(Table 1) List of studied samples with vestimentiferan tubes

Vestimentiferan tube worms are prominent members of modern methane seep communities and are totally reliant as adults on symbiotic sulphide-oxidizing bacteria for their nutrition. The sulphide is produced in the sediment by a biochemical reaction called the anaerobic oxidation of methane (AOM). A well-studied species from the Gulf of Mexico shows that seep vestimentiferans 'mine' sulphide from the sediment using root-like, thin walled, permeable posterior tube extensions, which can also be used to pump sulphate and possibly hydrogen ions from the soft tissue back into the sediment to increase the local rate of AOM. The 'root-balls' of exhumed seep vestimentiferans are intimately associated with carbonate nodules, which are a result of AOM. We have studied vestimentiferan specimens and associated carbonates from seeps at the Kouilou pockmark field on the Congo deep-sea fan and find that some of the posterior 'root' tubes of living specimens are enclosed with carbonate indurated sediment and other, empty examples are partially or completely replaced by the carbonate mineral aragonite. This replacement occurs from the outside of the tube wall inwards and leaves fine-scale relict textures of the original organic tube wall. The process of mineralization is unknown, but is likely a result of post-mortem microbial decay of the tube wall proteins by microorganisms or the precipitation from locally high flux of AOM derived carbonate ions. The aragonite-replaced tubes from the Kouilou pockmarks show similar features to carbonate tubes in ancient seep deposits and make it more likely that many of these fossil tubes are those of vestimentiferans. These observations have implications for the supposed origination of this group, based on molecular divergence estimates.

Genotypic data for nine microsatellite loci for the seagrass Zostera muelleri collections from Lake Macquarie, NSW, Australia

Seagrasses are ecosystem engineers that offer important habitat for a large number of species and provide a range of ecosystem services. Many seagrass ecosystems are dominated by a single species; with research showing that genotypic diversity at fine spatial scales plays an important role in maintaining a range of ecosystem functions. However, for most seagrass species, information on fine-scale patterns of genetic variation in natural populations is lacking. In this study we use a hierarchical sampling design to determine levels of genetic and genotypic diversity at different spatial scales (centimeters, meters, kilometers) in the Australian seagrass Zostera muelleri. Our analysis shows that at fine-spatial scales (< 1 m) levels of genotypic diversity are relatively low (R (Plots) = 0.37 ± 0.06 SE), although there is some intermingling of genotypes. At the site (10's m) and meadow location (km) scale we found higher levels of genotypic diversity (R (sites) = 0.79 ± 0.04 SE; R (Locations) = 0.78 ± 0.04 SE). We found some sharing of genotypes between sites within meadows, but no sharing of genotypes between meadow locations. We also detected a high level of genetic structuring between meadow locations (FST = 0.278). Taken together, our results indicate that both sexual and asexual reproduction are important in maintaining meadows of Z. muelleri. The dominant mechanism of asexual reproduction appears to occur via localised rhizome extension, although the sharing of a limited number of genotypes over the scale of 10's of metres could also result from the localised dispersal and recruitment of fragments. The large number of unique genotypes at the meadow scale indicates that sexual reproduction is important in maintaining these populations, while the high level of genetic structuring suggests little gene flow and connectivity between our study sites. These results imply that recovery from disturbances will occur through both sexual and asexual regeneration, but the limited connectivity at the landscape-scale implies that recovery at meadow-scale losses is likely to be limited.

Hydrochemistry, phytoplankton pigment concentration and phytoplankton abundance in water samples obtained in the Kuroshio Extension Front in October 2009

This data was collected during a cruise to the Kuroshio Extension Front in October 2009. Several chemical and biological parameters were measured: dissolved nutrients, picophytoplankton (by flow cytometry), microphytoplankton (by light microscopy) and phytoplankton pigments (HPLC).

