Using individual tracking data to validate the predictions of species distribution models

The authors would like to thank the College of Life Sciences of Aberdeen University and Marine Scotland Science which funded CP's PhD project. Skate tagging experiments were undertaken as part of Scottish Government project SP004. We thank Ian Burrett for help in catching the fish and the other fishermen and anglers who returned tags. We thank José Manuel Gonzalez-Irusta for extracting and making available the environmental layers used as environmental covariates in the environmental suitability modelling procedure. We also thank Jason Matthiopoulos for insightful suggestions on habitat utilization metrics as well as Stephen C.F. Palmer, and three anonymous reviewers for useful suggestions to improve the clarity and quality of the manuscript.

Estimating density of a rare and cryptic high-mountain Galliform species, the Buff-throated Partridge Tetraophasis szechenyii

Estimates of abundance or density are essential for wildlife management and conservation. There are few effective density estimates for the Buff-throated Partridge Tetraophasis szechenyii, a rare and elusive high-mountain Galliform species endemic to western China. In this study, we used the temporary emigration N-mixture model to estimate density of this species, with data acquired from playback point count surveys around a sacred area based on indigenous Tibetan culture of protection of wildlife, in Yajiang County, Sichuan, China, during April–June 2009. Within 84 125-m radius points, we recorded 53 partridge groups during three repeats. The best model indicated that detection probability was described by covariates of vegetation cover type, week of visit, time of day, and weather with weak effects, and a partridge group was present during a sampling period with a constant probability. The abundance component was accounted for by vegetation association. Abundance was substantially higher in rhododendron shrubs, fir-larch forests, mixed spruce-larch-birch forests, and especially oak thickets than in pine forests. The model predicted a density of 5.14 groups/km², which is similar to an estimate of 4.7 – 5.3 groups/km² quantified via an intensive spot-mapping effort. The post-hoc estimate of individual density was 14.44 individuals/km², based on the estimated mean group size of 2.81. We suggest that the method we employed is applicable to estimate densities of Buff-throated Partridges in large areas. Given importance of a mosaic habitat for this species, local logging should be regulated. Despite no effect of the conservation area (sacred) on the abundance of Buff-throated Partridges, we suggest regulations linking the sacred mountain conservation area with the official conservation system because of strong local participation facilitated by sacred mountains in land conservation.

What you find depends on where you look: responses to proximate habitat vary with landscape context

There is persistent interest in understanding responses of passerine birds to habitat fragmentation, but research findings have been inconsistent and sometimes contradictory in conclusions about how birds respond to characteristics of sites they occupy, such as habitat patch size or edge density. We examined whether these inconsistencies could result from differences in the amount of habitat in the surrounding landscape, e.g., for woodland birds, the amount of tree cover in the surrounding landscape. We compared responses of 22 woodland bird species to proximate-scale tree cover in open landscapes versus wooded landscapes. Our main expectation was that woodland birds would tolerate less suitable sites (less tree cover at the site scale) in open environments where they had little choice–where little tree cover was available in the surrounding area. We compared responses using logistic regression coefficients and loess plots in open and wooded landscapes in eastern North Dakota, USA. Responses to proximate-scale tree cover were stronger, not weaker, as expected, in open landscapes. In some cases the sign of the response changed from positive to negative in contrasting landscapes. We draw two conclusions: First, observed responses to proximate habitat measures such as habitat extent or edge density cannot be interpreted reliably unless landscape context is specified. Second, birds appear more selective, not less so, where habitat is sparse. Habitat loss and fragmentation at the landscape scale are likely to reduce the usefulness of local habitat conservation, and regional drivers in land-use change can have important effects for site-scale habitat use.

