Co-Producing a Shared Characterization of Depredation in the Gulf of Mexico Reef Fish Fishery: Comprehensive Report

Depredation, defined as the partial or complete removal of a hooked fish by a non-target species, is a cryptic form of mortality that can affect the accuracy of stock assessments and species management efforts. Accounting for depredation is crucial to minimize uncertainty in stock assessment models and to obtain accurate and reliable fisheries catch data. If these interactions are frequent, failure to properly quantify this form of mortality can lead to the underestimation of reef fish population removals, inappropriate harvest recommendations, and stakeholder unrest. In recent years, depredation has escalated in the Gulf of Mexico (GoM) reef fish fishery. Although GoM reef fish fishery stakeholders (fishermen) have actively pushed for resource managers to implement solutions to address these increasingly pervasive interactions, a comprehensive characterization of this issue is lacking, and trends surrounding GoM reef fish depredation – as well as factors that impact depredation – have not been adequately described or evaluated. Therefore, the objective of this project was to co-produce a shared characterization of the impacts of depredation in the GoM reef fish fishery. To accomplish this, we employed a three-phased approach consisting of synthesis (phase 1), survey (phase 2), and feedback (phase 3). During phase 1, we synthesized data from the NOAA Fisheries Southeast Fisheries Science Center (SEFSC) GoM Reef Fish Observer Program, the largest and longest depredation-related dataset available. Marked increases in depredation were shown starting in 2017 for both bottom longline and vertical longline, particularly in the Eastern GoM. To complement the analysis of the commercial sector from phase 1, we designed and implemented an electronic survey of private recreational anglers in phase 2. Survey results demonstrate that anglers across the GoM routinely experience depredation and have identified a variety of influential factors such as geographic location and depth. Surprisingly, depredation has not affected fishing behavior for the majority of those surveyed. Findings from the commercial fishery (phase 1) and private recreational fishery (phase 2) were then presented to a representative group of (predominantly) charter-for-hire fishermen during an in-person, collaborative participatory modeling workshop (phase 3). These stakeholders provided unique insights, suggesting that factors like the length of the red snapper fishing season, recreational angler high-grading, and a diminished GoM shrimp trawl fleet, have led to increases in depredation. Perhaps more importantly, these stakeholders noted a growing disconnect between their on-the-water observations (i.e., increased depredation), and what they perceived as an increasing desire from NOAA Fisheries and the general public to protect all sharks. Notably, these sentiments resulted in a lack of trust with respect to shark science, stock assessments, and resource management. Ultimately, this planning project led to a deeper understanding of shark depredation in the GoM commercial, private recreational, and charter-for-hire fisheries. Project findings formed the basis of a comprehensive Research and Development Plan and an Application Plan. In addition, data and insights from this planning project contributed to a peer-reviewed depredation review (Mitchell et al. 2022), a stock assessment report (Drymon et al. 2022), a manuscript in prep (Duffin et al.), five conference presentations, and three outreach products.

β3 integrins : negative regulators of angiogenesis

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Biology, 2002.Includes bibliographical references (leaves 199-219).A method was developed to isolate and purify primary murine endothelial cells from lung tissue (MLEC). The cells generated by this method were characterized by immuno-fluorescence detection and FACS analysis and expressed specific antigens including PECAM-1, ICAM-1, ICAM-2, VCAM-1 and VE-cadherin. Using this method, cells from wild-type and beta 3-integrin-deficient animals were purified and used to determine the specificity of a novel potential anti-angiogenic drug. This study shows that tumstatin, a fragment of the alpha 3 chain of collagen IV, inhibits proliferation, inhibits total protein synthesis and specifically inhibits CAP-dependent protein synthesis in MLEC. These effects do not occur when beta 3-null MLEC are treated with tumstatin or any of its derivatives. Nor do they occur in mouse embryonic fibroblasts which do express beta 3 integrin. The inhibition by tumstatin also occurs in in vivo angiogenesis assayed using a Matrigel plug insert. Similarly to in vitro assays, tumstatin failed to inhibit angiogenesis in beta 3 integrin-deficient animals. These results suggest that avf33 integrin is necessary but not sufficient for the activity of tumstatin. Further studies are required to identify avf33 integrin-associated factors in endothelial cells which determine tumstatin's endothelial cell specificity. Matrigel plug assays were also used to demonstrate that the loss of beta-3 integrin enhanced VEGF-induced angiogenesis. Results also show that VEGF-induced angiogenesis was enhanced in aortic ring explants from beta 3-null animals. These data suggest a new role for beta 3 integrin as a negative regulator of angiogenesis, both as a receptor for an endogenous inhibitory molecule and as an inhibitor of VEGF-induced angiogenesis.by Julie C. Lively.Ph.D

Data from: Within-population covariation between sexual reproduction and susceptibility to local parasites