Density of 9 sediment cores from the Weddell Sea

The wet bulk density is one of the most important parameters of the physical and geological properties of marine sediments. The density is connected directly with sedimentation history and a few sedirnent properties. Knowledge of the fine scale density-depth structure is the base for many model calculations, for both sedimentological and palaeoclimatic research. A density measurement system was designed and built at the Alfred Wegener Institute in Bremerhaven for measuring the wet buk density of sediment cores with high resolution in a non-destructive way. The density is deterrnined by measuring the absorption of Gamma-rays in the sediment. This principle has been used since the 50's in materials research and in the geosciences. In the present case, Cs137 is used as the radioactive source and the intensity is measured by a detector system (scintillator and photomultiplier). Density values are obtainable in both longitudinal core sections and planar cross-sections (the latter are a function of the axial rotation angle). Special studies on inhomogenity can be applied with core rotation. Detection of ice rafted debris (IRD) is made possible with this option. The processes that run the density measurement system are computer controlled. Besides the absorption measurement the core diameter at every measurement point is determined with a potentiometric system. The data values taken are stored on a personal computer. Before starting routine measurements on the sediment cores, a few experiments conceming the statistical aspects of the gamma-ray signal and its accuracy were carried out. These experiments led to such things as the optimum operational parameters. A high spatial resolution in the mm-range is possible with the 4mm-thin gamma-ray measurements. Within five seconds the wet bulk density can be deterrnined with an absolute accuracy of 1%. A comparison between data measured with the new system and conventional measurements on core samples after core splitting shows an agreement within +I- 5% for most of the values. For this thesis, density determinations were carried out on ten sediment cores. A few sediment characteristics are obtainable from using just the standard measurement results without core rotation. In addition to differentes and steps in the absolute density range, variations in the "frequency" of the density-depth structure can be detected due to the close spatial measurement interval and high resolution. Examples from measurements with small (9°) and great (90°) angle increments show that abrupt and smooth transitional changes of sedirnent layers as well as ice rafted debris of several dimensions can be detected and distiflguished clearly. After the presentation of the wet bulk density results, a comparison with data from other investigations was made. Measurements of the electrical resistivity correlated very well with the density data because both parameters are closely related to the porosity of the sedirnent. Additionally, results from measurements of the magnetic susceptibility and from ultra-sonic wave velocity investigations were considered for a integrative interpretation. The correlation of these both parameters and wet bulk density data is strongly dependent on the local (environmental) conditions. Finally, the densities were compared with recordings from sediment-echographic soundings and an X-ray computer tomography analysis. The individual results of all investigations were then finally combined into an accurate picture of the core. Problems of ambiguity, which exist when just one Parameter is determined alone, can be reduced more or less according to the number of parameters and sedimentary characteristics measured. The important role of the density data among other parameters of such an integrated interpretation is evident. Evidence of this role include the high resolution of the measurement, the excellent accuracy and the key position within methods and parameters concerning marine sediments.

Tidal-induced mixing and diapycnal nutrient fluxes in the Mauritanian upwelling region

The Mauritanian coastal area is one of the most biologically productive upwelling regions in the world ocean. Shipboard observations carried out during maximum upwelling season and short-term moored observations are used to investigate diapycnal mixing processes and to quantify diapycnal fluxes of nutrients. The observations indicate strong tide-topography interactions that are favored by near-critical angles occurring on large parts of the continental slope. Moored velocity observations reveal the existence of highly nonlinear internal waves and bores and levels of internal wave spectra are strongly elevated near the buoyancy frequency. Dissipation rates of turbulent kinetic energy at the slope and shelf determined from microstructure measurements in the upper 200 m averages to ? = 5 × 10-8 W kg-1. Particularly elevated dissipation rates were found at the continental slope close to the shelf break, being enhanced by a factor of 100 to 1000 compared to dissipation rates farther offshore. Vertically integrated dissipation rates per unit volume are strongest at the upper continental slope reaching values of up to 30 mW m-2. A comparison of fine-scale parameterizations of turbulent dissipation rates for shelf regions and the open ocean to the measured dissipation rates indicates deficiencies in reproducing the observations. Diapycnal nitrate fluxes above the continental slope at the base of the mixed layer yielding a mean value of 12 × 10-2 µmol m-2 s-1 are amongst the largest published to date. However, they seem to only represent a minor contribution (10% to 25%) to the net community production in the upwelling region.

