Marcelino de la Cruz

King Juan Carlos University | URJC · Biology and Geology

Background and aims: Arbuscular mycorrhizal (AM) fungi enhance the uptake of water and minerals to the plant hosts, alleviating plant stress. Therefore, AM fungal-plant interactions are particularly important in drylands and other stressful ecosystems. We aimed to determine the combined and independent effects of above- and belowground plant commu...

Ecological processes such as seed dispersal or plant–plant interactions and environmental constraints such as climate or soil heterogeneity are known to influence establishment, and thus the spatial patterns of plant communities and populations. In this study, we hypothesized that key functional traits such as the specific leaf area (SLA), reproduc...

Key message In this work, we highlighted the importance of the phenotypic structure of forest in regulating inter-tree competition with scattered individuals showing larger growth than close neighbours, with lower growth rates. Abstract Plant interactions are among the fundamental processes shaping the structure and functioning of ecosystems as th...

El libro va dirigido a estudiantes, profesores e investigadores del ámbito de las ciencias naturales que deseen iniciarse en el mundo de la investigación, entender en profundidad algunas de las principales técnicas de análisis de datos utilizadas en el ámbito de la ecología, o conocer la implementación de dichas técnicas en R, uno de los lenguajes...

Despite noticeable concern about the deforestation rate worldwide, the forest surface in Europe has considerably expanded over the past centuries as a consequence of the rural exodus and abandonment of agrarian practices. Tree recruitment associated with forest regrowth is a multi-stage process influenced by several biotic and abiotic factors. Yet,...

Global change pressures are jeopardizing the functioning and structure of most tropical forests and clouding the future for their biodiversity and provided services. Although the impact of direct destruction through deforestation and fragmentation is currently in the research portfolio, overgrazing, which is more diffuse and generalized but chronic...

Plant trait-based ecology is a powerful extension of the attempt of community ecolo-gists to unveil assembly mechanisms. However, the two main expected determinants of community assembly, niche and neutral processes, can be confused under this framework. Here, we propose to move from trait-based to phenotype-based community ecology, accounting for...

Understanding constraints to phenotypic plasticity is key given its role on the response of organisms to environmental change. It has been suggested that phenotypic integration, the structure of trait covariation, could limit trait plasticity. However, the relationship between plasticity and integration is far from resolved. Using a database of fun...

Aims An unresolved question in plant ecology is whether diversity of the aboveground and belowground compartments of a plant community is similar at different neighbourhood scales. We investigated how the similarity between both compartments varies with the aboveground sampling grain and if significant discrepancies exist between aboveground and b...

Trait-based ecology suggests that abiotic filtering is the main mechanism structuring the regional species pool in different subsets of habitat-specific species. At more local spatial scales, other ecological processes may add on giving rise to complex patterns of functional diversity (FD). Understanding how assembly processes operating on the habi...

Roots are assumed to play a major role in structuring soil microbial communities, but most studies exploring the relationships between microbes and plants at the community level have only used aboveground plant distribution as a proxy. However, a decoupling between belowground and aboveground plant components may occur due to differential spreading...

Aim Plant recruitment may occur immediately after seed dispersal from the mother plant, or be delayed through the formation of soil seed banks. These strategies are known to be mediated by adaptations of seed dispersal and reproductive phenology, which if analyzed together can provide valuable information about the regeneration strategies of specie...

Questions The current paradigm of plant community assembly relies on a set of processes operating at particular spatial scales. It is assumed that as the spatial scale becomes finer, environmental filtering loses its importance in favor of biotic interactions and neutral processes. Thus, at the very fine spatial scale represented by a rectangular p...

Friendly introduction to writing functions in R with ecological applications.

The functioning of plant communities is strongly influenced by the number of species in the community and their spatial arrangement. This is because plants interact with their nearest neighbors and this interaction is expected to be stronger when the interacting individuals are ecologically similar in terms of resource use. Recent evidence shows th...

Plant to plant interactions are probably the most important driver of species coexistence at fine spatial scales, but their detection represents a challenge in Ecology. Spatial point pattern analysis (SPPA) is likely the approach most used to identify them, however, it suffers from some limitations related to the over‐simplification of individuals...

