SESAM - a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages

Two different approaches currently prevail for predicting spatial patterns of species assemblages. The first approach (macroecological modelling, MEM) focuses directly on realised properties of species assemblages, whereas the second approach (stacked species distribution modelling, S-SDM) starts with constituent species to approximate assemblage properties. Here, we propose to unify the two approaches in a single 'spatially-explicit species assemblage modelling' (SESAM) framework. This framework uses relevant species source pool designations, macroecological factors, and ecological assembly rules to constrain predictions of the richness and composition of species assemblages obtained by stacking predictions of individual species distributions. We believe that such a framework could prove useful in many theoretical and applied disciplines of ecology and evolution, both for improving our basic understanding of species assembly across spatio-temporal scales and for anticipating expected consequences of local, regional or global environmental changes. In this paper, we propose such a framework and call for further developments and testing across a broad range of community types in a variety of environments.

Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.

DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5'-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.

Canonical correspondence analysis in social science research

The use of simple and multiple correspondence analysis is well-established in socialscience research for understanding relationships between two or more categorical variables.By contrast, canonical correspondence analysis, which is a correspondence analysis with linearrestrictions on the solution, has become one of the most popular multivariate techniques inecological research. Multivariate ecological data typically consist of frequencies of observedspecies across a set of sampling locations, as well as a set of observed environmental variablesat the same locations. In this context the principal dimensions of the biological variables aresought in a space that is constrained to be related to the environmental variables. Thisrestricted form of correspondence analysis has many uses in social science research as well,as is demonstrated in this paper. We first illustrate the result that canonical correspondenceanalysis of an indicator matrix, restricted to be related an external categorical variable, reducesto a simple correspondence analysis of a set of concatenated (or stacked ) tables. Then weshow how canonical correspondence analysis can be used to focus on, or partial out, aparticular set of response categories in sample survey data. For example, the method can beused to partial out the influence of missing responses, which usually dominate the results of amultiple correspondence analysis.

General trends in world biogeographic literature: a preliminary bibliometric analysis

Records with the search string biogeograph* were collected from the Science Citation Index (SCI). A total of 3456 records were downloaded for the 1945-2006 period from titles of articles and reviews, and 10,543 records were downloaded for 1991-2006, taking into consideration also abstracts and keywords. Temporal trends of publications, geographical and institutional distribution of the research output, authorship, and core journals were evaluated. There were as many as 122 countries carrying out biogeographic research; in the most recent period, USA is the top producing country, followed by the United Kingdom, Australia, France, Germany, Spain, and Canada. There were 17,493 authors contributing to the field. During 1991-2006 there were 4098 organizations with authors involved in biogeographic research; institutions with higher number of papers are the Natural History Museum (United Kingdom), the University of California, Berkeley (USA), the Museum National d'Histoire Naturelle (France), the Universidad Nacional Autónoma de México (Mexico), the American Museum of Natural History (USA) and the Russian Academy of Sciences (Russia). Research articles are spread over a variety of journals, with the Journal of Biogeography, Molecular Phylogenetics and Evolution, Molecular Ecology, and Biological Journal of the Linnean Society being the core journals. From 28,759 keywords retrieved those with the highest frequency were evolution, phylogeny, diversity, mitochondrial DNA, pattern(s), systematics, and population(s). We conclude that publications on biogeography have increased substantially during the last years, especially since 1998. The preferred journal for biogeographic papers is the Journal of Biogeography. Most frequent keywords seem to indicate that biogeography fits well within both evolutionary biology and ecology, with molecular biology and phylogenetics being important factors that drive their current development.

