Multiple approaches and novel techniques to study the spatial ecology of marine vertebrates

To mitigate potential negative impacts to marine vertebrates it is necessary to gain, and build on, knowledge and understanding of their spatial ecology. Aerial and ship based surveys, as well as satellite telemetry data, have allowed for growing insight into habitat use across a broad spectrum of migratory marine species. Furthermore, these data have often enabled characterisation of anthropogenic impacts and identified potential conservation management strategies. This thesis seeks to investigate the spatial ecology of marine vertebrates using sea turtles as a study group. Data for inter-nesting and post-nesting sea turtles are analysed, and where possible, threats investigated. The analyses presented here integrate the use of multiple spatial ecological tools, including aerial surveys, satellite tracking, remote sensing, Geographical Information Systems (GIS) and habitat modelling. Many of the analytical processes employed formulate novel methodologies, as well as build upon and develop existing techniques. For post-nesting turtles, foraging and migratory data are analysed, and observed and modelled habitat niches described. Putative threats from fisheries and climate change are investigated, and where appropriate, contextualised with data describing limits of Marine Protected Areas (MPAs). For inter-nesting turtles, at-sea distributions and coastal density patterns are explored. Vessel Monitoring System (VMS) and Automatic Identification System (AIS) data are used to elucidate shipping densities; spatial patterns of threat from fisheries, and other maritime industries are inferred. Aerial survey data are used to ascertain potential impacts to turtles on nesting beaches. Throughout this thesis spatially explicit areas are identified where concentrated conservation efforts could be applied. Furthermore, many of these analyses highlight that conservation policy must recognise the spatial extent of migratory species, and be flexible and adaptive to accommodate potential range shifts under climate change. Much of the presented analyses assimilate data from multiple sources to provide large datasets; allowing analyses to be made that would be otherwise unfeasible. Finally, this thesis demonstrates the utility of developing and applying novel analytical methodologies to these data to investigate the spatial ecology of marine vertebrates of conservation concern. As such, it is likely that many of the analytical techniques presented here could be adapted and applied to other widely dispersed marine vertebrate species to help inform global conservation planning and practice

Cnidaria in UK coastal waters: description of spatio-temporal patterns and inter-annual variability

Note that the accepted version of this paper is available on open access in ORE at: http://hdl.handle.net/10871/15245Concern has been expressed over future biogeographical expansion and habitat capitalization by species of the phylum Cnidaria, as this may have negative implications on human activities and ecosystems. There is, however, a paucity of knowledge and understanding of jellyfish ecology, in particular species distribution and seasonality. Recent studies in the UK have principally focused on the Celtic, Irish and North Seas, but all in isolation. In this study we analyse data from a publicly- driven sightings scheme across UK coastal waters (2003–2011; 9 years), with the aim of increasing knowledge on spatial and temporal patterns and trends. We describe inter-annual variability, seasonality and patterns of spatial distribution, and compare these with existing historic literature. Although incidentally-collected data lack quantification of effort, we suggest that with appropriate data management and interpretation, publicly-driven, citizen-science-based, recording schemes can provide for large-scale (spatial and temporal) coverage that would otherwise be logistically and financially unattainable. These schemes may also contribute to baseline data from which future changes in patterns or trends might be identified. We further suggest that findings from such schemes may be strengthened by the inclusion of some element of effort-corrected data collection

Predicting habitat suitability for basking sharks (Cetorhinus maximus) in UK waters using ensemble ecological niche modelling

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.The basking shark (Cetorhinus maximus) is an endangered species in the north-east Atlantic, having been historically over exploited. Whilst near-shore aggregation hotspots in the UK have been identified, robust knowledge on species distribution and abundance outside these areas remains limited. Research techniques, such as habitat modelling, could however be used to gain a greater knowledge of the species distribution to inform management plans to aid population recovery. For large mobile species gathering wide-scale distribution data can be financially and logistically challenging. In lieu of conducting a UK-wide expensive strategic survey for basking sharks, we use data from two regional-scale surveys, which were conducted in southwest England and western Scotland, and use an Ensemble Ecological Niche Model (EENM) to produce a spatially explicit map of habitat suitability. When compared against a ~20-year database of public sightings of basking sharks across UK coastal seas (to 6 nautical miles offshore), patterns of habitat suitability yielded a statistically significant agreement with areas known to support basking shark sightings. EENMs could be used to advise Marine Protected Area (MPA) selection, as well as to inform environmental impact assessments for offshore developments. The application of EENM outputs could be wide-reaching and benefit not only basking sharks but other large mobile marine species in the north-east Atlantic

