Abundance and opal input of radiolarian species of two sediment cores from the Atlantic sector of the Southern Ocean

Radiolarian-based paleoceanographic reconstructions generally use the abundance of selected radiolarian species. However, the recent focus on the opal flux and the development of isotope measurements in biogenic opal and the organic matter embedded in it demands a better knowledge of the origin of the opal. We present here an estimation of the opal content of the skeleton of 63 radiolarian species from two sites in the Southern Ocean. The skeletons are modelled as associations of simple geometrical shapes, and the volume thus obtained is combined with opal density to obtain the amount of opal. These data are, thus, used to determine the most important opal carriers in the radiolarian assemblage in both cores.

Optimal sampling strategy for estimation of spatial genetic structure in tree populations

Fine-scale spatial genetic structure (SGS) in natural tree populations is largely a result of restricted pollen and seed dispersal. Understanding the link between limitations to dispersal in gene vectors and SGS is of key interest to biologists and the availability of highly variable molecular markers has facilitated fine-scale analysis of populations. However, estimation of SGS may depend strongly on the type of genetic marker and sampling strategy (of both loci and individuals). To explore sampling limits, we created a model population with simulated distributions of dominant and codominant alleles, resulting from natural regeneration with restricted gene flow. SGS estimates from subsamples (simulating collection and analysis with amplified fragment length polymorphism (AFLP) and microsatellite markers) were correlated with the 'real' estimate (from the full model population). For both marker types, sampling ranges were evident, with lower limits below which estimation was poorly correlated and upper limits above which sampling became inefficient. Lower limits (correlation of 0.9) were 100 individuals, 10 loci for microsatellites and 150 individuals, 100 loci for AFLPs. Upper limits were 200 individuals, five loci for microsatellites and 200 individuals, 100 loci for AFLPs. The limits indicated by simulation were compared with data sets from real species. Instances where sampling effort had been either insufficient or inefficient were identified. The model results should form practical boundaries for studies aiming to detect SGS. However, greater sample sizes will be required in cases where SGS is weaker than for our simulated population, for example, in species with effective pollen/seed dispersal mechanisms.

Tradeoffs of different types of species occurrence data for use in systematic conservation planning

Data on the occurrence of species are widely used to inform the design of reserve networks. These data contain commission errors (when a species is mistakenly thought to be present) and omission errors (when a species is mistakenly thought to be absent), and the rates of the two types of error are inversely related. Point locality data can minimize commission errors, but those obtained from museum collections are generally sparse, suffer from substantial spatial bias and contain large omission errors. Geographic ranges generate large commission errors because they assume homogenous species distributions. Predicted distribution data make explicit inferences on species occurrence and their commission and omission errors depend on model structure, on the omission of variables that determine species distribution and on data resolution. Omission errors lead to identifying networks of areas for conservation action that are smaller than required and centred on known species occurrences, thus affecting the comprehensiveness, representativeness and efficiency of selected areas. Commission errors lead to selecting areas not relevant to conservation, thus affecting the representativeness and adequacy of reserve networks. Conservation plans should include an estimation of commission and omission errors in underlying species data and explicitly use this information to influence conservation planning outcomes.

Classification of Chenopodium Genus Populations and Species Based on Continuous and Categorical Variables

2000 Mathematics Subject Classification: 62P10, 62H30

Estimation of sea surface temperature from sediment core PS1768-8

The quantitative diatom analysis of 218 surface sediment samples recovered in the Atlantic and western Indian sector of the Southern Ocean is used to define a base of reference data for paleotemperature estimations from diatom assemblages using the Imbrie and Kipp transfer function method. The criteria which justify the exclusion of samples and species out of the raw data set in order to define a reference database are outlined and discussed. Sensitivity tests with eight data sets were achieved evaluating the effects of overall dominance of single species, different methods of species abundance ranking, and no-analog conditions (e.g., Eucampia Antarctica) on the estimated paleotemperatures. The defined transfer functions were applied on a sediment core from the northern Antarctic zone. Overall dominance of Fragilariopsis kerguelensis in the diatom assemblages resulted in a close affinity between paleotemperature curve and relative abundance pattern of this species downcore. Logarithmic conversion of counting data applied with other ranking methods in order to compensate the dominance of F. kerguelensis revealed the best statistical results. A reliable diatom transfer function for future paleotemperature estimations is presented.