Projected responses of North American grassland songbirds to climate change and habitat availability at their northern range limits in Alberta, Canada

Across North America, grassland songbirds have undergone steep population declines over recent decades, commonly attributed to agricultural intensification. Understanding the potential interactions between the impacts of climate change on the future distributions of these species and the availability of suitable vegetation for nesting can support improved risk assessments and conservation planning for this group of species. We used North American bioclimatic niche models to examine future changes in suitable breeding climate for 15 grassland songbird species at their current northern range limits along the boreal forest–prairie ecotone in Alberta, Canada. Our climate suitability projections, combined with the current distribution of native and tame pasture and cropland in Alberta, suggest that some climate-mediated range expansion of grassland songbirds in Alberta is possible. For six of the eight species projected to experience expansions of suitable climate area in Alberta, this suitable climate partly overlaps the current distribution of suitable land cover. Additionally, for more than half of the species examined, most of the area of currently suitable climate was projected to remain suitable to the end of the century, highlighting the importance of Alberta for the long-term persistence of these species. Some northern prairie-endemic species exhibited substantial projected northward shifts of both the northern and southern edges of the area of suitable climate. Baird’s Sparrow (Ammodramus bairdii) and Sprague’s Pipit (Anthus spragueii), both at-risk grassland specialists, are predicted to have limited climate stability within their current ranges, and their expansion into new areas of suitable climate may be limited by the availability of suitable land cover. Our results highlight the importance of the preservation and restoration of remaining suitable grassland habitat within areas of projected climate stability and beyond current northern range limits for the long-term persistence of many grassland songbird species in the face of climate change.

Prioritizing tropical habitats for long-distance migratory songbirds: an assessment of habitat quality at a stopover site in Colombia

Long-distance migratory birds are declining globally and migration has been identified as the primary source of mortality in this group. Despite this, our lack of knowledge of habitat use and quality at stopovers, i.e., sites where the energy for migration is accumulated, remains a barrier to designing appropriate conservation measures, especially in tropical regions. There is therefore an urgent need to assess stopover habitat quality and concurrently identify efficient and cost-effective methods for doing so. Given that fuel deposition rates directly influence stopover duration, departure fuel load, and subsequent speed of migration, they are expected to provide a direct measure of habitat quality and have the advantage of being measurable through body-mass changes. Here, we examined seven potential indicators of quality, including body-mass change, for two ecologically distinct Neotropical migratory landbirds on stopover in shade-coffee plantations and tropical humid premontane forest during spring migration in Colombia: (1) rate of body-mass change; (2) foraging rate; (3) recapture rate; (4) density; (5) flock size; (6) age and sex ratios; and (7) body-mass distribution. We found higher rates of mass change in premontane forest than in shade-coffee in Tennessee Warbler Oreothlypis peregrina, a difference that was mirrored in higher densities and body masses in forest. In Gray-cheeked Thrush Catharus minimus, a lack of recaptures in shade-coffee and higher densities in forest, also suggested that forest provided superior fueling conditions. For a reliable assessment of habitat quality, we therefore recommend using a suite of indicators, taking into account each species’ ecology and methodological considerations. Our results also imply that birds stopping over in lower quality habitats may spend a longer time migrating and require more stopovers, potentially leading to important carryover effects on reproductive fitness. Evaluating habitat quality is therefore imperative prior to defining the conservation value of newly identified stopover regions.

Data to Decision in a Dynamic Ocean: Robust Species Distribution Models and Spatial Decision Frameworks

Human use of the oceans is increasingly in conflict with conservation of endangered species. Methods for managing the spatial and temporal placement of industries such as military, fishing, transportation and offshore energy, have historically been post hoc; i.e. the time and place of human activity is often already determined before assessment of environmental impacts. In this dissertation, I build robust species distribution models in two case study areas, US Atlantic (Best et al. 2012) and British Columbia (Best et al. 2015), predicting presence and abundance respectively, from scientific surveys. These models are then applied to novel decision frameworks for preemptively suggesting optimal placement of human activities in space and time to minimize ecological impacts: siting for offshore wind energy development, and routing ships to minimize risk of striking whales. Both decision frameworks relate the tradeoff between conservation risk and industry profit with synchronized variable and map views as online spatial decision support systems.

