Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins

Over the past two decades, many ingenious efforts have been made in protein remote homology detection. Because homologous proteins often diversify extensively in sequence, it is challenging to demonstrate such relatedness through entirely sequence-driven searches. Here, we describe a computational method for the generation of `protein-like' sequences that serves to bridge gaps in protein sequence space. Sequence profile information, as embodied in a position-specific scoring matrix of multiply aligned sequences of bona fide family members, serves as the starting point in this algorithm. The observed amino acid propensity and the selection of a random number dictate the selection of a residue for each position in the sequence. In a systematic manner, and by applying a `roulette-wheel' selection approach at each position, we generate parent family-like sequences and thus facilitate an enlargement of sequence space around the family. When generated for a large number of families, we demonstrate that they expand the utility of natural intermediately related sequences in linking distant proteins. In 91% of the assessed examples, inclusion of designed sequences improved fold coverage by 5-10% over searches made in their absence. Furthermore, with several examples from proteins adopting folds such as TIM, globin, lipocalin and others, we demonstrate that the success of including designed sequences in a database positively sensitized methods such as PSI-BLAST and Cascade PSI-BLAST and is a promising opportunity for enormously improved remote homology recognition using sequence information alone.

Looking for safe harbor in a crowded sea: Coastal space use conflict and marine renewable energy development

Technological advances in the marine renewable energy industry and increased clarity about the leasing and licensing process are fostering development proposals in both state and federal waters. The ocean is becoming more industrialized and competition among all marine space users is developing (Buck et al. 2004). More spatial competition can lead to conflict between ocean users themselves, and to tensions that spill over to include other stakeholders and the general public (McGrath 2004). Such conflict can wind up in litigation, which is costly and takes agency time and financial resources away from other priorities. As proposals for marine renewable energy developments are evaluated, too often decision-makers lack the tools and information to properly account for the cumulative effects and the tradeoffs associated with alternative human uses of the ocean. This paper highlights the nature of marine space conflicts associated with marine renewable energy literature highlights key issues for the growth of the marine renewable energy sector in the United States. (PDF contains 4 pages)

Manage one beach or two? Movements and space-use of the threatened hooded plover (Thinornis rubricollis) in south-eastern Australia

An understanding of space use and dispersal of a wildlife species is essential for effective management. We examined the movements of a beach-dwelling, threatened population of hooded plover (Thinornis rubricollis) in southern central Victoria, Australia, by analysing sightings of colour-banded birds (4897 sightings; 194 birds tracked for up to 9 years). Most movements were relatively short (5050 ± 305 m), with 61.4% <1 km and 95.3% <20 km; they lacked directional or sexual bias. The extent of coastline used by individual birds was 47.8 ± 58.0 km. Regional differences in average distances moved by adults were apparent. For adults, movement rates (mean distance per day) were higher during the non-breeding season than during the breeding season. Non-breeding adults generally remained close to their partners (non-breeding, 456.3 ± 163.9 m; breeding, 148.2 ± 45.3 m). Largest flock sizes were recorded during the non-breeding period, and flocking was not uniformly distributed along the coast but appeared to be concentrated in particular locations. The frequency of pair cohesion (i.e. when the distance between partners was zero on a given day) was similar during the breeding (69.6%) and non-breeding seasons (67.7%). Breeding territories (kernel analysis) were 36.7 ± 5.7 ha and overlapped from year to year in all cases (23 pairwise comparisons; 47.9 ± 7.1% overlap). The high fidelity and constancy of territories confirms they warrant ongoing management investment, although the species relies on a matrix of breeding and non-breeding sites. The latter appear to occur in specific parts of the coast and warrant enhanced protection and more research attention. Fragmentation of the breeding population might occur where habitat is rendered unsuitable for > ~50 km.

The central-place territorial model does not apply to space-use by juvenile brook charr Salvelinus fontinalis in lakes

1. Territoriality is widely accepted as the mechanism responsible for density-dependent mortality, emigration, and 'self-thinning' of populations of juvenile salmonine fishes in streams. Numerous studies have focused on territoriality exclusively in stream (lotic) environments and thus have fostered a stereotyped view of juvenile salmonines as sedentary and territorial. We term this behavioural paradigm the central-place territorial model (CPTM).

2. We tested predictions characterizing the CPTM for young-of-the-year (YOY) brook charr (Salvelinus fontinalis) in two Canadian lakes to determine if territoriality may also potentially limit space and population size of brook charr in lakes.

3. Our findings were not consistent with the CPTM. Fish in both lakes were not central-place forages. Maximum displacement distance did not increase with body length as predicted by the general salmonine model of Grant and Kramer (1990). Net displacement distanced increased with the proportion of time spent moving. Aggressive frequency was greatest for fish which spent large proportions of time moving and did not defend from a central-place.