Georeferenced standardized apparent wave power along the coastline of Cabrera National Park for analysis of essential habitats of littoral species

Wind- induced exposure is one of the major forces shaping the geomorphology and biota in coastal areas. The effect of wave exposure on littoral biota is well known in marine environments (Ekebon et al., 2003; Burrows et al., 2008). In the Cabrera Archipelago National Park wave exposure has demostrated to have an effect on the spatial distribution of different stages of E.marginatus (Alvarez et al., 2010). Standarized average wave exposures during 2008 along the Cabrera Archipelago National park coast line were calculated to be applied in studies of littoral species distribution within the archipelago. Average wave exposure (or apparent wave power) was calculated for points located 50 m equidistant on the coastline following the EXA methodology (EXposure estimates for fragmented Archipelagos) (Ekebon et al., 2003). The average wave exposures were standardized from 1 to 100 (minimum and maximum in the area), showing coastal areas with different levels of mea wave exposure during the year. Input wind data (direction and intensity) from 2008 was registered at the Cabrera mooring located north of Cabrera Archipelago. Data were provided by IMEDEA (CSIC-UIB, TMMOS http://www.imedea.uib-csic.es/tmoos/boyas/). This cartography has been developed under the framework of the project EPIMHAR, funded by the National Park's Network (Spanish Ministry of Environment, Maritime and Rural Affairs, reference: 012/2007 ). Part of this work has been developed under the research programs funded by "Fons de Garantia Agrària i Pesquera de les Illes Balears (FOGAIBA)".

Relative abundance of diatom species in surface samples from the Southern Ocean, Sea ice species

Diatoms from 228 Southern Ocean core-top sediment samples were examined to determine the geographic distributions of 32 major diatom species/taxa preserved in the sediments of three zonally-distinct regions; Sea Ice, Open Ocean and the Tropical/Subtropical. In the first of three papers, 14 species/taxa occurring in the region where sea ice covers the ocean surface on an annual basis are geographically documented. Comparisons are drawn between the diatom abundances on the sea floor, sea ice parameters (annual duration and concentration in February and September) and February sea-surface temperature. Such parameters are commonly used in reconstructing past oceanographic conditions in the Sea Ice and Open Ocean zones. Analysis of the geographic patterns and sea-surface parameter correlations reveals species-specific distributions regulated primarily by sea ice coverage and sea-surface temperature, which support the use of diatom remains for the estimation of these past sea-surface environmental parameters. Comparison with reliable accounts of the 14 species from the sediments or plankton also provides the first glimpses into species-specific ecology and habitat linkages.

A Parameter Estimation and Identifiability Analysis Methodology Applied to a Street Canyon Air Pollution Model

Mathematical models are increasingly used in environmental science thus increasing the importance of uncertainty and sensitivity analyses. In the present study, an iterative parameter estimation and identifiability analysis methodology is applied to an atmospheric model – the Operational Street Pollution Model (OSPMr). To assess the predictive validity of the model, the data is split into an estimation and a prediction data set using two data splitting approaches and data preparation techniques (clustering and outlier detection) are analysed. The sensitivity analysis, being part of the identifiability analysis, showed that some model parameters were significantly more sensitive than others. The application of the determined optimal parameter values was shown to succesfully equilibrate the model biases among the individual streets and species. It was as well shown that the frequentist approach applied for the uncertainty calculations underestimated the parameter uncertainties. The model parameter uncertainty was qualitatively assessed to be significant, and reduction strategies were identified.

Development of single nucleotide polymorphism (SNP) markers from the mango (Mangifera indica) transcriptome for mapping and estimation of genetic diversity

The development of molecular markers for genomic studies in Mangifera indica (mango) will allow marker-assisted selection and identification of genetically diverse germplasm, greatly aiding mango breeding programs. We report here our identification of thousands of unambiguous molecular markers that can be easily assayed across genotypes of the species. With origin centered in Southeast Asia, mangos are grown throughout the tropics and subtropics as a nutritious fruit that exhibits remarkable intraspecific phenotypic diversity. With the goal of building a high density genetic map, we have undertaken discovery of sequence variation in expressed genes across a broad range of mango cultivars. A transcriptome sequence reference was built de novo from extensive sequencing and assembly of RNA from cultivar 'Tommy Atkins'. Single nucleotide polymorphisms (SNPs) in protein coding transcripts were determined from alignment of RNA reads from 24 mango cultivars of diverse origins: 'Amin Abrahimpur' (India), 'Aroemanis' (Indonesia), 'Burma' (Burma), 'CAC' (Hawaii), 'Duncan' (Florida), 'Edward' (Florida), 'Everbearing' (Florida), 'Gary' (Florida), 'Hodson' (Florida), 'Itamaraca' (Brazil), 'Jakarata' (Florida), 'Long' (Jamaica), 'M. Casturi Purple' (Borneo), 'Malindi' (Kenya), 'Mulgoba' (India), 'Neelum' (India), 'Peach' (unknown), 'Prieto' (Cuba), 'Sandersha' (India), 'Tete Nene' (Puerto Rico), 'Thai Everbearing' (Thailand), 'Toledo' (Cuba), 'Tommy Atkins' (Florida) and 'Turpentine' (West Indies). SNPs in a selected subset of protein coding transcripts are currently being converted into Fluidigm assays for genotyping of mapping populations and germplasm collections. Using an alternate approach, SNPs (144) discovered by sequencing of candidate genes in 'Kensington Pride' have already been converted and used for genotyping.

