Multiple csv worksheets for data analysis and modelling

There are numerous examples of phenological shifts that are recognized both as indicators of climate change and drivers of ecosystem change. A pressing challenge is to understand the causal mechanisms by which climate affects phenology. We combined annual population census data and individual longitudinal data (1992–2018) on grey seals,Halicheorus grypus, to quantify the relationship between pupping season phenology and sea surface temperature. A temperature increase of 2°C was associated with a pupping season advance of approximately seven days at the population level. However, we found that maternal age, rather than sea temperature, accounted for changes in pupping date by individuals. Warmer years were associated with an older average age of mothers, allowing us to explain phenological observations in terms of a changing population age structure. Finally, we developed a matrix population model to test whether our observations were consistent with changes to the stable age distribution. This could not fully account for observed phenological shift, strongly suggesting transient modification of population age structure, for example owing to immigration. We demonstrate a novel mechanism for phenological shifts under climate change in long-lived, age- or stage-structured species with broad implications for dynamics and resilience, as well as population management.

Abstract Conservation and population management decisions often rely on population models parameterized using census data. However, the sampling regime, precision, sample size, and methods used to collect census data are usually heterogeneous in time and space. Decisions about how to derive population‐wide estimates from this patchwork of data are complicated and may bias estimated population dynamics, with important implications for subsequent management decisions. Here, we explore the impact of site selection and data aggregation decisions on pup survival estimates, and downstream estimates derived from parameterized matrix population models (MPMs), using a long‐term dataset on grey seal (Halichoerus grypus) pup survival from southwestern Wales. The spatiotemporal and methodological heterogeneity of the data are fairly typical for ecological census data and it is, therefore, a good model to address this topic. Data were collected from 46 sampling locations (sites) over 25 years, and we explore the impact of data handling decisions by varying how years and sampling locations are combined to parameterize pup survival in population‐level MPMs. We focus on pup survival because abundant high‐quality data are available on this developmental stage. We found that survival probability was highly variable with most variation being at the site level, and poorly correlated among sampling sites. This variation could generate marked differences in predicted population dynamics depending on sampling strategy. The sample size required for a confident survival estimate also varied markedly geographically. We conclude that for populations with highly variable vital rates among sub‐populations, site selection and data aggregation methods are important. In particular, including peripheral or less frequently used areas can introduce substantial variation into population estimates. This is likely to be context‐dependent, but these choices, including the use of appropriate weights when summarizing across sampling areas, should be explored to ensure that management actions are successful.

Grey seals ( Halichoerus grypus ) are a qualifying feature of three special areas of conservation (SACs) in Wales, yet relatively little is known of their site use along this coastline. Since 1992, many individuals and organisations have contributed to a grey seal photographic identification database held by Natural Resources Wales, which is one of the largest and oldest of its kind, providing key information from grey seal haul-out sites around the Celtic and Irish Seas. Here, we investigated spatial connectivity of haul-out sites and fidelity of adult females to breeding sites. The minimum number of adult female grey seals using the area between 1992 and 2016 was 2688. Individual capture histories and relative spatial transition probabilities ( P ij ) between pairs of location groups were calculated. Adjacent locations were highly connected (e.g. Lleyn Peninsula and Bardsey, P ij = 0.7) but connections spanned the entire region, up to 230 km apart (e.g. Skomer and Dee Estuary, P ij = 0.004). Resights were recorded within SACs (e.g. Lleyn Peninsula and Bardsey [Lleyn Peninsula and the Sarnau SAC], P ij = 0.7), between SACs (e.g. Bardsey and Skomer [Pembrokeshire Marine], P ij = 0.03), between SACs and non-designated areas (e.g. Skerries and Bardsey, P ij = 0.09) and between sites outside any protected area (e.g. Dee Estuary and Anglesey, P ij = 0.5). While inter-annual fidelity to breeding sites was high ( P ij = 0.82–1), individual female grey seals moved throughout the region. This evidence of extensive site use beyond protected areas is important for the management and conservation of grey seals around Wales.