For siting offshore wind energy development (OWED) in the U.S. Atlantic (chapter 4), bird density maps are combined across species with weights of OWED sensitivity to collision and displacement and 10 km2 sites are compared against OWED profitability based on average annual wind speed at 90m hub heights and distance to transmission grid. A spatial decision support system enables toggling between the map and tradeoff plot views by site. A selected site can be inspected for sensitivity to a cetaceans throughout the year, so as to capture months of the year which minimize episodic impacts of pre-operational activities such as seismic airgun surveying and pile driving.

Routing ships to avoid whale strikes (chapter 5) can be similarly viewed as a tradeoff, but is a different problem spatially. A cumulative cost surface is generated from density surface maps and conservation status of cetaceans, before applying as a resistance surface to calculate least-cost routes between start and end locations, i.e. ports and entrance locations to study areas. Varying a multiplier to the cost surface enables calculation of multiple routes with different costs to conservation of cetaceans versus cost to transportation industry, measured as distance. Similar to the siting chapter, a spatial decisions support system enables toggling between the map and tradeoff plot view of proposed routes. The user can also input arbitrary start and end locations to calculate the tradeoff on the fly.

Essential to the input of these decision frameworks are distributions of the species. The two preceding chapters comprise species distribution models from two case study areas, U.S. Atlantic (chapter 2) and British Columbia (chapter 3), predicting presence and density, respectively. Although density is preferred to estimate potential biological removal, per Marine Mammal Protection Act requirements in the U.S., all the necessary parameters, especially distance and angle of observation, are less readily available across publicly mined datasets.

In the case of predicting cetacean presence in the U.S. Atlantic (chapter 2), I extracted datasets from the online OBIS-SEAMAP geo-database, and integrated scientific surveys conducted by ship (n=36) and aircraft (n=16), weighting a Generalized Additive Model by minutes surveyed within space-time grid cells to harmonize effort between the two survey platforms. For each of 16 cetacean species guilds, I predicted the probability of occurrence from static environmental variables (water depth, distance to shore, distance to continental shelf break) and time-varying conditions (monthly sea-surface temperature). To generate maps of presence vs. absence, Receiver Operator Characteristic (ROC) curves were used to define the optimal threshold that minimizes false positive and false negative error rates. I integrated model outputs, including tables (species in guilds, input surveys) and plots (fit of environmental variables, ROC curve), into an online spatial decision support system, allowing for easy navigation of models by taxon, region, season, and data provider.

For predicting cetacean density within the inner waters of British Columbia (chapter 3), I calculated density from systematic, line-transect marine mammal surveys over multiple years and seasons (summer 2004, 2005, 2008, and spring/autumn 2007) conducted by Raincoast Conservation Foundation. Abundance estimates were calculated using two different methods: Conventional Distance Sampling (CDS) and Density Surface Modelling (DSM). CDS generates a single density estimate for each stratum, whereas DSM explicitly models spatial variation and offers potential for greater precision by incorporating environmental predictors. Although DSM yields a more relevant product for the purposes of marine spatial planning, CDS has proven to be useful in cases where there are fewer observations available for seasonal and inter-annual comparison, particularly for the scarcely observed elephant seal. Abundance estimates are provided on a stratum-specific basis. Steller sea lions and harbour seals are further differentiated by ‘hauled out’ and ‘in water’. This analysis updates previous estimates (Williams & Thomas 2007) by including additional years of effort, providing greater spatial precision with the DSM method over CDS, novel reporting for spring and autumn seasons (rather than summer alone), and providing new abundance estimates for Steller sea lion and northern elephant seal. In addition to providing a baseline of marine mammal abundance and distribution, against which future changes can be compared, this information offers the opportunity to assess the risks posed to marine mammals by existing and emerging threats, such as fisheries bycatch, ship strikes, and increased oil spill and ocean noise issues associated with increases of container ship and oil tanker traffic in British Columbia’s continental shelf waters.

