Sparse species interactions reproduce abundance correlation patterns in microbial communities.

During the last decades, macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full understanding of the dynamical processes behind them. In particular, abundance fluctuations of different species are found to be correlated, both across time and across communities in metagenomic samples. Reproducing such correlations through appropriate population models remains an open challenge. The present paper tackles this problem and points to sparse species interactions as a necessary mechanism to account for them. Specifically, we discuss several possibilities to include interactions in population models and recognize Lotka-Volterra constants as a successful ansatz. For this, we design a Bayesian inference algorithm to extract sets of interaction constants able to reproduce empirical probability distributions of pairwise correlations for diverse biomes. Importantly, the inferred models still reproduce well-known single-species macroecological patterns concerning abundance fluctuations across both species and communities. Endorsed by the agreement with the empirically observed phenomenology, our analyses provide insights into the properties of the networks of microbial interactions, revealing that sparsity is a crucial feature.

Triadic influence as a proxy for compatibility in social relationships.

Networks of social interactions are the substrate upon which civilizations are built. Often, we create new bonds with people that we like or feel that our relationships are damaged through the intervention of third parties. Despite their importance and the huge impact that these processes have in our lives, quantitative scientific understanding of them is still in its infancy, mainly due to the difficulty of collecting large datasets of social networks including individual attributes. In this work, we present a thorough study of real social networks of 13 schools, with more than 3,000 students and 60,000 declared positive and negative relationships, including tests for personal traits of all the students. We introduce a metric-the "triadic influence"-that measures the influence of nearest neighbors in the relationships of their contacts. We use neural networks to predict the sign of the relationships in these social networks, extracting the probability that two students are friends or enemies depending on their personal attributes or the triadic influence. We alternatively use a high-dimensional embedding of the network structure to also predict the relationships. Remarkably, using the triadic influence (a simple one-dimensional metric) achieves the best accuracy, and adding the personal traits of the students does not improve the results, suggesting that the triadic influence acts as a proxy for the social compatibility of students. We postulate that the probabilities extracted from the neural networks-functions of the triadic influence and the personalities of the students-control the evolution of real social networks, opening an avenue for the quantitative study of these systems.

The turning point and end of an expanding epidemic cannot be precisely forecast.

Epidemic spread is characterized by exponentially growing dynamics, which are intrinsically unpredictable. The time at which the growth in the number of infected individuals halts and starts decreasing cannot be calculated with certainty before the turning point is actually attained; neither can the end of the epidemic after the turning point. A susceptible-infected-removed (SIR) model with confinement (SCIR) illustrates how lockdown measures inhibit infection spread only above a threshold that we calculate. The existence of that threshold has major effects in predictability: A Bayesian fit to the COVID-19 pandemic in Spain shows that a slowdown in the number of newly infected individuals during the expansion phase allows one to infer neither the precise position of the maximum nor whether the measures taken will bring the propagation to the inhibition regime. There is a short horizon for reliable prediction, followed by a dispersion of the possible trajectories that grows extremely fast. The impossibility to predict in the midterm is not due to wrong or incomplete data, since it persists in error-free, synthetically produced datasets and does not necessarily improve by using larger datasets. Our study warns against precise forecasts of the evolution of epidemics based on mean-field, effective, or phenomenological models and supports that only probabilities of different outcomes can be confidently given.

Identification of potential invasive alien species in Spain through horizon scanning.

Invasive alien species have widespread impacts on native biodiversity and ecosystem services. Since the number of introductions worldwide is continuously rising, it is essential to prevent the entry, establishment and spread of new alien species through a systematic examination of future potential threats. Applying a three-step horizon scanning consensus method, we evaluated non-established alien species that could potentially arrive, establish and cause major ecological impact in Spain within the next 10 years. Overall, we identified 47 species with a very high risk (e.g. Oreochromis niloticus, Popillia japonica, Hemidactylus frenatus, Crassula helmsii or Halophila stipulacea), 61 with high risk, 93 with moderate risk, and 732 species with low risk. Many of the species categorized as very high or high risk to Spanish biodiversity are either already present in Europe and neighbouring countries or have a long invasive history elsewhere. This study provides an updated list of potential invasive alien species useful for prioritizing efforts and resources against their introduction. Compared to previous horizon scanning exercises in Spain, the current study screens potential invaders from a wider range of terrestrial, freshwater, and marine organisms, and can serve as a basis for more comprehensive risk analyses to improve management and increase the efficiency of the early warning and rapid response framework for invasive alien species. We also stress the usefulness of measuring agreement and consistency as two different properties of the reliability of expert scores, in order to more easily elaborate consensus ranked lists of potential invasive alien species.

