An ecological characterization of Salt River Bay National Historical Park and Ecological Preserve, U.S. Virgin Islands

Salt River Bay National Historical Park and Ecological Preserve (hereafter, SARI or the park) was created in 1992 to preserve, protect, and interpret nationally significant natural, historical, and cultural resources (United States Congress 1992). The diverse ecosystem within it includes a large mangrove forest, a submarine canyon, coral reefs, seagrass beds, coastal forests, and many other natural and developed landscape elements. These ecosystem components are, in turn, utilized by a great diversity of flora and fauna. A comprehensive spatial inventory of these ecosystems is required for successful management. To meet this need, the National Oceanic and Atmospheric Administration (NOAA) Biogeography Program, in consultation with the National Park Service (NPS) and the Government of the Virgin Islands Department of Planning and Natural Resources (VIDPNR), conducted an ecological characterization. The characterization consists of three complementary components: a text report, digital habitat maps, and a collection of historical aerial photographs. This ecological characterization provides managers with a suite of tools that, when coupled with the excellent pre-existing body of work on SARI resources, enables improved research and monitoring activities within the park (see Appendix F for a list of data products).

ARTSCENE: A Neural System for Natural Scene Classification

How do humans rapidly recognize a scene? How can neural models capture this biological competence to achieve state-of-the-art scene classification? The ARTSCENE neural system classifies natural scene photographs by using multiple spatial scales to efficiently accumulate evidence for gist and texture. ARTSCENE embodies a coarse-to-fine Texture Size Ranking Principle whereby spatial attention processes multiple scales of scenic information, ranging from global gist to local properties of textures. The model can incrementally learn and predict scene identity by gist information alone and can improve performance through selective attention to scenic textures of progressively smaller size. ARTSCENE discriminates 4 landscape scene categories (coast, forest, mountain and countryside) with up to 91.58% correct on a test set, outperforms alternative models in the literature which use biologically implausible computations, and outperforms component systems that use either gist or texture information alone. Model simulations also show that adjacent textures form higher-order features that are also informative for scene recognition.

On the multiple ecological roles of water in river networks

The distribution and movement of water can influence the state and dynamics of terrestrial and aquatic ecosystems through a diversity of mechanisms. These mechanisms can be organized into three general categories wherein water acts as (1) a resource or habitat for biota, (2) a vector for connectivity and exchange of energy, materials, and organisms, and (3) as an agent of geomorphic change and disturbance. These latter two roles are highlighted in current models, which emphasize hydrologic connectivity and geomorphic change as determinants of the spatial and temporal distributions of species and processes in river systems. Water availability, on the other hand, has received less attention as a driver of ecological pattern, despite the prevalence of intermittent streams, and strong potential for environmental change to alter the spatial extent of drying in many regions. Here we summarize long-term research from a Sonoran Desert watershed to illustrate how spatial patterns of ecosystem structure and functioning reflect shifts in the relative importance of different 'roles of water' across scales of drainage size. These roles are distributed and interact hierarchically in the landscape, and for the bulk of the drainage network it is the duration of water availability that represents the primary determinant of ecological processes. Only for the largest catchments, with the most permanent flow regimes, do flood-associated disturbances and hydrologic exchange emerge as important drivers of local dynamics. While desert basins represent an extreme case, the diversity of mechanisms by which the availability and flow of water influence ecosystem structure and functioning are general. Predicting how river ecosystems may respond to future environmental pressures will require clear understanding of how changes in the spatial extent and relative overlap of these different roles of water shape ecological patterns. © 2013 Sponseller et al.

Ecological homogenization of urban USA

A visually apparent but scientifically untested outcome of land-use change is homogenization across urban areas, where neighborhoods in different parts of the country have similar patterns of roads, residential lots, commercial areas, and aquatic features. We hypothesize that this homogenization extends to ecological structure and also to ecosystem functions such as carbon dynamics and microclimate, with continental-scale implications. Further, we suggest that understanding urban homogenization will provide the basis for understanding the impacts of urban land-use change from local to continental scales. Here, we show how multi-scale, multidisciplinary datasets from six metropolitan areas that cover the major climatic regions of the US (Phoenix, AZ; Miami, FL; Baltimore, MD; Boston, MA; Minneapolis-St Paul, MN; and Los Angeles, CA) can be used to determine how household and neighborhood characteristics correlate with land-management practices, land-cover composition, and landscape structure and ecosystem functions at local, regional, and continental scales. © The Ecological Society of America.