Starting with marine animal observations at specific coordinates and times, I combine these data with environmental data, often satellite derived, to produce seascape predictions generalizable in space and time. These habitat-based models enable prediction of encounter rates and, in the case of density surface models, abundance that can then be applied to management scenarios. Specific human activities, OWED and shipping, are then compared within a tradeoff decision support framework, enabling interchangeable map and tradeoff plot views. These products make complex processes transparent for gaming conservation, industry and stakeholders towards optimal marine spatial management, fundamental to the tenets of marine spatial planning, ecosystem-based management and dynamic ocean management.

Habitat Use of the Key Largo Woodrat (Neotoma floridana smalli)

Key Largo woodrats are an endangered subspecies with an extremely limited habitat. This study sought to understand woodrat habitat preferences in order to guide management. Woodrats build stick nests from natural and artificial materials, so nest distribution and nest occupancy were used as indicators of preference. Distribution was determined by nest surveys, and remote cameras were used to assess occupancy. Forest structure, human disturbance, nest, and animal presence metrics were also collected. More nests were found along abandoned roads than along forest transects and more artificial nests were occupied than natural nests. These findings indicate that woodrats prefer areas with human disturbance, rather than forest age and structure as previously believed. This may have consequences on woodrat management, as it suggests that man-made materials are currently needed by woodrats even in a protected natural area.

Isotopic measurements of 3 foraminifer species from ODP Hole 171-1050C

Analysis of 944 single specimens of three species of late Maastrichtian planktonic foraminifera (Racemiguembelina fructicosa, Contusotruncana contusa, and Rugoglobigerina rugosa) from 38 samples spanning the last 3 Myr of the Cretaceous shows consistent isotopic trends through time, consistent isotopic differences among taxa, and high within-sample isotopic variability throughout. Within-sample variability does not change systematically through time for any taxon, but average d18O values decrease by approx. 1.5 per mill, and average d13C values diverge up section. Comparing taxa, average d18O values are similar within most samples, but average d13C values generally decrease from R. fructicosa to R. rugosa to C. contusa. In addition, the within-sample variability of individual d13C measurements is larger for R. fructicosa than for either C. contusa or R. rugosa, an observation which is consistent with a photosymbiotic habitat for R. fructicosa. In terms of Maastrichtian paleoceanography the negative d18O trend of approx. 1.5 per mill corresponds to a temperature increase of approx. 6°C, and the divergence of d13C values up section suggests an increasingly stratified water column in the western Atlantic through the late Maastrichtian. We suggest that these trends are best explained by increasing import of South Atlantic waters into the North Atlantic and an intensification of the Northern Hemisphere polar front.

Relative abundance of diatom species in surface samples from the Southern Ocean, Sea ice species

Diatoms from 228 Southern Ocean core-top sediment samples were examined to determine the geographic distributions of 32 major diatom species/taxa preserved in the sediments of three zonally-distinct regions; Sea Ice, Open Ocean and the Tropical/Subtropical. In the first of three papers, 14 species/taxa occurring in the region where sea ice covers the ocean surface on an annual basis are geographically documented. Comparisons are drawn between the diatom abundances on the sea floor, sea ice parameters (annual duration and concentration in February and September) and February sea-surface temperature. Such parameters are commonly used in reconstructing past oceanographic conditions in the Sea Ice and Open Ocean zones. Analysis of the geographic patterns and sea-surface parameter correlations reveals species-specific distributions regulated primarily by sea ice coverage and sea-surface temperature, which support the use of diatom remains for the estimation of these past sea-surface environmental parameters. Comparison with reliable accounts of the 14 species from the sediments or plankton also provides the first glimpses into species-specific ecology and habitat linkages.

