Raccoon ecology database: A resource for population dynamics modelling and meta-analysis

The value of scientific studies increases and is extended when their data are stored in a manageable and accessible format. This is demonstrated through development of a raccoon ecology database (REDB) to store, manage and disseminate available peer-reviewed and unpublished data on raccoon (Procyon lotor) biology, ecology and raccoon rabies, including citations for data sources. Over 800 documents were identified and citations for them entered into the database as literature references. Approximately 1000 trait values were entered from almost 200 of these sources. These data included estimates of population density, survival rates, rabies incubation period, litter size, body weight, dispersal distance and home-range size, often by age or sex class. Each datum is linked to a citation for its source, and to information about location and land use in the study area, time of year the study was undertaken, sample size, and variance. The relational database design enables querying and easy updating and manipulation of data.

The relational data model is presented, as is its application in further developing an individual-based, spatially-explicit population model of raccoon rabies. Using information queried from the REDB benefits model development by: i) assessing the appropriateness of input parameter values, ii) providing sources for citing input values, iii) parameterising the model to different geographic regions, iv) enabling meta-analyses for evaluating model structure, as well as further contributing to parameterisation at specific locations, and v) providing biologically appropriate parameter input values for model sensitivity testing. The REDB is a useful research resource that will increase in value with ongoing inclusion of data from future raccoon and raccoon rabies studies and serves as a model for database design and research applications to other species. The database and an empty database for use with other species are available online (http://redb.nrdpfc.ca).     

Seed banks of a southern Australian wetland: the influence of water regime on the final floristic composition

The sediments of a southern Australian wetland complex were investigated to determine the germinable seed bank. The number of seeds ranged from 22,000 to 78,000 m^–2. Non-metric multi dimensional scaling (NMS) ordination based upon species composition separated the four basins but each contained the representatives of the major functional groups: terrestrial, amphibious and submerged. To test the influence of water regime on the final floristic composition derived from these seed banks, sediments were positioned at three elevations (0, 30 and 80 cm) and subjected to three hydrologic regimes (static water level, and draw down rates of 2.5 and 7 cm week^–1). Species compositions were analysed after 98 days via ordination. Despite significant differences in the initial seed bank composition the final floristic compositions were correlated with the water regime and independent of the initial seed bank composition. Species groups were segregated on a basis of whether sediments were continuously exposed to the atmosphere, the rate of draw down and the water depth. Moist sediments were dominated by species belonging to all the main functional groups. Sediments subject to rapid drying were dominated by terrestrial species whereas sediments that were flooded for the majority of the time were dominated by submerged species.     

Diatoms of Lake Peipsi-Pihkva: a floristic and ecological review

463 taxa of diatoms have been recorded from the pelagic and littoral plankton, benthos and periphyton of Lake Peipsi-Pihkva. This typical eutrophic plain lake has many common features with large lakes of both Central and North Europe. As to the richness of diatom taxa, L. Peipsi- Pihkva surpasses other eutrophic lowland lakes, which can be explained by the size of this lake, and by the variety of living conditions in it. The list of taxa as well as notes about rare and phytogeographically interesting diatoms are presented.Deceased.     

Diversity and ecological characteristics of vascular flora in Mediterranean temporary pools

Vascular flora of Mediterranean temporary pools has been studied with the aims to define its diversity and to individuate the ecological characteristics of the different plant groups associated with this relevant and endangered habitat type. Overall, 246 species were found of which 108 were terrestrial, 57 generalist of aquatic or wet habitats and 81 typical of temporary water and strongly linked to temporary pools. The results suggest that: (i) vascular flora associated with Sardinian Mediterranean temporary pools is rich and diversified; (ii) rare ferns are better represented than previously reported; (iii) plant species are generally heliophilous and acidophilous, specialized temporary pool species mainly differing from the unspecialized ones in relationship to their soil moisture requirements; (iv) these habitats are particularly important for maintaining regional freshwater biodiversity.     

The ecological significance of annuals on a Mediterranean grassland (Mt Ventoux,France)