Experiment: changing carbonate chemistry influence on coccoliths formed by Emiliania huxleyi

The coccolithophore Emiliania huxleyi is a marine phytoplankton species capable of forming small calcium carbonate scales (coccoliths) which cover the organic part of the cell. Calcification rates of E. huxleyi are known to be sensitive to changes in seawater carbonate chemistry. It has, however, not yet been clearly determined how these changes are reflected in size and weight of individual coccoliths and which specific parameter(s) of the carbonate system drive morphological modifications. Here, we compare data on coccolith size, weight, and malformation from a set of five experiments with a large diversity of carbonate chemistry conditions. This diversity allows distinguishing the influence of individual carbonate chemistry parameters such as carbon dioxide (CO2), bicarbonate (HCO3- ), carbonate ion (CO32-), and protons (H+) on the measured parameters. Measurements of fine-scale morphological structures reveal an increase of coccolith malformation with decreasing pH suggesting that H+ is the major factor causing malformations. Coccolith distal shield area varies from about 5 to 11 µm2. Changes in size seem to be mainly induced by varying [HCO3- ] and [H+] although influence of [CO32-] cannot be entirely ruled out. Changes in coccolith weight were proportional to changes in size. Increasing CaCO3 production rates are reflected in an increase in coccolith weight and an increase of the number of coccoliths formed per unit time. The combined investigation of morphological features and coccolith production rates presented in this study may help to interpret data derived from sediment cores, where coccolith morphology is used to reconstruct calcification rates in the water column.

Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in Northwestern Spain

This paper presents a detailed genetic study of Castanea sativa in El Bierzo, a major nut production region with interesting features. It is located within a glacial refuge at one extreme of the distribution area (northwest Spain); it has a centenary tradition of chestnut management; and more importantly, it shows an unusual degree of genetic isolation. Seven nuclear microsatellite markers were selected to analyze the genetic variability and structure of 169 local trees grafted for nut production. We analyzed in the same manner 62 local nuts. The selected loci were highly discriminant for the genotypes studied, giving a combined probability of identity of 6.1 × 10−6. An unprecedented density of trees was sampled for this project over the entire region, and nuts were collected representing 18 cultivars marketed by local producers. Several instances of misclassification by local growers were detected. Fixation index estimates and analysis of molecular variance (AMOVA) data are supportive of an unexpectedly high level of genetic differentiation in El Bierzo, larger than that estimated in a previous study with broader geographical scope but based on limited local sampling (Pereira-Lorenzo et al., Tree Genet Genomes 6: 701–715, 2010a). Likewise, we have determined that clonality due to grafting had been previously overestimated. In line with these observations, no significant spatial structure was found using both a model-based Bayesian procedure and Mantel’s tests. Taken together, our results evidence the need for more fine-scale genetic studies if conservation strategies are to be efficiently improved.

Maintaining distances with the engineer: patterns of coexistence in plant communities beyond the patch-bare dichotomy