Ecological effects of the North Atlantic oscillation

Climatic oscillations as reflected in atmospheric modes such as the North Atlantic Oscillation (NAO) may be seen as a proxy for regulating forces in aquatic and terrestrial ecosystems. Our review highlights the variety of climate processes related to the NAO and the diversity in the type of ecological responses that different biological groups can display. Available evidence suggests that the NAO influences ecological dynamics in both marine and terrestrial systems, and its effects may be seen in variation at the individual, population and community levels. The ecological responses to the NAO encompass changes in timing of reproduction, population dynamics, abundance, spatial distribution and interspecific relationships such as competition and predator-prey relationships. This indicates that local responses to large-scale changes may be more subtle than previously suggested. We propose that the NAO effects may be classified as three types: direct, indirect and integrated. Such a classification will help the design and interpretation of analyses attempting to relate ecological changes to the NAO and, possibly, to climate in general.

A new procedure to optimize the selection of groups in a classification tree

Agglomerative cluster analyses encompass many techniques, which have been widely used in various fields of science. In biology, and specifically ecology, datasets are generally highly variable and may contain outliers, which increase the difficulty to identify the number of clusters. Here we present a new criterion to determine statistically the optimal level of partition in a classification tree. The criterion robustness is tested against perturbated data (outliers) using an observation or variable with values randomly generated. The technique, called Random Simulation Test (RST), is tested on (1) the well-known Iris dataset [Fisher, R.A., 1936. The use of multiple measurements in taxonomic problems. Ann. Eugenic. 7, 179–188], (2) simulated data with predetermined numbers of clusters following Milligan and Cooper [Milligan, G.W., Cooper, M.C., 1985. An examination of procedures for determining the number of clusters in a data set. Psychometrika 50, 159–179] and finally (3) is applied on real copepod communities data previously analyzed in Beaugrand et al. [Beaugrand, G., Ibanez, F., Lindley, J.A., Reid, P.C., 2002. Diversity of calanoid copepods in the North Atlantic and adjacent seas: species associations and biogeography. Mar. Ecol. Prog. Ser. 232, 179–195]. The technique is compared to several standard techniques. RST performed generally better than existing algorithms on simulated data and proved to be especially efficient with highly variable datasets.

Marine ecosystem services: Linking indicators to their classification

There is a multitude of ecosystem service classifications available within the literature, each with its own advantages and drawbacks. Elements of them have been used to tailor a generic ecosystem service classification for the marine environment and then for a case study site within the North Sea: the Dogger Bank. Indicators for each of the ecosystem services, deemed relevant to the case study site, were identified. Each indicator was then assessed against a set of agreed criteria to ensure its relevance and applicability to environmental management. This paper identifies the need to distinguish between indicators of ecosystem services that are entirely ecological in nature (and largely reveal the potential of an ecosystem to provide ecosystem services), indicators for the ecological processes contributing to the delivery of these services, and indicators of benefits that reveal the realized human use or enjoyment of an ecosystem service. It highlights some of the difficulties faced in selecting meaningful indicators, such as problems of specificity, spatial disconnect and the considerable uncertainty about marine species, habitats and the processes, functions and services they contribute to.

Biological and ecological traits of marine species

This paper reviews the utility and availability of biological and ecological traits for marine species so as to prioritise the development of a world database on marine species traits. In addition, the ‘status’ of species for conservation, that is, whether they are introduced or invasive, of fishery or aquaculture interest, harmful, or used as an ecological indicator, were reviewed because these attributes are of particular interest to society. Whereas traits are an enduring characteristic of a species and/or population, a species status may vary geographically and over time. Criteria for selecting traits were that they could be applied to most taxa, were easily available, and their inclusion would result in new research and/or management applications. Numerical traits were favoured over categorical. Habitat was excluded as it can be derived from a selection of these traits. Ten traits were prioritized for inclusion in the most comprehensive open access database on marine species (World Register of Marine Species), namely taxonomic classification, environment, geography, depth, substratum, mobility, skeleton, diet, body size and reproduction. These traits and statuses are being added to the database and new use cases may further subdivide and expand upon them.

Tillin, H. & Tyler-Walters, H., 2014. Assessing the sensitivity of subtidal sedimentary habitats to pressures associated with marine activities. Phase 2 Report – Literature review and sensitivity assessments for ecological groups for circalittoral and offshore Level 5 biotopes. JNCC Report No. 512B, 260 pp.