Using Cumulative Impact Mapping to Prioritize Marine Conservation Efforts in Equatorial Guinea

This is the final version. Available on open access from Frontiers Media via the DOI in this recordData Availability Statement Ensemble ecological niche models (EENMs) and threat maps (anthropogenic footprint, cumulative impact, and cumulative utilization and impact) for each species (Atlantic humpback dolphin Sousa teuszii; bottlenose dolphin Tursiops truncatus; humpback whale Megaptera novaeangliae; leatherback Dermochelys coriacea; and olive ridley sea turtle Lepidochelys olivacea) are available from the Dryad Digital Repository doi: 10.5061/dryad.v6wwpzgr9 (Trew et al., 2019).Marine biodiversity is under extreme pressure from anthropogenic activity globally, leading to calls to protect at least 10% of the world’s oceans within marine protected areas (MPAs) and other effective area-based conservation measures. Fulfilling such commitments, however, requires a detailed understanding of the distribution of potentially detrimental human activities, and their predicted impacts. One such approach that is being increasingly used to strengthen our understanding of human impacts is cumulative impact mapping; as it can help identify economic sectors with the greatest potential impact on species and ecosystems in order to prioritize conservation management strategies, providing clear direction for intervention. In this paper, we present the first local cumulative utilization impact mapping exercise for the Bioko-Corisco-Continental area of Equatorial Guinea’s Exclusive Economic Zone – situated in the Gulf of Guinea, one of the most important and least studied marine regions in the Eastern Central Atlantic. This study examines the potential impact of ten direct anthropogenic activities on a suite of key marine megafauna species and reveals that the most suitable habitats for these species, located on the continental shelf, are subject to the highest threat scores. However, in some coastal areas, the persistence of highly suitable habitat subject to lower threat scores suggests that there are still several strategic areas that are less impacted by human activity that may be suitable sites for protected area expansion. Highlighting both the areas with potentially the highest impact, and those with lower impact levels, as well as particularly damaging activities can inform the direction of future conservation initiatives in the region.Waitt FoundationWildlife Conservation SocietyDarwin InitiativeDepartment for Environment, Food and Rural Affairs (Defra)Waterloo FoundationNatural Environment Research Council (NERC)Marine Turtle Conservation Fund (United States Fish and Wildlife Service, United States Department of the Interior)Vaalco EnergyHarvest Natural ResourcesSea World and Busch Gardens Conservation FundTullow OilOld Dominion UniversityWWFWildlife Conservation SocietyUniversity of Exete

Long term underwater sound measurements in the shipping noise indicator bands 63 Hz and 125 Hz from the port of Falmouth Bay, UK

PublishedThis is an open access article.Chronic low-frequency anthropogenic sound, such as shipping noise, may be negatively affecting marine life. The EU's Marine Strategy Framework Directive (MSFD) includes a specific indicator focused on this noise. This indicator is the yearly average sound level in third-octave bands with centre frequencies at 63 Hz and 125 Hz. These levels are described for Falmouth Bay, UK, an active port at the entrance to the English Channel. Underwater sound was recorded for 30 min h− 1 over the period June 2012 to November 2013 for a total of 435 days. Mean third-octave levels were louder in the 125-Hz band (annual mean level of 96.0 dB re 1 μPa) than in the 63-Hz band (92.6 dB re 1 μPa). These levels and variations are assessed as a function of seasons, shipping activity and wave height, providing comparison points for future monitoring activities, including the MSFD and emerging international regulation.This work is funded by the European Social Fund (ESF), the Peninsula Research Institute for Marine Renewable Energy (PRIMaRE; funded by the South West Regional Development Agency), MERiFIC (funded by the European Regional Development Fund through the Interreg IV-A programme), the Technology Strategy Board (TSB), and Fred Olsen Renewables. We are sincerely thankful to David Raymond and David Parish (U. of Exeter) for their technical support, particularly with mooring development and equipment maintenance and servicing and deployment through this project

