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.

Mineral-magnetic record of Late Quaternary climatic changes in a high Alpine lake

The magnetic properties of a sediment core from a high altitude lake in the Swiss Alps were compared with palynological and geochemical data to link climatic and mineral magnetic variations. According to pollen data, the sediments extend from the present to the Younger Dryas, i.e., they cover more than 10,000 years of environmental change in the Alps. The major change in magnetic properties corresponds to the climatic warming of the early Holocene. High-coercivity magnetic minerals that characterize the Late Glacial period almost disappeared during the Holocene and the concentration of ferrimagnetic minerals increased sharply. The contribution of superparamagnetic grains also decreased in the Holocene sediments. Similar variations in {SP} content and coercivity, of smaller magnitude, are found in the Holocene and are interpreted to represent minor climatic variations. Comparison with the historical record of the last 1000 years confirms this interpretation. The magnetic mineralogy, the superparamagnetic contents, and the {IRM} intensity in the coarse-grained, Late Glacial sediments are similar to those measured in the catchment bedrock. This indicates a detrital origin. The different properties and the higher concentration of magnetic minerals in the Holocene sediments are due to authigenic phases. Magnetic properties provide a high resolution record of climatic change. They are sensitive even to small variations that are not recorded in the pollen or {LOI} data. Magnetic parameters show fine-scale variation and constitute a valuable supplement to conventional climatic indicators.

Global 2009 1km MODIS (MOD35/MOD09) cloud frequency and MOD35 processing path

Identifying cloud interference in satellite-derived data is a critical step toward developing useful remotely sensed products. Most MODIS land products use a combination of the MODIS (MOD35) cloud mask and the 'internal' cloud mask of the surface reflectance product (MOD09) to mask clouds, but there has been little discussion of how these masks differ globally. We calculated global mean cloud frequency for both products, for 2009, and found that inflated proportions of observations were flagged as cloudy in the Collection 5 MOD35 product. These erroneously categorized areas were spatially and environmentally non-random and usually occurred over high-albedo land-cover types (such as grassland and savanna) in several regions around the world. Additionally, we found that spatial variability in the processing path applied in the Collection 5 MOD35 algorithm affects the likelihood of a cloudy observation by up to 20% in some areas. These factors result in abrupt transitions in recorded cloud frequency across landcover and processing-path boundaries impeding their use for fine-scale spatially contiguous modeling applications. We show that together, these artifacts have resulted in significantly decreased and spatially biased data availability for Collection 5 MOD35-derived composite MODIS land products such as land surface temperature (MOD11) and net primary productivity (MOD17). Finally, we compare our results to mean cloud frequency in the new Collection 6 MOD35 product, and find that landcover artifacts have been reduced but not eliminated. Collection 6 thus increases data availability for some regions and land cover types in MOD35-derived products but practitioners need to consider how the remaining artifacts might affect their analysis.

Sea ice habitat characteristics and number of narwhal (Monodon monoceros) sightings in Disko Bay, West Greenland

There is a paucity of information on abundance, densities, and habitat selection of narwhals Monodon monoceros in the offshore pack ice of Baffin Bay, West Greenland, despite the critical importance of winter foraging regions and considerable sea ice declines in the past decades. We conducted a double-platform visual aerial survey over a narwhal wintering ground to obtain pack ice densities and develop the first fully corrected abundance estimate using point conditional mark-recapture distance sampling. Continuous video recording and digital images taken along the trackline allowed for in situ quantification of winter narwhal habitat and for the estimation of fine-scale narwhal habitat selection and habitat-specific sighting probabilities. Abundance at the surface was estimated at 3484 (coefficient of variation [CV] = 0.46) including whales missed by observers. The fully corrected abundance of narwhals was 18 044 (CV = 0.46), or approximately one-quarter of the entire Baffin Bay population. The narwhal wintering ground surveyed (~9500 km**2) had 2.4 to 3.2% open water based on estimates from satellite imagery (NASA Moderate Resolution Imaging Spectroradiometer) and 1565 digital photographic images collected on the trackline. Thus, the ~18 000 narwhals had access to 233 km**2 of open water, resulting in an average density of ~77 narwhals/km**2 open water. Narwhal sighting probability near habitats with <10% or 10 to 50% open water was significantly higher than sighting probability in habitats with >50% open water, suggesting narwhals select optimal foraging areas in dense pack ice regardless of open water availability. This study provides the first quantitative ecological data on densities and habitat selection of narwhals in pack ice foraging regions that are rapidly being altered with climate change.

