Slopes of Avian Species-Area Relationships, Human Population Density, and Environmental Factors

There is increasing interest in how humans influence spatial patterns in biodiversity. One of the most frequently noted and marked of these patterns is the increase in species richness with area, the species-area relationship (SAR). SARs are used for a number of conservation purposes, including predicting extinction rates, setting conservation targets, and identifying biodiversity hotspots. Such applications can be improved by a detailed understanding of the factors promoting spatial variation in the slope of SARs, which is currently the subject of a vigorous debate. Moreover, very few studies have considered the anthropogenic influences on the slopes of SARs; this is particularly surprising given that in much of the world areas with high human population density are typically those with a high number of species, which generates conservation conflicts. Here we determine correlates of spatial variation in the slopes of species-area relationships, using the British avifauna as a case study. Whilst we focus on human population density, a widely used index of human activities, we also take into account (1) the rate of increase in habitat heterogeneity with increasing area, which is frequently proposed to drive SARs, (2) environmental energy availability, which may influence SARs by affecting species occupancy patterns, and (3) species richness. We consider environmental variables measured at both local (10 km x 10 km) and regional (290 km x 290 km) spatial grains, but find that the former consistently provides a better fit to the data. In our case study, the effect of species richness on the slope SARs appears to be scale dependent, being negative at local scales but positive at regional scales. In univariate tests, the slope of the SAR correlates negatively with human population density and environmental energy availability, and positively with the rate of increase in habitat heterogeneity. We conducted two sets of multiple regression analyses, with and without species richness as a predictor. When species richness is included it exerts a dominant effect, but when it is excluded temperature has the dominant effect on the slope of the SAR, and the effects of other predictors are marginal.

Characterizing Aquifer Heterogeneity Using Bacterial and Bacteriophage Tracers

Gravel aquifers act as important potable water sources in central western Europe yet they are subject to numerous contamination pressures. Compositional and textural heterogeneity makes protection zone delineation around groundwater supplies in these units challenging; artificial tracer testing aids characterization. This paper reappraises previous tracer test results in light of new geological and microbiological data. Comparative passive gradient testing, using a fluorescent solute (Uranine), virus (H40/1 bacteriophage), and comparably sized bacterial tracers Escherichia coli and Pseudomonas putida, was used to investigate a calcareous gravel aquifer’s ability to remove microbiological contaminants at a test site near Munich, Germany. Test results revealed E. coli relative recoveries could exceed those of H40/1 at monitoring wells 10 m and 20 m from an injection well by almost four times; P. putida recoveries varied by a factor of up to three between wells. Application of filtration theory suggested greater attenuation of H40/1 relative to similarly charged E. coli occurred due to differences in microorganism size, while estimated collision efficiencies appeared comparable. By contrast, more positively charged P. putida experienced greater attenuation at one monitoring point, while lower attenuation rates at the second location indicated the influence of geochemical heterogeneity. Test findings proved consistent with observations from nearby fresh outcrops that suggested thin open framework gravel beds dominated mass transport in the aquifer, while discrete intervals containing stained clasts reflect localized geochemical heterogeneity. Study results highlight the utility of reconciling outcrop observations with artificial tracer test responses, using microbiological tracers with well-defined properties, to characterize aquifer heterogeneity.

Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci

The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.

Genetic determinants of clinical heterogeneity in sickle cell disease

L’anémie falciforme est une maladie monogénique causée par une mutation dans le locus de la β-globine. Malgré le fait que l’anémie falciforme soit une maladie monogénique, cette maladie présente une grande hétérogénéité clinique. On présume que des facteurs environnementaux et génétiques contribuent à cette hétérogénéité. Il a été observé qu’un haut taux d’hémoglobine fœtale (HbF) diminuait la sévérité et la mortalité des patients atteints de l’anémie falciforme. Le but de mon projet était d’identifier des variations génétiques modifiant la sévérité clinique de l’anémie falciforme. Dans un premier temps, nous avons effectué la cartographie-fine de trois régions précédemment associées avec le taux d’hémoglobine fœtale. Nous avons ensuite effectué des études d’association pan-génomiques avec deux complications cliniques de l’anémie falciforme ainsi qu’avec le taux d’hémoglobine fœtale. Hormis les régions déjà identifiées comme étant associées au taux d’hémoglobine fœtale, aucun locus n’a atteint le niveau significatif de la puce de génotypage. Pour identifier des groupes de gènes modérément associés au taux d’hémoglobine fœtale qui seraient impliqués dans de mêmes voies biologiques, nous avons effectué une étude des processus biologiques. Finalement, nous avons effectué l’analyse de 19 exomes de patients Jamaïcains ayant des complications cliniques mineures de l’anémie falciforme. Compte tenu de la taille des cohortes de réplication disponibles, nous n’avons pas les moyens de valider statistiquement les variations identifiées par notre étude. Cependant, nos résultats fournissent de bons gènes candidats pour des études fonctionnelles et pour les réplications futures. Nos résultats suggèrent aussi que le β-hydroxybutyrate en concentration endogène pourraient influencer le taux d’hémoglobine fœtale. De plus, nous montrons que la cartographie-fine des régions associées par des études pan-génomiques peut identifier des signaux d’association additionnels et augmenter la variation héritable expliquée par cette région.

