A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis

<p>Abstract</p> <p>Background</p> <p>The difficulty in elucidating the genetic basis of complex diseases roots in the many factors that can affect the development of a disease. Some of these genetic effects may interact in complex ways, proving undetectable by current single-locus methodology.</p> <p>Results</p> <p>We have developed an analysis tool called Hypothesis Free Clinical Cloning (HFCC) to search for genome-wide epistasis in a case-control design. HFCC combines a relatively fast computing algorithm for genome-wide epistasis detection, with the flexibility to test a variety of different epistatic models in multi-locus combinations. HFCC has good power to detect multi-locus interactions simulated under a variety of genetic models and noise conditions. Most importantly, HFCC can accomplish exhaustive genome-wide epistasis search with large datasets as demonstrated with a 400,000 SNP set typed on a cohort of Parkinson's disease patients and controls.</p> <p>Conclusion</p> <p>With the current availability of genetic studies with large numbers of individuals and genetic markers, HFCC can have a great impact in the identification of epistatic effects that escape the standard single-locus association analyses.</p

Piezometric and ground deformation relationship at Almonte-Marismas aquifer (Andalucía, Spain)

[EN] Groundwater is one of the most important hydric resources of the Spain territory. Nevertheless, heavy groundwater withdrawal generates severe consequences, being land subsidence one of them. The Interferometric Synthetic Aperture Radar (InSAR) technique have been recently exploited to detect and monitor aquifer related deformations. In the present work, relationship between piezometric levels drawdowns and land subsidence has been studied for the higher withdrawals areas within Almonte-Marismas aquifer system (which holds the Doñana Natural Space). Four datasets of radar satellite images, obtained from Sentine-1 satellite, have been processed using the InSAR technique in the period 2014 - 2020. Results show that in some of these areas, like those surrounding El Rocío and Matalascañas villages, the correlation between these two variables is high.[ES] El agua subterránea es uno de los recursos hídricos más importantes en el territorio español. La gran cantidad de agua que se retira de ellos puede tener graves consecuencias, entre las que destaca, en algunos acuíferos, la subsidencia del terreno. La técnica de interferometría radar (InSAR), ha sido desarrollada en las últimas décadas para detectar y monitorear las deformaciones relacionadas con los acuíferos. En este trabajo se estudia la posible relación existente entre la variación de los niveles piezométricos y el movimiento del terreno en zonas con grandes extracciones del acuífero Almonte-Marismas (sobre el que se ubica el Espacio Natural de Doñana). Para ello, se han analizado los datos de deformación del terreno obtenidos del satélite Sentinel-1 en el periodo 2014-2020 Los resultados muestran que, en alguna de estas zonas, como las cercanas a las poblaciones de El Rocío y Matalascañas, la correlación entre ambas variables es alta.Este trabajo es parte de las actividades subvencionadas dentro del Sistema Nacional de Garantía Juvenil (PEJ2018-002477), financiado por la Fundación Tripartita para la Formación en el Empleo, la iniciativa YEI (Youth Employment Initiative) y el Fondo Social Europeo (FSE). Los datos Copernicus Sentinel-1 se obtuvieron y procesaron en la plataforma GEP de la ESA en el marco del GEP Early Adopters Programme. Agradecemos al IGME y a la CHG por proporcionar los datos de piezometría, así como a la Junta de Andalucía por suministrar los datos meteorológicos.González-Jiménez, M.; Guardiola-Albert, C.; Aguilera-Alonso, H.; Béjar- Pizarro, M.; Herrera, G.; Ezquerro, P.; López-Vinielles, J.... (2021). Estudio de la relación entre la piezometría y la deformación del terreno en el acuífero Almonte-Marismas (Andalucía, España). En Proceedings 3rd Congress in Geomatics Engineering. Editorial Universitat Politècnica de València. 102-108. https://doi.org/10.4995/CiGeo2021.2021.12675OCS10210

Monitoring and current research of groundwater resources and recharge in the Doñana Natural area (SE Spain)

30 p. Incluye versión abreviada en castellanoThis chapter presents the monitoring and research of groundwater resources and natural recharge in the Doñana Natural Area. The subchapter “Monitoring networks for Groundwater Resources and Recent Management Issues of the Doñana” deals with the history and current state of the official monitoring networks for piezometry and hydrochemistry. In the second subchapter “Application of Models in Recent Management and Forecasting of Resources” the current research and the model based water management issues are presented. The third subchapter “Main Knowledge existing on Groundwater Natural Chemical Composition and Contaminant Processes in the Eolian Mantle Aquifer Sector of the Doñana (SW Spain)” provides an overview of hydrochemical research carried out in the eolian part of the aquifer. Subchapter 4 “Active Monitoring Network for Recharge Measurements in the Doñana National Park” presents the current monitoring network for groundwater recharge.Instituto Geológico y Minero de España, EspañaUniversidad Politécnica de Cartagena, EspañaUniversidad Politécnica de Cataluña, EspañaReal Academia de Ciencias Exactas, Físicas y Naturales, EspañaInstituto Andaluz de Investigación y Formación Agraria y Pesquera, EspañaUniversidad de Córdoba, Españ