Most work on plant community ecology has been performed aboveground, neglecting the processes that occur in the soil. DNA metabarcoding, where multiple species are computationally identified in bulk samples, can help overcome the logistical limitations involved in sampling plant communities belowground. A major limitation of this methodology is, ho...

Manual of the R package Rramas. Analyzes and predicts from matrix population models (Caswell 2006) <doi:10.1002/9781118445112.stat07481>.

Questions Positive and negative associations among species influence the structure of plant communities. Yet, how these plant associations are assembled at the community level is poorly understood. We propose a new approach that combines spatial ecology, network theory and trait‐based ecology to examine the assembly of plant–plant associations at...

Tests the observed overlapping polygon area in a collection of polygons against a null model of random rotation, as explained in De la Cruz et al. (2017) <doi:10.13140/RG.2.2.12825.72801>

This vignette explains how to read shapefile data into R for use the overlapptest package. This vignette is part of the documentation included in overlapptest version 1.0. T

We assessed the relative importance of dispersal limitation, environmental heterogeneity and their joint effects as determinants of the spatial patterns of 229 species in the moist tropical forest of Barro Colorado Island (Panama). We differentiated five types of species according to their dispersal syndrome; autochorous, anemochorous, and zoochoro...

Mean cluster size by dispersal syndrome. Mean cluster size (σ) ± Standard Error of the five types of species according to their dispersal syndromes (autochorous, anemochorous, and zoochorous species with small, medium-size and large fruits). Black dots and lines indicate resulting values for 189 species by selecting the best fitting model among hom...

Bandwidth for inhomogeneous processes. Number (n) of species in each dispersal syndrome described by each of the two inhomogeneous point processes considered; Inhomogeneous Poisson process (IPP) and Inhomogeneous Poisson cluster process (IPCP). These processes model the effects of environmental heterogeneity, and the joint effect between dispersal...

Dispersal syndrome and spatial point process fitted to each species. Best fit: spatial point process fitted for each species. Inhomogeneous Poisson process (IPP), homogeneous Poisson cluster process (HPCP); inhomogeneous Poisson cluster process (IPCP). Dispersal: dispersal syndrome assigned to each species. Animal1: zoochorous (fruit size < 2 cm);...

Spatial point processes. Mathematical details of the three spatial point processes: Inhomogeneous Poisson Processes (IPP), Homogeneous Poisson cluster process (HPCP), Inhomogeneous Poisson cluster process (IPCP). (DOCX)

SHARELINK: https://authors.elsevier.com/a/1V-y7,XRNLVEF- The estimated potential of landscape metrics as a surrogate for biodiversity is strongly dependent on the spatial analytical unit used for evaluation. We assessed the relationship between terrestrial vertebrate species richness (total and taxonomic) and structural landscape heterogeneity, te...

Endozoochory is a prominent form of seed dispersal in tropical dry forests. Most extant megafauna that perform such seed dispersal are ungulates, which can also be seed predators. White-tailed deer (Odocoileus virginianus) is one of the last extant megafauna of Neotropical dry forests, but whether it serves as a legitimate seed disperser is poorly...

Provides histograms, boxplots and dotplots as alternatives to scatterplots of data when plotting fitted logistic regressions.

The study by Bastin et al. (Reports, 12 May 2017, p. 635) is based on an incomplete delimitation of dry forest distribution and on an old and incorrect definition of drylands. Its sampling design includes many plots located in humid ecosystems and ignores critical areas for the conservation of dry forests. Therefore, its results and conclusions may...

Ecologists have recognised the effects of biotic interactions on the spatial distribution of living organisms. Yet, the spatial structure of plant interaction networks in real-world ecosystems has remained elusive so far. Using spatial pattern and network analyses, we found that alpine plant communities are organised in spatially variable and compl...

The recent Global Drylands Assessment of forests is based on both an incomplete delimitation of dry forests distribution and on an old and incorrect delimitation of drylands. Its sampling design includes a large proportion of plots located in humid ecosystems and ignores critical areas for the conservation of dry forests. Therefore its results and...

Script to document numbers, statistics and maps in the technical comment on ”The extent of forest in dryland biomes”.

Manual of the R package "idar" (Individual Diversity-Area Relationships). Functions to compute and test individual (species, phylogenetic and functional) diversity-area relationships , i.e., how species-, phylogenetic-and functional-diversity varies with spatial scale around the individuals of some species in a community.

Most ecological theories that aim to explain coexistence in megadiverse communities employ a set of three rules to describe the stochastic geometry of biodiversity: (i) individuals exhibit intraspecific clustering; (ii) species abundances vary according to a log‐normal distribution and (iii) the spatial arrangement between species is independent. T...

Working with fully mapped communities provides the ecologist the opportunity to estimate precisely who interacts with who, how frequently and which of those interactions are important for the assembly of the community. Most analyses of fully mapped communities have employed point pattern analysis techniques, as these extract the maximum information...

An important component to resolve contemporary debates in ecology about niches versus neutrality lies in our ability to understand how deterministic and stochastic processes interact in space and time to structure biodiversity. Plant interactions are fundamental processes for structuring plant communities, and are usually considered as deterministi...

Most ecological studies that involve point pattern analyses are based on a single plot, which prevent the separation of the effects of various processes that could act simultaneously, as well as limiting the conclusions that can be extracted from these studies. However, considering the spatial distribution of individuals in several plots as replica...

Spatial patterns of plant species are determined by an array of ecologica factors including biotic and abiotic environmental constraints and intrinsic species traits. Thus, an observed aggregated pattern may be the result of short-distance dispersal, the presence of habitat heterogeneity, plant-plant interactions or a combination of the above. Here...

Background: The traditional markets in southern Ecuador and within the Andean region are especially important for plant resource trading among local people, even since before Spanish colonization; therefore, ethnobotanical studies are currently necessary and important. These strategic spaces persist for the traditional medicine cultural value refl...

The dwarf mistletoe, Arceuthobium oxycedri, is found on populations of Juniperus oxycedrus, in central Spain. This species can have negative effects on the physiology of its host, including mortality. Understanding the mechanisms that control its distribution and dispersal is critical to assessing its potential for spread. We assessed dwarf mistlet...

Evaluating community assembly through the use of functional traits is a promising tool for testing predictions arising from Niche and Coexistence theories. Although interactions among neighboring species and their inter-specific differences are known drivers of coexistence with a strong spatial signal, assessing the role of individual species on th...

Understanding biological invasions patterns and mechanisms is highly needed for forecasting and managing these processes and their negative impacts. At small scales, ecological processes driving plant invasions are expected to produce a spatially explicit pattern driven by propagule pressure and local ground heterogeneity. Our aim was to determine...

Deforestation and fragmentation are major components of global change; both are contributing to the rapid loss of tropical forest area with important implications for ecosystem functioning and biodiversity conservation. The forests of South Ecuador are a biological 'hotspot' due to their high diversity and endemism levels. We examined the deforesta...

QuestionsShrublands often exhibit very high levels of species richness. We ask which mechanisms underlie plant species co-existence in a hyper-diverse Mediterranean shrubland, and the scales at which individual species exert their effects during organization of diversity in these communities.LocationBrea de Tajo, Madrid, Spain.Methods We computed t...

Manual of the R package "selectspm 0.2". Functions to Select Point Pattern Models Based on Minimum Contrast, AIC and Goodness of Fit

Some wrappers, functions and data sets for spatial point pattern analysis (mainly based on spatstat), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones''

Documents Phytosociologiques N.S., 8: 173-183.

Understanding how diversity is maintained in species-rich communities, such as tropical forests, remains a challenge in ecology. Recent work suggests that the controversy between competing theories could be better resolved by considering the spatial scale at which different processes rule community assembly.Here we use individual species-area relat...

Manual of the R package "replicatedpp2w": A Two-Way ANOVA-Like Method to Analyze Replicated Point Patterns. Test for effects of both individual factors and their interaction on replicated spatial patterns in a two factorial design.

Spatial patterns of adult plants are a consequence of several ecological processes related to seed dispersal and recruitment. Dispersal limitation, mediated by dispersal syndrome, is considered a key factor in the formation of adult plant spatial patterns. Although this initial pattern determined by dispersal has been thoroughly studied, the subseq...

Supplementary material for the paper "Does spatial heterogeneity blur the signature of dispersal syndromes on spatial patterns of woody species? A test in a tropical dry forest"

Deforestation and fragmentation are major components of global change; both are contributing to the rapid loss of tropical forest area with important implications for ecosystem functioning and biodiversity conservation. The forests of South Ecuador are a biological 'hotspot' due to their high diversity and endemism levels. We examined the deforesta...

