Assessment of the population structure and temporal changes in spatial dynamics and genetic characteristics of the Atlantic bluefin tuna under a fishery independent framework.

As a large and long-lived species with high economic value, restricted spawning areas and short spawning periods, the Atlantic bluefin tuna (BFT; Thunnus thynnus) is particularly susceptible to over-exploitation. Although BFT have been targeted by fisheries in the Mediterranean Sea for thousands of years, it has only been in these last decades that the exploitation rate has reached far beyond sustainable levels. An understanding of the population structure, spatial dynamics, exploitation rates and the environmental variables that affect BFT is crucial for the conservation of the species. The aims of this PhD project were 1) to assess the accuracy of larval identification methods, 2) determine the genetic structure of modern BFT populations, 3) assess the self-recruitment rate in the Gulf of Mexico and Mediterranean spawning areas, 4) estimate the immigration rate of BFT to feeding aggregations from the various spawning areas, and 5) develop tools capable of investigating the temporal stability of population structuring in the Mediterranean Sea. Several weaknesses in modern morphology-based taxonomy including demographic decline of expert taxonomists, flawed identification keys, reluctance of the taxonomic community to embrace advances in digital communications and a general scarcity of modern user-friendly materials are reviewed. Barcoding of scombrid larvae revealed important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. Using a Genotyping-by-Sequencing a panel of 95 SNPs was developed and used to characterize the population structuring of BFT and composition of adult feeding aggregations. Using novel molecular techniques, DNA was extracted from bluefin tuna vertebrae excavated from late iron age, ancient roman settlements Byzantine-era Constantinople and a 20th century collection. A second panel of 96 SNPs was developed to genotype historical and modern samples in order to elucidate changes in population structuring and allele frequencies of loci associated with selective traits.

Anadromous Rainbow Smelt and Tomcod in Connecticut: Assessment of populations, conservation status, and need for restoration plan

(beginning of rainbow smelt executive summary) Evidence indicates that anadromous rainbow smelt (Osmerus mordax) populations in Connecticut and elsewhere in the northeast United States have severely declined. Several sampling programs have documented declines in Connecticut’s smelt populations over the last three decades (Marcy 1976a, Marcy 1976b, Millstone Environmental Laboratory 2005). Similar declines have also been documented in the Hudson River (ASA Analysis & Communication 2005) and in Massachusetts (personal communication, Brad Chase, MA Division of Marine Fisheries 2004). Recreational and commercial fisheries in the region for this species have virtually ceased (Blake and Smith 1984). The Connecticut Fish Advisory Committee of the Endangered Species Program has recommended that rainbow smelt be listed as threatened in Connecticut, and the National Marine Fisheries Service (2004) has recently listed rainbow smelt as a Federal Species of Concern. The purpose of this project is to develop an environmental history of rainbow smelt in Connecticut and surrounding regions, and document the current status of populations in Connecticut waters. An environmental history that assesses trends in abundance, environmental threats and historical efforts to ameliorate the threats will contribute to regional efforts to conserve these fish. Comprehensive review of the regional literature and trends associated with rainbow smelt has not been undertaken since Kendall (1926). Assessment of current abundance, distribution, areas of critical habitat, and whether the species is presently reproducing in state waters is critical for clarifying conservation status, designing a monitoring program and developing a recovery or enhancement plan, if this appears to be necessary. (beginning of tomcod executive summary) Atlantic tomcod (Microgadus tomcod) are believed to have declined significantly in Connecticut and other estuaries of the Northeast and Middle Atlantic states. Several monitoring programs indicate that the species is scarce and/or declining in the region’s estuaries (Gottschall and Pacileo 2004, Molnar 2004, Millstone Environmental Laboratory 2005, ASA Analysis and Communication 2005). Once-active recreational (NMFS MRFSS 2005, http://www.st.nmfs.gov) and commercial fisheries for this species in Connecticut are now dormant. For the past 10 years, the Connecticut Fish Advisory Committee of the Endangered Species Program has recommended that studies be undertaken to quantify the status of tomcod populations and to determine if conservation actions should be initiated. The purpose of this project is to develop an environmental history of Atlantic tomcod in Connecticut and surrounding regions, and document the current status of populations in Connecticut waters. An environmental history that assesses trends in abundance, environmental threats and historical efforts to ameliorate the threats will contribute to regional efforts to conserve these fish. Assessment of current abundance, distribution, areas of critical habitat, and whether the species is presently reproducing in state waters is critical for determining conservation status, designing a monitoring program and developing a recovery or enhancement plan, if this appears to be necessary.