4. Fish in both lakes were rarely aggressive, highly active, and often moved back over the same areas. However, lake fish which migrated to a tributary stream had no net displacement (central-place foraging) illustrating the immediate effects of current on foraging tactics and space-use.

5. The effect of hydrodynamic environment (flowing vs. still water) on fish behaviour needs to be explicitly considered in future models of salmonine behaviour.

Sex-biased space-use response to urbanization in an endemic urban adapter

Urbanization impacts on the composition and distribution of wildlife. The tawny frogmouth (Podargus strigoides) is an endemic, nocturnal bird species widespread throughout Australia with recent research highlighting high densities within urban environments. The aim of this study was to investigate homerange size and land-use in response to a gradient of urbanization by determining (a) the key land-use types influencing home-range size and location in the urban landscape (b) whether urbanization impacts on home-range size; and (c) whether the response to urbanization is gender specific. Twelve birds, seven male and five female were radio-tracked within a study zone located in Melbourne, Australia. We used minimum convex polygons (MCP) 95% and 50% fixed-kernel isopleths to calculate home-range size and areas of core use within each home-range. In both the landscape and core areas of their home-range, birds positioned their home-range in areas with more trees, avoiding impervious surfaces and utilizing grassed areas. Male mean kernel home-range was 17.65 ± 4.35 ha and female 6.55 ± 1.40 ha. Male home-ranges contained higher levels of impervious surfaces than females. Modelling demonstrated that as urbanization intensified the home-range size of males increased whereas female home-ranges remained static in size. This research identifies land-use selection and highlights the possibility that spatial behaviour in the species is sex-biased in response to a gradient of urbanization. © 2014 Elsevier B.V.

(Tables 1,2) Tracking records and space use statistics of polar bears (Ursus maritimus) in Storfjorden, Svalbard

Arctic sea ice is declining rapidly, making it vital to understand the importance of different types of sea ice for ice-dependent species such as polar bears Ursus maritimus. In this study we used GPS telemetry (25 polar bear tracks obtained in Svalbard, Norway, during spring) and high-resolution synthetic aperture radar (SAR) sea-ice data to investigate fine-scale space use by female polar bears. Space use patterns differed according to reproductive state; females with cubs of the year (COYs) had smaller home ranges and used fast-ice areas more frequently than lone females. First-passage time (FPT) analysis revealed that females with COYs displayed significantly longer FPTs near (<10 km) glacier fronts than in other fast-ice areas; lone females also increased their FPTs in such areas, but they also frequently used drifting pack ice. These results clearly demonstrate the importance of fast-ice areas, in particular close to glacier fronts, especially for females with COYs. Access to abundant and predictable prey (ringed seal pups), energy conservation and reluctance to cross large open water areas are possible reasons for the observed patterns. However, glacier fronts are retracting in Svalbard, and declines in land-fast ice have been notable over the past decade. The eventual disappearance of these important habitats might become critical for the survival of polar bear cubs in Svalbard and other regions with similar habitat characteristics. Given the relatively small size of many fast-ice areas in Svalbard, the results observed in this study would not have been revealed using less accurate location data or lower-resolution sea-ice data.

Resource partitioning in sympatric delphinids: Space use and habitat preferences of Australian snubfin and Indo-Pacific humpback dolphins

1. Many species of delphinids co-occur in space and time. However, little is known of their ecological interactions and the underlying mechanisms that mediate their coexistence. 2. Snubfin Orcaella heinsohni, and Indo-Pacific humpback dolphins Sousa chinensis, live in sympatry throughout most of their range in Australian waters. I conducted boat-based surveys in Cleveland Bay, north-east Queensland, to collect data on the space and habitat use of both species. Using Geographic Information Systems, kernel methods and Euclidean distances I investigated interspecific differences in their space use patterns, behaviour and habitat preferences. 3. Core areas of use (50% kernel range) for both species were located close to river mouths and modified habitat such as dredged channels and breakwaters close to the Port of Townsville. Foraging and travelling activities were the dominant behavioural activities of snubfin and humpback dolphins within and outside their core areas. 4. Their representative ranges (95% kernel range) overlapped considerably, with shared areas showing strong concordance in the space use by both species. Nevertheless, snubfin dolphins preferred slightly shallower (1-2 m) waters than humpback dolphins (2-5 m). Additionally, shallow areas with seagrass ranked high in the habitat preferences of snubfin dolphins, whereas humpback dolphins favoured dredged channels. 5. Slight differences in habitat preferences appear to be one of the principal factors maintaining the coexistence of snubfin and humpback dolphins. I suggest diet partitioning and interspecific aggression as the major forces determining habitat selection in these sympatric species.