Cognitive resource allocation determines the organization of personal networks.

The typical human personal social network contains about 150 relationships including kin, friends, and acquaintances, organized into a set of hierarchically inclusive layers of increasing size but decreasing emotional intensity. Data from a number of different sources reveal that these inclusive layers exhibit a constant scaling ratio of [Formula: see text] While the overall size of the networks has been connected to our cognitive capacity, no mechanism explaining why the networks present a layered structure with a consistent scaling has been proposed. Here we show that the existence of a heterogeneous cost to relationships (in terms of time or cognitive investment), together with a limitation in the total capacity an individual has to invest in them, can naturally explain the existence of layers and, when the cost function is linear, explain the scaling between them. We develop a one-parameter Bayesian model that fits the empirical data remarkably well. In addition, the model predicts the existence of a contrasting regime in the case of small communities, such that the layers have an inverted structure (increasing size with increasing emotional intensity). We test the model with five communities and provide clear evidence of the existence of the two predicted regimes. Our model explains, based on first principles, the emergence of structure in the organization of personal networks and allows us to predict a rare phenomenon whose existence we confirm empirically.

Ecological quality assessement of marinas: An integrative approach combining biological and environmental data.

The importance of marinas as infrastructures for recreational boating is increasing substantially. However, information on their soft-bottom benthic communities, a key tool for managing programmes, is still scarce. We combined environment features with macro- and meiofaunal soft-bottom community information for assessing the ecological status of marinas with an integrative approach. To address this issue, we focused on eight marinas of the Southern Iberian Peninsula. Macro- and meiofauna data revealed high benthic heterogeneity at a spatial scale. The environmental variables which correlated best with macrofauna were mainly phosphorus, granulometry, and total organic carbon, and secondarily important variables were faecal coliforms, the biocide Irgarol, and heavy metals; total hydrocarbon concentration was also significant for meiofauna. Annelida was the dominant phylum in terms of number of species (37%) and abundance (66%) and were better descriptors of the environmental conditions than Arthropoda and Mollusca. Although identification to the species level is desirable and mandatory for assessing biological pollution, significant differences among marinas and correlations between fauna and abiotic variables were already detected at the level of family and order. This implies that biota assessment at higher levels may still be useful in monitoring programmes limited by time and budget constraints. The major novelty of this study lies in the development of an integrative assessment method based on the following selected ecological indicators: Marinas Environmental Pollution Index (MEPI), Biocontamination Index (BCI), macrofaunal biotic indices (AMBI, M-AMBI, BENTIX, MEDOCC and BENFES), macrofaunal taxa richness and Shannon-Wiener's diversity, and nematode:copepod index. This approach was able to discriminate marinas of the Southern Iberian Peninsula based on their ecological status, which ranged from poor to good. The method can be useful to design standards for assigning "sustainable quality seals" to those marinas with better values of ecological indicators.

Disentangling the effects of selection and loss bias on gene dynamics.

We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size. Free-living microbes evolve under stronger selection for gene retention than parasites. Different classes of MGE show a broad range of fitness effects, from the nearly neutral transposons to prophages, which are actively eliminated by selection. Genes involved in antiparasite defense, on average, incur a fitness cost to the host that is at least as high as the cost of plasmids. This cost is probably due to the adverse effects of autoimmunity and curtailment of horizontal gene transfer caused by the defense systems and selfish behavior of some of these systems, such as toxin-antitoxin and restriction modification modules. Transposons follow a biphasic dynamics, with bursts of gene proliferation followed by decay in the copy number that is quantitatively captured by the model. The horizontal gene transfer to loss ratio, but not duplication to loss ratio, correlates with genome size, potentially explaining increased abundance of neutral and costly elements in larger genomes.

Sheldon spectrum and the plankton paradox: two sides of the same coin-a trait-based plankton size-spectrum model.

The Sheldon spectrum describes a remarkable regularity in aquatic ecosystems: the biomass density as a function of logarithmic body mass is approximately constant over many orders of magnitude. While size-spectrum models have explained this phenomenon for assemblages of multicellular organisms, this paper introduces a species-resolved size-spectrum model to explain the phenomenon in unicellular plankton. A Sheldon spectrum spanning the cell-size range of unicellular plankton necessarily consists of a large number of coexisting species covering a wide range of characteristic sizes. The coexistence of many phytoplankton species feeding on a small number of resources is known as the Paradox of the Plankton. Our model resolves the paradox by showing that coexistence is facilitated by the allometric scaling of four physiological rates. Two of the allometries have empirical support, the remaining two emerge from predator-prey interactions exactly when the abundances follow a Sheldon spectrum. Our plankton model is a scale-invariant trait-based size-spectrum model: it describes the abundance of phyto- and zooplankton cells as a function of both size and species trait (the maximal size before cell division). It incorporates growth due to resource consumption and predation on smaller cells, death due to predation, and a flexible cell division process. We give analytic solutions at steady state for both the within-species size distributions and the relative abundances across species.

Enumerating secondary structures and structural moieties for circular RNAs.

A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of RNA sequences, with the folded configurations standing as a proxy for the phenotype. Here, we count the secondary structures of circular RNAs of length n and calculate the asymptotic distributions of different structural moieties, such as stems or hairpin loops, by means of symbolic combinatorics. Circular RNAs differ in essential ways from their linear counterparts. From the mathematical viewpoint, the enumeration of the corresponding secondary structures demands the use of combinatorial techniques additional to those used for linear RNAs. The asymptotic number of secondary structures for circular RNAs grows as ann-5/2, with a depending on particular constraints applied to the secondary structure. As it occurs with linear RNA, the abundance of any structural moiety is normally distributed in the limit n→∞, with a mean and a variance that increase linearly with n.

Heterogeneous networks do not promote cooperation when humans play a Prisoner's Dilemma.

It is not fully understood why we cooperate with strangers on a daily basis. In an increasingly global world, where interaction networks and relationships between individuals are becoming more complex, different hypotheses have been put forward to explain the foundations of human cooperation on a large scale and to account for the true motivations that are behind this phenomenon. In this context, population structure has been suggested to foster cooperation in social dilemmas, but theoretical studies of this mechanism have yielded contradictory results so far; additionally, the issue lacks a proper experimental test in large systems. We have performed the largest experiments to date with humans playing a spatial Prisoner's Dilemma on a lattice and a scale-free network (1,229 subjects). We observed that the level of cooperation reached in both networks is the same, comparable with the level of cooperation of smaller networks or unstructured populations. We have also found that subjects respond to the cooperation that they observe in a reciprocal manner, being more likely to cooperate if, in the previous round, many of their neighbors and themselves did so, which implies that humans do not consider neighbors' payoffs when making their decisions in this dilemma but only their actions. Our results, which are in agreement with recent theoretical predictions based on this behavioral rule, suggest that population structure has little relevance as a cooperation promoter or inhibitor among humans.

Morphology of the first zoeal stages of five species of the portunid genus Callinectes (Decapoda, Brachyura) hatched at the laboratory.

The genus Callinectes Stimpson, 1860 currently consists of 16 species, six of which are reported in Brazilian coast. In the present study, the first zoeal stages of Callinectes bocourti, C. danae, C. exasperatus, C. ornatus and C. sapidus from Brazil were obtained from ovigerous females. The morphological and meristic characters of all these larval stages are described and illustrated. Those of C. bocourti, C. danae and C. sapidus are redescribed and compared with the previous descriptions, and differences are listed. Larval characters of these species were examined for interspecific differences, as well as larval features to distinguish the genus Callinectes within Portunidae. In addition, other portunid genera and species with a known first zoeal stage are compared, with special attention to those species present in the same geographical area. Our findings concord with some previous molecular studies, and we discuss the complexity within the group.