Population monitoring for kangaroo management

In wildlife management, the program of monitoring will depend on the management objective. If the objective is damage mitigation, then ideally it is damage that should be monitored. Alternatively, population size (N) can be used as a surrogate for damage, but the relationship between N and damage obviously needs to be known. If the management objective is a sustainable harvest, then the system of monitoring will depend on the harvesting strategy. In general, the harvest strategy in all states has been to offer a quota that is a constant proportion of population size. This strategy has a number of advantages over alternative strategies, including a low risk of over- or underharvest in a stochastic environment, simplicity, robustness to bias in population estimates and allowing harvest policy to be proactive rather than reactive. However, the strategy requires an estimate of absolute population size that needs to be made regularly for a fluctuating population. Trends in population size and in various harvest statistics, while of interest, are secondary. This explains the large research effort in further developing accurate estimation methods for kangaroo populations. Direct monitoring on a large scale is costly. Aerial surveys are conducted annually at best, and precision of population estimates declines with the area over which estimates are made. Management at a fine scale (temporal or spatial) therefore requires other monitoring tools. Indirect monitoring through harvest statistics and habitat models, that include rainfall or a greenness index from satellite imagery, may prove useful.

Intertidal habitat conservation: identifying conservation targets in the absence of detailed biological information

1. Growing concern associated with threats to the marine environment has resulted in an increased demand for marine reserves that conserve representative and adequate examples of biodiversity. Often, the decisions about where to locate reserves must be made in the absence of detailed information on the patterns of distribution of the biota. Alternative approaches are required that include defining habitats using surrogates for biodiversity. Surrogate measures of biodiversity enable decisions about where to locate marine reserves to be made more reliably in the absence of detailed data on the distribution of species. 2. Intertidal habitat types derived using physical properties of the shoreline were used as a surrogate for intertidal biodiversity to assist with the identification of sites for inclusion in a candidate system of intertidal marine reserves for 17 463 km of the mainland coast of Queensland, Australia. This represents the first systematic approach, on essentially one-dimensional data, using fine-scale (tens to hundreds of metres) intertidal habitats to identify a system of marine reserves for such a large length of coast. A range of solutions would provide for the protection of a representative example of intertidal habitats in Queensland. 3. The design and planning of marine and terrestrial protected areas systems should not be undertaken independently of each other because it is likely to lead to inadequate representation of intertidal habitats in either system. The development of reserve systems specially designed to protect intertidal habitats should be integrated into the design of terrestrial and marine protected area systems. Copyright (c) 2005 John Wiley & Sons, Ltd.

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.

Microhabitat use by black-faced impala in the Etosha National Park, Namibia

We Studied microhabitat use by black-faced impala in different herd types during the rut in the cold dry seasons of 2001 and 2002 in the Etosha National Park, Namibia. We investigated whether black-faced impala select feeding sites consistently for their microhabitat characteristics in 2 vegetation types, Karstveld and Tamboti Woodland. We also investigated intra-population differences in microhabitat use between herds of different types. In both habitats, sites used by impala for feeding were more likely to be in the shade, within 2 m of the edges of wooded areas and grassy clearings, with high visibility at I m height, and with lower grass swords than nearby nonfeeding sites. In Karstveld, feeding sites of impala were also located closer to the nearest shrub than were nonfeeding sites. A degree of fine-scale sexual segregation in microhabitat use was demonstrated, but it was not consistent across habitats. Incorporating these trends in the microhabitat use of black-faced impala into management, decisions should maximize the success Of Small populations released at selected off-park sites.