Temporal distribution of Aedes aegypti Linnaeus (Diptera, Culicidae), in a Hospital in Cuiabá, State of Mato Grosso, Brazil

This study aimed at registering and monitoring the presence of Aedes aegypti in the University Hospital Júlio Muller, Cuiabá-MT, as well as investigating the influence of temperature and rainfall on its temporal distribution and egg densities in ovitraps. The study was performed from April/2007 to March/2008, utilizing ovitraps with 10% of hay infusion and a wood paddle as an oviposition substrate. For surveillance, one ovitrap was placed in each of the 12 points distributed throughout the hospital. Ovitraps were collected monthly at the end of a 5-day installation period. After egg counting, wood paddles were immersed in water to allow larval eclosion for species identification through optical microscopy. Egg Density Index (EDI), Positive Ovitraps Index (POI), and Mean Number of Eggs (MNE) were used for data analysis. The presence of A. aegypti in the hospital was registered throughout the study period, except in July. The MNE was proportionally higher in the internal area (n= 8.47 eggs/paddle) when compared to the external area (n= 5.46 eggs/paddle), and was higher in September/October 2007 and January/February 2008. A significant increase in EDI, POI and MNE was registered in periods where the average temperature was higher, and the increase in POI was also concomitant with an increase in rainfall. The continuous presence of A. aegypti in the hospital throughout the study period, points out the need of including this mosquito in the arthropod control list in this environment. This is particularly important, considering that A. aegypti is an important vector of several arboviroses.

Dinámica espacio temporal en la ecología trófica de la anchoveta (Engraulis ringens Jenyns, 1842; pisces: engraulide) en el mar peruano

El objetivo de este trabajo es estudiar las variaciones ontogénicas, espaciales y nictemerales en la dieta de la anchoveta peruana (Engraulis ringens). El trabajo se basa en el análisis de contenido estomacal de 13 430 anchovetas (peces de 4 a 19,5 cm) muestreados durante 22 cruceros de investigación realizados a bordo de las embarcaciones científicas del Instituto del Mar del Perú durante el período 1996-2003. Previo a los análisis estadísticos la contribución de cada grupo de presa fue convertido a carbonó. Los datos fueron procesados por medio de estadística uni y multivariada en función de la talla de la anchoveta, la latitud, la distancia de la costa, la distancia del borde de la plataforma continental y el período nictemeral. Los resultados enseñan que la anchoveta se alimenta mayormente de zooplancton cualquier sea su tamaño o su distribución espaciotemporal. La anchoveta cambio gradualmente su dieta a lo largo de su ciclo de vida. Así, los individuos mas pequeños han ingerido mayormente copépodos calanoideos (68.0%) y eufausidos (23.3%), mientras que los individuos mas grandes ingirieron mayormente eufausidos (84.9%) y copépodos calanoideos (11.5%). Latitudinalmente, la mayor contribución de los copépodos calanoideos se observó en las zonas de afloramiento de Chicama y San Juan, con el 52.3% y 47.5%, respectivamente. Hasta los 160 km de distancia de la costa, no se ha observado un patrón regular en la contribución de las principales presas, mientras que por fuera, se insinúa un patrón caracterizado por el predominio de los eufausidos (>84%) y la menor contribución de copépodos calanoideos (<14,1%). En la plataforma continental los eufausidos contribuyeron con el 55.6% y los copépodos calanoideos con el 36.9%; mientras que por fuera de esa zona, los eufausidos se incrementaron al 75.3% y los copépodos calanoideos disminuyeron al 20.1%. Al considerar el período nictemeral, el ítem presa predominante durante el día fueron los eufausidos (52.7%) seguido de los copépodos calanoideos (40.9%); mientras que durante la noche, los eufausidos se incrementaron al 80.2% y los copépodos calanoideos disminuyeron al 15.7%. Estos resultados contradicen lo que se conocía acerca de la variabilidad de la dieta de la anchoveta, desestimándose: (i) que en el norte es fitoplanctívora y en el sur es zooplanctívora; (ii) que la fracción zooplanctónica es mayor en la zona oceánica. Asimismo, se ha demostrado que: (i) la anchoveta es principalmente zooplanctófaga durante su ciclo de vida, con modificaciones que corresponden a la mayor ingesta de presas pequeñas cuando son juveniles y de presas grandes cuando son adultas, (ii) en la zona de influencia de la plataforma continental consume aproximadamente el doble de copépodos calanoideos que en la zona oceánica, y aproximadamente una tercera parte menos de eufausidos en la zona interna que en la zona oceánica, y (iii) durante la noche y el día ingiere principalmente eufausidos pero la contribución de los copépodos calanoideos sube al 40%.