Taxonomic study of the Pagurus forbesii "complex" (Crustacea: Decapoda: Paguridae). Description of Pagurus pseudosculptimanus sp. nov. from Alborán Sea (Southern Spain, Western Mediterranean Sea).

Study of hermit crabs from Alboran Sea has allowed recognition of two different morphological forms under what had been understood as Pagurus forbesii. Based on morphological observations with various species of Pagurus, and molecular studies, a new species is described as P. pseudosculptimanus. An overview of species of Pagurus from the eastern Atlantic and Mediterranean Sea is provided.

Two cases of pseudohermaphroditism in loggerhead sea turtles Caretta caretta.

Two juvenile (curved carapace lengths: 28 and 30 cm) loggerhead sea turtles Caretta caretta with precocious male external characteristics were admitted to the ARCA del Mar rescue area at the Oceanogràfic Aquarium in Valencia, Spain, in 2009 and 2010. Routine internal laparoscopic examination and subsequent histopathology confirmed the presence of apparently healthy internal female gonads in both animals. Extensive tissue biopsy and hormone induction assays were consistent with female sex. To the best of our knowledge, this is the first report of pseudohermaphroditism in loggerhead sea turtles based on sexual external characteristics and internal laparoscopic examination. Our findings suggest that the practice of using external phenotypical characteristics as the basis for gender identification in sea turtles should be reevaluated. Future research should focus on detecting more animals with sexual defects and their possible effects on the sea turtle population.

Stability of the personal relationship networks in a longitudinal study of middle school students.

The personal network of relationships is structured in circles of friendships, that go from the most intense relationships to the least intense ones. While this is a well established result, little is known about the stability of those circles and their evolution in time. To shed light on this issue, we study the temporal evolution of friendships among teenagers during two consecutive academic years by means of a survey administered on five occasions. We show that the first two circles, best friends and friends, can be clearly observed in the survey but also that being in one or the other leads to more or less stable relationships. We find that being in the same class is one of the key drivers of friendship evolution. We also observe an almost constant degree of reciprocity in the relationships, around 60%, a percentage influenced both by being in the same class and by gender homophily. Not only do our results confirm the mounting evidence supporting the circle structure of human social networks, but they also show that these structures persist in time despite the turnover of individual relationships-a fact that may prove particularly useful for understanding the social environment in middle schools.

Trends in the decapod crustacean community at the southernmost estuary of the Atlantic coast of Europe.

Climate change may enhance the establishment of introduced species, as well as the poleward shift in distribution of numerous species over decades. Long-term research and monitoring of an ecosystem at the southernmost point of the Atlantic coast of Europe should be an important priority in order to detect and understand trends in species composition and the related environmental changes. The Guadalquivir estuary (South West Spain) is more likely to suffer the exacerbated effects of climate change due to its location in the Mediterranean-climate zone. The long-term data set between 1997 and 2006 has allowed us to analyse the variability of the natural and anthropogenic stressors. The mean interannual dissimilarity of the estuarine fauna (Bray-Curtis dissimilarity index) has showed important differences throughout the years, and the species that most contributed to these differences were the exotic species capable of completing their life cycles. This long-term monitoring of the estuarine community has allowed us to anticipate future events and ecological risk assessment in European waters.

A horizon scan exercise for aquatic invasive alien species in Iberian inland waters.

As the number of introduced species keeps increasing unabatedly, identifying and prioritising current and potential Invasive Alien Species (IAS) has become essential to manage them. Horizon Scanning (HS), defined as an exploration of potential threats, is considered a fundamental component of IAS management. By combining scientific knowledge on taxa with expert opinion, we identified the most relevant aquatic IAS in the Iberian Peninsula, i.e., those with the greatest geographic extent (or probability of introduction), severe ecological, economic and human health impacts, greatest difficulty and acceptability of management. We highlighted the 126 most relevant IAS already present in Iberian inland waters (i.e., Concern list) and 89 with a high probability of being introduced in the near future (i.e., Alert list), of which 24 and 10 IAS, respectively, were considered as a management priority after receiving the highest scores in the expert assessment (i.e., top-ranked IAS). In both lists, aquatic IAS belonging to the four thematic groups (plants, freshwater invertebrates, estuarine invertebrates, and vertebrates) were identified as having been introduced through various pathways from different regions of the world and classified according to their main functional feeding groups. Also, the latest update of the list of IAS of Union concern pursuant to Regulation (EU) No 1143/2014 includes only 12 top-ranked IAS identified for the Iberian Peninsula, while the national lists incorporate the vast majority of them. This fact underlines the great importance of taxa prioritisation exercises at biogeographical scales as a step prior to risk analyses and their inclusion in national lists. This HS provides a robust assessment and a cost-effective strategy for decision-makers and stakeholders to prioritise the use of limited resources for IAS prevention and management. Although applied at a transnational level in a European biodiversity hotspot, this approach is designed for potential application at any geographical or administrative scale, including the continental one.