Human activities within the marine environment give rise to a number of pressures on seabed habitats. Improved understanding of the sensitivity of subtidal sedimentary habitats is required to underpin the management advice provided for Marine Protected Areas, as well as supporting other UK marine monitoring and assessment work. The sensitivity of marine sedimentary habitats to a range of pressures induced by human activities has previously been systematically assessed using approaches based on expert judgement for Defra Project MB0102 (Tillin et al. 2010). This previous work assessed sensitivity at the level of the broadscale habitat and therefore the scores were typically expressed as a range due to underlying variation in the sensitivity of the constituent biotopes. The objective of this project was to reduce the uncertainty around identifying the sensitivity of selected subtidal sedimentary habitats by assessing sensitivity, at a finer scale and incorporating information on the biological assemblage, for 33 Level 5 circalittoral and offshore biotopes taken from the Marine Habitat Classification of Britain and Ireland (Connor et al. 2004). Two Level 6 sub-biotopes were also included in this project as these contain distinctive characterising species that differentiate them from the Level 5 parent biotope. Littoral, infralittoral, reduced and variable salinity sedimentary habitats were excluded from this project as the scope was set for assessment of circalittoral and offshore sedimentary communities. This project consisted of three Phases. • Phase 1 - define ecological groups based on similarities in the sensitivity of characterising species from the Level 5 and two Level 6 biotopes described above. • Phase 2 - produce a literature review of information on the resilience and resistance of characterising species of the ecological groups to pressures associated with activities in the marine environment. • Phase 3 - to produce sensitivity assessment ‘proformas’ based on the findings of Phase 2 for each ecological group. This report outlines results of Phase 2. The Tillin et al., (2010) sensitivity assessment methodology was modified to use the best available scientific evidence that could be collated within the project timescale. An extensive literature review was compiled, for peer reviewed and grey literature, to examine current understanding about the effects of pressures from human activities on circalittoral and offshore sedimentary communities in UK continental shelf waters, together with information on factors that contribute to resilience (recovery) of marine species. This review formed the basis of an assessment of the sensitivity of the 16 ecological groups identified in Phase 1 of the project (Tillin & Tyler-Walters 2014). As a result: • the state of knowledge on the effects of each pressure on circalittoral and offshore benthos was reviewed; • the resistance, resilience and, hence, sensitivity of sixteen ecological groups, representing 96 characteristic species, were assessed for eight separate pressures; • each assessment was accompanied by a detailed review of the relevant evidence; Assessing the sensitivity of subtidal sedimentary habitats to pressures associated with human activities • knowledge gaps and sources of uncertainty were identified for each group; • each assessment was accompanied by an assessment of the quality of the evidence, its applicability to the assessment and the degree of concordance (agreement) between the evidence, to highlight sources of uncertainty as an assessment of the overall confidence in the sensitivity assessment, and finally • limitations in the methodology and the application of sensitivity assessments were outlined. This process demonstrated that the ecological groups identified in Phase 1 (Tillin & Tyler-Walters 2014) were viable groups for sensitivity assessment, and could be used to represent the 33 circalittoral and offshore sediments biotopes identified at the beginning of the project. The results of the sensitivity assessments show: • the majority of species and hence ecological groups in sedimentary habitats are sensitive to physical change, especially loss of habitat and sediment extraction, and change in sediment type; • most sedimentary species are sensitive to physical damage, e.g. abrasion and penetration, although deep burrowing species (e.g. the Dublin Bay prawn - Nephrops norvegicus and the sea cucumber - Neopentadactyla mixta) are able to avoid damaging effects to varying degrees, depending on the depth of penetration and time of year; • changes in hydrography (wave climate, tidal streams and currents) can significantly affect sedimentary communities, depending on whether they are dominated by deposit, infaunal feeders or suspension feeders, and dependant on the nature of the sediment, which is itself modified by hydrography and depth; • sedentary species and ecological groups that dominate the top-layer of the sediment (either shallow burrowing or epifaunal) remain the most sensitive to physical damage; • mobile species (e.g. interstitial and burrowing amphipods, and perhaps cumaceans) are the least sensitive to physical change or damage, and hydrological change as they are already adapted to unstable, mobile substrata; • sensitivity to changes in organic enrichment and hence oxygen levels, is variable between species and ecological groups, depending on the exact habitat preferences of the species in question, although most species have at least a medium sensitivity to acute deoxygenation; • there is considerable evidence on the effects of bottom-contact fishing practices and aggregate dredging on sedimentary communities, although not all evidence is directly applicable to every ecological group; • there is lack of detailed information on the physiological tolerances (e.g. to oxygenation, salinity, and temperature), habitat preferences, life history and population dynamics of many species, so that inferences has been made from related species, families, or even the same phylum; • there was inadequate evidence to assess the effects of non-indigenous species on most ecological groups, and Assessing the sensitivity of subtidal sedimentary habitats to pressures associated with human activities • there was inadequate evidence to assess the effects of electromagnetic fields and litter on any ecological group. The resultant report provides an up-to-date review of current knowledge about the effects of pressures resulting from human activities of circalittoral and offshore sedimentary communities. It provides an evidence base to facilitate and support the provision of management advice for Marine Protected Areas, development of UK marine monitoring and assessment, and conservation advice to offshore marine industries. However, such a review will require at least annual updates to take advantage of new evidence and new research as it becomes available. Also further work is required to test how ecological group assessments are best combined in practice to advise on the sensitivity of a range of sedimentary biotopes, including the 33 that were originally examined.

Nomenclature and syntaxonomic notes on some high-rank syntaxa of the European grassland vegetation

We present descriptions of a new order (Ranunculo cortusifolii-Geranietalia reuteri and of a new alliance (Stachyo lusitanicae-Cheirolophion sempervirentis) for the herbaceous fringe communities of Macaronesia and of the southwestern Iberian Peninsula, respectively. A new alliance, the Polygalo mediterraneae-Bromion erecti (mesophilous post-cultural grasslands), was introduced for the Peninsular Italy. We further validate and typify the Armerietalia rumelicae (perennial grasslands supported by nutrient-poor on siliceous bedrocks at altitudes characterized by the submediterranean climate of central-southern Balkan Peninsula), the Securigero-Dasypyrion villosae (lawn and fallow-land tall-grass annual vegetation of Italy), and the Cirsio vallis-demoni-Nardion (acidophilous grasslands on siliceous substrates of the Southern Italy). Nomenclatural issues (validity, legitimacy, synonymy, formal corrections) have been discussed and clarified for the following names: Brachypodio-Brometalia, Bromo pannonici-Festucion csikhegyensis, Corynephoro-Plantaginion radicatae, Heleochloion, Hieracio-Plantaginion radicatae, Nardetea strictae, Nardetalia strictae, Nardo-Callunetea, Nardo-Galion saxatilis, Oligo-Bromion, Paspalo-Heleochloetalia, Plantagini-Corynephorion and Scorzoneret alia villosae. 

“Islands” in Holocene forests: implications for forest openness, landscape clearance and “culture-steppe” species

Human activity has undoubtedly had a major impact on Holocene forested ecosystems, with the concurrent expansion of plants and animals associated with cleared landscapes and pasture, also known as 'culture-steppe'. However, this anthropogenic perspective may have underestimated the contribution of autogenic disturbance (e.g. wind-throw, fire), or a mixture of autogenic and anthropogenic processes, within early Holocene forests. Entomologists have long argued that the north European primary forest was probably similar in structure to pasture woodland. This idea has received support from the conservation biologist Frans Vera, who has recently strongly argued that the role of large herbivores in maintaining open forests in the primeval landscapes of Europe has been seriously underestimated. This paper reviews this debate from a fossil invertebrate perspective and looks at several early Holocene insect assemblages. Although wood taxa are indeed important during this period, species typical of open areas and grassland and dung beetles, usually associated with the dung of grazing animals, are persistent presences in many early woodland faunas. We also suggest that fire and other natural disturbance agents appear to have played an important ecological role in some of these forests, maintaining open areas and creating open vegetation islands within these systems. More work, however, is required to ascertain the role of grazing animals, but we conclude that fossil insects have a significant contribution to make to this debate. This evidence has fundamental implications in terms of how the palaeoecological record is interpreted, particularly by environmental archaeologists and palaeoecologists who may be more interested in identifying human-environment interactions rather than the ecological processes which may be preserved within palaeoecological records.

Homogeneous habitat can meet the discrete and varied resource requirements of hares but may set an ecological trap

In common with other farmland species, hares (Lepus spp.) are in widespread decline in agricultural landscapes due to agricultural intensification and habitat loss. We examined the importance of habitat heterogeneity to the Irish hare (Lepus timidus hibernicus) in a pastoral landscape. We used radio-tracking during nocturnal active and diurnal inactive periods throughout one year. In autumn, winter and spring, hares occupied a heterogeneous combination of improved grassland, providing food, and Juncus-dominated rough pasture, providing refuge. In summer, hares significantly increased their use of improved grassland. This homogeneous habitat can fulfil the discrete and varied resource requirements of hares for feeding and shelter at certain times of year. However, improved grassland may be a risky habitat for hares as silage harvesting occurs during their peak birthing period of late spring and early summer. We therefore posit the existence of a putative ecological trap inherent to a homogeneous habitat of perceived high value that satisfies the hares' habitat requirements but which presents risks at a critical time of year. To test this hypothesis in relation to hare populations, work is required to provide data on differential leveret mortality between habitat types.

Distribution of the common lizard (Zootoca vivipara) and landscape favourability for the species in Northern Ireland

The common lizard (Zootoca vivipara) is Ireland’s only native reptile, forming a key part of the island’s biodiversity. However, there is a general paucity of distributional and abundance data for the species. In this study, we collated incidental records for common lizard sightings to define the distribution of the species in Northern Ireland. Maximum entropy modelling was employed to describe species-habitat associations. The resulting predicted landscape favourability was used to evaluate the current status of the species based on the distribution of its maximum potential range in relation to the degree of fragmentation of remaining suitable habitat. In common with previous studies in the Republic of Ireland, sightings were highly clustered indicating under-recording, observer bias, and fragmentation of suitable habitat. A total of 98 records were collated from 1905 to 2009. The species was recorded in 63 (ca. 34%) of 186 × 10 km Northern Irish grid squares. Lizard occurrence was strongly and positively associated with landscapes dominated by heathland, bog and coastal habitats. The single best approximating model correctly classified the presence of lizards in 84.2% of cases. Upland heath, lowland raised bog and sand dune systems are all subject to Habitat Action Plans in Northern Ireland and are threatened by conversion to agriculture, afforestation, invasive species encroachment and infrastructural development. Consequently, remaining common lizard populations are likely to be small, isolated and highly fragmented. Establishment of an ecological network to preserve connectivity of remaining heath and bog will not only benefit remaining common lizard populations but biodiversity in general.

Lake restoration in terms of ecological resilience: a numerical study of biomanipulations under bistable conditions

An abstract version of the comprehensive aquatic simulation model (CASM) is found to exhibit bistability under intermediate loading of nutrient input, supporting the alternative-stable-states theory and field observations for shallow lakes. Our simulations of biomanipulations under the bistable conditions reveal that a reduction in the abundance of zooplanktivorous fish cannot switch the system from a turbid to a clear state. Rather, a direct reduction of phytoplankton and detritus was found to be most effective to make this switch in the present model. These results imply that multiple manipulations may be effective for practical restorations of lakes. We discuss the present results of biomanipulations in terms of ecological resilience in multivariable systems or natural systems.

Landscape effects on extremely fragmented populations of a rare solitary bee, Colletes floralis

Globally there is concern over the decline of bees, an ecologically important group of pollinating insects. Genetic studies provide insights into population structure that are crucial for conservation management but that would be impossible to obtain by conventional ecological methods. Yet conservation genetic studies of bees have primarily focussed on social species rather than the more species-rich solitary bees. Here we investigate the population structure of Colletes floralis, a rare and threatened solitary mining bee, in Ireland and Scotland using nine microsatellite loci. Genetic diversity was surprisingly as high in Scottish (Hebridean island) populations at the extreme northwestern edge of the species range as in mainland Irish populations further south. Extremely high genetic differentiation among populations was detected; multilocus FST was up to 0.53, and G’ST and Dest were even higher (maximum: 0.85 and 1.00 respectively). A pattern of isolation by distance was evident for sites separated by land. Water appears to act as a substantial barrier to gene flow yet sites separated by sea did not exhibit isolation by distance. Colletes floralis populations are extremely isolated and probably not in regional migration-drift equilibrium. GIS-based landscape genetic analysis reveals urban areas as a potential and substantial barrier to gene flow. Our results highlight the need for urgent site-specific management action to halt the decline of this and potentially other rare solitary bees.