Manual of the R package "selectspm". Functions to fit and select point patterns models based on minimum contrast and AIC.

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 analysi...

Although tree ferns are an important component of temperate and tropical forests, very little is known about their ecology. Their peculiar biology (e.g., dispersal by spores and two-phase life cycle) makes it difficult to extrapolate current knowledge on the ecology of other tree species to tree ferns. In this paper, we studied the effects of negat...

The presence of compatible fungi is necessary for epiphytic orchid recruitment. Thus, identifying associated mycorrhizal fungi at the population level is essential for orchid conservation. Recruitment patterns may also be conditioned by factors such as seed dispersal range and specific environmental characteristics. In a forest plot, all trees with...

Questions(1) Does climate amelioration in semi-arid ecosystems increase seed bank richness and seed density in both total and persistent seed banks? (2) Does herbivory modulate climate effects on soil seed banks? (3) Is this effect mediated by changes in the above-ground vegetation? (4) To what extent do environmental conditions affect similarity b...

Positive plant interactions have strong effects on plant diversity at several spatial scales, expanding species distribution under stressful conditions. We evaluated the joint effect of climate and grazing on the nurse effect of Croton wagneri, by monitoring several community attributes at two spatial scales: microhabitat and plant community. Two v...

Manual of the R package tgram. Functions to compute and plot tracheidograms.

Manual of the R package "dixon". Function to test spatial segregation and association based in contingency table analysis of nearest neighbour counts following Dixon (2002). Some fortran code has been included to the original dixon2002 function of the ecespa package to improve speed.

Manual of the R package "mpmcorrelogram". Functions to compute and plot multivariate (partial) Mantel correlograms.

Se considera que el aclareo por denso-dependencia es uno de los mecanismos clave implicados en la coexistencia de especies en bosques tropicales (Zimmerman 2008, Wright 2002). Este proceso tiene una importante manifestación espacial derivada del aclareo de las poblaciones de plántulas que presentan elevadas densidades conespecíficas locales. El res...

Como continuación del libro publicado en 2008 (Introducción al Análisis Espacial de Datos en Ecología y Ciencias Ambientales: Métodos y Aplicaciones), la presente obra presenta algunos avances en el campo de la ecología espacial. El libro consta de 16 capítulos divididos en dos grandes apartados: i) conceptos y técnicas para el análisis espacial de...

Los bosques secos neotropicales son reconocidos como uno de los ecosistemas más amenazados del mundo. La acelerada pérdida de cobertura vegetal de estos bosques ha ocasionado que, en la actualidad, se encuentren restringidos a una pequeña fracción de su área de distribución histórica. Conocer su diversidad biológica, así como cuáles son los factore...

Persistence and abundance of species is determined by habitat availability and the ability to disperse and colonize habitats at contrasting spatial scales. Favourable habitat fragments are also heterogeneous in quality, providing differing opportunities for establishment and affecting the population dynamics of a species. Based on these principles,...

This study examines the seed dispersal spectrum of the tropical dry forests of Southern Ecuador, in an effort to contribute to the knowledge of the complex dynamics of tropical dry forests. Seed dispersal spectrum was described for a total number of 160 species. Relationships of dispersal syndromes with plant growth form and climatic seasonality we...

How do tree species identity, microhabitat and water availability affect inter- and intra-specific interactions between juvenile and adult woody plants? Continental Mediterranean forests in Alto Tajo Natural Park, Guadalajara, Spain. A total of 2066 juveniles and adults of four co-occurring tree species were mapped in 17 plots. The frequency of juv...

Melocactus ernestii Vaupel ssp. ernestii occurs in discontinuous outcrops in eastern Brazil. We investigated the spatio-temporal pattern of mortality events and survival of seedlings of M. ernestii relationship with plants and perennials, from the use of plots, assigned with the aid of measuring tapes, which were taken the Cartesian coordinates of...

Because climate can affect xylem cell anatomy, series of intra-annual cell anatomical features have the potential to retrospectively supply seasonal climatic information. In this study, we explored the ability to extract information about water stress conditions from tracheid features of the Mediterranean conifer Juniperus thurifera L. Tracheidogra...