Responding to the challenges of Water and Global Warming: Environmental Hydrogeology and Global Change Research Group (HYGLO-Lab)

[EN] The current Global Warming of planet Earth is probably the most important geological phenomenon in the last 20,000 years of its history and for human race. This process is having nowadays notable effects on the climate, ecosystems and natural resources. Possibly the most important renewable geological resource is water. One of the most strategic phases of the water cycle is groundwater. Despite its low visibility, quantitatively (and qualitatively too) it is essential for life on Planet Earth. Foreseeable consequences on groundwater due to climate change and sea level rise will be very significant. Hydrogeology can provide answers to many of the questions that are beginning to be raised in relation to these impacts and their effects. Environmental hydrogeology is a way of understanding the set of disciplines mixed in Hydrogeology as a Science of Nature. The HYGLO-Lab Research Group of the IGME-CSIC National Center attempts, through its lines of research, with a double global and local component, to provide answers to some of these questions.Peer reviewe

Vapor flow control in dune sediments under dry bare soil conditions.

The study presents daily values of inward and outward vapor flux crossing the soil-atmosphere boundary in dependence on meteorological parameters and soil moisture. Measurements of vapor flux, soil moisture and meteorological parameters were evaluated during days without rainfall between 2015 and 2019. Vapor flux data were obtained at 1 min intervals by a precision lysimeter installed in the Doñana National Park, southwest Spain. Meteorological data were measured on-site at 10-min intervals, including temperature, relative humidity, wind velocity and net radiation. After manual and automatic noise elimination of the lysimeter data, time series of a summer and winter period were generated for selected relevant parameters. Furthermore, daily cumulative data of inward and outward vapor flux were calculated for the entire period and analyzed for their control by meteorological parameters and soil moisture. Results show moderate correlations of daily outward vapor flux on the diurnal amplitudes of temperature and humidity whereas daily inward vapor indicates moderate correlations with temperature and soil moisture. A correction coefficient for potential evaporation to estimate actual evaporation was determined based on soil moisture and air temperature.Unidad de Sevilla, Instituto Geológico y Minero de España, EspañaDepartament d'Enginyeria Civil i Ambiental, Universitat Politècnica de Catalunya, EspañaGrupo de Hidrogeología, Universitat Politècnica de Catalunya, EspañaGrupo de Hidrogeología, Consejo Superior de Investigaciones Científicas, Españ

Datos y retos para una gestión sostenible de los recursos hídricos subterráneos en Doñana

Peer reviewe

Actualización de la recarga aplicada al modelo matemático del acuífero de Doñana (Andalucía occidental)

Presentado en el XI Simposio del Agua en Andalucía (Granada, 13 a 16 de noviembre de 2023). - Tomo 4[ES] Este trabajo propone una nueva zonificación de la recarga del acuífero de Doñana con el fin de adaptar los límites a la delimitación de las actuales Masas de Aguas Subterráneas y dar un enfoque hidrogeológico más estricto. Se basa en la distribución litológica, textura del suelo, usos del territorio, tipos de cultivo y/o distribución de comunidades vegetales. Se ha realizado un análisis espacio-temporal a partir de Sistemas de Información Geográfica y estudios del suelo no tenidos en cuenta anteriormente. Como resultado, la superficie aflorante queda subdividida en 18 zonas que representan 7 conjuntos litológicos con diferentes permeabilidades. Se ha diferenciado con mayor detalle el tipo de ocupación del suelo en los afloramientos más permeables representados por arenas eólicas, gravas, arenas y limos (zonas urbanas, con cultivos intensivos, bajo plástico, extensivos, forestal o vegetación dispersa). La recarga procedente de la lluvia se estima a nivel diario aplicando el Balance de Agua del Suelo basado en el modelo T de Thornthwaite y Mather (1955). A cada zona se aplica la serie climática más representativa en función de su distribución geográfica y se asignan los parámetros de capacidad de retención de agua en el suelo y coeficiente de escorrentía deducidos del análisis de la zonificación. La recarga media obtenida (241,8 hm³/a) es aplicable al modelo matemático en régimen estacionario. Asimismo, se indican las pautas a seguir para su aplicación en régimen transitorio actualizado al periodo hidrológico 1975/76-2020/21.Este trabajo se ha realizado en el marco del convenio del IGME-CSIC con la Confederación Hidrográfica del Guadalquivir, para la mejora del conocimiento hidrogeológico en el marco de la planificación hidrológica (2020-2024), en su Actividad nº 11 “Actualización del modelo matemático del acuífero de Doñana”. Zonificación y estimación de la recarga para el modelo matemático del acuífero Almonte-Marismas (Doñana).Peer reviewe

