Maximum likelihood methods and their application in neighbourhood models

Los métodos de máxima verosimilitud (MMV) ofrecen un marco alternativo a la estadística frecuentista convencional, alejándose del uso del p-valor para el rechazo de una única hipótesis nula y optando por el uso de las verosimilitudes para evaluar el grado de apoyo en los datos a un conjunto de hipótesis alternativas (o modelos) de interés para el investigador. Estos métodos han sido ampliamente aplicados en ecología en el marco de los modelos de vecindad. Dichos modelos usan una aproximación espacialmente explícita para describir procesos demográficos de plantas o procesos ecosistémicos en función de los atributos de los individuos vecinos. Se trata por tanto de modelos fenomenológicos cuya principal utilidad radica en funcionar como herramientas de síntesis de los múltiples mecanismos por los que las especies pueden interactuar e influenciar su entorno, proporcionando una medida del efecto per cápita de individuos de distintas características (ej. tamaño, especie, rasgos fisiológicos) sobre los procesos de interés. La gran ventaja de aplicar los MMV en el marco de los modelos de vecindad es que permite ajustar y comparar múltiples modelos que usen distintos atributos de los vecinos y/o formas funcionales para seleccionar aquel con mayor soporte empírico. De esta manera, cada modelo funcionará como un “experimento virtual” para responder preguntas relacionadas con la magnitud y extensión espacial de los efectos de distintas especies coexistentes, y extraer conclusiones sobre posibles implicaciones para el funcionamiento de comunidades y ecosistemas. Este trabajo sintetiza las técnicas de implementación de los MMV y los modelos de vecindad en ecología terrestre, resumiendo su uso hasta la fecha y destacando nuevas líneas de aplicación.Maximum likelihood methods (MLM) offer an alternative framework to the traditional frequentist approach of data analysis, where the use of p-values to reject a single null (usually trivial) hypothesis is replaced by the use of likelihoods to evaluate the support in the data for a set of alternative working hypotheses of scientific relevance. These methods have been widely applied in the ecological framework of the neighbourhood models. These models use a spatially-explicit approach to describe demographic or ecosystem processes as a function of the attributes of neighbouring plants. They are therefore phenomenological models that serve as a tool of synthesis of the multiple mechanisms by which species can interact and modify its immediate environment, offering an estimate of the per-capita influence of individuals of different characteristics (e.g. size, species, functional traits) on the processes of study. A fundamental advantage of applying MMV in the framework of the neighbourhood models is that it allows fitting and comparing multiple models that use contrasting neighbour attributes and/or functional forms to select the one with the largest empirical support. In this way, each model works as a “virtual experiment” to answer questions related with the magnitude and spatial extent of the effects of different coexisting species and their potential implications for the function of communities and ecosystems. This paper reviews the use of MMV and neighborhood models in terrestrial ecology, synthesizing the state of the art and emphasizing new avenues of application

Effects of Quercus suber Decline on Woody Plant Regeneration: Potential Implications for Successional Dynamics in Mediterranean Forests