A study was carried out on a Mediterranean limestone grassland to search for the ecological significance of the occurrence of annuals. In the studied grassland, most of annuals are concentrated in patches. Authors tested if annuals (1) correspond to the R-strategy (ruderal) according to Grime's theory, i. e. they are adapted to live in disturbed, productive habitats, or (2) if they present an adaptation to a xeric climate in keeping with Raunkiaer.The correspondence analyses and the examination of plants strategies reveal that:(1) annuals are grouped with the more xerophytic perennials in the ordination,(2) the cover of annuals is higher in plots with a high cover of S species (stress-tolerators) and a lower cover of C species (competitors) and CS species (intermediate strategy).These results constitute arguments to integrate annuals of Mediterranean grasslands into stress-tolerators. In the discussion are examined the importance of patches in which annuals are preferentially located. Although patches are generated by disturbances, the presence of annuals is explained by their life cycle fitting the microclimate variations, characterized by an extreme summer drought. Their cycle is not adapted here to the frequency of disturbances (unless the summer drought is considered as annual disturbance - this last point of view is discussed). In the studied grassland, annuals are then better thought of as highly developed stress-tolerators than as ruderals. A generalization is put forward by distinguishing two cases: in xeric habitats, annuals are stress-tolerant, and in productive habitats, they are ruderal.Nomenclature: follows Kerguélen (1993)     

PeptideDepot: Flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information

Recently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through MS/MS. Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to various experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker‐driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end‐users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our high throughput autonomous proteomic pipeline used in the automated acquisition and post‐acquisition analysis of proteomic data.     

Nitrogen-fixing legumes and silvigenesis in a rain forest in French Guiana: a taxonomic and ecological approach

The nodulation status and nodule morphology of 62 taxa of Leguminosae in a rain forest in French Guiana are reported according to the taxonomy of the family. The N₂-fixing species are then fitted into 'functional groups' according to their behaviour towards illumination, in order to evaluate their importance in the global dynamics of the stand. The results showed that 67% of the observed species were nodulated (50, 71 and 77% of the Caesalpiniaceae, Mimosaceae and Papilionaceae, respectively). In the Caesalpiniaceae, nodule-like structures were reported in the genus Crudia and in the species Senna quinquangulata , although this needs to be confirmed. All the nodules studied in this subfamily were astragaloid and mucunoid. In the Mimosaceae, the ability of a new genus ( Balizia ) to form nodules was reported, as well as nodulation on aerial roots in Inga stipularis . The nodules studied were mainly mucunoid. In the Papilionaceae, nodulation on aerial roots in Poecilanthe hostmannii and on conventional roots of the genus Paramachaerium were reported for the first time. All types of nodular structures were found in this subfamily but the structures were quite uniform at the tribal level. These are consistent with suggestions that nodule morphology has a taxonomic value. Eight functional groups of N₂-fixing species are proposed, ranging from light dependance to shade tolerance. These results indicate the important role played by N₂-fixing species in the global dynamics of the stand and that N inputs by N₂ fixation were continuous along the gradient of energetic resources that characterizes the silvigenetic process. The interactions between the photosynthetic capacities of the species and the ability to fix N₂ in low light conditions are discussed.     

Functional traits predict drought performance and distribution of Mediterranean woody species

Water availability is one of the key environmental factors that affect plant establishment and distribution. In many regions water availability will decline with climate change, exposing small seedlings to a greater likelihood of drought. In this study, 17 leaves, stem, root, and whole-plant traits of ten woody Mediterranean species were measured under favourable growing conditions and seedling drought survival was evaluated during a simulated dry-down episode. The aims of this study were: i) to assess drought survival of different species, ii) to analyse which functional traits predict drought survival time, and iii) to explain species distribution in the field, based on species drought survival and drought strategies. Drought survival time varied ten-fold across species, from 19 to 192 days. Across species, drought survival was positively related to the rooting depth per leaf area, i.e., the ability to acquire water from deeper soil layers while reducing transpiring leaf area. Drought survival time was negatively related to species ability to grow quickly, as indicated by high relative growth and net assimilation rates. Drought survival also explained species distribution in the field. It was found that species were sorted along a continuum, ranging between two contrasting species functional extremes based on functional traits and drought performance. One extreme consisted of acquisitive fast-growing deciduous species, with thin, soft metabolically active leaves, with high resource use and vulnerability to drought. The opposite extreme consisted of conservative slow-growing evergreen species with sclerophyllous leaves, deep roots, a low transpiring area, and low water use, resulting in high drought survival and drought tolerance. The results show that these drought strategies shape species distribution in this Mediterranean area.     

Transcending data gaps: a framework to reduce inferential errors in ecological analyses

The analysis of functional diversity (FD) has gained increasing importance due to its generality and utility in ecology. In particular, patterns in the spatial distribution and temporal change of FD are being used to predict locations and functional groups that are immediately vulnerable to global changes. A major impediment to the accurate measurement of FD is the pervasiveness of missing data in trait datasets. While such prevalent data gaps can engender misleading inferences in FD analyses, we currently lack any practical guide to handle missing data in trait datasets. Here, we identify significant mismatches between true FD and values derived from datasets that contain missing data. We demonstrate that imputing missing data with a phylogeny‐informed approach reduces the risk of misinterpretation of FD patterns, and provides baseline information against which central questions in ecology can be evaluated.     