Optimal management of natural resources. Accounting for heterogeneity

Dynamic optimization methods have become increasingly important over the last years in economics. Within the dynamic optimization techniques employed, optimal control has emerged as the most powerful tool for the theoretical economic analysis. However, there is the need to advance further and take account that many dynamic economic processes are, in addition, dependent on some other parameter different than time. One can think of relaxing the assumption of a representative (homogeneous) agent in macro- and micro-economic applications allowing for heterogeneity among the agents. For instance, the optimal adaptation and diffusion of a new technology over time, may depend on the age of the person that adopted the new technology. Therefore, the economic models must take account of heterogeneity conditions within the dynamic framework. This thesis intends to accomplish two goals. The first goal is to analyze and revise existing environmental policies that focus on defining the optimal management of natural resources over time, by taking account of the heterogeneity of environmental conditions. Thus, the thesis makes a policy orientated contribution in the field of environmental policy by defining the necessary changes to transform an environmental policy based on the assumption of homogeneity into an environmental policy which takes account of heterogeneity. As a result the newly defined environmental policy will be more efficient and likely also politically more acceptable since it is tailored more specifically to the heterogeneous environmental conditions. Additionally to its policy orientated contribution, this thesis aims making a methodological contribution by applying a new optimization technique for solving problems where the control variables depend on two or more arguments --- the so-called two-stage solution approach ---, and by applying a numerical method --- the Escalator Boxcar Train Method --- for solving distributed optimal control problems, i.e., problems where the state variables, in addition to the control variables, depend on two or more arguments. Chapter 2 presents a theoretical framework to determine optimal resource allocation over time for the production of a good by heterogeneous producers, who generate a stock externalit and derives government policies to modify the behavior of competitive producers in order to achieve optimality. Chapter 3 illustrates the method in a more specific context, and integrates the aspects of quality and time, presenting a theoretical model that allows to determine the socially optimal outcome over time and space for the problem of waterlogging in irrigated agricultural production. Chapter 4 of this thesis concentrates on forestry resources and analyses the optimal selective-logging regime of a size-distributed forest.

Slopes of Avian Species-Area Relationships, Human Population Density, and Environmental Factors

There is increasing interest in how humans influence spatial patterns in biodiversity. One of the most frequently noted and marked of these patterns is the increase in species richness with area, the species–area relationship (SAR). SARs are used for a number of conservation purposes, including predicting extinction rates, setting conservation targets, and identifying biodiversity hotspots. Such applications can be improved by a detailed understanding of the factors promoting spatial variation in the slope of SARs, which is currently the subject of a vigorous debate. Moreover, very few studies have considered the anthropogenic influences on the slopes of SARs; this is particularly surprising given that in much of the world areas with high human population density are typically those with a high number of species, which generates conservation conflicts. Here we determine correlates of spatial variation in the slopes of species–area relationships, using the British avifauna as a case study. Whilst we focus on human population density, a widely used index of human activities, we also take into account (1) the rate of increase in habitat heterogeneity with increasing area, which is frequently proposed to drive SARs, (2) environmental energy availability, which may influence SARs by affecting species occupancy patterns, and (3) species richness. We consider environmental variables measured at both local (10 km × 10 km) and regional (290 km × 290 km) spatial grains, but find that the former consistently provides a better fit to the data. In our case study, the effect of species richness on the slope SARs appears to be scale dependent, being negative at local scales but positive at regional scales. In univariate tests, the slope of the SAR correlates negatively with human population density and environmental energy availability, and positively with the rate of increase in habitat heterogeneity. We conducted two sets of multiple regression analyses, with and without species richness as a predictor. When species richness is included it exerts a dominant effect, but when it is excluded temperature has the dominant effect on the slope of the SAR, and the effects of other predictors are marginal.