15 páginas.-- 2 figuras.-- 1 tabla.-- 82 referencias.--The online version of this article (doi:10.1007/s10021-016-0044-5) contains supplementary material, which is available to authorized usersIn the last two decades, widespread tree decline and mortality have been documented in forests worldwide. These mortality events usually show certain level of host-specificity, translating into rapid changes in the relative abundance of the adult community. Despite these short-term changes, it is poorly understood whether the decline and mortality of certain tree species are likely to result in long-term vegetation shifts. Trajectories of forest recovery and the probability of occurrence of permanent vegetation shifts are to a large extent determined by post-mortality regeneration dynamics. Using a spatially explicit neighborhood approach, we evaluated the spatial patterns of natural regeneration of the woody plant community in mixed Mediterranean forests affected by the decline of their dominant tree species, Quercus suber. We predicted the abundance, survival, and richness of the seedling and sapling bank as a function of the distribution and health status of the tree and shrub community. Results indicated that Q. suber decline had detectable effects on seedlings and saplings of coexistent woody species from very different functional groups (trees, shrubs, and lianas). The sign and magnitude of these effects varied substantially among coexistent species, which could imply shifts in the species ranking of seedling and sapling abundance, affecting successional trajectories and potentially leading to vegetation shifts. Because most of these changes pointed towards a loss of dominance of Q. suber, management strategies are urgently needed in order to attenuate adult mortality or promote its regeneration, counteracting the negative effects of global change drivers (exotic pathogens, climate change) on these valuable forests.This research was supported by the Ministerio de Ciencia e Innovación (MICIIN) projects INTERBOS (CGL2008-04503-C03-03), DIVERBOS (CGL2011-30285-C02-01), RETROBOS (CGL2011-26877), and RESTECO (CGL2014-52858-R), and the Junta de Andalucía project ANASINQUE (PGC2010-RNM-5782). BI was supported by a Formación de Personal Investigador (FPI)-MICINN Grant, J.M.A. by a Formación de Personal Universitario (FPU)-MEC Grant, and I.M.P.R. by a JAEdoc-Consejo Superior de Investigaciones Científicas (CSIC) contract.Peer reviewe

Fact Sheet: Virtual Research Environments in Agroecology Transition: Insights and Applications from the ALL-Ready Project

<p>Virtual Research Environments (VREs) are rapidly becoming a cornerstone in science, streamlining research processes and fostering collaboration. VREs are digital platforms in the form of a website designed to provide seamless access to all servicesa data user needs to do data-related work and collaborate with the community to create new knowledge.The All-Ready Agroecology VRE simplifies, centralize, digitalize and streamline the creation of interdisciplinary innovation ecosystems and communities via collaboration between Agroecology Living Labs and Research Infrastructures.The All-Ready Agroecology VRE catalyse change towards agroecology transition by providing users the opportunity to be inspired by others' ideas and innovations, learn by sharing and get advice from experts to build research solutions targeted to specific needs</p&gt

Spatial patterns of soil pathogens in declining Mediterranean forests: implications for tree species regeneration

11 pages, 5 figures, 2 tables, 66 references.Soil-borne pathogens are a key component of the belowground community because of the significance of their ecological and socio-economic impacts. However, very little is known about the complexity of their distribution patterns in natural systems. Here, we explored the patterns, causes and ecological consequences of spatial variability in pathogen abundance in Mediterranean forests affected by oak decline. • We used spatially explicit neighborhood models to predict the abundance of soil-borne pathogen species (Phytophthora cinnamomi, Pythium spiculum and Pythium spp.) as a function of local abiotic conditions (soil texture) and the characteristics of the tree and shrub neighborhoods (species composition, size and health status). The implications of pathogen abundance for tree seedling performance were explored by conducting a sowing experiment in the same locations in which pathogen abundance was quantified. • Pathogen abundance in the forest soil was not randomly distributed, but exhibited spatially predictable patterns influenced by both abiotic and, particularly, biotic factors (tree and shrub species). Pathogen abundance reduced seedling emergence and survival, but not in all sites or tree species. • Our findings suggest that heterogeneous spatial patterns of pathogen abundance at fine spatial scale can be important for the dynamics and restoration of declining Mediterranean forests.This study was supported by the Ministerio de Ciencia e Innovación (MICIIN) project INTERBOS (CGL2008-4503-C03-01), the Organismo Autónomo de Parques Nacionales/Ministerio de Medio Ambiente, Rural y Marino (OAPN⁄MIMARM) project DECALDO (091 ⁄ 2009) and European Fondo Europeo de Desarrollo Regional (FEDER) funds. B.I. was supported by a Formación de Personal Investigador (FPI)-MICIIN grant, J.M.A. by a Junta para la Ampliación de Estudios (JAE)pre-CSIC grant and I.M.P.R. by a JAEdoc-Consejo Superior de Investigaciones Científicas (CSIC) contract.Peer reviewe