Life‐history traits of the Northwest European flora: The LEDA database

Abstract. An international group of scientists is building a ‘trait base’, an open internet database of life‐history traits of the Northwest European flora (LEDA) that can be used as a tool in planning, in nature conservation and restoration, and in other applied research. The species‐trait matrix will comprise referenced information under control of an editorial board, for species of the Northwest European flora, combining existing information and additional measurements. The focus will be on 26 plant traits that describe three key features of plant dynamics: persistence, regeneration, and dispersability. Currently 35% of the species‐trait matrix has been filled; however, as the LEDA trait base consortium aims to deliver a database as complete as possible, all input from the scientific community is welcome.     

HTAPP: High‐throughput autonomous proteomic pipeline

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab‐based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic data sets is critically important. The high‐throughput autonomous proteomic pipeline described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is composed of a software that controls the acquisition of mass spectral data along with automation of post‐acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user‐configurable lab‐based relational database. The software design of high‐throughput autonomous proteomic pipeline focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples.     

Characterization of SCAR markers of Eimeria spp. of domestic fowl and construction of a public relational database (The Eimeria SCARdb)

This study reports the development and characterization of 151 sequence characterized amplified region (SCAR) markers for the seven Eimeria species that infect the domestic fowl. From this set, 84 markers are species-specific and 67 present partial specificity. The complete nucleotide sequence was derived for all markers, revealing the presence of micro- and minisatellite repetitive units in 22 SCARs, with up to five distinct repeat units being observed per marker. Only 15 markers showed significant hits in similarity searches against public sequence databases, thus confirming their anonymous and non-coding character. Finally, a relational database of the markers (the Eimeria SCARdb) was developed and made available on the Internet, providing a valuable resource of SCAR markers that can be useful for molecular diagnosis, and also for epizootiological, genetic variability and genome mapping studies.     

Dung beetle community (Coleoptera: Scarabaeidae: Scarabaeinae) in a tropical landscape at the Lachua Region,Guatemala

Biological diversity conservation within natural reserves has been prioritized, but conservation efforts outside protected areas (where most human activities take place) have been very little considered. In this scenario, an alternative agricultural practice that may reduce the impacts of fragmentation in outer landscapes is a perforation process, which involves conservation in agricultural fields surrounded by continuous forests. Such practices enhance the positive impact of ecological services on fields. In this study we analyzed the biological diversity state in perforation fields and their surrounding forests. The analysis was done using dung beetles as biological indicators. A nested pattern in dung beetles distribution was found, which ordered the surrounding continuous forest sites as the ones with the highest species richness, followed by the perforation fields, and placed the fragmentation practice fields (continuous agricultural fields surrounding forest patches) with the lowest one. Indicator species for perforation fields and surrounding continuous forests were chosen. In general, perforation practice fields differed in composition, based upon functional groups richness and identity; it also contained a higher species richness than the fragmentation practice. Agricultural practices that enhance biological diversity conservation such as perforation, should be recommended and considered in natural resource management by local communities in order to take advantage of ecological services that otherwise may be gradually lost.     

The analysis of convergence in ecological indicators: An application to the Mediterranean fisheries

Ecological indicators are increasingly used to examine the evolution of natural ecosystems and the impacts of human activities. Assessing their trends to develop comparative analyses is essential. We introduce the analysis of convergence, a novel approach to evaluate the dynamic and trends of ecological indicators and predict their behavior in the long-term. Specifically, we use a non-parametric estimation of Gaussian kernel density functions and transition probability matrix integrated in the R software. We validate the performance of our methodology through a practical application to three different ecological indicators to study whether Mediterranean countries converge towards similar fisheries practices. We focus on how distributions evolve over time for the Marine Trophic Index, the Fishing in Balance Index and the Expansion Factor during 1950–2010. Results show that Mediterranean countries persist in their fishery behaviors throughout the time series, although a tendency towards similar negative effects on the ecosystem is apparent in the long-term. This methodology can be easily reproduced with different indicators and/or ecosystems in order to analyze ecosystem dynamics.     

