Juan C. Alonso

Bio: Juan C. Alonso is an academic researcher from Spanish National Research Council. The author has contributed to research in topics: DNA & Bustard. The author has an hindex of 58, co-authored 359 publications receiving 11981 citations. Previous affiliations of Juan C. Alonso include University of Wisconsin-Madison & Max Planck Society.

Modelling landscape-scale habitat use using GIS and remote sensing : a case study with great bustards

Abstract: Summary 1. Many species are adversely affected by human activities at large spatial scales and their conservation requires detailed information on distributions. Intensive ground surveys cannot keep pace with the rate of land-use change over large areas and new methods are needed for regional-scale mapping. 2. We present predictive models for great bustards in central Spain based on readily available advanced very high resolution radiometer (AVHRR) satellite imagery combined with mapped features in the form of geographic information system (GIS) data layers. As AVHRR imagery is coarse-grained, we used a 12-month time series to improve the definition of habitat types. The GIS data comprised measures of proximity to features likely to cause disturbance and a digital terrain model to allow for preference for certain topographies. 3. We used logistic regression to model the above data, including an autologistic term to account for spatial autocorrelation. The results from models were combined using Bayesian integration, and model performance was assessed using receiver operating characteristics plots. 4. Sites occupied by bustards had significantly lower densities of roads, buildings, railways and rivers than randomly selected survey points. Bustards also occurred within a narrower range of elevations and at locations with significantly less variable terrain. 5. Logistic regression analysis showed that roads, buildings, rivers and terrain all contributed significantly to the difference between occupied and random sites. The Bayesian integrated probability model showed an excellent agreement with the original census data and predicted suitable areas not presently occupied. 6. The great bustard’s distribution is highly fragmented and vacant habitat patches may occur for a variety of reasons, including the species’ very strong fidelity to traditional sites through conspecific attraction. This may limit recolonization of previously occupied sites. 7. We conclude that AVHRR satellite imagery and GIS data sets have potential to map distributions at large spatial scales and could be applied to other species. While models based on imagery alone can provide accurate predictions of bustard habitats at some spatial scales, terrain and human influence are also significant predictors and are needed for finer scale modelling.

Genome Engineering Reveals Large Dispensable Regions in Bacillus subtilis

Abstract: Bacterial genomes contain 250 to 500 essential genes, as suggested by single gene disruptions and theoretical considerations. If this view is correct, the remaining nonessential genes of an organism, such as Bacillus subtilis, have been acquired during evolution in its perpetually changing ecological niches. Notably, approximately 47% of the approximately 4,100 genes of B. subtilis belong to paralogous gene families in which several members have overlapping functions. Thus, essential gene functions will outnumber essential genes. To answer the question to what extent the most recently acquired DNA contributes to the life of B. subtilis under standard laboratory growth conditions, we initiated a "reconstruction" of the B. subtilis genome by removing prophages and AT-rich islands. Stepwise deletion of two prophages (SPbeta, PBSX), three prophage-like regions, and the largest operon of B. subtilis (pks) resulted in a genome reduction of 7.7% and elimination of 332 genes. The resulting strain was phenotypically characterized by metabolic flux analysis, proteomics, and specific assays for protein secretion, competence development, sporulation, and cell motility. We show that genome engineering is a feasible strategy for functional analysis of large gene clusters, and that removal of dispensable genomic regions may pave the way toward an optimized Bacillus cell factory.

Large-scale habitat selection by agricultural steppe birds in Spain: identifying species–habitat responses using generalized additive models

Abstract: Summary 1 Predictive models of species’ distributions are used increasingly in ecological studies investigating features as varied as biodiversity, habitat selection and interspecific competition. In a pilot study, we based a successful model for the great bustard Otis tarda on advanced very high resolution radiometer (AVHRR) satellite data, which offer attractive predictor variables because of the global coverage, high temporal frequency of overpasses and low cost. We wished to assess whether the approach could be applied at very large spatial scales, and whether the coarse resolution of the imagery (1 km 2 ) would limit application to those bird species with large home ranges or to simple recognition of broad habitat types. 2 We modelled the distributions of three agricultural steppe birds over the whole of Spain using a common set of predictor variables, including AVHRR imagery. The species, great bustard, little bustard Tetrax tetrax and calandra lark Melanocorhypha calandra , have similar habitat requirements but differently sized home ranges, and are all species of conservation concern. Good models would reveal differences in distribution between the species and have high predictive power despite the large geographical extent covered. 3 Generalized additive models (GAMs) were built with the presence–absence of the species as the response variable. Individual species’ responses to the habitat variables were identified using partial fits and compared with each other. We found that this modelling framework could successfully distinguish the habitats selected by the three species, while the response curves indicated how the habitats differed. Model fits and cross-validations assessed using receiver operating characteristic (ROC) plots showed the models to be successful and robust. 4 We overlaid the predictive maps to identify key areas for agricultural steppe birds in Spain and compared these with the present network of protected sites in two sample regions. In Castilla Leon the provision of protected sites appears appropriate, but in Castilla La Mancha large areas of apparently suitable habitat have no protection. 5 These results confirm that large-scale models are able to increase our understanding of species’ ecology and provide data for conservation planning. AVHRR imagery, in combination with other variables, has sufficient resolution to model a range of bird species, and GAMs have the flexibility to model subtle species–habitat responses.