Impact of tree decline on spatial patterns of seedling-mycorrhiza interactions: Implications for regeneration dynamics in Mediterranean forests

9 páginas.-- 3 figuras.-- 80referencias.-- Appendix A. Supplementary material Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.foreco.2015.05. 014.In the last decades, an increasing number of forest decline events and widespread tree mortality have been reported worldwide as a consequence of different global change drivers. Such a general decrease in tree health and cover has a large potential to impact mycorrhizal communities, but this issue remains largely unexplored.We used a Bayesian framework to analyze the impact of Quercus suber decline on spatial patterns of seedling-mycorrhiza interactions in mixed Mediterranean forests in Southern Spain, and evaluate the relative importance of this symbiosis as a driver of oak seedling establishment.Our models showed that the spatial variability found in the patterns of oak seedling colonization by both arbuscular mycorrhizas and ectomycorrhizas was partially linked to the process of Q. suber decline. Moreover, seedling survival and growth was influenced by the intensity of mycorrhizal colonization, but in quite unexpected ways. Arbuscular mycorrhizas had a larger effect on seedling performance than ectomycorrhizas, and the effects of both groups were negative or neutral but never positive.We conclude that because the spatial distribution of the seedling-mycorrhiza association responded to the identity and health status of individual trees, and mycorrhizal infection did in turn affect seedling performance, tree decline might affect forest dynamics through changes in plant-soil biota feedbacks.We thank the director and technical staff of Los Alcornocales Natural Park for facilities and support to carry out the field work. We are also indebted to Eduardo Gutiérrez, Ana Pozuelos, Maite Domínguez-Núñez, Adela Moreno and several students for invaluable laboratory and field assistance, and to I. Ibáñez for data analysis assistance. This research was supported by the Ministerio de Ciencia e Innovación (MICIIN) projects INTERBOS (CGL2008-04503-C03-03), DIVERBOS (CGL2011-30285-C02-01) and RETROBOS (CGL2011-26877), and the Junta de Andalucía project ANASINQUE (PGC2010-RNM-5782). BI was supported by a Formación de Personal Investigador (FPI)-MICINN grant, J.M.A. by a Formación de Personal Universitario (FPU)-MEC grant and I.M.P.R. by a JAEdoc-Consejo Superior de Investigaciones Científicas (CSIC) contract.Peer reviewe

Spatial patterns of Phytophthora cinnamomi in declining Mediterranean forests: implications for tree species regeneration

Presentado a The Sixth Meeting of the IUFRO Working Party 7‐02‐09, celebrado en Córdoba (España) del 9-14 de septiembre de 2012. Enlazamos con http://hdl.handle.net/10261/57038; http://hdl.handle.net/10261/57042Soil‐borne pathogens are a key component of the belowground community due to the significance of their ecological and socio‐economic impacts. However, very little is known about the complexity of their distribution patterns in natural systems.Peer reviewe

SIFOMED: el suelo como parte integrante del ecosistema

Póster presentado por el grupo Sistemas Forestales Mediterráneos (SIFOMed) en la Jornada: EL IRNAS Y EL SUELO: Alianza y Complicidad. JORNADA DEL AÑO INTERNACIONAL DE LOS SUELOS 30 de octubre de 2015Páginas Web del grupo http://www.irnas.csic.es/sifomed/El grupo SIFOMed tiene como objetivo el estudio de la dinámica y funcionamiento de los ecosistemas forestales mediterráneos, prestando especial atención a su respuesta frente al cambio global. Desarrollamos investigación básica en las áreas de ecología vegetal y de ecosistemas, con una fuerte componente aplicada a la restauración y conservación de sistemas perturbados. En general, nuestros estudios conectan el componente aéreo y edáfico del ecosistema, analizando las interacciones directas o indirectas entre plantas, microorganismos y animales.Peer reviewe

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved