Phenex: ontological annotation of phenotypic diversity.

BACKGROUND: Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. CONCLUSIONS/SIGNIFICANCE: Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

Marine microplankton diversity database

Many macroecological theories have been developed to study the diversity on our planet. All these theories require the existence of consistent databases to test their predictions. In this work, we compiled a data set of marine microplankton species abundances at 788 stations with an extensive geographical coverage. Data were collected on different oceanographic cruises between 1992 and 2002. This database consists of abundances (cells/mL) for each species at each station and depth, together with estimates of the biomass and biovolume for each species. One of the key strengths in this database is that species identifications were made by the same taxonomist, which provides greater strength to the collection and ensures that estimates of species diversity are reliable. Environmental information has also been compiled at each station (chlorophyll, temperature, photosynthetically active radiation [PAR], nutrients) in order to have a characterization of the study area and to be used in studies on the environmental and biological controls of marine biodiversity.

Diversity of functional groups in the vegetation sandy seashore of the Grande, Anclitas and Caguamas Cays (Jardines de la Reina Archipelago, Cuba)

Sandy shores are known to be extreme ecosystems where the vegetation has evolved many morphological and physiological adaptations for its survival. With the aim of identify possible relationships between the vegetation´s functional diversity with abiotic factors and its corresponding quantification, we collected data on the abundance and richness of the sandy coast vegetation complex in Grande, Anclitas and Caguamas keys. Its flora is largely characterized by the dominance of hemicryptophytes and chamaephytes plants with nanophyllous leaves and displaying dispersal syndromes such as zoochory and anemochory. However, the functional groups´ richness, in the present study, varies from one key to another. Functional diversity is similar between the wet and dry seasons, and its spatial variation is influenced by the interplay of the set of abiotic factors herein studied.

Global latitudinal variations in marine copepod diversity and environmental factors

Latitudinal gradients in diversity are among the most striking features in ecology. For terrestrial species, climate (i.e. temperature and precipitation) is believed to exert a strong influence on the geographical distributions of diversity through its effects on energy availability. Here, we provide the first global description of geographical variation in the diversity of marine copepods, a key trophic link between phytoplankton and fish, in relation to environmental variables. We found a polar-tropical difference in copepod diversity in the Northern Hemisphere where diversity peaked at subtropical latitudes. In the Southern Hemisphere, diversity showed a tropical plateau into the temperate regions. This asymmetry around the Equator may be explained by climatic conditions, in particular the influence of the Inter-Tropical Convergence Zone, prevailing mainly in the northern tropical region. Ocean temperature was the most important explanatory factor among all environmental variables tested, accounting for 54 per cent of the variation in diversity. Given the strong positive correlation between diversity and temperature, local copepod diversity, especially in extra-tropical regions, is likely to increase with climate change as their large-scale distributions respond to climate warming.

Biological Communities at Marine Shallow-Water Vent and Seep Sites

The review compiles, for the first time, data on the communities at 62 shallow-water hydrothermal vent and cold seep sites. ‘Shallow sites’ are defined as sites no deeper than 200 m. The communities at these sites are also compared with communities in reducing sediments at similar depths. Below 200 m, vent and seep obligate species tend to dominate the fauna living in areas where reducing fluids are released from the seabed. At the shallow sites, vent and seep obligate species of fauna are rare, only eight having being reported from shallow vents. No definite seep obligates have been found. Shallow vents and seeps are colonized by communities that consist of a subset of the background fauna, especially those species that are less sensitive to hydrogen sulphide toxicity. Conversely the zones directly surrounding shallow vent and seeps sites with varied topography, substrate type and food supply, often have a higher species diversity than the background area. The reasons for these differences are discussed.

Effect of habitat fragmentation on levels and patterns of genetic diversity in natural populations of the peat moss Polytrichum commune

Peat bogs represent unique ecosystems that are under particular threat from fragmentation due to peat harvesting, with only 38% of the original peatland in Europe remaining intact and unaffected by peat cutting, drainage and silviculture. In this study, we have used microsatellite markers to determine levels and patterns of genetic diversity in both cut and uncut natural populations of the peat moss Polytrichum commune. Overall diversity levels suggest that there is more genetic variation present than had previously been assumed for bryophytes. Despite this, diversity values from completely cut bogs were found to be lower than those from uncut peatlands (average 0.729 versus 0.880). In addition, the genetic diversity was more highly structured in the cut populations, further suggesting that genetic drift is already affecting genetic diversity in peat bogs subjected to fragmentation.