SCUBA divers as oceanographic samplers: The potential of dive computers to augment aquatic temperature monitoring

Monitoring temperature of aquatic waters is of great importance, with modelled, satellite and in-situ data providing invaluable insights into long-term environmental change. However, there is often a lack of depth-resolved temperature measurements. Recreational dive computers routinely record temperature and depth, so could provide an alternate and highly novel source of oceanographic information to fill this data gap. In this study, a citizen science approach was used to obtain over 7,000 scuba diver temperature profiles. The accuracy, offset and lag of temperature records was assessed by comparing dive computers with scientific conductivity-temperature-depth instruments and existing surface temperature data. Our results show that, with processing, dive computers can provide a useful and novel tool with which to augment existing monitoring systems all over the globe, but especially in under-sampled or highly changeable coastal environments

Here today, here tomorrow: Beached timber in Gabon, a persistent threat to nesting sea turtles

notes:types: JOURThe African country of Gabon has seen decadal increases in commercial logging. An unforeseen consequence of this has been that many coastal areas, including several National Parks and Reserves, have suffered severe pollution from beached timber. This has the potential to adversely affect nesting sea turtles, particularly the leatherback turtle (Dermochelys coriacea) for which Gabon constitutes the world’s largest rookery. In this study, we analyse aerial survey data (2003, 2007 and 2011) to determine the temporal persistence and spatial extent of beached timber, and by integrating spatial data on nesting, ascertain regions where beached timber poses the greatest threat to nesting leatherback turtles. There was no marked difference in the number of beached logs recorded across the study area during the period, with 15,160, 13,528 and 17,262 logs recorded in the three years, respectively. There was, however, a significant difference in abundance of beached logs among geographical areas. Analysis highlighted two coastal areas where nesting leatherback turtles were likely to be at greatest risk from beached timber. At one such site, Kingere, within Pongara National Park, where both logs and turtle densities are high, monitoring in 2006/2007 and 2007/2008 suggested that between 1.6% and 4.4% of leatherback turtles could be entrapped at this site. Given the dynamic nature of Gabon’s coastal environment, and the potential limitations of aerial surveys, densities of beached timber could be greater than this analysis reveals. We also propose, that despite recent export restrictions of whole logs, their environmental persistence potentially represents a long-term problem

A novel approach to estimate the distribution, density and at-sea risks of a centrally-placed mobile marine vertebrate

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Formulating management strategies for mobile marine species is challenging, as knowledge is required of distribution, density, and overlap with putative threats. As a step towards assimilating knowledge, ecological niche models may identify likely suitable habitats for species, but lack the ability to enumerate species densities. Traditionally, this has been catered for by sightings-based distance sampling methods that may have practical and logistical limitations. Here we describe a novel method to estimate at-sea distribution and densities of a marine vertebrate, using historic aerial surveys of Gabonese leatherback turtle (Dermochelys coriacea) nesting beaches and satellite telemetry data of females at sea. We contextualise modelled patterns of distribution with putative threat layers of boat traffic, including fishing vessels and large ship movements, using Vessel Monitoring System (VMS) and Automatic Identification System (AIS) data. We identify key at-sea areas in which protection for inter-nesting leatherback turtles could be considered within the coastal zone of Gabonese Exclusive Economic Zone (EEZ). Our approach offers a holistic technique that merges multiple datasets and methodologies to build a deeper and insightful knowledge base with which to manage known activities at sea. As such, the methodologies presented in this study could be applied to other species of sea turtles for cumulative assessments; and with adaptation, may have utility in defining critical habitats for other central-place foragers such as pinnipeds, or sea bird species. Although our analysis focuses on a single species, we suggest that putative threats identified within this study (fisheries, seismic activity, general shipping) likely apply to other mobile marine vertebrates of conservation concern within Gabonese and central African coastal waters, such as olive ridley sea turtles (Lepidochelys olivacea), humpback dolphins (Sousa teuszii) and humpback whales (Megaptera novaeangliae).We thank the following for support and funding: CARPE (Central African Regional Program for the Environment, Darwin Initiative, EAZA ShellShock Campaign, Gabon Sea Turtle Partnership with funding from the Marine Turtle Conservation Fund (United States Fish and Wildlife Service, U.S. Department of the Interior), Harvest Energy, Large Pelagics Research Centre at the University of Massachusetts (Boston), NERC, Vaalco Energy and the Wildlife Conservation Society. We are sincerely grateful to the field teams and logistics staff who assisted in the aerial and ground surveys and with field-site assistance. BJG and MJW receive funding from the Natural Environment Research Council (NE/J012319/1), the European Union and the Darwin Initiative