Estimating the hidden number of scrapie affected holdings in great Britain using a simple, truncated count model allowing for heterogeneity.

None of the current surveillance streams monitoring the presence of scrapie in Great Britain provide a comprehensive and unbiased estimate of the prevalence of the disease at the holding level. Previous work to estimate the under-ascertainment adjusted prevalence of scrapie in Great Britain applied multiple-list capture–recapture methods. The enforcement of new control measures on scrapie-affected holdings in 2004 has stopped the overlapping between surveillance sources and, hence, the application of multiple-list capture–recapture models. Alternative methods, still under the capture–recapture methodology, relying on repeated entries in one single list have been suggested in these situations. In this article, we apply one-list capture–recapture approaches to data held on the Scrapie Notifications Database to estimate the undetected population of scrapie-affected holdings with clinical disease in Great Britain for the years 2002, 2003, and 2004. For doing so, we develop a new diagnostic tool for indication of heterogeneity as well as a new understanding of the Zelterman and Chao’s lower bound estimators to account for potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a special, locally truncated Poisson likelihood equivalent to a binomial likelihood. This understanding allows the extension of the Zelterman approach by means of logistic regression to include observed heterogeneity in the form of covariates—in case studied here, the holding size and country of origin. Our results confirm the presence of substantial unobserved heterogeneity supporting the application of our two estimators. The total scrapie-affected holding population in Great Britain is around 300 holdings per year. None of the covariates appear to inform the model significantly.

Estimating the hidden number of scrapie affected holdings in great Britain using a simple, truncated count model allowing for heterogeneity

None of the current surveillance streams monitoring the presence of scrapie in Great Britain provide a comprehensive and unbiased estimate of the prevalence of the disease at the holding level. Previous work to estimate the under-ascertainment adjusted prevalence of scrapie in Great Britain applied multiple-list capture-recapture methods. The enforcement of new control measures on scrapie-affected holdings in 2004 has stopped the overlapping between surveillance sources and, hence, the application of multiple-list capture-recapture models. Alternative methods, still under the capture-recapture methodology, relying on repeated entries in one single list have been suggested in these situations. In this article, we apply one-list capture-recapture approaches to data held on the Scrapie Notifications Database to estimate the undetected population of scrapie-affected holdings with clinical disease in Great Britain for the years 2002, 2003, and 2004. For doing so, we develop a new diagnostic tool for indication of heterogeneity as well as a new understanding of the Zelterman and Chao's lower bound estimators to account for potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a special, locally truncated Poisson likelihood equivalent to a binomial likelihood. This understanding allows the extension of the Zelterman approach by means of logistic regression to include observed heterogeneity in the form of covariates-in case studied here, the holding size and country of origin. Our results confirm the presence of substantial unobserved heterogeneity supporting the application of our two estimators. The total scrapie-affected holding population in Great Britain is around 300 holdings per year. None of the covariates appear to inform the model significantly.

Good and bad increases in ecological awareness: environmental differentiation revisited

We analyze a vertically differentiated market, assuming that conventional and green firms' products have different impacts on the environment. Heterogeneous consumers choose to be supplied by a conventional or a green firm, depending on their extra willingness to pay for a green product and the relative prices of the products in the market. We show that environmental awareness campaigns may have a negative impact on total welfare. This possibility is shown to exist without consumer misperceptions about the quality of green products and ruling out changes in the coverage and the structure of the market. Surprisingly, both conventional and green firms may benefit from heterogeneity-enhancing awareness campaigns, while social welfare is more likely to be enhanced by heterogeneity-reducing ones.

Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications

Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such heterogeneous tumor progression. Evolutionary biology can provide important insights into this process. In particular, experimental evolution studies of microbial populations, which exist as clonal populations that can diversify into multiple subclones, have revealed important evolutionary processes driving heterogeneity within a population. There are transferrable lessons that can be learnt from these studies that will help us to understand the process of intra-tumor heterogeneity in the clinical setting. In this review, we summarize drivers of microbial diversity that have been identified, such as mutation rate and environmental influences, and discuss how knowledge gained from microbial experimental evolution studies may guide us to identify and understand important selective factors that promote intra-tumor heterogeneity. Furthermore, we discuss how these factors could be used to direct and optimize research efforts to improve patient care, focusing on therapeutic resistance. Finally, we emphasize the need for longitudinal studies to address the impact of these potential tumor heterogeneity-promoting factors on drug resistance, metastatic potential and clinical outcome.