Two-phase plant communities with an engineer conforming conspicuous patches and affecting the performance and patterns of coexisting species are the norm under stressful conditions. To unveil the mechanisms governing coexistence in these communities at multiple spatial scales, we have developed a new point-raster approach of spatial pattern analysis, which was applied to a Mediterranean high mountain grassland to show how Festuca curvifolia patches affect the local distribution of coexisting species. We recorded 22 111 individuals of 17 plant perennial species. Most coexisting species were negatively associated with F. curvifolia clumps. Nevertheless, bivariate nearest-neighbor analyses revealed that the majority of coexisting species were confined at relatively short distances from F. curvifolia borders (between 0-2 cm and up to 8 cm in some cases). Our study suggests the existence of a fine-scale effect of F. curvifolia for most species promoting coexistence through a mechanism we call 'facilitation in the halo'. Most coexisting species are displaced to an interphase area between patches, where two opposite forces reach equilibrium: attenuated severe conditions by proximity to the F. curvifolia canopy (nutrient-rich islands) and competitive exclusion mitigated by avoiding direct contact with F. curvifolia.

Geografía del carbono en alta resolución en bosque tropical amazónico del Ecuador mediante sensores aerotransportados

La estimación de la biomasa de la vegetación terrestre en bosque tropical no sólo es un área de investigación en rápida expansión, sino también es un tema de gran interés para reducir las emisiones de carbono asociadas a la deforestación y la degradación forestal (REDD+). Las estimaciones de densidad de carbono sobre el suelo (ACD) en base a inventarios de campo y datos provenientes de sensores aerotransportados, en especial con sensores LiDAR, han conducido a un progreso sustancial en el cartografiado a gran escala de las reservas de carbono forestal. Sin embargo, estos mapas de carbono tienen incertidumbres considerables, asociadas generalmente al proceso de calibración del modelo de regresión utilizado para producir los mapas. En esta tesis se establece una metodología para la calibración y validación de un modelo general de estimación de ACD usando LiDAR en un sector del Parque Nacional Yasuní en Ecuador. En el proceso de calibración del modelo se considera el tamaño y la ubicación de las parcelas, la influencia de la topografía y la distribución espacial de la biomasa. Para el análisis de los datos se utilizan técnicas geoestadísticas en combinación con variables geomorfométricas derivadas de datos LiDAR, y se propone un esquema de muestreo estratificado por posiciones topográficas (valle, ladera y cima). La validación del modelo general para toda la zona de estudio presentó valores de RMSE = 5.81 Mg C ha-1, R2 = 0.94 y sesgo = 0.59, mientras que, al considerar las posiciones topográficas, el modelo presentó valores de RMSE = 1.67 Mg C ha-1, R2 = 0.98 y sesgo = 0.23 para el valle; RMSE = 3.13 Mg C ha-1, R2 = 0.98 y sesgo = - 0.34 para la ladera; y RMSE = 2.33 Mg C ha-1, R2 = 0.97 y sesgo = 0.74 para la cima. Los resultados obtenidos demuestran que la metodología de muestreo estratificado por posiciones topográficas propuesto, permite calibrar de manera efectiva el modelo general con las estimaciones de ACD en campo, logrando reducir el RMSE y el sesgo. Los resultados muestran el potencial de los datos LiDAR para caracterizar la estructura vertical de la vegetación en un bosque altamente diverso, permitiendo realizar estimaciones precisas de ACD, y conocer patrones espaciales continuos de la distribución de la biomasa aérea y del contenido de carbono en la zona de estudio. ABSTRACT Estimating biomass of terrestrial vegetation in tropical forest is not only a rapidly expanding research area, but also a subject of tremendous interest for reducing carbon emissions associated with deforestation and forest degradation (REDD+). The aboveground carbon density estimates (ACD) based on field inventories and airborne sensors, especially LiDAR sensors have led to a substantial progress in large-scale mapping of forest carbon stocks. However, these carbon maps have considerable uncertainties generally associated with the calibration of the regression model used to produce these maps. This thesis establishes a methodology for calibrating and validating a general ACD estimation model using LiDAR in Ecuador´s Yasuní National Park. The size and location of the plots are considered in the model calibration phase as well as the influence of topography and spatial distribution of biomass. Geostatistical analysis techniques are used in combination with geomorphometrics variables derived from LiDAR data, and then a stratified sampling scheme considering topographic positions (valley, slope and ridge) is proposed. The validation of the general model for the study area showed values of RMSE = 5.81 Mg C ha-1, R2 = 0.94 and bias = 0.59, while considering the topographical positions, the model showed values of RMSE = 1.67 Mg C ha-1, R2 = 0.98 and bias = 0.23 for the valley; RMSE = 3.13 Mg C ha-1, R2 = 0.98 and bias = - 0.34 for the slope; and RMSE = 2.33 Mg C ha-1, R2 = 0.97 and bias = 0.74 for the ridge. The results show that the stratified sampling methodology taking into account topographic positions, effectively calibrates the general model with field estimates of ACD, reducing RMSE and bias. The results show the potential of LiDAR data to characterize the vertical structure of vegetation in a highly diverse forest, allowing accurate estimates of ACD, and knowing continuous spatial patterns of biomass distribution and carbon stocks in the study area.