Control of trace metal distribution and variability in an interdunal wetland

[EN] Trace elements are serious pollutants in the natural environment and are of increasing concern due to the adverse effects at global scale. To refine the current understanding of trace metal distribution and variability in natural environments, concentrations of dissolved trace metals (Ag, Al, As, B, Ba, Be, Co, Cr, Cd, Cu, Fe, Hg, Mo, Ni, Pb, Sb, Se, Th,Tl, U, V, Mn, Zn), major ions, inorganic nutrients (NO3, PO4), TOC and stable isotopes of water were determined in water samples from rainwater, seven piezometers and a pond in the coastal Doñana wetland during four sampling campaigns between 2017 and 2019. Results show clear evaporation signatures of stable isotopes in the pond but not in the groundwater. Hydrochemical analyses yield significant, systematic changes in groundwater trace metal and nutrient composition along the flowpath from the dune belt to the pond, controlled by organic matter in the sediments. Whereas major ions reached maximum concentrations in the pond due to evapoconcentration, most trace metals showed highest concentrations at sites with lower redox levels, except for B, As and U, which showed very high concentrations in the pond. Cu, Zn, Ni, Sb and Tl yielded higher median concentrations in rainwater than in most of the groundwater points and in case of Cu and Zn higher even than in surface water which points to an atmospheric input source of these elements. Temporal variability of trace metals was related to lower hydraulic heads after an elongated dry period which led to lower redox levels and higher concentrations of most of the trace elements whereas major ions showed more constant concentration levels. This is of special concern regarding climate change and the predicted higher frequency of prolonged dry periods, which could modify the natural hydrochemical patterns in undisturbed wetlands systems.This work has been financed by the CLIGRO Project (MICINN, CGL2016-77473-C3-1-R) of the Spanish National Plan for Scientific and Technical Research and Innovation. The infrastructure has been co-financed by European Research Funds (SE Scientific Infrastructures and Techniques and Equipment 388 2013, IGME13-1E-2113). The contracts of Lidia Molano Leno (PEJ-2014-A-68763) and Daniel Jesus Martinez Suárez (PTA2014-09579-I) were financed by the Ministry of Economy, Industry and Competitiveness of Spain (MINECO) and co-financed by the European Investment Bank (EIB) and the European Social Fund (ESF). The contract of Carmen Serrano Hidalgo was funded by the Industrial PhD grant supported by the Autonomous Region of Madrid, Spain (IND2018/AMB-9553). This work is also a contribution to the Andalusian research groups RNM-308 (Group of Hydrogeology) and RNM-126 (Group of water resources), the Lower Guadalquivir Basin convention between the CN IGME CSIC and Confederación Hidrológica del Guadalquivir (CHG) as well as the convention between Pablo de Olavide University and the Guadalquivir River Basin Board (Hydrological monitoring and modeling in Doñana temporary ponds).Peer reviewe

Investigating the impact of climate change on groundwater recharge using a high precision meteo lysimeter in a dune belt of the Doñana National Park

Congress on Groundwater and Global Change in the Western Mediterranean (2017. Granada)Although precise weighing lysimeters are mostly installed for agricultural purposes in crop-producing areas, these instruments are also useful in areas of ecological interest where soil and aquifer recharge-discharge processes need to be better understood. In September 2015 a high precision meteo-lysimeter was installed in a coastal dune of the Doñana Natural Reserve to quantify the recharge in dune belts, and to estimate its dependence on regional climate trends. In addition to the lysimeter, also six soil moisture sensors (model CS650) and 2 meteorological stations were installed. The first results show recharge rates of natural precipitation ranging from 19 to 97%, depending on the meteorological conditions and the initial soil moisture. The lysimeter-measured rainfall generally exceeded the measurements of the tipping bucket. Also the contribution of the dew was detected by the lysimeter. A soil water model is currently being set up to simulate recharge, soil water movement, evaporation and percolation, as well as to quantify uncertainty and noise effects.Unidad de Sevilla, Instituto Geológico y Minero de España, EspañaInstituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica, EspañaDepartamento de Agronomía, Universidad de Córdoba, EspañaPeer reviewe

A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis

Background: The difficulty in elucidating the genetic basis of complex diseases roots in the many factors that can affect the development of a disease. Some of these genetic effects may interact in complex ways, proving undetectable by current single-locus methodology. Results: We have developed an analysis tool called Hypothesis Free Clinical Cloning (HFCC) to search for genome-wide epistasis in a case-control design. HFCC combines a relatively fast computing algorithm for genome-wide epistasis detection, with the flexibility to test a variety of different epistatic models in multi-locus combinations. HFCC has good power to detect multi-locus interactions simulated under a variety of genetic models and noise conditions. Most importantly, HFCC can accomplish exhaustive genome-wide epistasis search with large datasets as demonstrated with a 400,000 SNP set typed on a cohort of Parkinson's disease patients and controls. Conclusion: With the current availability of genetic studies with large numbers of individuals and genetic markers, HFCC can have a great impact in the identification of epistatic effects that escape the standard single-locus association analyses