Present bias predicts participation in payments for environmental services: evidence from a behavioral experiment in Uganda

Farmers are necessary agents in global efforts to conserve the environment now that croplands and pastures together constitute the largest terrestrial system on Earth – covering some 48% of ice-free land surface. Whereas standard economic models predict that farmers will participate in conservation programs so long as they are profitable, empirical findings from behavioral economics point to a number of normally unobservable preferences that may influence the decision-making process. This study tests, for the first time, whether heterogeneity in behavioral preferences correlates with decisions to participate in Payments for Environmental Services (PES) programs. We elicit individual trust and time preferences using economic experiments and link resulting measures to household survey data and participation decisions in a Ugandan PES program. We find that farmers who exhibit a preference for proximate gains – present-biased preferences – are 47.7% more likely to participate in the program than those who show time-consistent or future-biased preferences. This result has implications for ongoing and planned PES programs involving farmers, particularly in Africa, by highlighting a potential relationship between payment timing and participation, and further validates the use of behavioral experiments in explaining real-world decisions.

Unexpected genetic heterogeneity in a large consanguineous Brazilian pedigree presenting deafness

Nonsyndromic autosomal recessive deafness accounts for 80% of hereditary deafness. To date, 52 loci responsible for autosomal recessive deafness have been mapped and 24 genes identified. Here, we report a large inbred Brazilian pedigree with 26 subjects affected by prelingual deafness. Given the extensive consanguinity found in this pedigree, the most probable pattern of inheritance is autosomal recessive. However, our linkage and mutational analysis revealed, instead of an expected homozygous mutation in a single gene, two different mutant alleles and a possible third undetected mutant allele in the MYO15A gene (DFNB3 locus), as well as evidence for other causes for deafness in the same pedigree. Among the 26 affected subjects, 15 were homozygous for the novel c.10573delA mutation in the MYO15A gene, 5 were compound heterozygous for the mutation c.10573delA and the novel deletion c.9957_9960delTGAC and one inherited only a single c.10573delA mutant allele, while the other one could not be identified. Given the extensive consanguinity of the pedigree, there might be at least one more deafness locus segregating to explain the condition in some of the subjects whose deafness is not clearly associated with MYO15A mutations, although overlooked environmental causes could not be ruled out. Our findings illustrate a high level of etiological heterogeneity for deafness in the family and highlight some of the pitfalls of genetic analysis of large genes in extended pedigrees, when homozygosity for a single mutant allele is expected.

Genetic heterogeneity of within-family variance of body weight in Atlantic salmon (Salmo salar)

BACKGROUND: Canalization is defined as the stability of a genotype against minor variations in both environment and genetics. Genetic variation in degree of canalization causes heterogeneity of within-family variance. The aims of this study are twofold: (1) quantify genetic heterogeneity of (within-family) residual variance in Atlantic salmon and (2) test whether the observed heterogeneity of (within-family) residual variance can be explained by simple scaling effects. RESULTS: Analysis of body weight in Atlantic salmon using a double hierarchical generalized linear model (DHGLM) revealed substantial heterogeneity of within-family variance. The 95% prediction interval for within-family variance ranged from ~0.4 to 1.2 kg2, implying that the within-family variance of the most extreme high families is expected to be approximately three times larger than the extreme low families. For cross-sectional data, DHGLM with an animal mean sub-model resulted in severe bias, while a corresponding sire-dam model was appropriate. Heterogeneity of variance was not sensitive to Box-Cox transformations of phenotypes, which implies that heterogeneity of variance exists beyond what would be expected from simple scaling effects. CONCLUSIONS: Substantial heterogeneity of within-family variance was found for body weight in Atlantic salmon. A tendency towards higher variance with higher means (scaling effects) was observed, but heterogeneity of within-family variance existed beyond what could be explained by simple scaling effects. For cross-sectional data, using the animal mean sub-model in the DHGLM resulted in biased estimates of variance components, which differed substantially both from a standard linear mean animal model and a sire-dam DHGLM model. Although genetic differences in canalization were observed, selection for increased canalization is difficult, because there is limited individual information for the variance sub-model, especially when based on cross-sectional data. Furthermore, potential macro-environmental changes (diet, climatic region, etc.) may make genetic heterogeneity of variance a less stable trait over time and space.

Dependence of anuran diversity on environmental descriptors in farmland ponds

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)