Chloroplast DNA footprints of postglacial recolonization by oaks

Recolonization of Europe by forest tree species after the last glaciation is well documented in the fossil pollen record. This spread may have been achieved at low densities by rare events of long-distance dispersal, rather than by a compact wave of advance, generating a patchy genetic structure through founder effects. In long-lived oak species, this structure could still be discernible by using maternally transmitted genetic markers. To test this hypothesis, a fine-scale study of chloroplast DNA (cpDNA) variability of two sympatric oak species was carried out in western France. The distributions of six cpDNA length variants were analyzed at 188 localities over a 200 × 300 km area. A cpDNA map was obtained by applying geostatistics methods to the complete data set. Patches of several hundred square kilometers exist which are virtually fixed for a single haplotype for both oak species. This local systematic interspecific sharing of the maternal genome strongly suggests that long-distance seed dispersal events followed by interspecific exchanges were involved at the time of colonization, about 10,000 years ago.

Molecular heterochrony in the early development of Drosophila

Heterochrony, the relative change of developmental timing, is one of the major modes of macroevolutionary change; it identifies temporally disassociated units of developmental evolution. Here, we report the results of a fine-scale temporal study for the expression of the developmental gene hairy and morphological development in three species of Drosophila, D. melanogaster, D. simulans, and D. pseudoobscura. The results suggest that between and among closely related species, temporal displacement of ontogenetic trajectory is detected even at the earliest stage of development. Overall, D. simulans shows the earliest expression, followed by D. melanogaster, and then by D. pseudoobscura. Setting D. melanogaster as the standard, we find the approximate time to full expression is accelerated by 13 min, 48 s in D. simulans and retarded by 24 min in D. pseudoobscura. Morphologically, again with D. melanogaster setting the standard, initiation of cellularization is faster in D. simulans by 15 min, 42 s; and initiation of morphogenesis is faster in D. simulans by 18 min, 7 s. These results seem to be consistent with the finding that the approximate time to full expression of hairy is accelerated by 13 min, 48 s in D. simulans. On the other hand, the same morphological events are delayed by 5 min, 32 s, and by 11 min, 32 s, respectively, in D. pseudoobscura. These delays are small, compared with the 24-min delay in full expression. The timing changes, in total, seem consistent with continuous phyletic evolution of temporal trajectories. Finally, we speculate that epigenetic interactions of hairy expression timing and cell-cycle timing may have led to morphological differences in the terminal system of the larvae.

