Leakage in BICEP3 and Keck CMB Data from 2016 to 2018

The Bicep/Keck Array experiment is a series of small-aperture refracting telescopes observing degree-scale Cosmic Microwave Background polarization from the South Pole in search of a primordial B-mode signature. As a pair differencing experiment, an important systematic that must be controlled is the differential beam response between the co-located, orthogonally polarized detectors. We use high-fidelity, in-situ measurements of the beam response to estimate the temperature-to-polarization (T → P) leakage in our latest data including observations from 2016 through 2018. This includes three years of Bicep3 observing at 95 GHz, and multifrequency data from Keck Array. Here we present band-averaged far-field beam maps, differential beam mismatch, and residual beam power (after filtering out the leading difference modes via deprojection) for these receivers. We show preliminary results of "beam map simulations," which use these beam maps to observe a simulated temperature (no Q/U) sky to estimate T → P leakage in our real data

Observing low elevation sky and the CMB Cold Spot with BICEP3 at the South Pole

BICEP3 is a 520 mm aperture on-axis refracting telescope at the South Pole, which observes the polarization of the cosmic microwave background (CMB) at 95 GHz to search for the B-mode signal from inflationary gravitational waves. In addition to this main target, we have developed a low-elevation observation strategy to extend coverage of the Southern sky at the South Pole, where BICEP3 can quickly achieve degree-scale E-mode measurements over a large area. An interesting E-mode measurement is probing a potential polarization anomaly around the CMB Cold Spot. During the austral summer seasons of 2018-19 and 2019-20, BICEP3 observed the sky with a flat mirror to redirect the beams to various low elevation ranges. The preliminary data analysis shows degree-scale E-modes measured with high signal-to-noise ratio

Loss of coral reef growth capacity to track future increases in sea level

Water-depths above coral reefs is predicted to increase due to global sea-level rise (SLR). As ecological degradation inhibits the vertical accretion of coral reefs, it is likely that coastal wave exposure will increase but there currently exists a lack of data in projections concerning local rates of reef growth and local SLR. In this study we have aggregated ecological data of more than 200 tropical western Atlantic and Indian Ocean reefs and calculated their vertical growth which we have then compared with recent and projected rates of SLR across different Representative Concentration Pathway (RCP) scenarios. While many reefs currently show vertical growth that would be sufficient to keep-up with recent historic SLR, future projections under scenario RCP4.5 reveal that without substantial ecological recovery many reefs will not have the capacity to track SLR. Under RCP8.5, we predict that mean water depth will increase by over half a metre by 2100 across the majority of reefs. We found that coral cover strongly predicted whether a reef could track SLR, but that the majority of reefs had coral cover significantly lower than that required to prevent reef submergence. To limit reef submergence, and thus the impacts of waves and storms on adjacent coasts, climate mitigation and local impacts that reduce coral cover (e.g., local pollution and physical damage through development land reclamation) will be necessary

Re-evaluating Atlantic cod mortality including lobster bycatch: where could we be today?

Full accounting of fisheries mortality is one of the most tractable ways to improve stock assessments. However, it can be challenging to obtain in cases when missing catch comes from small-scale nontarget fisheries unrequired to report incidental catch. Atlantic cod (Gadus morhua) in the Gulf of Maine (GoM), USA, once served as a regionally important fishery, but has been serially depleted to <5% of historic spawning stock biomass. Recent management efforts to rebuild GoM cod have largely failed. We test the hypothesis that unaccounted bycatch of Atlantic cod in the Maine American lobster (Homarus americanus) fishery is a substantial missing piece in the GoM Atlantic cod assessment. We integrated multiple scenarios of hind-casted discards into the two accepted regional cod assessment models from 1982 to 2016. Incorporation of discards improved the assessment bias for both models (10%–15%), increased estimates of spawning stock biomass (4%), and decreased estimates of fishing mortality (9%). A novel evaluation of longitudinal model bias suggests that alternative modelling approaches or specifications may be warranted. We highlight the importance of accounting for all fishery-related mortality and the need for methods to deliver more comprehensive estimates from both target and nontarget fisheries.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Optimal weighting in species habitat modelling: a case study from Ommastrehpes bartramii in the Northwest Pacific Ocean

The weighting of environmental variables in habitat modelling is important, especially for species with a poorly understood distribution. Traditional weighting schemes, such as arithmetic or geometric mean, often cause “gradient” habitat distribution patterns. We develop a new methodology that determines optimal variable weighting via a structured sensitivity analysis approach. This method considers the full spectrum of weighting combinations and uses multiple model selection criteria to select the best fit. We use a Northwest Pacific neon flying squid fishery dataset (1998-2012) to compare our ‘BEST-HSI’ with the traditional fixed methods, as well as to the more recent machine learning approach: boosted regression tree. Approaches were evaluated based on differences in habitat metrics, such as continuity, magnitude, and ratio of estimated unfavourable/favourable habitat. The BEST-HSI model generally outperformed the other three methods, though habitat metrics notably differed depending on weighting schemes used. The BEST-HSI approach is an efficient exploratory tool to investigate empirical relationships between organism presence and the environment, particularly for species with little known life history or migration information.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author