A virtual species set for robust and reproducible species distribution modelling tests

Predicting species potential and future distribution has become a relevant tool in biodiversity monitoring and conservation.In this data article we present the suitability map of a virtual species generated based on two bioclimatic variables, and a dataset containing more than 700,000 random observations at the extent of Europe. The dataset includes spatial attributes such as: distance to roads, protected areas, country codes, and the habitat suitability of two spatially clustered species (grassland and forest species) and a wide-spread species.

Indication strength of coenological similarity patterns based on genus-level taxon lists and prevalence distribution

Several methods and indicators can be used to evaluate the coenological state of a given habitat, the ones which can be created simply, quickly, standardizably and reliably and which can be used to exactly quantify the state of a given habitat in point of numbers can be of outstanding practical importance in ecology. One possible method is the examination of the genera which can be found in a given habitat in great abundance and have little number of species and various ecological characteristics. For this purpose one of the most appropriate groups is that of ground-dwelling oribatid mites (Acari: Oribatida). In our research, joining the bioindication methodological project of the “Adaptation to Climate Change” Research Group of the Hungarian Academy of Sciences, the indication strength of genus-level taxon lists and the effects of the main pattern-generating factors creating similarity patterns were analysed with the help of data series on oribatid mites collected by us and originating from literature. Our aim was to develop a method with the help of which the difference expressed with distance functions between two oribatid mite genus lists originating from any sources can correspond to spatial and temporal scales. Our results prove that these genus lists are able to express the spatial distance of the habitats. With the help of this base of comparison changes in disturbed or transformed habitats can be expressed by means of oribatid mite communities, with spatial and temporal distances.

Distribution and ecology of amphibians and reptiles in a fragmented landscape, northeastern Bolivia

Habitat loss and fragmentation have been implicated as driving forces behind recent waves of extinction. The regional landscape where this study occurred is a mosaic of forest and grassland, and therefore provides an ideal system with which to investigate the implications of habitat patchiness for the distribution and ecology of organisms. Here I describe patterns of amphibian and reptile distribution among and within habitats at the study site, investigate associations between habitat and community structure, describe nested subset patterns on forest islands, and quantify the relationship between body size and density across ecological scales and taxonomic groups. ^ Species richness did not vary across habitats, between forest island isolation classes or between island edges and cores. In contrast, species composition varied at all three ecological scales, reflecting differences in the distribution of both forest and open-habitat affiliated species. Species composition was associated with multivariate habitat profiles, with differences occurring along the isolation gradient of forest islands rather than the area gradient. The relationship between species composition and habitat was stronger for amphibians than for reptiles, a pattern that may be ascribed to physiological differences between the two groups. Analysis of nested subset pattern of community structure indicated that species composition of islands is nested as a function of isolation. Four species whose distribution on forest islands seems to be dispersal-limited drive the relationship between nestedness and isolation. Although there were several examples of shifts in body size across spatial scales and taxonomic groups, body size was not associated with density as predicted by theory, which may reflect differences between real and habitat islands, or differential responses of poikilothermic vertebrates to changes in density relative to homeotherms. ^ Taken together, the strongest result to emerge from this research is the importance of isolation, rather than area, on community structure in this system. Much evidence suggested that different ecological groups of species show distinct patterns of distribution both within and among habitat types. This suggests that species distributions at this site are not the result of 'neutral' processes at the community level, but rather reflect fundamental differences in the ecology of component species. ^

Influence of teleost abundance on the distribution and abundance of sharks in Florida Bay, USA

Understanding the factors that influence the distribution and abundance of predators, including sharks, is important for predicting the impacts of human changes to the environment. Such studies are particularly important in Florida Bay, USA where there are planned large-scale changes to patterns of freshwater input from the Everglades ecosystem. Studies of many marine predators suggest that links between predator and prey habitat use may vary with spatial scale, but there have been few studies of the role of prey distribution in shaping habitat use and abundance of sharks. We used longline catches of sharks and trawls for potential teleost prey to determine the influence of teleost abundance on shark abundance at the scale of regions and habitats in Florida Bay. We found that shark catch per unit effort (CPUE) was not linked to CPUE ofteleosts at the scale of sampling sites, but shark CPUE was positively correlated with the mean CPUE for teleosts within a region. Although there does not appear to be a strong match between the abundance of teleosts and sharks at small spatial scales, regional shark abundance is likely driven, at least partially, by the availability of prey. Management strategies that influence teleost abundance will have cascading effects to higher trophic levels in Florida Bay.