On the coexistence of cooperators,defectors and conditional cooperators in the multiplayer iterated Prisoner's Dilemma.

Recent experimental evidence [Grujic Fosco, Araujo, Cuesta, Sánchez, 2010. Social experiments in the mesoscale: humans playing a spatial Prisoner's dilemma. PLoS ONE 5, e13749] on the spatial Prisoner's Dilemma suggests that players choosing to cooperate or not on the basis of their previous action and the actions of their neighbors coexist with steady defectors and cooperators. We here study the coexistence of these three strategies in the multiplayer iterated Prisoner's Dilemma by means of the replicator dynamics. We consider groups with n=2, 3, 4 and 5 players and compute the payoffs to every type of player as the limit of a Markov chain where the transition probabilities between actions are found from the corresponding strategies. We show that for group sizes up to n=4 there exists an interior point in which the three strategies coexist, the corresponding basin of attraction decreasing with increasing number of players, whereas we have not been able to locate such a point for n=5. We analytically show that in the limit n --> ∞ no interior points can arise. We conclude by discussing the implications of this theoretical approach on the behavior observed in experiments.

Free-energy density functional for Strauss's model of transitive networks.

Ensemble models of graphs are one of the most important theoretical tools to study complex networks. Among them, exponential random graphs (ERGs) have proven to be very useful in the analysis of social networks. In this paper we develop a technique, borrowed from the statistical mechanics of lattice gases, to solve Strauss's model of transitive networks. This model was introduced long ago as an ERG ensemble for networks with high clustering and exhibits a first-order phase transition above a critical value of the triangle interaction parameter where two different kinds of networks with different densities of links (or, alternatively, different clustering) coexist. Compared to previous mean-field approaches, our method describes accurately even small networks and can be extended beyond Strauss's classical model-e.g., to networks with different types of nodes. This allows us to tackle, for instance, models with node homophily. We provide results for the latter and show that they accurately reproduce the outcome of Monte Carlo simulations.

Two new hermit crab species of Diogenes (Crustacea: Decapoda: Diogenidae) from Atlanto-Mediterranean coasts of Iberian Peninsula: Poleward migrants or merely overlooked indigenous species?

A new hermit crab species of the genus Diogenes with reddish-orange cheliped, Diogenes erythromanus sp. nov., is described and illustrated based on specimens from the Mediterranean coasts of the Iberian Peninsula, southern Spain. In addition, a second morphotype originating from Mauritanian waters and morphologically very close to D. erythromanus sp. nov. is described as a different species, D. arguinensis sp. nov. The new species are here compared to morphologically similar congeners, especially to those inhabiting the same geographical range. Diogenes erythromanus sp. nov. is distinguishable from other Diogenes primarily by the shape and armature of the left cheliped, with a palm slightly higher than long, with a ridge of spines running along the proximal lower margin that continues with a series of spinose rows forming a central band parallel to the upper margin of the palm. The palm in D. arguinensis sp. nov. is longer than high and shows similar proximal ridge, but without central spinose ridge. The shape of the cheliped is also different in D. arguinensis sp. nov., with long dactylus, which is also flattened and twisted. Sequences from two mitochondrial and one nuclear genes, and comparative analyses with other available sequences for the genus, are also included. Molecular phylogenetic analyses support the morphological delimitation, with D. erythromanus sp. nov. and D. arguinensis sp. nov. forming a separate group, more related to other tropical species, which raises different possible explanations for its presence in the Iberian Peninsula.