Acoustic telemetry and network analysis reveal the space use of multiple reef predators and enhance marine protected area design

Marine protected areas (MPAs) are commonly employed to protect ecosystems from threats like overfishing. Ideally, MPA design should incorporate movement data from multiple target species to ensure sufficient habitat is protected. We used long-term acoustic telemetry and network analysis to determine the fine-scale space use of five shark and one turtle species at a remote atoll in the Seychelles, Indian Ocean, and evaluate the efficacy of a proposed MPA. Results revealed strong, species-specific habitat use in both sharks and turtles, with corresponding variation in MPA use. Defining the MPA's boundary from the edge of the reef flat at low tide instead of the beach at high tide (the current best in Seychelles) significantly increased the MPA's coverage of predator movements by an average of 34%. Informed by these results, the larger MPA was adopted by the Seychelles government, demonstrating how telemetry data can improve shark spatial conservation by affecting policy directly.

Acoustic telemetry and network analysis reveal the space use of multiple reef predators and enhance marine protected area design

Marine protected areas (MPAs) are commonly employed to protect ecosystems from threats like overfishing. Ideally, MPA design should incorporate movement data from multiple target species to ensure sufficient habitat is protected. We used long-term acoustic telemetry and network analysis to determine the fine-scale space use of five shark and one turtle species at a remote atoll in the Seychelles, Indian Ocean, and evaluate the efficacy of a proposed MPA. Results revealed strong, species-specific habitat use in both sharks and turtles, with corresponding variation in MPA use. Defining the MPA's boundary from the edge of the reef flat at low tide instead of the beach at high tide (the current best in Seychelles) significantly increased the MPA's coverage of predator movements by an average of 34%. Informed by these results, the larger MPA was adopted by the Seychelles government, demonstrating how telemetry data can improve shark spatial conservation by affecting policy directly.

Markov models and network analysis reveal sex-specific differences in the space-use of a coastal apex predator

Understanding the links between external variables such as habitat and interactions with conspecifics and animal space-use is fundamental to developing effective management measures. In the marine realm, automated acoustic tracking has become a widely used method for monitoring the movement of free-ranging animals, yet researchers generally lack robust methods for analysing the resulting spatial-usage data. In this study, acoustic tracking data from male and female broadnose sevengill sharks Notorynchus cepedianus, collected in a system of coastal embayments in southeast Tasmania were analyzed to examine sex-specific differences in the sharks' coastal space-use and test novel methods for the analysis of acoustic telemetry data. Sex-specific space-use of the broadnose sevengill shark from acoustic telemetry data was analysed in two ways: The recently proposed spatial network analysis of between-receiver movements was employed to identify sex-specific space-use patterns. To include the full breadth of temporal information held in the data, movements between receivers were furthermore considered as transitions between states of a Markov chain, with the resulting transition probability matrix allowing the ranking of the relative importance of different parts of the study area. Both spatial network and Markov chain analysis revealed sex-specific preferences of different sites within the study area. The identification of priority areas differed for the methods, due to the fact that in contrast to network analysis, our Markov chain approach preserves the chronological sequence of detections and accounts for both residency periods and movements. In addition to adding to our knowledge of the ecology of a globally distributed apex predator, this study presents a promising new step towards condensing the vast amounts of information collected with acoustic tracking technology into straightforward results which are directly applicable to the management and conservation of any species that meet the assumptions of our model.

Patterns in the space use of the Bearded Reedling, Panurus biarmicus, on the Tay Reedbeds, Scotland