Lists of seamounts and knolls in different formats

Seamounts and knolls are 'undersea mountains', the former rising more than 1000 m from the sea floor. These features provide important habitats for aquatic predators, demersal deep-sea fish and benthic invertebrates. However most seamounts have not been surveyed and their numbers and locations are not well known. Previous efforts to locate and quantify seamounts have used relatively coarse bathymetry grids. Here we use global bathymetric data at 30 arc-second resolution to identify seamounts and knolls. We identify 33,452 seamounts and 138,412 knolls, representing the largest global set of identified seamounts and knolls to date. We compare estimated seamount numbers, locations, and depths with validation sets of seamount data from New Zealand and Azores. This comparison indicates the method we apply finds 94% of seamounts, but may overestimate seamount numbers along ridges and in areas where faulting and seafloor spreading creates highly complex topography. The seamounts and knolls identified herein are significantly geographically biased towards areas surveyed with ship-based soundings. As only 6.5% of the ocean floor has been surveyed with soundings it is likely that new seamounts will be uncovered as surveying improves. Seamount habitats constitute approximately 4.7% of the ocean floor, whilst knolls cover 16.3%. Regional distribution of these features is examined, and we find a disproportionate number of productive knolls, with a summit depth of <1.5 km, located in the Southern Ocean. Less than 2% of seamounts are within marine protected areas and the majority of these are located within exclusive economic zones with few on the High Seas. The database of seamounts and knolls resulting from this study will be a useful resource for researchers and conservation planners.

First record of Antipathella subpinnata in the Azores

The first record of Antipathella subpinnata ( Ellis and Solander, 1786) for the Azores archipelago is presented based on bottom longline by-catch analysis and ROV seafloor surveys, extending the species western-most boundary of distribution in the NE Atlantic. The species was determined using classic taxonomy and molecular analysis targeting nuclear DNA. Although maximum spine height on Azorean colonies branchlets is slightly smaller than that reported from Mediterranean colonies (0.12 vs 0.16 mm), the analysis of partial 18S rDNA, complete ITS1, 5.8S, ITS2 and partial 28S rDNA suggests that the Azorean and Mediterranean specimens belong to the same species. Video surveys of an A. subpinnata garden detected near Pico Island are used to provide the first in situ description of the species habitat in the region and the first detailed description of a black coral garden in the NE Atlantic. With A. subpinnata being the only coral found between 150 and 196 m depths, this is the deepest black coral garden recorded in the NE Atlantic and the first one to be monospecific. The species exhibited a maximum density of 2.64 colonies/m**2 and occurred across a surface area estimated at 67,333 m**2, yielding a local population estimate of 50,500 colonies.

Raster grids detailing habitat suitability for Lophelia pertusa reefs in the Irish continental margin

This dataset contains raster grids in GeoTIFF format describing the habitat suitability for living Lophelia pertusa reefs in the Irish continental margin (extended continental shelf claim). The habitat suitability map is given in continuous and binary (based on the 10th percentile threshold) format. The geographic extent is 25°53.801'W - 6°42.401'W and 46°45.033'N - 57°27.033'N. The spatial resolution is 0.01°x0.01°. The map projection is WGS 1984.

Occurrence (presence-only) of living Lophelia pertusa reefs in the Irish continental margin

The present data set was used as a training set for a Habitat Suitability Model. It contains occurrence (presence-only) of living Lophelia pertusa reefs in the Irish continental margin, which were assembled from databases, cruise reports and publications. A total of 4423 records were inspected and quality assessed to ensure that they (1) represented confirmed living L. pertusa reefs (so excluding 2900 records of dead and isolated coral colony records); (2) were derived from sampling equipment that allows for accurate (<200 m) geo-referencing (so excluding 620 records derived mainly from trawling and dredging activities); and (3) were not duplicated. A total of 245 occurrences were retained for the analysis. Coral observations are highly clustered in regions targeted by research expeditions, which might lead to falsely inflated model evaluation measures (Veloz, 2009). Therefore, we coarsened the distribution data by deleting all but one record within grid cells of 0.02° resolution (Davies & Guinotte 2011). The remaining 53 points were subject to a spatial cross-validation process: a random presence point was chosen, grouped with its 12 closest neighbour presence points based on Euclidean distance and withheld from model training. This process was repeated for all records, resulting in 53 replicates of spatially non-overlapping sets of test (n=13) and training (n=40) data. The final 53 occurrence records were used for model training.

