Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura

Background: Transposable elements (TEs) constitute a substantial amount of all eukaryotic genomes. They induce an important proportion of deleterious mutations by insertion into genes or gene regulatory regions. However, their mutational capabilities are not always adverse but can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution and activity in the genomes of populations under different environmental and demographic regimes, is important to understand their role in species evolution. In this work we study the chromosomaldistribution of two TEs, gypsy and bilbo, in original and colonizing populations of Drosophilasubobscura to reveal the putative effect of colonization on their insertion profile.Results: Chromosomal frequency distribution of two TEs in one original and three colonizingpopulations of D. subobscura, is different. Whereas the original population shows a low insertionfrequency in most TE sites, colonizing populations have a mixture of high (frequency ¿ 10%) andlow insertion sites for both TEs. Most highly occupied sites are coincident among colonizingpopulations and some of them are correlated to chromosomal arrangements. Comparisons of TEcopy number between the X chromosome and autosomes show that gypsy occupancy seems to becontrolled by negative selection, but bilbo one does not. Conclusion: These results are in accordance that TEs in Drosophila subobscura colonizing populations are submitted to a founder effect followed by genetic drift as a consequence of colonization. This would explain the high insertion frequencies of bilbo and gypsy in coincident sites of colonizing populations. High occupancy sites would represent insertion events prior to colonization. Sites of low frequency would be insertions that occurred after colonization and/orcopies from the original population whose frequency is decreasing in colonizing populations. Thiswork is a pioneer attempt to explain the chromosomal distribution of TEs in a colonizing specieswith high inversion polymorphism to reveal the putative effect of arrangements in TE insertionprofiles. In general no associations between arrangements and TE have been found, except in a fewcases where the association is very strong. Alternatively, founder drift effects, seem to play aleading role in TE genome distribution in colonizing populations.

Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

Background: Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment andinnate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Results:Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection arefrequent on genes that are known to be at bifurcation points, and that are identified as beingin key position by a network-level analysis such as MGAT3 and GCS1.Conclusions: These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.

Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.

Endogenous population subgroups: the best population partition and optimal number of groups

The aim of this paper is to suggest a method to find endogenously the points that group the individuals of a given distribution in k clusters, where k is endogenously determined. These points are the cut-points. Thus, we need to determine a partition of the N individuals into a number k of groups, in such way that individuals in the same group are as alike as possible, but as distinct as possible from individuals in other groups. This method can be applied to endogenously identify k groups in income distributions: possible applications can be poverty

Modelling of bird distribution under complex mediterranean landscape dynamics: open habitat birds and fire (MEDFIRE)

Report for the scientific sojourn at the Simon Fraser University, Canada, from July to September 2007. General context: landscape change during the last years is having significant impacts on biodiversity in many Mediterranean areas. Land abandonment, urbanisation and specially fire are profoundly transforming large areas in the Western Mediterranean basin and we know little on how these changes influence species distribution and in particular how these species will respond to further change in a context of global change including climate. General objectives: integrate landscape and population dynamics models in a platform allowing capturing species distribution responses to landscape changes and assessing impact on species distribution of different scenarios of further change. Specific objective 1: develop a landscape dynamic model capturing fire and forest succession dynamics in Catalonia and linked to a stochastic landscape occupancy (SLOM) (or spatially explicit population, SEPM) model for the Ortolan bunting, a species strongly linked to fire related habitat in the region. Predictions from the occupancy or spatially explicit population Ortolan bunting model (SEPM) should be evaluated using data from the DINDIS database. This database tracks bird colonisation of recently burnt big areas (&50 ha). Through a number of different SEPM scenarios with different values for a number of parameter, we should be able to assess different hypothesis in factors driving bird colonisation in new burnt patches. These factors to be mainly, landscape context (i.e. difficulty to reach the patch, and potential presence of coloniser sources), dispersal constraints, type of regenerating vegetation after fire, and species characteristics (niche breadth, etc).

On the density distribution across space: a probabilistic approach

This paper aims at providing a Bayesian parametric framework to tackle the accessibility problem across space in urban theory. Adopting continuous variables in a probabilistic setting we are able to associate with the distribution density to the Kendall's tau index and replicate the general issues related to the role of proximity in a more general context. In addition, by referring to the Beta and Gamma distribution, we are able to introduce a differentiation feature in each spatial unit without incurring in any a-priori definition of territorial units. We are also providing an empirical application of our theoretical setting to study the density distribution of the population across Massachusetts.