Distribution of Diatoms and Development of Diatom-Based Models for Inferring Salinity and Nutrient Concentrations in Florida Bay and Adjacent Coastal Wetlands of South Florida (USA)

The composition and distribution of diatom algae inhabiting estuaries and coasts of the subtropical Americas are poorly documented, especially relative to the central role diatoms play in coastal food webs and to their potential utility as sentinels of environmental change in these threatened ecosystems. Here, we document the distribution of diatoms among the diverse habitat types and long environmental gradients represented by the shallow topographic relief of the South Florida, USA, coastline. A total of 592 species were encountered from 38 freshwater, mangrove, and marine locations in the Everglades wetland and Florida Bay during two seasonal collections, with the highest diversity occurring at sites of high salinity and low water column organic carbon concentration (WTOC). Freshwater, mangrove, and estuarine assemblages were compositionally distinct, but seasonal differences were only detected in mangrove and estuarine sites where solute concentration differed greatly between wet and dry seasons. Epiphytic, planktonic, and sediment assemblages were compositionally similar, implying a high degree of mixing along the shallow, tidal, and storm-prone coast. The relationships between diatom taxa and salinity, water total phosphorus (WTP), water total nitrogen (WTN), and WTOC concentrations were determined and incorporated into weighted averaging partial least squares regression models. Salinity was the most influential variable, resulting in a highly predictive model (r apparent 2  = 0.97, r jackknife 2  = 0.95) that can be used in the future to infer changes in coastal freshwater delivery or sea-level rise in South Florida and compositionally similar environments. Models predicting WTN (r apparent 2  = 0.75, r jackknife 2  = 0.46), WTP (r apparent 2  = 0.75, r jackknife 2  = 0.49), and WTOC (r apparent 2  = 0.79, r jackknife 2  = 0.57) were also strong, suggesting that diatoms can provide reliable inferences of changes in solute delivery to the coastal ecosystem.

Ecology and distribution of diatoms in Biscayne Bay, Florida (USA): Implications for bioassessment and paleoenvironmental studies

The spatial and temporal distribution of planktonic, sediment-associated and epiphytic diatoms among 58 sites in Biscayne Bay, Florida was examined in order to identify diatom taxa indicative of different salinity and water quality conditions, geographic locations and habitat types. Assessments were made in contrasting wet and dry seasons in order to develop robust assessment models for salinity and water quality for this region. We found that diatom assemblages differed between nearshore and offshore locations, especially during the wet season when salinity and nutrient gradients were steepest. In the dry season, habitat structure was primary determinant of diatom assemblage composition. Among a suite of physicochemical variables, water depth and sediment total phosphorus (STP) were most strongly associated with diatom assemblage composition in the dry season, while salinity and water total phosphorus (TP) were more important in the wet season. We used indicator species analysis (ISA) to identify taxa that were most abundant and frequent at nearshore and offshore locations, in planktonic, epiphytic and benthic habitats and in contrasting salinity and water quality regimes. Because surface water concentrations of salts, total phosphorus, nitrogen (TN) and organic carbon (TOC) are partly controlled by water management in this region, diatom-based models were produced to infer these variables in modern and retrospective assessments of management-driven changes. Weighted averaging (WA) and weighted averaging partial least squares (WA-PLS) regressions produced reliable estimates of salinity, TP, TN and TOC from diatoms (r2 = 0.92, 0.77, 0.77 and 0.71, respectively). Because of their sensitivity to salinity, nutrient and TOC concentrations diatom assemblages should be useful in developing protective nutrient criteria for estuaries and coastal waters of Florida.