Ecological temporal stability of Staphylococcus aureus nasal carriage.

We described the colonization dynamics of Staphylococcus aureus in a group of 266 healthy carriers over a period of approximately 1 year. We used precise genotyping methods, i.e., amplified fragment length polymorphism (AFLP), spa typing, and double-locus sequence typing (DLST), to detect changes in strain identity. Strain change took place rather rarely: out of 89 carriers who had initially been colonized, only 7 acquired a strain different from the original one. Approximately one-third of the carriers eliminated the colonization, and a similar number became newly colonized. Some of these events probably represent detection failure rather than genuine colonization loss or acquisition. Lower bacterial counts were associated with increased probability of eliminating the colonization. We have confirmed a high mutation rate in the spa locus: 6 out of 53 strains underwent mutation in the spa locus. There was no overall change in S. aureus genotype composition.

Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?

Aquaporins (AQPs) are membrane channels belonging to the major intrinsic proteins family and are known for their ability to facilitate water movement. While in Populus trichocarpa, AQP proteins form a large family encompassing fifty-five genes, most of the experimental work focused on a few genes or subfamilies. The current work was undertaken to develop a comprehensive picture of the whole AQP gene family in Populus species by delineating gene expression domain and distinguishing responsiveness to developmental and environmental cues. Since duplication events amplified the poplar AQP family, we addressed the question of expression redundancy between gene duplicates. On these purposes, we carried a meta-analysis of all publicly available Affymetrix experiments. Our in-silico strategy controlled for previously identified biases in cross-species transcriptomics, a necessary step for any comparative transcriptomics based on multispecies design chips. Three poplar AQPs were not supported by any expression data, even in a large collection of situations (abiotic and biotic constraints, temporal oscillations and mutants). The expression of 11 AQPs was never or poorly regulated whatever the wideness of their expression domain and their expression level. Our work highlighted that PtTIP1;4 was the most responsive gene of the AQP family. A high functional divergence between gene duplicates was detected across species and in response to tested cues, except for the root-expressed PtTIP2;3/PtTIP2;4 pair exhibiting 80% convergent responses. Our meta-analysis assessed key features of aquaporin expression which had remained hidden in single experiments, such as expression wideness, response specificity and genotype and environment interactions. By consolidating expression profiles using independent experimental series, we showed that the large expansion of AQP family in poplar was accompanied with a strong divergence of gene expression, even if some cases of functional redundancy could be suspected.

Single-trial topographic analysis of human EEG: A new image of event-related potentials

We present a novel approach for analyzing single-trial electroencephalography (EEG) data, using topographic information. The method allows for visualizing event-related potentials using all the electrodes of recordings overcoming the problem of previous approaches that required electrode selection and waveforms filtering. We apply this method to EEG data from an auditory object recognition experiment that we have previously analyzed at an ERP level. Temporally structured periods were statistically identified wherein a given topography predominated without any prior information about the temporal behavior. In addition to providing novel methods for EEG analysis, the data indicate that ERPs are reliably observable at a single-trial level when examined topographically.

Stationarity analysis of historical flood series in France and Spain (14th-20th centuries)