Estimation of mercury background values in sediment and biota of the Bijagós archipelago, Guinea-Bissau

This work evaluates the mercury (Hg) contamination status (sediments and biota) of the Bijagós archipelago, off the coast of Guinea-Bissau. Sediments exhibited very low concentrations (<1-12ngg(-1)), pointing to negligible sources of anthropogenic Hg in the region. Nevertheless, Hg is well correlated to the fine fraction, aluminium, and loss on ignition, indicating the effect of grain size and organic matter content on the presence of Hg in sediments. Mercury in the bivalves Tagelus adansoni and Senilia senilis did not vary considerably among sites, ranging within narrow intervals (0.09-0.12 and 0.12-0.14μgg(-1) (dry weight), respectively). Divergent substrate preferences/feeding tactics may justify slight differences between species. The value 11ngg(-1) is proposed as the sediment background concentration for this West-African coastal region, and concentrations within the interval 8-10ngg(-1) (wet weight) may be considered as reference range for S. senilis and T. adansoni in future monitoring studies.

Umbrella pine above ground biomass estimation with very high spatial resolution satellite images

Above ground biomass is frequently estimated with forest inventory data and an extrapolation method for the per unit area evaluations. This procedure is labour demanding and costly. In this study above ground biomass functions, whose independent variable is crown horizontal projection, were developed. Multi-resolution segmentation method and object-oriented classification, based on very high spatial resolution satellite images, were used to obtain the area of tree crown horizontal projection for umbrella pine (Pinus pinea L.). A set of inventory plots were measured and with existing allometric functions for this species above ground biomass per tree and per plot were calculated. The two data sets were used to fit linear functions both for individual plot and their cumulative values. The results show a good performance of the models. Errors smaller than 10% are obtained for stand areas greater than 1.4 ha. These functions have the advantages of estimating above ground biomass for all the area under study or surveillance, not requiring forest inventory; allow monitoring in short time periods; and are easily implemented in a geographical information system environment.

Above ground biomass estimation in Mediterranean multiple use systems with high spatial resolution satellite images

Forest biomass has been having an increasing importance in the world economy and in the evaluation of the forests development and monitoring. It was identified as a global strategic reserve, due to its applications in bioenergy, bioproduct development and issues related to reducing greenhouse gas emissions. The estimation of above ground biomass is frequently done with allometric functions per species with plot inventory data. An adequate sampling design and intensity for an error threshold is required. The estimation per unit area is done using an extrapolation method. This procedure is labour demanding and costly. The mail goal of this study is the development of allometric functions for the estimation of above ground biomass with ground cover as independent variable, for forest areas of holm aok (Quercus rotundifolia), cork oak (Quercus suber) and umbrella pine (Pinus pinea) in multiple use systems. Ground cover per species was derived from crown horizontal projection obtained by processing high resolution satellite images, orthorectified, geometrically and atmospheric corrected, with multi-resolution segmentation method and object oriented classification. Forest inventory data were used to estimate plot above ground biomass with published allometric functions at tree level. The developed functions were fitted for monospecies stands and for multispecies stands of Quercus rotundifolia and Quercus suber, and Quercus suber and Pinus pinea. The stand composition was considered adding dummy variables to distinguish monospecies from multispecies stands. The models showed a good performance. Noteworthy is that the dummy variables, reflecting the differences between species, originated improvements in the models. Significant differences were found for above ground biomass estimation with the functions with and without the dummy variables. An error threshold of 10% corresponds to stand areas of about 40 ha. This method enables the overall area evaluation, not requiring extrapolation procedures, for the three species, which occur frequently in multispecies stands.