Distribution of Diatoms Along Environmental Gradients in the Charlotte Harbor, Florida (USA), Estuary and Its Watershed: Implications for Bioassessment of Salinity and Nutrient Concentrations

The relative abundance of diatom species in different habitats can be used as a tool to infer prior environmental conditions and evaluate management decisions that influence habitat quality. Diatom distribution patterns were examined to characterize relationships between assemblage composition and environmental gradients in a subtropical estuarine watershed. We identified environmental correlates of diatom distribution patterns across the Charlotte Harbor, Florida, watershed; evaluated differences among three major river drainages; and determined how accurately local environmental conditions can be predicted using inference models based on diatom assemblages. Sampling locations ranged from freshwater to marine (0.1–37.2 ppt salinity) and spanned broad nutrient concentration gradients. Salinity was the predominant driver of difference among diatom assemblages across the watershed, but other environmental variables had stronger correlations with assemblages within the subregions of the three rivers and harbor. Eighteen indicator taxa were significantly affiliated with subregions. Relationships between diatom taxon distributions and salinity, distance from the harbor, total phosphorus (TP), and total nitrogen (TN) were evaluated to determine the utility of diatom assemblages to predict environmental values using a weighted averaging-regression approach. Diatom-based inferences of these variables were strong (salinity R 2 = 0.96; distance R 2 = 0.93; TN R 2 = 0.83; TP R 2 = 0.83). Diatom assemblages provide reliable estimates of environmental parameters on different spatial scales across the watershed. Because many coastal diatom taxa are ubiquitous, the diatom training sets provided here should enable diatom-based environmental reconstructions in subtropical estuaries that are being rapidly altered by land and water use changes and sea level rise.

Woody Plant Invasion into the Freshwater Marl Prairie Habitat of the Cape Sable Seaside Sparrow: Final Report

In the fall of 2005, U.S. Fish and Wildlife Services (USFWS) contracted with Florida International University (FIU) to study the physical and biological drivers underlying the distribution of woody plant species in the marl prairie habitat of the Cape Sable Seaside Sparrow (CSSS). This report presents what we have learned about woody plant encroachment based on studies carried out during the period 2006-2008. The freshwater marl prairie habitat currently occupied by the Cape Sable seaside sparrow (CSSS; Ammodramus maritimus mirabilis) is a dynamic mosaic comprised of species-rich grassland communities and tree islands of various sizes, densities and compositions. Landscape heterogeneity and the scale of vegetative components across the marl prairie is primarily determined by hydrologic conditions, biological factors (e.g. dispersal and growth morphology), and disturbances such as fire. The woody component of the marl prairie landscape is subject to expansion through multiple positive feedback mechanisms, which may be initiated by recent land use change (e.g. drainage). Because sparrows are known to avoid areas where the woody component is too extensive, a better understanding of invasion dynamics is needed to ensure proper management.

The rodent fauna of Long Pine Key, Everglades National Park: a comparison of habitat types

Rodents are often involved at several stages of trophic dynamics. Consequently they often play crucial roles in the structure and function of many complex ecological systems. This study sought to address the lack of baseline data concerning rodents in tropical areas, and south Florida in particular. Live trapping took place in the four major habitat types of the Long Pine Key area of Everglades National Park over the course of one year. I compared population structures and abundance of murid rodents in the four habitat types, and tested multiple weather variables for their effectiveness as predictors of rodent abundance. I found the Long Pine Key area to be depauperate in terms of species diversity. Each of the four species of rodent encountered favored a particular habitat type. The density of the understory vegetation and the avoidance of avian predators in particular appear to be the most important factors in the distribution and abundance of rodents in the Long Pine Key area of Everglades National Park.

Distribuição e uso de habitat por peixes recifais em um gradiente ambiental: estudo de caso em recifes areníticos

There are several abiotic factors reported in the literature as regulators of the distribution of fish species in marine environments. Among them stand out structural complexity of habitat, benthic composition, depth and distance from the coast are usually reported as positive influencers in the diversity of difentes species, including reef fish. These are dominant elements in reef systems and considered high ecological and socioeconomic importance. Understanding how the above factors influence the distribution and habitat use of reef fish communities are important for their management and conservation. Thus, this study aims to evaluate the influence of these variables on the community of reef fishes along an environmental gradient of depth and distance from shore base in sandstone reefs in the coast of state of Rio Grande do Norte, Brazil. These variables are also used for creating a simple predictive model reef fish biomass for the environment studied. Data collection was performed through visual surveys in situ, and recorded environmental data (structural complexity of habitat, type of coverage of the substrate, benthic invertebrates) and ecological (wealth, abundance and reef fish size classes). As a complement, information on the diet were raised through literature and the biomass was estimated from the length-weight relationship of each species. Overall, the reefs showed a low coverage by corals and the Shallow reefs, Intermediate I and II dominated by algae and the Funds by algae and sponges. The complexity has increased along the gradient and positively influenced the species richness and abundance. Both attributes influenced in the structure of the reef fish community, increasing the richness, abundance and biomass of fish as well as differentiating the trophic structure of the community along the depth gradient and distance from the coast. Distribution and use of habitat by recifas fish was associated with food availability. The predictor model identified depth, roughness and coverage for foliose algae, calcareous algae and soft corals as the most significant variables influencing in the biomass of reef fish. In short, the description and understanding of these patterns are important steps to elucidate the ecological processes. In this sense, our approach provides a new understanding of the structure of the reef fish community of Rio Grande do Norte, allowing understand a part of a whole and assist future monitoring actions, evaluation, management and conservation of these and other reefs of Brazil.

An evaluation of home range models for marine fish tracking and fine scale habitat use and movement patterns of age 1 Greenland cod (Gadus macrocephalus ogac)

My thesis examines fine-scale habitat use and movement patterns of age 1 Greenland cod (Gadus macrocephalus ogac) tracked using acoustic telemetry. Recent advances in tracking technologies such as GPS and acoustic telemetry have led to increasingly large and detailed datasets that present new opportunities for researchers to address fine-scale ecological questions regarding animal movement and spatial distribution. There is a growing demand for home range models that will not only work with massive quantities of autocorrelated data, but that can also exploit the added detail inherent in these high-resolution datasets. Most published home range studies use radio-telemetry or satellite data from terrestrial mammals or avian species, and most studies that evaluate the relative performance of home range models use simulated data. In Chapter 2, I used actual field-collected data from age-1 Greenland cod tracked with acoustic telemetry to evaluate the accuracy and precision of six home range models: minimum convex polygons, kernel densities with plug-in bandwidth selection and the reference bandwidth, adaptive local convex hulls, Brownian bridges, and dynamic Brownian bridges. I then applied the most appropriate model to two years (2010-2012) of tracking data collected from 82 tagged Greenland cod tracked in Newman Sound, Newfoundland, Canada, to determine diel and seasonal differences in habitat use and movement patterns (Chapter 3). Little is known of juvenile cod ecology, so resolving these relationships will provide valuable insight into activity patterns, habitat use, and predator-prey dynamics, while filling a knowledge gap regarding the use of space by age 1 Greenland cod in a coastal nursery habitat. By doing so, my thesis demonstrates an appropriate technique for modelling the spatial use of fish from acoustic telemetry data that can be applied to high-resolution, high-frequency tracking datasets collected from mobile organisms in any environment.

Mapped distribution of intertidal habitats in Australia between 1999 and 2014, link to data in ArcGIS format (29 MB)

Shorebirds have declined severely across the East Asian-Australasian Flyway. Many species rely on intertidal habitats for foraging, yet the distribution and conservation status of these habitats across Australia remain poorly understood. Here, we utilised freely available satellite imagery to produce the first map of intertidal habitats across Australia. We estimated a minimum intertidal area of 9856 km**2, with Queensland and Western Australia supporting the largest areas. Thirty-nine percent of intertidal habitats were protected in Australia, with some primarily within marine protected areas (e.g. Queensland) and others within terrestrial protected areas (e.g. Victoria). In fact, three percent of all intertidal habitats were protected both by both marine and terrestrial protected areas. To achieve conservation targets, protected area boundaries must align more accurately with intertidal habitats. Shorebirds use intertidal areas to forage and supratidal areas to roost, so a coordinated management approach is required to account for movement of birds between terrestrial and marine habitats. Ultimately, shorebird declines are occurring despite high levels of habitat protection in Australia. There is a need for a concerted effort both nationally and internationally to map and understand how intertidal habitats are changing, and how habitat conservation can be implemented more effectively.