This thesis presents research into the space use of a specialist reedbed Passerine, the Bearded Reedling, or Bearded Tit, Panurus biarmicus, with a view to inform the conservation of this species and reedbeds as a whole. How a species uses space, and how space use changes between individuals or over time, can influence: the ability to forage and hunt effectively, breeding success, susceptibility to predation, genetic health, disease spread, robustness against environmental change and ultimately, colonisation or extinction. Thus, understanding the space use of animals can provide critical insight into ecological systems. Birds offer interesting models when studying animal space use, as, by being intrinsically mobile, many bird species can occupy multiple spatial scales. As a consequence of being completely dependent on patchy and ephemeral reedbed habitats, the Bearded Reedling, has a clustered, inhomogeneous distribution throughout its range. This drives the existence of distinct spatial scales upon which space use studies should be characterised. Distribution and movement within a single reedbed can be considered local-scale, while spatial processes between reedbeds can be considered wide-scale. Temporal processes may act upon both of these scales. For example, changing interactions with predators may influence nest positioning at a local-scale, while seasonal changes in resource requirements might drive processes such as migration at a wide-scale. The Bearded Reedling has a wide temperate breeding range, extending over much of Eurasia. On the IUCN’s red list, it is listed as ‘of least concern’, with an estimated European population between 240,000-480,000 breeding pairs. Despite its relatively favourable conservation status, its dependence on reedbed habitats drives a fragmented distribution, with populations being concentrated in small, isolated, stands. Over the last century reedbed wetlands have suffered rapid declines caused by drainage schemes undertaken to improve land for development or agriculture. Additionally, many remaining reed stands are subject to extensive commercial management to produce thatch or biofuel. Conversely, in other areas, management is driven by conservation motives which recognise the present threats to reedbeds, and aim to encourage the diversity of species associated with these habitats. As the Bearded Reedling is fundamentally linked to the quality and structure of a reed stand, understanding the space use of this species will offer information for the direct conservation of this specialist species, and for the effects of reedbed management as a whole. This thesis first presents studies of space use at a local-scale. All local-scale research is conducted at the Tay Reedbeds in eastern Scotland. Mist netting and bird ringing data are used within capture recapture models, which include an explicit spatial component, to gain insight into the abundance of the Bearded Reedling on the Tay. This abundance estimation approach suggests the Tay reedbeds are a stronghold for this species on the British Isles, and that, as a high latitude site, the Tay may have importance for range expansion. A combination of transect surveys and radio-tracking data are then used to establish the local-scale space use of this species during the breeding and autumnal seasons. These data are related to changes in the structure of reed caused by local management in the form of mosaic winter reed cutting. Results suggest that birds exploit young and cut patches of reed as foraging resources when they are available, and that old, unmanaged reed is critical for nesting and winter foraging. Further local-scale studies concern the spatial patterns in the nesting habits of this species. Mosaic reed cutting creates clear edges in a reedbed. Artificial nests placed in the Tay Reedbeds demonstrate increased nest predation rates closer to the edges of cut patches. Additionally, high predation rates become reduced as the cut reed re-grows, suggesting that reed cutting may increase accessibility of the stand to predators. As Bearded Reedling nests are uncommon and difficult to locate, the timing, site selection and structure of a sample of real nests from the Tay is then detailed. These demonstrate an early, and relatively rigid breeding onset in this species, the importance of dense, compacted reeds as nesting sites and a degree of flexibility in nest structure. Conservation efforts will also benefit from studies into wide-scale spatial processes. These may be important when establishing how colonisation events occur and when predicting the effects of climatic change. The Bearded Reedling has been traditionally considered a resident species which only occasionally undertakes wide-scale, between-reedbed, movements. Indeed, the ecology of this species suggests strict year round local residency to reedbeds, with distinct seasonal changes in diet allowing occupation of these habitats year round. The European ringing recoveries of this species, since the 1970s are investigated to better characterise the wider movements of specialist resident. These suggest residency in southern populations, but higher instances of movement than expected in more northerly regions. In these regions wide-scale movement patterns resemble those of partial regular migratory species. An understanding of local and wide-scale spatial processes can offer a strong foundation on which to build conservation strategies. This thesis aims to use studies of space use to provide this foundation for the Bearded Reedling and offer further insight into the ecology of reedbed habitats as a whole. The thesis concludes by proposing an effective strategy for the conservation management of reedbeds that will especially benefit the Bearded Reedling.

Habitat heterogeneity and use of physical acoustic space in anuran communities in southeastern Brazil.

We intended to verify if structural and physiognomical characteristics of water bodies influence on the degree of overlap among calling sites of 23 anurans species, if anuran species use different calling sites in different water bodies, and if there is some relationship between the degree of advertisement call (based on seven call features) and calling site differentiation. Then, we determined calling sites (based in four variables) and recorded the advertisement call for anuran species that occurred in 10 water bodies of northwestern São Paulo State. We also determined the environmental heterogeneity (based in four environmental descriptors) for each water body. Males of most species used similar calling sites in each water body, probably because of the high uniformity of the environment, as a consequence of agricultural impacts on edge vegetation of the studied ponds. Most species (18 out of 19 species) called from different sites in the ponds where they occurred, which can be associated with differences in horizontal and vertical distribution of vegetation in the studied ponds. From the 19 species analyzed, only males of Pseudopaludicola aff. saltica called in sites with the same characteristics in different ponds. Advertisement call of Hylidae species was more similar to each other than were Leiuperidae and Leptodactylidae among themselves. The aquatic/terrestrial anurans (Bufonidae, Leiuperidae, Leptodactylidae and Microhylidae) occupied similar calling sites but presented quite distinct advertisement calls, while Hylidae species presented an inverse pattern: a high similarity on advertisement call features but used different calling sites, which indicates a niche complementarity between physical (calling site use) and acoustic (advertisement call) space use.