The benthic foraminiferal community in a naturally CO2-rich coastal habitat of the southwestern Baltic Sea

It is expected that the calcification of foraminifera will be negatively affected by the ongoing acidification of the oceans. Compared to the open oceans, these organisms are subjected to much more adverse carbonate system conditions in coastal and estuarine environments such as the southwestern Baltic Sea, where benthic foraminifera are abundant. This study documents the seasonal changes of carbonate chemistry and the ensuing response of the foraminiferal community with bi-monthly resolution in Flensburg Fjord. In comparison to the surface pCO2, which is close to equilibrium with the atmosphere, we observed large seasonal fluctuations of pCO2 in the bottom and sediment pore waters. The sediment pore water pCO2 was constantly high during the entire year ranging from 1244 to 3324 µatm. Nevertheless, in contrast to the bottom water, sediment pore water was slightly supersaturated with respect to calcite as a consequence of higher alkalinity (AT) for most of the year. Foraminiferal assemblages were dominated by two calcareous species, Ammonia aomoriensis and Elphidium incertum, and the agglutinated Ammotium cassis. The one-year cycle was characterised by seasonal community shifts. Our results revealed that there is no dynamic response of foraminiferal population density and diversity to elevated sediment pore water pCO2. Surprisingly, the fluctuations of sediment pore water undersaturation (Omega calc) co-vary with the population densities of living Ammonia aomoriensis. Further, we observed that most of the tests of living calcifying foraminifera were intact. Only Ammonia aomorienis showed dissolution and recalcification structures on the tests, especially at undersaturated conditions. Therefore, the benthic community is subjected to high pCO2 and tolerates elevated levels as long as sediment pore water remains supersaturated. Model calculations inferred that increasing atmospheric CO2 concentrations will finally lead to a perennial undersaturation in sediment pore waters. Whereas benthic foraminifera indeed may cope with a high sediment pore water pCO2, the steady undersaturation of sediment pore waters would likely cause a significant higher mortality of the dominating Ammonia aomoriensis. This shift may eventually lead to changes in the benthic foraminiferal communities in Flensburg Fjord, as well as in other regions experiencing naturally undersaturated Omega calc levels.

Ecophysiology of Adonis distorta, a high-mountain species endemic of the Central Apennines

Morphological, anatomical and physiological plant and leaf traits of A. distorta, an endemic species of the Central Apennines on the Majella Massif, growing at 2,675 m a.s.l, were analyzed. The length of the phenological cycle starts immediately after the snowmelt at the end of May, lasting 128 ± 10 days. The low A. distorta height  (Hmax= 64 ± 4 mm) and total leaf area (TLA= 38 ± 9 cm2) associated to a high leaf mass area (LMA =11.8±0.6 mg cm−2) and a relatively high leaf tissue density (LTD = 124.6±14.3 mg cm−3) seem to be adaptive traits to the stress factors of the environment where it grows. From a physiological point of view, the high A. distorta photosynthetic rates (PN =19.6 ± 2.3 µmol m−2 s−1) and total chlorophyll content (Chla+b = 0.88 ± 0.13 mg g−1) in July are justified by the favorable temperature. PN decreases by 87% in September at the beginning of plant senescence. Photosynthesis and leaf respiration (RD) variations allow A. distorta to maintain a positive carbon balance during the growing season becoming indicative of the efficiency of plant carbon use. The results could be an important tool for conservation programmes of the A. distorta wild populations.

Application of computer-aided tomography techniques to visualize kelp holdfast structure reveals the importance of habitat complexity for supporting marine biodiversity

Ecosystem engineers that increase habitat complexity are keystone species in marine systems, increasing shelter and niche availability, and therefore biodiversity. For example, kelp holdfasts form intricate structures and host the largest number of organisms in kelp ecosystems. However, methods that quantify 3D habitat complexity have only seldom been used in marine habitats, and never in kelp holdfast communities. This study investigated the role of kelp holdfasts (Laminaria hyperborea) in supporting benthic faunal biodiversity. Computer-aided tomography (CT-) scanning was used to quantify the three-dimensional geometrical complexity of holdfasts, including volume, surface area and surface fractal dimension (FD). Additionally, the number of haptera, number of haptera per unit of volume, and age of kelps were estimated. These measurements were compared to faunal biodiversity and community structure, using partial least-squares regression and multivariate ordination. Holdfast volume explained most of the variance observed in biodiversity indices, however all other complexity measures also strongly contributed to the variance observed. Multivariate ordinations further revealed that surface area and haptera per unit of volume accounted for the patterns observed in faunal community structure. Using 3D image analysis, this study makes a strong contribution to elucidate quantitative mechanisms underlying the observed relationship between biodiversity and habitat complexity. Furthermore, the potential of CT-scanning as an ecological tool is demonstrated, and a methodology for its use in future similar studies is established. Such spatially resolved imager analysis could help identify structurally complex areas as biodiversity hotspots, and may support the prioritization of areas for conservation.