Interdisciplinary frameworks for studying natural hazards and their temporal trends have an important potential in data generation for risk assessment, land use planning, and therefore the sustainable management of resources. This paper focuses on the adjustments required because of the wide variety of scientific fields involved in the reconstruction and characterisation of flood events for the past 1000 years. The aim of this paper is to describe various methodological aspects of the study of flood events in their historical dimension, including the critical evaluation of old documentary and instrumental sources, flood-event classification and hydraulic modelling, and homogeneity and quality control tests. Standardized criteria for flood classification have been defined and applied to the Isère and Drac floods in France, from 1600 to 1950, and to the Ter, the Llobregat and the Segre floods, in Spain, from 1300 to 1980. The analysis on the Drac and Isère data series from 1600 to the present day showed that extraordinary and catastrophic floods were not distributed uniformly in time. However, the largest floods (general catastrophic floods) were homogeneously distributed in time within the period 1600¿1900. No major flood occurred during the 20th century in these rivers. From 1300 to the present day, no homogeneous behaviour was observed for extraordinary floods in the Spanish rivers. The largest floods were uniformly distributed in time within the period 1300-1900, for the Segre and Ter rivers.

Heel and toe clearance estimation for gait analysis using wireless inertial sensors.

Tripping is considered a major cause of fall in older people. Therefore, foot clearance (i.e., height of the foot above ground during swing phase) could be a key factor to better understand the complex relationship between gait and falls. This paper presents a new method to estimate clearance using a foot-worn and wireless inertial sensor system. The method relies on the computation of foot orientation and trajectory from sensors signal data fusion, combined with the temporal detection of toe-off and heel-strike events. Based on a kinematic model that automatically estimates sensor position relative to the foot, heel and toe trajectories are estimated. 2-D and 3-D models are presented with different solving approaches, and validated against an optical motion capture system on 12 healthy adults performing short walking trials at self-selected, slow, and fast speed. Parameters corresponding to local minimum and maximum of heel and toe clearance were extracted and showed accuracy ± precision of 4.1 ± 2.3 cm for maximal heel clearance and 1.3 ± 0.9 cm for minimal toe clearance compared to the reference. The system is lightweight, wireless, easy to wear and to use, and provide a new and useful tool for routine clinical assessment of gait outside a dedicated laboratory.

The application of trend surface models to the analysis of time factors in Swiss cancer mortality.

To study different temporal components on cancer mortality (age, period and cohort) methods of graphic representation were applied to Swiss mortality data from 1950 to 1984. Maps using continuous slopes ("contour maps") and based on eight tones of grey according to the absolute distribution of rates were used to represent the surfaces defined by the matrix of various age-specific rates. Further, progressively more complex regression surface equations were defined, on the basis of two independent variables (age/cohort) and a dependent one (each age-specific mortality rate). General patterns of trends in cancer mortality were thus identified, permitting definition of important cohort (e.g., upwards for lung and other tobacco-related neoplasms, or downwards for stomach) or period (e.g., downwards for intestines or thyroid cancers) effects, besides the major underlying age component. For most cancer sites, even the lower order (1st to 3rd) models utilised provided excellent fitting, allowing immediate identification of the residuals (e.g., high or low mortality points) as well as estimates of first-order interactions between the three factors, although the parameters of the main effects remained still undetermined. Thus, the method should be essentially used as summary guide to illustrate and understand the general patterns of age, period and cohort effects in (cancer) mortality, although they cannot conceptually solve the inherent problem of identifiability of the three components.

Tough adults, frail babies: an analysis of stress sensitivity across early life-history stages of widely introduced marine invertebrates

All ontogenetic stages of a life cycle are exposed to environmental conditions so that population persistence depends on the performance of both adults and offspring. Most studies analysing the influence of abiotic conditions on species performance have focussed on adults, while studies covering early life-history stages remain rare. We investigated the responses of early stages of two widely introduced ascidians, Styela plicata and Microcosmus squamiger, to different abiotic conditions. Stressors mimicked conditions in the habitats where both species can be found in their distributional ranges and responses were related to the selection potential of their populations by analysing their genetic diversity. Four developmental stages (egg fertilisation, larval development, settlement, metamorphosis) were studied after exposure to high temperature (30°C), low salinities (26 and 22 ) and high copper concentrations (25, 50 and 100 µg/L). Although most stressors effectively led to failure of complete development (fertilisation through metamorphosis), fertilisation and larval development were the most sensitive stages. All the studied stressors affected the development of both species, though responses differed with stage and stressor. S. plicata was overall more resistant to copper, and some stages of M. squamiger to low salinities. No relationship was found between parental genetic composition and responses to stressors. We conclude that successful development can be prevented at several life-history stages, and therefore, it is essential to consider multiple stages when assessing species' abilities to tolerate stress. Moreover, we found that early development of these species cannot be completed under conditions prevailing where adults live. These populations must therefore recruit from elsewhere or reproduce during temporal windows of more benign conditions. Alternatively, novel strategies or behaviours that increase overall reproductive success might be responsible for ensuring population survival.