Optimal latent period in a bacteriophage population model structured by infection-age

We study the lysis timing of a bacteriophage population by means of a continuously infection-age-structured population dynamics model. The features of the model are the infection process of bacteria, the natural death process, and the lysis process which means the replication of bacteriophage viruses inside bacteria and the destruction of them. We consider that the length of the lysis timing (or latent period) is distributed according to a general probability distribution function. We have carried out an optimization procedure and we have found the latent period corresponding to the maximal fitness (i.e. maximal growth rate) of the bacteriophage population.

Population genetic structure and demography analysis in palinurus elephas populations from atlantic and mediterranean waters

Report for the scientific sojourn at the University of Reading, United Kingdom, from January until May 2008. The main objectives have been firstly to infer population structure and parameters in demographic models using a total of 13 microsatellite loci for genotyping approximately 30 individuals per population in 10 Palinurus elephas populations both from Mediterranean and Atlantic waters. Secondly, developing statistical methods to identify discrepant loci, possibly under selection and implement those methods using the R software environment. It is important to consider that the calculation of the probability distribution of the demographic and mutational parameters for a full genetic data set is numerically difficult for complex demographic history (Stephens 2003). The Approximate Bayesian Computation (ABC), based on summary statistics to infer posterior distributions of variable parameters without explicit likelihood calculations, can surmount this difficulty. This would allow to gather information on different demographic prior values (i.e. effective population sizes, migration rate, microsatellite mutation rate, mutational processes) and assay the sensitivity of inferences to demographic priors by assuming different priors.

Association between HIV status and HIV knowledge in the population attending Non-Governmental Organizations to perform the rapid HIV test in Catalonia

Human Immunodeficiency Virus continues to be a pandemic. Spain is one of the European countries with the highest incidence of HIV. Within Catalonia, Spain many projects have been implemented with the intention of improving HIV knowledge and lowering the incidence. HIV knowledge is also known to have a positive effect on lowering stigma and discrimination of the people living with HIV. However, few studies study the distribution of HIV knowledge and its association to HIV status, age, sex, geographical zone of origin and level of education within the same study. Objectives: To identify if HIV knowledge is associated with HIV status, age, sex, geographical zone of origin and level of education. Method: Quantitative, cross-sectional, centre-based study comprising of people receiving an HIV test in Catalonia, Spain. Data will be collected from the 11 HIV Non-Governmental Organisations in Catalonia, Spain. The Brief HIV Knowledge Scale will be used to assess HIV knowledge; information from the HIV test session will be used to assess HIV status, age, sex, geographic zone of origin and level of education. The association between HIV knowledge and the afore mentioned variables will then be calculated.

A finite-population revenue management model and a risk-ratio procedure for the joint estimation of population size and parameters

Many dynamic revenue management models divide the sale period into a finite number of periods T and assume, invoking a fine-enough grid of time, that each period sees at most one booking request. These Poisson-type assumptions restrict the variability of the demand in the model, but researchers and practitioners were willing to overlook this for the benefit of tractability of the models. In this paper, we criticize this model from another angle. Estimating the discrete finite-period model poses problems of indeterminacy and non-robustness: Arbitrarily fixing T leads to arbitrary control values and on the other hand estimating T from data adds an additional layer of indeterminacy. To counter this, we first propose an alternate finite-population model that avoids this problem of fixing T and allows a wider range of demand distributions, while retaining the useful marginal-value properties of the finite-period model. The finite-population model still requires jointly estimating market size and the parameters of the customer purchase model without observing no-purchases. Estimation of market-size when no-purchases are unobservable has rarely been attempted in the marketing or revenue management literature. Indeed, we point out that it is akin to the classical statistical problem of estimating the parameters of a binomial distribution with unknown population size and success probability, and hence likely to be challenging. However, when the purchase probabilities are given by a functional form such as a multinomial-logit model, we propose an estimation heuristic that exploits the specification of the functional form, the variety of the offer sets in a typical RM setting, and qualitative knowledge of arrival rates. Finally we perform simulations to show that the estimator is very promising in obtaining unbiased estimates of population size and the model parameters.