Evolutionary biology has yet to reconcile the ubiquity of sex with its costs relative to asexual reproduction. Here, we test the hypothesis that coevolving parasites maintain sex in their hosts. Specifically, we examined the distributions of sexual reproduction and susceptibility to local parasites within a single population of freshwater snails (Potamopyrgus antipodarum). Susceptibility to local trematode parasites (Microphallus sp.) is a relative measure of the strength of coevolutionary selection in this system. Thus, if coevolving parasites maintain sex, sexual snails should be common where susceptibility is high. We tested this prediction in a mixed population of sexual and asexual snails by measuring the susceptibility of snails from multiple sites in a lake. Consistent with the prediction, the frequency of sexual snails was tightly and positively correlated with susceptibility to local parasites. Strikingly, in just two years, asexual females increased in frequency at sites where susceptibility declined. We also found that the frequency of sexual females covaries more strongly with susceptibility than with the prevalence of Microphallus infection in the field. In linking susceptibility to the frequency of sexual hosts, our results directly implicate spatial variation in coevolutionary selection in driving the geographic mosaic of sex

coordinates

This file contains the latitude and longitude for each of the 13 sites sampled in this study. Coordinates were obtained from Google Earth. Data columns are as follows: (1) site (n=13); (2) latitude; (3) longitude

Antimicrobial Resistant Bacteria in Shrimp and Shrimp Farms of Bangladesh

The purpose of this study was to investigate the presence of pathogenic bacteria, specifically Escherichia coli and Salmonella and Vibrio species, and their antimicrobial resistance in shrimp aquaculture facilities of Bagerhat (Bangladesh). Sediment samples were collected from both Penaeus monodon and Macrobrachium rosenbergii farms and shrimp samples from the Macrobrachium rosenbergii facility. The abovementioned bacteria were not found, but five Enterobacterales (Proteus penneri, Proteus alimentorum, Morganella morganii, Enterobacter hormaechei subsp. xiangfangensis and Plesiomonas shigelloides) were detected. This is the first documented case of Enterobacter hormaechei subsp. xiangfangensis in a shrimp farm. Nine antibiotics—ampicillin, gentamicin, chloramphenicol, oxytetracycline, nitrofurantoin, levofloxacin, ciprofloxacin, azithromycin, and co-trimoxazole—were selected for antibiotic resistance testing, and the majority (88.9%) had at least one isolate that was resistant. Across sources, 78.0% of isolates were resistant to at least one antimicrobial, and multidrug resistance was also detected in 29.3% of all isolates. Despite the low number of samples analyzed, nine in total, the results of this experiment emphasize that shrimp farms in Bagerhat may have a problem with antimicrobial-resistant bacteria. This could have negative impacts on shrimp quality and consumers’ health

experimental data

This file contains the full results of the inoculation experiment from which susceptibility and the proportion of sexual females were determined for 13 sites in each of three years. Juvenile snails from each were exposed to high doses of parasites from Lake Alexandrina. Following parasite development, snails were evaluated for sex, infection and reproductive mode. Data columns are as follows: (1) year (n=3; 2013, 2014, and 2015); (2) site (n=13); (3) replicate (n=3-6 depending on year); (4) sexual: number of sexual females in the replicate; (5) asexual: the number of asexual females; (6) healthy: the total number of healthy females; (7) infected: the total number of females infected with Microphallus; (8) healthy_sexual: the number of healthy, sexual females; (9) infected_sexual: the number of sexual females infected with Microphallus. Columns 4 and 5 give the proportion of sexual females at a site. Columns 6 and 7 give overall susceptibility, while 8 and 9 give susceptibility of sexual females only. In 2014, the proportion of sexual females was obtained from 6 experimental replicates, and susceptibility from 3

field data

This file contains data for individual female snails collected from our 13 field sites in 2014 and 2015. These data were used in validating our results for variation in the proportion of sexual females between sites and for estimating the infection prevalence of sexual females. Data columns are as follows: (1) year (n=2); site (n=13); (3) length: shell length in millimeters; (4) infected: 0 for healthy, 1 for castrated with Microphallus; (5) ploidy: 2 for diploid sexual and 3 for triploid asexual

prevalence

This file contains the length-corrected estimates of infection prevalence for each site in 2013 through 2015. Length-corrected estimates are given for all females and for sexual females only. The length-corrected estimates of infection prevalence for all females were obtained from Gibson et al. (2016, Am Nat). The raw data for those estimates are associated with that publication – Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.t89hc. The length-corrected estimates of infection prevalence for sexual females only were obtained in the same manner as described in Gibson et al. (2016, Am Nat): they are the estimated marginal means for infection prevalence obtained from a generalized linear model with site, year, their interaction and shell length (mm, covariate) as predictors of the probability of infection of an individual, sexual female. The raw data for those estimates are included in this Dryad data package, with field_data.csv. Infection prevalence of sexual females was only available for 2014-2015. Data columns are as follows: (1) year (n=3); (2) site (n=13); (3) prevalence_lc: length-corrected prevalence for all females; (4) prevalence_sexual_lc: length-corrected prevalence for sexual females

temporal change

This file contains the change in susceptibility and proportion sexual females at each site through time. The change is calculated as the value in 2015 minus the value in 2013. Data columns are as follows: (1) site (n=13); (2) sex: change in the proportion of sexual females; (3) susceptibility: change in overall susceptibility; (4) sexual_susceptibility: change in susceptibility of sexual females