Assessing large-scale wildlife responses to human infrastructure development.

Abstract: Habitat loss and deterioration represent the main threats to wildlife species, and are closely linked to the expansion of roads and human settlements. Unfortunately, large-scale effects of these structures remain generally overlooked. Here, we analyzed the European transportation infrastructure network and found that 50% of the continent is within 1.5 km of transportation infrastructure. We present a method for assessing the impacts from infrastructure on wildlife, based on functional response curves describing density reductions in birds and mammals (e.g., road-effect zones), and apply it to Spain as a case study. The imprint of infrastructure extends over most of the country (55.5% in the case of birds and 97.9% for mammals), with moderate declines predicted for birds (22.6% of individuals) and severe declines predicted for mammals (46.6%). Despite certain limitations, we suggest the approach proposed is widely applicable to the evaluation of effects of planned infrastructure developments under multiple scenarios, and propose an internationally coordinated strategy to update and improve it in the future.

Plasmid copy-number control and better-than-random segregation genes of pSM19035 share a common regulator

Abstract: Transcription initiation of the copy-number control and better-than-random segregation genes of the broad-host-range and low-copy-number plasmid pSM19035 are subjected to repression by the autoregulated pSM19035-encoded ω product in Bacillus subtilis cells. The promoters of the copS (Pcop1 and Pcop2), δ (Pδ), and ω (Pω) genes have been mapped. These promoters are embedded in a set of either seven copies of a 7-bp direct repeat or in a block consisting of two 7-bp direct repeats and one 7-bp inverted repeat; the blocks are present either two or three times. The cooperative binding of ω protein to the repeats on the Pcop1, Pcop2, Pδ, and Pω promoters represses transcription initiation by a mechanism that does not exclude σARNAP from the promoters. These results indicate that ω protein regulates plasmid maintenance by controlling the copy number on the one hand and by regulating the amount of proteins required for better-than-random segregation on the other hand.

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Abstract: The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated. It is found that the correlation between these two estimates is large when the sample size is small, and decreases slowly as the sample size increases. Using the relationship obtained, a statistical method for testing the neutral mutation hypothesis is developed. This method needs only the data of DNA polymorphism, namely the genetic variation within population at the DNA level. A simple method of computer simulation, that was used in order to obtain the distribution of a new statistic developed, is also presented. Applying this statistical method to the five regions of DNA sequences in Drosophila melanogaster, it is found that large insertion/deletion (greater than 100 bp) is deleterious. It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

Abstract: The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Methods to account for spatial autocorrelation in the analysis of species distributional data : a review

Abstract: Species distributional or trait data based on range map (extent-of-occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species’ distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method’s implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing

Using the satellite-derived NDVI to assess ecological responses to environmental change

Abstract: Assessing how environmental changes affect the distribution and dynamics of vegetation and animal populations is becoming increasingly important for terrestrial ecologists to enable better predictions of the effects of global warming, biodiversity reduction or habitat degradation. The ability to predict ecological responses has often been hampered by our rather limited understanding of trophic interactions. Indeed, it has proven difficult to discern direct and indirect effects of environmental change on animal populations owing to limited information about vegetation at large temporal and spatial scales. The rapidly increasing use of the Normalized Difference Vegetation Index (NDVI) in ecological studies has recently changed this situation. Here, we review the use of the NDVI in recent ecological studies and outline its possible key role in future research of environmental change in an ecosystem context.

Evolution and the Theory of Games

Abstract: In the Hamadryas baboon, males are substantially larger than females. A troop of baboons is subdivided into a number of ‘one-male groups’, consisting of one adult male and one or more females with their young. The male prevents any of ‘his’ females from moving too far from him. Kummer (1971) performed the following experiment. Two males, A and B, previously unknown to each other, were placed in a large enclosure. Male A was free to move about the enclosure, but male B was shut in a small cage, from which he could observe A but not interfere. A female, unknown to both males, was then placed in the enclosure. Within 20 minutes male A had persuaded the female to accept his ownership. Male B was then released into the open enclosure. Instead of challenging male A , B avoided any contact, accepting A’s ownership.