Period-Luminosity-Colour distribution and classification of Galactic oxygen-rich LPVs I. Luminosity calibrations

The absolute K magnitudes and kinematic parameters of about 350 oxygen-rich Long-Period Variable stars are calibrated, by means of an up-to-date maximum-likelihood method, using HIPPARCOS parallaxes and proper motions together with radial velocities and, as additional data, periods and V-K colour indices. Four groups, differing by their kinematics and mean magnitudes, are found. For each of them, we also obtain the distributions of magnitude, period and de-reddened colour of the base population, as well as de-biased period-luminosity-colour relations and their two-dimensional projections. The SRa semiregulars do not seem to constitute a separate class of LPVs. The SRb appear to belong to two populations of different ages. In a PL diagram, they constitute two evolutionary sequences towards the Mira stage. The Miras of the disk appear to pulsate on a lower-order mode. The slopes of their de-biased PL and PC relations are found to be very different from the ones of the Oxygen Miras of the LMC. This suggests that a significant number of so-called Miras of the LMC are misclassified. This also suggests that the Miras of the LMC do not constitute a homogeneous group, but include a significant proportion of metal-deficient stars, suggesting a relatively smooth star formation history. As a consequence, one may not trivially transpose the LMC period-luminosity relation from one galaxy to the other.

Statistical properties of new neutrality tests against population growth.

A number of statistical tests for detecting population growth are described. We compared the statistical power of these tests with that of others available in the literature. The tests evaluated fall into three categories: those tests based on the distribution of the mutation frequencies, on the haplotype distribution, and on the mismatch distribution. We found that, for an extensive variety of cases, the most powerful tests for detecting population growth are Fu"s FS test and the newly developed R2 test. The behavior of the R2 test is superior for small sample sizes, whereas FS is better for large sample sizes. We also show that some popular statistics based on the mismatch distribution are very conservative. Key words: population growth, population expansion, coalescent simulations, neutrality tests

Morphometric relationhip in the Chaetognath Sagitta setosa Muller 1847: within population versus between population variability.

Sagitta setosa is a neritic Chaetognath exhibiting a discontinuous geographic distribution. To assess the influence of its discontinuous geographic distribution on morphometric variability between isolated populations, we conducted a biometric study of S. setosa from three different locations: Goteborg and Plymouth (North Atlantic) and Barcelona ( Western Mediterranean). Out results do indicate some disparity between the populations that is reflected not in size differences, largely determined by water temperature, but in shape (body proportions).

Optimal latent period in a bacteriophage population model structured by infection-age

We study the lysis timing of a bacteriophage population by means of a continuously infection-age-structured population dynamics model. The features of the model are the infection process of bacteria, the death process, and the lysis process which means the replication of bacteriophage viruses inside bacteria and the destruction of them. The time till lysis (or latent period) is assumed to have an arbitrary distribution. We have carried out an optimization procedure, and we have found that the latent period corresponding to maximal fitness (i.e. maximal growth rate of the bacteriophage population) is of fixed length. We also study the dependence of the optimal latent period on the amount of susceptible bacteria and the number of virions released by a single infection. Finally, the evolutionarily stable strategy of the latent period is also determined as a fixed period taking into account that super-infections are not considered

Multimorbidity patterns in a national representative sample of the Spanish adult population.

BACKGROUND: In the context of population aging, multimorbidity has emerged as a growing concern in public health. However, little is known about multimorbidity patterns and other issues surrounding chronic diseases. The aim of our study was to examine multimorbidity patterns, the relationship between physical and mental conditions and the distribution of multimorbidity in the Spanish adult population. METHODS: Data from this cross-sectional study was collected from the COURAGE study. A total of 4,583 participants from Spain were included, 3,625 aged over 50. An exploratory factor analysis was conducted to detect multimorbidity patterns in the population over 50 years of age. Crude and adjusted binary logistic regressions were performed to identify individual associations between physical and mental conditions. RESULTS: THREE MULTIMORBIDITY PATTERNS ROSE: 'cardio-respiratory' (angina, asthma, chronic lung disease), 'mental-arthritis' (arthritis, depression, anxiety) and the 'aggregated pattern' (angina, hypertension, stroke, diabetes, cataracts, edentulism, arthritis). After adjusting for covariates, asthma, chronic lung disease, arthritis and the number of physical conditions were associated with depression. Angina and the number of physical conditions were associated with a higher risk of anxiety. With regard to multimorbidity distribution, women over 65 years suffered from the highest rate of multimorbidity (67.3%). CONCLUSION: Multimorbidity prevalence occurs in a high percentage of the Spanish population, especially in the elderly. There are specific multimorbidity patterns and individual associations between physical and mental conditions, which bring new insights into the complexity of chronic patients. There is need to implement patient-centered care which involves these interactions rather than merely paying attention to individual diseases.