Univariate versus multivariate modeling of panel data

Panel data can be arranged into a matrix in two ways, called 'long' and 'wide' formats (LFand WF). The two formats suggest two alternative model approaches for analyzing paneldata: (i) univariate regression with varying intercept; and (ii) multivariate regression withlatent variables (a particular case of structural equation model, SEM). The present papercompares the two approaches showing in which circumstances they yield equivalent?insome cases, even numerically equal?results. We show that the univariate approach givesresults equivalent to the multivariate approach when restrictions of time invariance (inthe paper, the TI assumption) are imposed on the parameters of the multivariate model.It is shown that the restrictions implicit in the univariate approach can be assessed bychi-square difference testing of two nested multivariate models. In addition, commontests encountered in the econometric analysis of panel data, such as the Hausman test, areshown to have an equivalent representation as chi-square difference tests. Commonalitiesand differences between the univariate and multivariate approaches are illustrated usingan empirical panel data set of firms' profitability as well as a simulated panel data.

Natural or naturalized? phylogeography suggests that the abundant sea urchin arbacia lixula Is a recent Colonizer of the Mediterranean

We present the global phylogeography of the black sea urchin Arbacia lixula, an amphi-Atlantic echinoid with potential to strongly impact shallow rocky ecosystems. Sequences of the mitochondrial cytochrome c oxidase gene of 604 specimens from 24 localities were obtained, covering most of the distribution area of the species, including the Mediterranean and both shores of the Atlantic. Genetic diversity measures, phylogeographic patterns, demographic parameters and population differentiation were analysed. We found high haplotype diversity but relatively low nucleotide diversity, with 176 haplotypes grouped within three haplogroups: one is shared between Eastern Atlantic (including Mediterranean) and Brazilian populations, the second is found in Eastern Atlantic and the Mediterranean and the third is exclusively from Brazil. Significant genetic differentiation was found between Brazilian, Eastern Atlantic and Mediterranean regions, but no differentiation was found among Mediterranean sub-basins or among Eastern Atlantic sub-regions. The star-shaped topology of the haplotype network and the unimodal mismatch distributions of Mediterranean and Eastern Atlantic samples suggest that these populations have suffered very recent demographic expansions. These expansions could be dated 94-205 kya in the Mediterranean, and 31-67 kya in the Eastern Atlantic. In contrast, Brazilian populations did not show any signature of population expansion. Our results indicate that all populations of A. lixula constitute a single species. The Brazilian populations probably diverged from an Eastern Atlantic stock. The present-day genetic structure of the species in Eastern Atlantic and the Mediterranean is shaped by very recent demographic processes. Our results support the view (backed by the lack of fossil record) that A. lixula is a recent thermophilous colonizer which spread throughout the Mediterranean during a warm period of the Pleistocene, probably during the last interglacial. Implications for the possible future impact of A. lixula on shallow Mediterranean ecosystems in the context of global warming trends must be considered.

Thermodynamic stability of nanosized multicomponent bubbles/droplets: The square gradient theory and the capillary approach

Formation of nanosized droplets/bubbles from a metastable bulk phase is connected to many unresolved scientific questions. We analyze the properties and stability of multicomponent droplets and bubbles in the canonical ensemble, and compare with single-component systems. The bubbles/droplets are described on the mesoscopic level by square gradient theory. Furthermore, we compare the results to a capillary model which gives a macroscopic description. Remarkably, the solutions of the square gradient model, representing bubbles and droplets, are accurately reproduced by the capillary model except in the vicinity of the spinodals. The solutions of the square gradient model form closed loops, which shows the inherent symmetry and connected nature of bubbles and droplets. A thermodynamic stability analysis is carried out, where the second variation of the square gradient description is compared to the eigenvalues of the Hessian matrix in the capillary description. The analysis shows that it is impossible to stabilize arbitrarily small bubbles or droplets in closed systems and gives insight into metastable regions close to the minimum bubble/droplet radii. Despite the large difference in complexity, the square gradient and the capillary model predict the same finite threshold sizes and very similar stability limits for bubbles and droplets, both for single-component and two-component systems.