Tracking biological invasions in space and time: elucidating the invasive history of the green alga Codium fragile using old DNA

With the advent of 'ancient DNA' studies on preserved material of extant and extinct species, museums and herbaria now represent an important although still underutilized resource in molecular ecology. The ability to obtain sequence data from archived specimens can reveal the recent history of cryptic species and introductions. We have analysed extant and herbarium samples of the highly invasive green alga Codium fragile, many over 100 years old, to identify cryptic accessions of the invasive strain known as C. fragile ssp. tomentosoides, which can be identified by a unique haplotype. Molecular characterization of specimens previously identified as native in various regions shows that the invasive tomentosoides strain has been colonizing new habitats across the world for longer than records indicate, in some cases nearly 100 years before it was noticed. It can now be found in the ranges of all the other native haplotypes detected, several of which correspond to recognized subspecies. Within regions in the southern hemisphere there was a greater diversity of haplotypes than in the northern hemisphere, probably as a result of dispersal by the Antarctic Circumpolar Current. The findings of this study highlight the importance of herbaria in preserving contemporaneous records of invasions as they occur, especially when invasive taxa are cryptic.

Phenotypic diversity amongst strains of Pleurotus sajor-caju: implications for cultivation in and environments

In arid regions, biodiversity and biomass are limited by water availability, and this problem has been compounded by desertification associated with global climate change. The saprotrophic macrofungi that are indigenous to hot subtropical and tropical regions, such as Pleurotus spp., can play key roles in water sequestration, nutrient cycling, human nutrition, and bioremediation of waste materials. We studied 15 strains of Pleurotus sajor-caju, a widespread and phenotypically-diverse species, to establish variability in growth response and primordium development over a range of stress parameters: osmotic potential (-0.5 to -5 MPa), temperature (5-40 degrees C) and pH (2-12). The initiation of primordia precedes basidiome production and therefore represents a key stage in bioremediation strategies and fungi-driven nutrient cycles. Primordia were produced at low pH (4-6), at suboptimal growth temperatures (<or =25 degrees C), and under moderate water stress (-0.5 to -3.5 MPa). Although the growth windows for different strains were similar, their maximum growth rates and the optimum conditions for growth varied. We discuss the phenotypic diversity of Pleurotus strains and discuss their potential for cultivation, bioremediation and ecological regeneration.

Cryptic species diversity in a widespread bumble bee complex revealed using mitochondrial DNA RFLPs

Cryptic species diversity is thought to be common within the class Insecta, posing problems for basic ecological and population genetic studies and conservation management. Within the temperate bumble bee (Bombus spp.) fauna, members of the subgenus Bombus sensu stricto are amongst the most abundant and widespread. However, their species diversity is controversial due to the extreme difficulty or inability morphologically to identify the majority of individuals to species. Our character-based phylogenetic analyses of partial CO1 (700 bp) from 39 individuals spread across their sympatric European ranges provided unequivocal support for five taxa (3-22 diagnostic DNA base pair sites per species). Inclusion of 20 Irish specimens to the dataset revealed >= 2.3% sequence divergence between taxa and 200 m) whilst B. cryptarum was relatively more abundant at higher altitudes. Bombus magnus was rarely encountered at urban sites. Both B. lucorum and B. terrestris are nowadays reared commercially for pollination and transported globally. Our RFLP approach to identify native fauna can underpin ecological studies of these important cryptic species as well as the impact of commercial bumble bees on them.

Understanding genetic diversity of the liver fluke Fasciola hepatica

Economical breeding is important to obtain maximum gain from the breeding in the animal sector. The economic loss has to be eliminated or should be minimized. The liver fluke, Fasciola hepatica, present mostly in sheep and dairy cattle affect the yield of animals and even cause their death. To eliminate or minimize the impact of these parasites on the animals, it is important to understand the genetic diversity of the liver fluke populations and the relationship between parasite and host at regional bases. This research was carried out to determine diversity by sequence analysis of the mitochondrial ND1 gene and ribosomal ITS1 region.

Tentacular diversity in deep-sea deposit-feeding holothurians: implications for biodiversity in the deep sea

The tentacles of deep-sea holothurians show a wide range of morphological diversity. The present paper examines gross tentacle morphology in surface deposit feeding holothurians from a range of bathymetric depths. Species studied included the elasipods: Oneirophanta mutabilis, Psychropotes longicauda and Benthogone rosea and the aspidochirotids: Paroriza prouhoi, Pseudostichopus sp., Bathyplotes natans and Paroriza pallens. The sympatric abyssal species Oneirophanta mutabilis, Psychropotes longicauda and Pseudostichopus sp. show subtle differences in diet and the structure and filling patterns of the gut that suggest differences in feeding strategies which may represent one mechanism to overcome competition for food resources in an environment where nutrient resources are considered to be, at least periodically, limiting. Interspecific differences in tentacle functional morphology and digestive strategies, which reflects taxonomic diversity could be explained in terms of Sanders'; Stability–Time Hypothesis. Since different tentacle types will turn over sediments to different extents, their impact on sedimentary communities will be enormous so that high diversity in meiofaunal communities may be explained most simply by Dayton and Hessler's Biological Disturbance Hypothesis.