Rapid plant diversification: Planning for an evolutionary future

Systematic conservation planning is a branch of conservation biology that seeks to identify spatially explicit options for the preservation of biodiversity. Alternative systems of conservation areas are predictions about effective ways of promoting the persistence of biodiversity; therefore, they should consider not only biodiversity pattern but also the ecological and evolutionary processes that maintain and generate species. Most research and application, however, has focused on pattern representation only. This paper outlines the development of a conservation system designed to preserve biodiversity pattern and process in the context of a rapidly changing environment. The study area is the Cape Floristic Region (CFR), a biodiversity hotspot of global significance, located in southwestern Africa. This region has experienced rapid (post-Pliocene) ecological diversification of many plant lineages; there are numerous genera with large clusters of closely related species (flocks) that have subdivided habitats at a very fine scale. The challenge is to design conservation systems that will preserve both the pattern of large numbers of species and various natural processes, including the potential for lineage turnover. We outline an approach for designing a system of conservation areas to incorporate the spatial components of the evolutionary processes that maintain and generate biodiversity in the CFR. We discuss the difficulty of assessing the requirements for pattern versus process representation in the face of ongoing threats to biodiversity, the difficulty of testing the predictions of alternative conservation systems, and the widespread need in conservation planning to incorporate and set targets for the spatial components (or surrogates) of processes.

Structure and evolution of the compact radio source in NGC 1275.

Investigations of the fine-scale structure in the compact nucleus of the radio source 3C 84 in NGC 1275 (New General Catalogue number) are reported. Structural monitoring observations beginning as early as 1976, and continuing to the present, revealed subluminal motions in a jet-like relatively diffuse region extending away from a flat-spectrum core. A counterjet feature was discovered in 1993, and very recent nearly simultaneous studies have detected the same feature at five frequencies ranging from 5 to 43 GHz. The counterjet exhibits a strong low-frequency cutoff, giving this region of the source an inverted spectrum. The observations are consistent with a physical model in which the cutoff arises from free-free absorption in a volume that surrounds the core but obscures only the counterjet feature. If such a model is confirmed, very-long-baseline radio interferometry observations can then be used to probe the accretion region, outside the radio jet, on parsec scales.

Spatial Distribution of Marine Epibenthic Communities in the Hola Trough (Vesterålen, Northern Norway)

The Lofoten-Vesterålen marine shelf is one of the most geologically diverse coast and offshore margin areas in Norway. This leads to huge heterogeneity in marine environments, and often high biodiversity. However, little is known yet about the benthic communities in this region. Within the ARCTOS LoVe MarineEco project the epibenthic communities of the Hola trough (Vesterålen) are analysed to give a first description of their spatial distribution. In this trough both a complex hydrodynamic system and varied topographic submarine elements occur. Trawling samples were collected for two different approaches: one in a meso-scale and another in a small-scale. For the broad scale a transect consisting in three stations was developed, while for the fine scale a small area on a sand wave field, consisting in five stations called HolaBox, was sampled. All organisms were intended to be identified to species level and colonial fauna was discarded for the analysis. Different diversity indexes were assessed (Shannon index (H’) and Pielou’s eveness (J’)). Clustering and nMDS analyses identified four statistically significant groups in terms of abundance (ind./100m2). A total amount of 211 different taxa were found within all stations. The more outer part of the transect (close to the shelf edge) presented a huge abundance of organisms and was dominated by the hemi sessile tube-builder polychaetes Nothria conchylega and Eunice dubitata and the sea urchin Gacilechinus acutus, while the more inner parts presented less abundance of individuals. Probably some upwelling produced by the Norwegian Atlantic Current (NWAC) is influencing the shelf edge increasing the primary production and, therefore, enriching the seafloor in this region. The sand wave field presented two different groups with few amount of individuals. Small-scale variability could be produced by the high heterogeneity within the different types of sand waves, while the scarce abundance of animals can be produced by the permanent changing environment that movable sand waves produce. Here more active and mobile fauna was found such as brittle stars and hermit crabs (among others). Finally, a fourth group was found in the most inner station of the transect, laying on a ridge in the central part of the trough. This station, with coarse substrate, was mainly dominated again by brittle stars and sea urchins. We can conclude that this is a really heterogeneous trough in environments and therefore in communities (even in a local scale). More detailed studies that focus in the local environmental drivers have to be carried out to get an integrated understanding of the structure of benthic communities in this system.