Intertidal zonation and latitudinal gradients on macroalgal assemblages: Species,functional groups and thallus morphology approaches

Macroalgae are unavoidable biological elements when monitoring and assessing costal environments. However, these tasks can be difficult to address because macroalgae a) present a high natural variability across a range of spatial and temporal scales, b) they imply a high sampling and laboratory processing effort and good taxonomical expertise (as they are a very diverse group of species), and c) there is insufficient knowledge about their structural and functional characteristics. This work addressed how the vertical (intertidal zonation) and horizontal (latitudinal gradient) variability of macroalgae assemblages are structured across continental Portugal, as well as how some surrogates for species-level biodiversity measures (namely functional groups and thallus morphology approaches) respond to such large-scale variability. Particularly, it was tested if intertidal zonation patterns are higher than fine-scale horizontal variation, and however, if vertical variation decreases along broad-scale horizontal variation. To do so, cover per species was taken (using a photographical and GIS methodological approach) from five sites located along the shoreline and along respective upper- mid- and lower-intertidal zones. The work findings include that both intertidal and latitudinal gradients impose deep structural changes on assemblages patterns. That is, broad-scale processes along Portuguese latitudes act as strongly as vertical stress gradients on assemblages patterns. Functional groups and thallus morphology approaches were useful to generalize the latitudinal assemblages patterns, where some groups emerge at the expense of others, and may improve biodiversity understanding and ecological synthesis. Because these surrogates decrease taxonomical expertise needs and can provide insight into the functional structure of macroalgal communities, their patterns founded may be particularly useful as reference data for further monitoring, so that shifts in such patterns might represent early warning surrogate approaches to detect environmental impact changes. Ultimately, to generate broader databases on rocky shore assemblages diversity (from species-level to functional groups and thallus morphologies approaches) can be useful for large-scale comparisons and for establishing ecological reference conditions, including for monitoring programs and environmental impact studies.     

The RAINFOR database: monitoring forest biomass and dynamics

Problem: Data from over 100 permanent sample plots which have been studied for 10–20 years need a suitable system for storage which allows simple data manipulation and retrieval for analysis. Methods: A relational database linking tree records, taxonomic nomenclature and corresponding environmental data has been built in MS Access as part of the RAINFOR project. Conclusion: The database allows flexible and long‐term use of a large amount of data: more than 100 tree plots across Amazonia, incorporating over 80 000 records of individual trees and over 300 000 total records of tree diameter measurements from successive censuses. The database is designed to enable linkages to existing soil, floristic or plant‐trait databases. This database will be a useful tool for exploring the impact of environmental factors on forest structure and dynamics at local to continental scales, and long term changes in forest ecology. As an early example of its potential, we explore the impact of different methodological assumptions on estimates of tropical forest biomass and carbon storage.     

Saccharomyces genome database: underlying principles and organisation

A scientific database can be a powerful tool for biologists in an era where large-scale genomic analysis, combined with smaller-scale scientific results, provides new insights into the roles of genes and their products in the cell. However, the collection and assimilation of data is, in itself, not enough to make a database useful. The data must be incorporated into the database and presented to the user in an intuitive and biologically significant manner. Most importantly, this presentation must be driven by the user's point of view; that is, from a biological perspective. The success of a scientific database can therefore be measured by the response of its users - statistically, by usage numbers and, in a less quantifiable way, by its relationship with the community it serves and its ability to serve as a model for similar projects. Since its inception ten years ago, the Saccharomyces Genome Database (SGD) has seen a dramatic increase in its usage, has developed and maintained a positive working relationship with the yeast research community, and has served as a template for at least one other database. The success of SGD, as measured by these criteria, is due in large part to philosophies that have guided its mission and organisation since it was established in 1993. This paper aims to detail these philosophies and how they shape the organisation and presentation of the database.     

UNIQEM, a microbiological database: Problems and prospects

The UNIQEM database, designed to accumulate general microbiological data, is currently used to store and make available information about microorganisms studied and maintained at the Institute of Microbiology, Russian Academy of Sciences. UNIQEM can accumulate and maintain list-form information on a wide range of microorganisms (a property database) and facilitates collecting, processing, and publishing diverse data having to do with these microorganisms and their properties (a catalogue database). The database supports the retrieval of microorganisms by specifying an arbitrary set of their properties and has the potential for eventually evolving into a computer instrument for unattended identification of microorganisms. UNIQEMAkhlynin, D.S. and Gal’chenko, V.F., 1998.     

varver: a database of microsatellite variation in vertebrates

Understanding how genetic variation is maintained within a species is important in ecology, evolution, conservation and population genetics. Tremendous efforts have been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played a major role since the 1990s. Here we describe a comprehensive database, varver (Variation in Vertebrates) that provides complete information regarding microsatellite variation in natural populations of vertebrates. For each species, varver includes basic information of the species, a list of publications reporting the microsatellite variation, and tables of genetic variation within and between populations (heterozygosity and F_ST). The geographic location and rough sampling range are also shown for each sampled population. The database should be useful for researchers interested in not only specific species but also comparing multiple species. We discuss the utility of microsatellite data, particularly for meta‐analyses that involve multiple microsatellite loci from various species. We show that in such analyses, it is extremely important to correct for biases caused by differences in mutation rate, mainly due to repeat unit and number.