Systematics and phylogeography of the Dysdera erythrina species complex (Araneae, Dysderidae) in Sardinia

Sardinia is the second largest island in the Mediterranean and, together with Corsica and nearby mainland areas, one of the top biodiversity hotspots in the region. The origin of Sardinia traces back to the opening of the western Mediterranean in the late Oligocene. This geological event and the subsequent Messinian Salinity Crisis and Pleistocene glacial cycles have had a major impact on local biodiversity. The Dysdera woodlouse hunter spiders are one of the most diverse ground-dweller groups in the Mediterranean. Here we describe the first two species of this genus endemic to Sardinia: Dysdera jana sp. n. and Dysdera shardana sp. n. The two species show contrasting allopatric distribution: D. jana sp. n. is a narrow endemic while D. shardana sp. n. is distributed throughout most of the island. A multi-gene DNA sequence phylogenetic analys based on mitochondrial and nuclear genes supports the close relationships of the new species to the type species of the genus Dysdera erythrina. Age estimates reject Oligocene origin of the new Dysdera species and identify the Messinian Salinity Crises as the most plausible period for the split between Sardinian endemics and their closest relatives. Phylogeographic analysis reveals deep genetic divergences and population structure in Dysdera shardana sp. n., suggesting that restriction to gene flow probably due to environmental factors could explain local speciation events. Taxonomy, phylogeny, DNA sequencing, Mediterranean biogeography, phylogeography

A novel approach to analysing the regimes of temporary streams in relation to their controls on the composition and structure of aquatic biota

Temporary streams are those water courses that undergo the recurrent cessation of flow or the complete drying of their channel. The structure and composition of biological communities in temporary stream reaches are strongly dependent on the temporal changes of the aquatic habitats determined by the hydrological conditions. Therefore, the structural and functional characteristics of aquatic fauna to assess the ecological quality of a temporary stream reach cannot be used without taking into account the controls imposed by the hydrological regime. This paper develops methods for analysing temporary streams' aquatic regimes, based on the definition of six aquatic states that summarize the transient sets of mesohabitats occurring on a given reach at a particular moment, depending on the hydrological conditions: Hyperrheic, Eurheic, Oligorheic, Arheic, Hyporheic and Edaphic. When the hydrological conditions lead to a change in the aquatic state, the structure and composition of the aquatic community changes according to the new set of available habitats. We used the water discharge records from gauging stations or simulations with rainfall-runoff models to infer the temporal patterns of occurrence of these states in the Aquatic States Frequency Graph we developed. The visual analysis of this graph is complemented by the development of two metrics which describe the permanence of flow and the seasonal predictability of zero flow periods. Finally, a classification of temporary streams in four aquatic regimes in terms of their influence over the development of aquatic life is updated from the existing classifications, with stream aquatic regimes defined as Permanent, Temporary-pools, Temporary-dry and Episodic. While aquatic regimes describe the long-term overall variability of the hydrological conditions of the river section and have been used for many years by hydrologists and ecologists, aquatic states describe the availability of mesohabitats in given periods that determine the presence of different biotic assemblages. This novel concept links hydrological and ecological conditions in a unique way. All these methods were implemented with data from eight temporary streams around the Mediterranean within the MIRAGE project. Their application was a precondition to assessing the ecological quality of these streams.

Modeling and Classifying Breast Tissue Density in Mammograms

We present a new approach to model and classify breast parenchymal tissue. Given a mammogram, first, we will discover the distribution of the different tissue densities in an unsupervised manner, and second, we will use this tissue distribution to perform the classification. We achieve this using a classifier based on local descriptors and probabilistic Latent Semantic Analysis (pLSA), a generative model from the statistical text literature. We studied the influence of different descriptors like texture and SIFT features at the classification stage showing that textons outperform SIFT in all cases. Moreover we demonstrate that pLSA automatically extracts meaningful latent aspects generating a compact tissue representation based on their densities, useful for discriminating on mammogram classification. We show the results of tissue classification over the MIAS and DDSM datasets. We compare our method with approaches that classified these same datasets showing a better performance of our proposal

Spiders on a Hot Volcanic Roof: Colonisation Pathways and Phylogeography of the Canary Islands Endemic Trap-Door Spider Titanidiops canariensis (Araneae, Idiopidae)

Studies conducted on volcanic islands have greatly contributed to our current understanding of how organisms diversify. The Canary Islands archipelago, located northwest of the coast of northern Africa, harbours a large number of endemic taxa. Because of their low vagility, mygalomorph spiders are usually absent from oceanic islands. The spider Titanidiops canariensis, which inhabits the easternmost islands of the archipelago, constitutes an exception to this rule. Here, we use a multi-locus approach that combines three mitochondrial and four nuclear genes to investigate the origins and phylogeography of this remarkable trap-door spider. We provide a timeframe for the colonisation of the Canary Islands using two alternative approaches: concatenation and species tree inference in a Bayesian relaxed clock framework. Additionally, we investigate the existence of cryptic species on the islands by means of a Bayesian multi-locus species delimitation method. Our results indicate that T. canariensis colonised the Canary Islands once, most likely during the Miocene, although discrepancies between the timeframes from different approaches make the exact timing uncertain. A complex evolutionary history for the species in the archipelago is revealed, which involves two independent colonisations of Fuerteventura from the ancestral range of T. canariensis in northern Lanzarote and a possible back colonisation of southern Lanzarote. The data further corroborate a previously proposed volcanic refugium, highlighting the impact of the dynamic volcanic history of the island on the phylogeographic patterns of the endemic taxa. T. canariensis includes at least two different species, one inhabiting the Jandia peninsula and central Fuerteventura and one spanning from central Fuerteventura to Lanzarote. Our data suggest that the extant northern African Titanidiops lineages may have expanded to the region after the islands were colonised and, hence, are not the source of colonisation. In addition, T. maroccanus may harbour several cryptic species.