Resolving taxonomic uncertainty in vulnerable elasmobranchs : are the Madeira skate (Raja maderensis) and the thornback ray (Raja clavata) distinct species?

We are grateful to all those who helped with sample collection. This includes the MEDITS survey programme (IEO Mallorca) for Mediterranean samples. Portugal mainland samples were collected under the EU Data Collection Framework (DCF, PNAB). Azores specimens from the Department of Oceanography and Fisheries (DOP) of the University of the Azores (UAc) were collected under the project DEMERSAIS “Monitorização das espécies demersais dos Açores” financed by the Azorean government, and the project DEECON “Unravelling population connectivity for sustainable fisheries in the Deep Sea” project approved by the European Science Foundation (ESF) under the EUROCORES programme (proposal No 06-EuroDEEP-FP-008 & SFRH-EuroDEEP/0002/2007). This study was funded by the UK Natural Environment Research Council (NERC) Oceans 2025 Strategic Research Programme Theme 6 (Science for Sustainable Marine Resources). REB was supported by the Fisheries Society of the British Isles (FSBI), BSP was funded by the Fundação para a Ciência e a Tecnologia, SFRH/BPD/72351/2010 and JL was supported by The Alasdair Downes Marine Conservation Fund.

Why fisheries collapse and what to do about it.

With the collapse of fisheries in many parts of the world causing widespread economic harm, attention is focused on a possible cause and remedy of fishery collapse. Economic theory for managing a renewable resource, such as a fishery, leads to an ecologically unstable equilibrium as difficult to maintain as balancing a marble on top of a dome. A fishery should be managed for ecological stability instead--in the analogy, as easy to maintain as keeping a marble near the base of a bowl. The goal of ecological stability is achieved if the target stock is above that producing maximum sustainable yield and harvested at less than the maximum sustainable yield. The cost of managing for ecological stability, termed "natural insurance," is low if the fishery is sufficiently productive. This cost is shown to pay for itself over the long term in a variable and uncertain environment. An ecologically stable target stock may be attained either with annually variable quotas following current practice or, preferably, through a market mechanism whereby fish are taxed at dockside if caught when the stock was below target and are untaxed otherwise. In this regulatory environment, the goal of maximizing short-term revenue coincides with the goal of ecological stability, thereby also maximizing long-term revenue. This new approach to fishery management is illustrated with the recently collapsed Newfoundland fishing industry. The Newfoundland cod fishery is expected to rebuild to an ecologically stable level in about 9 years and thereafter support an annual harvest of about 75% of the 1981-1990 average.

Effects of climate change on fisheries : from a global to a regional perspective

Tese de doutoramento, Biologia (Biologia Marinha e Aquacultura), Universidade de Lisboa, Faculdade de Ciências, 2016

Evaluating conservation and fisheries management strategies by linking spatial prioritization software and ecosystem and fisheries modelling tools

Well-designed marine protected area (MPA) networks can deliver a range of ecological, economic and social benefits, and so a great deal of research has focused on developing spatial conservation prioritization tools to help identify important areas. However, whilst these software tools are designed to identify MPA networks that both represent biodiversity and minimize impacts on stakeholders, they do not consider complex ecological processes. Thus, it is difficult to determine the impacts that proposed MPAs could have on marine ecosystem health, fisheries and fisheries sustainability. Using the eastern English Channel as a case study, this paper explores an approach to address these issues by identifying a series of MPA networks using the Marxan and Marxan with Zones conservation planning software and linking them with a spatially explicit ecosystem model developed in Ecopath with Ecosim. We then use these to investigate potential trade-offs associated with adopting different MPA management strategies. Limited-take MPAs, which restrict the use of some fishing gears, could have positive benefits for conservation and fisheries in the eastern English Channel, even though they generally receive far less attention in research on MPA network design. Our findings, however, also clearly indicate that no-take MPAs should form an integral component of proposed MPA networks in the eastern English Channel, as they not only result in substantial increases in ecosystem biomass, fisheries catches and the biomass of commercially valuable target species, but are fundamental to maintaining the sustainability of the fisheries. Synthesis and applications. Using the existing software tools Marxan with Zones and Ecopath with Ecosim in combination provides a powerful policy-screening approach. This could help inform marine spatial planning by identifying potential conflicts and by designing new regulations that better balance conservation objectives and stakeholder interests. In addition, it highlights that appropriate combinations of no-take and limited-take marine protected areas might be the most effective when making trade-offs between long-term ecological benefits and short-term political acceptability.