Marine turtles are of conservation concern throughout their range, with past population declines largely due to exploitation through both legal and illegal take, and incidental capture in fisheries. Whilst much research effort has been focused on nesting beaches and elaborating migratory corridors, these species spend the vast majority of their life-cycle in foraging grounds, which are, in some species, quite discrete. To understand and manage these populations, empirical data are needed on distribution, space-use, and habitats to best inform design of protective measures. Here we describe space-use, occupancy, and wide-ranging movements derived from conventional flipper tagging and satellite tracking of sub-adult green turtles (Chelonia mydas) within the coastal waters of the Turks and Caicos Islands (TCI; 2011-2017). 623 turtles were fitted with flipper tags, with 69 subsequently recaptured, five of which in international waters. Sixteen individual turtles of between 63 and 81 cm curved carapace length were satellite tracked for a mean 226 days (range: 38-496). Data revealed extended periods of occupancy in the shallow coastal waters within a RAMSAR protected area. Satellite tracking and flipper tagging showed wide-ranging movements, with flipper tag recaptures occurring in waters off Nicaragua (n = 4), and Venezuela (n = 1). Also, four of 16 satellite tracked turtles exhibiting directed movements away (displaced 450 km) from TCI waters traveling through nine geo-political zones within the Caribbean-Atlantic basin, as well as on the High Seas. One turtle traveled to the Central American coast before settling on inshore habitat in Colombia's waters for 162 days before transmission ceased, indicating ontogenetic dispersal to a distant foraging habitat. These data highlight connectivity throughout the region, displaying key linkages between countries that have previously only been linked by genetic evidence. This study also provides evidence of the importance of the Turks and Caicos Islands marine protected area network and importance of effective management of the sea turtle fishery for regional green turtle populations.

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Biologging devices are used ubiquitously across vertebrate taxa in studies of movement and behavioural ecology to record data from organisms without the need for direct observation. Despite the dramatic increase in the sophistication of this technology, progress in reducing the impact of these devices to animals is less obvious, notwithstanding the implications for animal welfare. Existing guidelines focus on tag weight (e.g. the ‘5% rule'), ignoring aero/hydrodynamic forces in aerial and aquatic organisms, which can be considerable. Designing tags to minimize such impact for animals moving in fluid environments is not trivial, as the impact depends on the position of the tag on the animal, as well as its shape and dimensions. We demonstrate the capabilities of computational fluid dynamics (CFD) modelling to optimize the design and positioning of biologgers on marine animals, using the grey seal (Halichoerus grypus) as a model species. Specifically, we investigate the effects of (a) tag form, (b) tag size, and (c) tag position and quantify the impact under frontal hydrodynamic forces, as encountered by seals swimming at sea. By comparing a conventional versus a streamlined tag, we show that the former can induce up to 22% larger drag for a swimming seal; to match the drag of the streamlined tag, the conventional tag would have to be reduced in size by 50%. For the conventional tag, the drag induced can differ by up to 11% depending on the position along the seal's body, whereas for the streamlined tag this difference amounts to only 5%. We conclude by showing how the CFD simulation approach can be used to optimize tag design to reduce drag for aerial and aquatic species, including issues such as the impact of lateral currents (unexplored until now). We also provide a step‐by‐step guide to facilitate the implementation of CFD in biologging tag design.

Many marine megavertebrate taxa, including sea turtles, disperse widely from their hatching or birthing locations but display natal homing as adults. We used flipper tagging, satellite tracking and genetics to identify the origin of loggerhead turtles living in Amvrakikos Gulf, Greece. This location has been identified as hosting regionally important numbers of large-juvenile to adult sized turtles that display long-term residency and/or association to the area, and also presents a male biased sex ratio for adults. A total of 20 individuals were linked to nesting areas in Greece through flipper tagging and satellite telemetry, with the majority (16) associated with Zakynthos Island. One additional female was tracked from Amvrakikos Gulf to Turkey where she likely nested. Mitochondrial DNA mixed stock analyses of turtles captured in Amvrakikos Gulf (n = 95) indicated 82% of individuals originated from Greek nesting stocks, mainly from Zakynthos Island (63%), with lesser contributions from central Turkey, Cyprus and Libya. These results suggest that the male-biased sex ratio found in Amvrakikos Gulf may be driven by the fact that males breed twice as frequently on Zakynthos, resulting in their using foraging grounds of greater proximity to the breeding site. Conservation measures in localised foraging habitats for the protection of marine vertebrates, such as sea turtles, may have positive impacts on several disparate breeding stocks and the use of multiple methods to determine source populations can indicate the relative effectiveness of these measures.

Somatic growth is an integrated, individual‐based response to environmental conditions, especially in ectotherms. Growth dynamics of large, mobile animals are particularly useful as bio‐indicators of environmental change at regional scales. We assembled growth rate data from throughout the West Atlantic for green turtles, Chelonia mydas, which are long‐lived, highly migratory, primarily herbivorous mega‐consumers that may migrate over hundreds to thousands of kilometers. Our dataset, the largest ever compiled for sea turtles, has 9690 growth increments from 30 sites from Bermuda to Uruguay from 1973 to 2015. Using generalized additive mixed models, we evaluated covariates that could affect growth rates; body size, diet, and year have significant effects on growth. Growth increases in early years until 1999, then declines by 26% to 2015. The temporal (year) effect is of particular interest because two carnivorous species of sea turtles—hawksbills, Eretmochelys imbricata, and loggerheads, Caretta caretta—exhibited similar significant declines in growth rates starting in 1997 in the West Atlantic, based on previous studies. These synchronous declines in productivity among three sea turtle species across a trophic spectrum provide strong evidence that an ecological regime shift (ERS) in the Atlantic is driving growth dynamics. The ERS resulted from a synergy of the 1997/1998 El Niño Southern Oscillation (ENSO)—the strongest on record—combined with an unprecedented warming rate over the last two to three decades. Further support is provided by the strong correlations between annualized mean growth rates of green turtles and both sea surface temperatures (SST) in the West Atlantic for years of declining growth rates (r = −.94) and the Multivariate ENSO Index (MEI) for all years (r = .74). Granger‐causality analysis also supports the latter finding. We discuss multiple stressors that could reinforce and prolong the effect of the ERS. This study demonstrates the importance of region‐wide collaborations.

Somatic growth dynamics are an integrated response to environmental conditions. Hawksbill sea turtles (Eretmochelys imbricata) are long-lived, major consumers in coral reef habitats that move over broad geographic areas (hundreds to thousands of kilometers). We evaluated spatio-temporal effects on hawksbill growth dynamics over a 33-yr period and 24 study sites throughout the West Atlantic and explored relationships between growth dynamics and climate indices. We compiled the largest ever data set on somatic growth rates for hawksbills -3541 growth increments from 1980 to 2013. Using generalized additive mixed model analyses, we evaluated 10 covariates, including spatial and temporal variation, that could affect growth rates. Growth rates throughout the region responded similarly over space and time. The lack of a spatial effect or spatio-temporal interaction and the very strong temporal effect reveal that growth rates in West Atlantic hawksbills are likely driven by region-wide forces. Between 1997 and 2013, mean growth rates declined significantly and steadily by 18%. Regional climate indices have significant relationships with annual growth rates with 0- or 1-yr lags: positive with the Multivariate El Nino Southern Oscillation Index (correlation = 0.99) and negative with Caribbean sea surface temperature (correlation = -0.85). Declines in growth rates between 1997 and 2013 throughout the West Atlantic most likely resulted from warming waters through indirect negative effects on foraging resources of hawksbills. These climatic influences are complex. With increasing temperatures, trajectories of decline of coral cover and availability in reef habitats of major prey species of hawksbills are not parallel. Knowledge of how choice of foraging habitats, prey selection, and prey abundance are affected by warming water temperatures is needed to understand how climate change will affect productivity of consumers that live in association with coral reefs.

Marine turtles are considered keystone consumers in tropical coastal ecosystems and their decline through overexploitation has been implicated in the deterioration of reefs and seagrass pastures in the Caribbean. In the present study, we analysed stomach contents of green (Chelonia mydas) and hawksbill turtles (Eretmochelys imbricata) harvested in the legal turtle fishery of the Turks and Caicos Islands (Caribbean) during 2008-2010. Small juveniles to adult-sized turtles were sampled. Together with data from habitat surveys, we assessed diet composition and the taxonomic distinctness (and other species diversity measures) in the diets of these sympatric marine turtle species. The diet of green turtles (n=92) consisted of a total of 47 taxa: including three species of seagrass (present in 99% of individuals), 29 species of algae and eight sponge species. Hawksbill turtles (n=45) consumed 73 taxa and were largely spongivorous (16 species; sponges present in 100% of individuals) but also foraged on 50 species of algae (present in 73% of individuals) and three species of seagrass. Plastics were found in trace amounts in 4% of green turtle and 9% of hawksbill turtle stomach samples. We expected to find changes in diet that might reflect ontogenetic shifts from small (oceanic-pelagic) turtles to larger (coastal-benthic) turtles. Dietary composition (abundance and biomass), however, did not change significantly with turtle size, although average taxonomic distinctness was lower in larger green turtles. There was little overlap in prey between the two turtle species, suggesting niche separation. Taxonomic distinctness routines indicated that green turtles had the most selective diet, whereas hawksbill turtles were less selective than expected when compared with the relative frequency and biomass of diet items. We discuss these findings in relation to the likely important trophic roles that these sympatric turtle species play in reef and seagrass habitats.

Marine turtles are sensitive to harvesting because of life-cycle traits such as longevity, late maturity and natal philopatry. The take of nesting females is of conservation concern because they are key to population maintenance and has led to global efforts to protect this life stage. In the Turks and Caicos Islands (TCI; a UK Overseas Territory in the Caribbean), previous turtle fishery legislation protected nesting turtles on the beach but not in the water, where turtles over a minimum size were subject to legal take. In a 2-year study, we undertook nesting beach and in-water surveys, molecular analyses, satellite tracking and collation of fisheries landing data to investigate the populations of green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) turtles in the TCI and its turtle fishery. Adults were frequently taken in one of the region's largest legal and artisanal turtle fisheries. We suggest that nesting populations in the TCI, which contain genetically unique haplotypes, have diminished since the 1980s, likely as a result of the harvest of adults. Using these multiple lines of evidence, we highlight the inadequacies of the former fishery regulations and propose specific legislative amendments, which, as a result of this study, were implemented on 1 July 2014 by the TCI government. With good enforcement, these measures will protect adults breeding in the TCI and those from nesting rookeries in the region that use the waters of the TCI, improve the management of this fishery, and safeguard fisher livelihoods.

Disease in wildlife populations is often controlled through culling. But when healthy individuals are removed and diseased individuals are left in the population, it is anticipated that prevalence of disease increases. Although this scenario is presumably common in exploited populations where infected individuals are less marketable, it is not widely reported in the literature. We describe this scenario in a marine turtle fishery in the Turks and Caicos Islands (TCI), where green turtles are harvested for local consumption. During a two-year period, we recorded the occurrence of fibropapillomatosis (FP) disease in green turtles (Chelonia mydas) captured during in-water surveys and compared it with that of turtles landed in the fishery. 13.4% (n=32) of turtles captured during in-water surveys showed externally visible signs of FP. FP occurred at specific geographic locations where fishing also occurred. Despite the disease being prevalent in the size classes selected by fishers, FP was not present in any animals landed by the fishery (n=162). The majority (61%) of fishers interviewed expressed that they had caught turtles with FP. Yet, 82% of those that had caught turtles with the disease chose to return their catch to the sea, selectively harvesting healthy turtles and leaving those with the disease in the population. Our study illustrates that fisher choice may increase the prevalence of FP disease and highlights the importance of this widely neglected driver in the disease dynamics of exploited wildlife populations.

Grey seals (Halichoerus grypus) are a species of conservation concern that require Marine Protected Area management and population status assessment under the EU Habitats Directive. Aerial surveys are commonly used to monitor grey seal pup production at their globally important UK colonies. However, in Wales more than half of pups are born in cryptic breeding habitats such as sea caves. These cryptic habitats preclude the use of aerial monitoring methods and necessitate ground-based counts, which are costly in resources. In this study, we compare a ground-based pup production census with a reduced effort plot-sampling survey to estimate pup production, derive a total population size and assess cost effectiveness. Pup production in North Wales was estimated at 91 (95% confidence interval: 70–112) by the plot-sampling design and was a good approximation of the ‘true’ value of 96 derived from the census. The total population size in North Wales was estimated at between 242 and 307 grey seals. The plot-sampling design reduced survey effort by 46% and saved 30% on logistical costs compared to the full census. We outline the suitability of this method as part of a monitoring programme for grey seal pup production and suggest our approach may be applicable to other regions where grey seals use cryptic breeding habitat.