The temporal dynamics of resource use by frugivorous birds: a network approach

Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant frugivore interaction networks spanning two years in a Mediterranean shrubland community. Three main hypotheses dealing with the temporal variation of network properties were tested, examining the effects of abundance, switching behavior between alternative food resources, and morphological traits in determining consumer interaction patterns. Our results demonstrate that temporal variation in consumer interaction patterns is explained by short-term variation in resource and bird abundances and seasonal dietary switches between alternative resources (fleshy fruits and insects). Moreover, differences in beak morphology are associated with differences in switching behavior between resources, suggesting an important role of foraging adaptations in determining network patterns. We argue that beak shape adaptations might determine generalist and specialist feeding behaviors and thus the positions of consumer species within the network. Finally, we provide a preliminary framework to interpret phylogenetic signal in plant animal networks. Indeed, we show that the strength of the phylogenetic signal in networks depends on the relative importance of abundance, behavioral, and morphological variables. We show that these variables strongly differ in their phylogenetic signal. Consequently, we suggest that moderate and significant phylogenetic effects should be commonly observed in networks of species interactions. Read More: http://www.esajournals.org/doi/abs/10.1890/07-1939.1

Invasive species and habitat degradation in Iberian streams: an analysis of their role in freshwater fish diversity loss

Mediterranean endemic freshwater fish are among the most threatened biota in the world. Distinguishing the role of different extinction drivers and their potential interactions is crucial for achieving conservation goals. While some authors argue that invasive species are a main driver of native species declines, others see their proliferation as a co-occurring process to biodiversity loss driven by habitat degradation. It is difficult to discern between the two potential causes given that few invaded ecosystems are free from habitat degradation, and that both factors may interact in different ways. Here we analyze the relative importance of habitat degradation and invasive species in the decline of native fish assemblages in the Guadiana River basin (southwestern Iberian Peninsula) using an information theoretic approach to evaluate interaction pathways between invasive species and habitat degradation (structural equation modeling, SEM). We also tested the possible changes in the functional relationships between invasive and native species, measured as the per capita effect of invasive species, using ANCOVA. We found that the abundance of invasive species was the best single predictor of natives’ decline and had the highest Akaike weight among the set of predictor variables examined. Habitat degradation neither played an active role nor influenced the per capita effect of invasive species on natives. Our analyses indicated that downstream reaches and areas close to reservoirs had the most invaded fish assemblages, independently of their habitat degradation status. The proliferation of invasive species poses a strong threat to the persistence of native assemblages in highly fluctuating environments. Therefore, conservation efforts to reduce native freshwater fish diversity loss in Mediterranean rivers should focus on mitigating the effect of invasive species and preventing future invasions

Searching for consensus in ahp-group decision making. A bayesian perspective

This paper sets out to identify the initial positions of the different decisionmakers who intervene in a group decision making process with a reducednumber of actors, and to establish possible consensus paths between theseactors. As a methodological support, it employs one of the most widely-knownmulticriteria decision techniques, namely, the Analytic Hierarchy Process(AHP). Assuming that the judgements elicited by the decision makers follow theso-called multiplicative model (Crawford and Williams, 1985; Altuzarra et al.,1997; Laininen and Hämäläinen, 2003) with log-normal errors and unknownvariance, a Bayesian approach is used in the estimation of the relative prioritiesof the alternatives being compared. These priorities, estimated by way of themedian of the posterior distribution and normalised in a distributive manner(priorities add up to one), are a clear example of compositional data that will beused in the search for consensus between the actors involved in the resolution ofthe problem through the use of Multidimensional Scaling tools

The Role of the Delay Time in the Modeling of Biological Range Expansions

The time interval between successive migrations of biological species causes a delay time in the reaction-diffusion equations describing their space-time dynamics. This lowers the predicted speed of the waves of advance, as compared to classical models. It has been shown that this delay-time effect improves the modeling of human range expansions. Here, we demonstrate that it can also be important for other species. We present two new examples where the predictions of the time-delayed and the classical (Fisher) approaches are compared to experimental data. No free or adjustable parameters are used. We show that the importance of the delay effect depends on the dimensionless product of the initial growth rate and the delay time. We argue that the delay effect should be taken into account in the modeling of range expansions for biological species