Formation of aluminosilicate-bearing quartz veins in the Simano nappe (Central Alps): structural, thermobarometric and oxygen isotope constraints

We combined structural analysis, thermobarometry and oxygen isotope geochemistry to constrain the evolution of kyanite and/or andalusite-bearing quartz veins from the amphibolite facies metapelites of the Simano nappe, in the Central Alps of Switzerland. The Simano nappe records a complex polyphase tectonic evolution associated with nappe stacking during Tertiary Alpine collision (D1). The second regional deformation phase (132) is responsible for the main penetrative schistosity and mineral lineation, and formed during top-to-the-north thrusting. During the next stage of deformation (D3) the aluminosilicate-bearing veins formed by crystallization in tension gashes, in tectonic shadows of boudins, as well as along shear bands associated with top-to-the-north shearing. D2 and D3 are coeval with the Early Miocene metamorphic peak, characterised by kyanite + staurolite + garnet + biotite assemblages in metapelites. The peak pressure (P) and temperature (T) conditions recorded are constrained by multiple-equilibrium thermobarometry at 630 +/- 20 degrees C and 8.5 +/- 1 kbar (similar to 27 km depth), which is in agreement with oxygen isotope thermometry indicating isotopic equilibration of quartz-kyanite pairs at 670 +/- 50 degrees C. Quartz-kyanite pairs from the aluminosilicate-bearing quartz veins yield equilibration temperatures of 645 +/- 20 degrees C, confirming that the veins formed under conditions near metamorphic peak. Quartz and kyanite from veins and the surrounding metapelites have comparable isotopic compositions. Local intergranular diffusion in the border of the veins controls the mass-transfer and the growth of the product assemblage, inducing local mobilization of SiO2 and Al2O3. Andalusite is absent from the host rocks, but it is common in quartz veins, where it often pseudomorphs kyanite. For andalusite to be stable at T-max, the pressure in the veins must have been substantially lower than lithostatic. An alternative explanation consistent with structural observations would be inheritance by andalusite of the kyanite isotopic signature during polymorphic transformation after the metamorphic peak.

Spatial and temporal variability of crop yield and some Rhodic Hapludox properties under no-tillage

Soil properties are closely related with crop production and spite of the measures implemented, spatial variation has been repeatedly observed and described. Identifying and describing spatial variations of soil properties and their effects on crop yield can be a powerful decision-making tool in specific land management systems. The objective of this research was to characterize the spatial and temporal variations in crop yield and chemical and physical properties of a Rhodic Hapludox soil under no-tillage. The studied area of 3.42 ha had been cultivated since 1985 under no-tillage crop rotation in summer and winter. Yield and soil property were sampled in a regular 10 x 10 m grid, with 302 sample points. Yields of several crops were analyzed (soybean, maize, triticale, hyacinth bean and castor bean) as well as soil chemical (pH, Soil Organic Matter (SOM), P, Ca2+, Mg2+, H + Al, B, Fe, Mn, Zn, CEC, sum of bases (SB), and base saturation (V %)) and soil physical properties (saturated hydraulic conductivity, texture, density, total porosity, and mechanical penetration resistance). Data were analyzed using geostatistical analysis procedures and maps based on interpolation by kriging. Great variation in crop yields was observed in the years evaluated. The yield values in the Northern region of the study area were high in some years. Crop yields and some physical and soil chemical properties were spatially correlated.