Lithofacies distribution in the western Bay of Plenty, New Zealand

Sediment dynamics on a storm-dominated shelf (western Bay of Plenty, New Zealand) were mapped and analyzed using the newly developed multi-sensor benthic profiler MARUM NERIDIS III. An area of 60 km × 7 km between 2 and 35 m water depth was surveyed with this bottom-towed sled equipped with a high-resolution camera for continuous close-up seafloor photography and a CTD with connected turbidity sensor. Here we introduce our approach of using this multi-parameter dataset combined with sidescan sonography and sedimentological analyses to create detailed lithofacies and bedform distribution maps and to derive regional sediment transport patterns. For the assessment of sediment distribution, photographs were classified and their spatial distribution mapped out according to associated acoustic backscatter from a sidescan sonar. This provisional map was used to choose target locations for surficial sediment sampling and subsequent laboratory analysis of grain size distribution and mineralogical composition. Finally, photographic, granulometric and mineralogical facies were combined into a unified lithofacies map and corresponding stratigraphic model. Eight distinct types of lithofacies with seawards increasing grain size were discriminated and interpreted as reworked relict deposits overlain by post-transgressional fluvial sediments. The dominant transport processes in different water depths were identified based on type and orientation of bedforms, as well as bottom water turbidity and lithofacies distribution. Observed bedforms include subaquatic dunes, coarse sand ribbons and sorted bedforms of varying dimensions, which were interpreted as being initially formed by erosion. Under fair weather conditions, sediment is transported from the northwest towards the southeast by littoral drift. During storm events, a current from the southeast to the northweast is induced which is transporting sediment along the shore in up to 35 m water depth. Shorewards oriented cross-shore transport is taking place in up to 60 m water depth and is likewise initiated by storm events. Our study demonstrates how benthic photographic profiling delivers comprehensive compositional, structural and environmental information, which compares well with results obtained by traditional probing methods, but offers much higher spatial resolution while covering larger areas. Multi-sensor benthic profiling enhances the interpretability of acoustic seafloor mapping techniques and is a rapid and economic approach to seabed and habitat mapping especially in muddy to sandy facies.

Mapped cetacean habitat suitability and richness in the Azores, links to ArcGIS files

Marine spatial planning and ecological research call for high-resolution species distribution data. However, those data are still not available for most marine large vertebrates. The dynamic nature of oceanographic processes and the wide-ranging behavior of many marine vertebrates create further difficulties, as distribution data must incorporate both the spatial and temporal dimensions. Cetaceans play an essential role in structuring and maintaining marine ecosystems and face increasing threats from human activities. The Azores holds a high diversity of cetaceans but the information about spatial and temporal patterns of distribution for this marine megafauna group in the region is still very limited. To tackle this issue, we created monthly predictive cetacean distribution maps for spring and summer months, using data collected by the Azores Fisheries Observer Programme between 2004 and 2009. We then combined the individual predictive maps to obtain species richness maps for the same period. Our results reflect a great heterogeneity in distribution among species and within species among different months. This heterogeneity reflects a contrasting influence of oceanographic processes on the distribution of cetacean species. However, some persistent areas of increased species richness could also be identified from our results. We argue that policies aimed at effectively protecting cetaceans and their habitats must include the principle of dynamic ocean management coupled with other area-based management such as marine spatial planning.

Distribution, density and abundance of Antarctic ice seals off Queen Maud Land and the eastern Weddell Sea

The Antarctic Pack Ice Seal (APIS) Program was initiated in 1994 to estimate the abundance of four species of Antarctic phocids: the crabeater seal Lobodon carcinophaga, Weddell seal Leptonychotes weddellii, Ross seal Ommatophoca rossii and leopard seal Hydrurga leptonyx and to identify ecological relationships and habitat use patterns. The Atlantic sector of the Southern Ocean (the eastern sector of the Weddell Sea) was surveyed by research teams from Germany, Norway and South Africa using a range of aerial methods over five austral summers between 1996-1997 and 2000-2001. We used these observations to model densities of seals in the area, taking into account haul-out probabilities, survey-specific sighting probabilities and covariates derived from satellite-based ice concentrations and bathymetry. These models predicted the total abundance over the area bounded by the surveys (30°W and 10°E). In this sector of the coast, we estimated seal abundances of: 514 (95 % CI 337-886) x 10**3 crabeater seals, 60.0 (43.2-94.4) x 10**3 Weddell seals and 13.2 (5.50-39.7) x 10**3 leopard seals. The crabeater seal densities, approximately 14,000 seals per degree longitude, are similar to estimates obtained by surveys in the Pacific and Indian sectors by other APIS researchers. Very few Ross seals were observed (24 total), leading to a conservative estimate of 830 (119-2894) individuals over the study area. These results provide an important baseline against which to compare future changes in seal distribution and abundance.