Application of computer-aided tomography techniques to visualize kelp holdfast structure reveals the importance of habitat complexity for supporting marine biodiversity

Ecosystem engineers that increase habitat complexity are keystone species in marine systems, increasing shelter and niche availability, and therefore biodiversity. For example, kelp holdfasts form intricate structures and host the largest number of organisms in kelp ecosystems. However, methods that quantify 3D habitat complexity have only seldom been used in marine habitats, and never in kelp holdfast communities. This study investigated the role of kelp holdfasts (Laminaria hyperborea) in supporting benthic faunal biodiversity. Computer-aided tomography (CT-) scanning was used to quantify the three-dimensional geometrical complexity of holdfasts, including volume, surface area and surface fractal dimension (FD). Additionally, the number of haptera, number of haptera per unit of volume, and age of kelps were estimated. These measurements were compared to faunal biodiversity and community structure, using partial least-squares regression and multivariate ordination. Holdfast volume explained most of the variance observed in biodiversity indices, however all other complexity measures also strongly contributed to the variance observed. Multivariate ordinations further revealed that surface area and haptera per unit of volume accounted for the patterns observed in faunal community structure. Using 3D image analysis, this study makes a strong contribution to elucidate quantitative mechanisms underlying the observed relationship between biodiversity and habitat complexity. Furthermore, the potential of CT-scanning as an ecological tool is demonstrated, and a methodology for its use in future similar studies is established. Such spatially resolved imager analysis could help identify structurally complex areas as biodiversity hotspots, and may support the prioritization of areas for conservation.

The comparative effects of habitat complexity on faunal assemblages of northern temperate artificial and natural reefs

Several north temperate marine species were recorded on subtidal hard-substratum reef sites selected to produce a gradient of structural complexity. The study employed an established scuba-based census method, the belt transect. The three types of reef examined, with a measured gradient of increasing structural complexity, were natural rocky reef, artificial reef constructed of solid concrete blocks, and artificial reef made of concrete blocks with voids. Surveys were undertaken monthly over a calendar year using randomly placed fixed rope transects. For a number of conspicuous species of fish and invertebrates, significant differences were found between the levels of habitat complexity and abundance. Overall abundance for many of the species examined was 2-3 times higher on the complex artificial habitats than on simple artificial or natural reef habitats. The enhanced habitat availability produced by the increased structural complexity delivered through specifically designed artificial reefs may have the potential to augment faunal abundance while promoting species diversity. 

Extralimital Senegalese species during Marine Isotope Stages 5.5 and 11 in the Canary Islands (29 degrees N): Sea surface temperature estimates

[EN] The presence of Harpa doris Röding, 1798 in marine deposits of the last interglacial period, ~. 130-120. ka (marine isotope stage or MIS 5.5) in the Canary Islands (Gran Canaria, Lanzarote and Fuerteventura) enabled us to compare this occurrence with its present habitat in the Gulf of Guinea and the Cape Verde Islands, well to the south. This comparison leads to the conclusion that sea surface temperatures (SSTs) in the waters around the Canary Islands during the last interglacial period were at least 3.3. °C higher than today. H. doris is found in association with the large gastropod Persististrombus latus (Gmelin, 1791) as well as the coral Siderastrea radians (Pallas, 1766).