Factors driving patterns and trends in strandings of small cetaceans

The incidence of cetacean strandings is expected to depend on a combination of factors, including the dis- tribution and abundance of the cetaceans, their prey, and causes of mortality (e.g. natural, fishery bycatch), as well as currents and winds which affect whether carcasses reach the shore. We investigated spatiotemporal patterns and trends in the numbers of strandings of three species of small cetacean in Galicia (NW Spain) and their relationships with meteoro- logical, oceanographic, prey abundance and fishing-related variables, aiming to disentangle the relationship that may exist between these factors, cetacean abundance and mor- tality off the coast. Strandings of 1166 common dolphins (Delphinus delphis), 118 bottlenose dolphins (Tursiops truncatus) and 90 harbour porpoises (Phocoena phocoena) during 2000–2013 were analysed. Generalised additive and generalised additive-mixed model results showed that the variables which best explained the pattern of strandings of the three cetacean species were those related with local ocean meteorology (strength and direction of the North– South component of the winds and the number of days with South-West winds) and the winter North Atlantic Oscil- lation Index. There were no significant relationships with indices of fishing effort or landings. Only bottlenose dolphin showed possible fluctuations in local abundance over the study period. There was no evidence of long-term trends in number of strandings in any of the species and their abun- dances were, therefore, considered to have been relatively stable during the study period.Versión del editor2,01

Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals

This is the final version of the article. Available from Springer Nature via the DOI in this record.Connectivity is an important component of metapopulation dynamics in marine systems and can influence population persistence, migration rates and conservation decisions associated with Marine Protected Areas (MPAs). In this study, we compared the genetic diversity, gene flow and population structure of two octocoral species, Eunicella verrucosa and Alcyonium digitatum, in the northeast Atlantic (ranging from the northwest of Ireland and the southern North Sea, to southern Portugal), using two panels of thirteen and eight microsatellite loci, respectively. Our results identified regional genetic structure in E. verrucosa partitioned between populations from southern Portugal, northwest Ireland, and Britain/France; subsequent hierarchical analysis of population structure also indicated reduced gene flow between southwest Britain and northwest France. However, over a similar geographical area, A. digitatum showed little evidence of population structure, suggesting high gene flow and/or a large effective population size; indeed, the only significant genetic differentiation detected in A. digitatum occurred between North Sea samples and those from the English Channel/northeast Atlantic. In both species the vast majority of gene flow originated from sample sites within regions, with populations in southwest Britain being the predominant source of contemporary exogenous genetic variants for the populations studied. Unsurprisingly, historical patterns of gene flow appeared more complex, though again southwest Britain appeared an important source of genetic variation for both species. Our findings have major conservation implications, particularly for E. verrucosa, a protected species in UK waters and listed by the IUCN as ‘Vulnerable’, and for the designation and management of European MPAs.We thank Natural England (project No. RP0286, contract No. SAE 03-02-146), the NERC (grant No. NE/L002434/1) and the University of Exeter for funding this research. Additional funding for sample collection, travel and microsatellite development was provided by the EU Framework 7 ASSEMBLE programme, agreement no. 227799, and NERC grant No. NBAF-362