Small-scale fisheries (SSF) account for around half of the world's marine and inland fisheries, but their impact on the marine environment is usually under-estimated owing to difficulties in monitoring and regulation. Successful management of mixed SSF requires holistic approaches that sustainably exploit target species, consider non-target species and maintain fisher livelihoods. For two years, we studied the marine turtle fishery in the Turks and Caicos Islands (TCI) in the Wider Caribbean Region, where the main export fisheries are queen conch (Strombus gigas) and the spiny lobster (Panulirus argus); with fin-fish, green turtles (Chelonia mydas) and hawksbill turtles (Eretmochelys imbricata) taken for domestic consumption. We evaluate the turtle harvest in relation to the other fisheries and recommend legislation and management alternatives. We demonstrate the connectivity between multi-species fisheries and artisanal turtle capture: with increasing lobster catch-per-unit-effort (CPUE), hawksbill catch increased whilst green turtle catch decreased. With increasing conch CPUE, hawksbill catch declined and there was no demonstrable effect on green turtle catch. We estimate 176–324 green and 114–277 hawksbill turtles are harvested annually in TCI: the largest documented legal hawksbill fishery in the western Atlantic. Of particular concern is the capture of adult turtles. Current legislation focuses take on larger individuals that are key to population maintenance. Considering these data we recommend the introduction of maximum size limits for both species and a closed season on hawksbill take during the lobster fishing season. Our results highlight the need to manage turtles as part of a broader approach to SSF management.

Performance assessment, impact detection, and the assessment of regulatory compliance are common scientific problems for the management of protected areas. Some habitats in protected areas, however, are rare and/or variable and are not often selected for study by ecologists because they preclude comparison with controls and high community variability makes meaningful change detection difficult. Shallow coastal saline lagoons are habitats that experience comparatively high levels of stress due to high physical variability. Lagoons are rare, declining habitats found in coastal regions throughout Europe (and elsewhere) where they are identified as one of the habitats most in need of protected area management. The infauna in the sediments of 25 lagoons were sampled. Temporal and spatial variation in three of these [protected] lagoons was investigated further over 5 years. In a multivariate analysis of community structure similarities were found between some lagoons, but in other cases communities were unique or specific to only two sites. The protected lagoons with these unique/specific communities showed significant temporal and spatial variation, yet none of the changes observed were attributed to human impacts and were interpreted as inherent variability. Multivariate control charts can operate without experimental controls and were used to assess community changes within the context of ‘normal’ lagoon variability. The aim of control chart analysis is to characterize background variability in a parameter and identify when a new observation deviates more than expected. In only 1 year was variability more than expected and corresponded with the coldest December in over 100 years. Multivariate control charts are likely to have wide application in the management of protected areas and other natural systems where variability and/or rarity preclude conventional analytical and experimental approaches but where assessments of condition, impact or regulatory compliance are nonetheless required.

This study describes the impact of the first passage of two types of bottom-towed fishing gear on rare protected shellfish-reefs formed by the horse mussel Modiolus modiolus (L.). One of the study sites was trawled and the other was scallop-dredged. Divers collected HD video imagery of epifauna from quadrats at the two study sites and directed infaunal samples from one site. The total number of epifaunal organisms was significantly reduced following a single pass of a trawl (90%) or scallop dredge (59%), as was the diversity of the associated community and the total number of M. modiolus at the trawled site. At both sites declines in anthozoans, hydrozoans, bivalves, echinoderms and ascidians accounted for most of the change. A year later, no recovery was evident at the trawled site and significantly fewer infaunal taxa (polychaetes, malacostracans, bivalves and ophuroids) were recorded in the trawl track. The severity of the two types of impact reflected the undisturbed status of the habitats compared to previous studies. As a 'priority habitat' the nature of the impacts described on M. modiolus communities are important to the development of conservation management policy and indicators of condition in Marine Protected Areas (EU Habitats Directive) as well as indicators of 'Good Environmental Status' under the European Union Marine Strategy Framework Directive. Conservation managers are under pressure to support decisions with good quality evidence. Elsewhere, indirect studies have shown declines of M. modiolus biogenic communities in fishing grounds. However, given the protected status of the rare habitat, premeditated demonstration of direct impact is unethical or illegal in Marine Protected Areas. This study therefore provides a unique opportunity to investigate the impact from fishing gear whilst at the same time reflecting on the dilemma of evidence-based conservation management.