Galactic Archaeology and Minimum Spanning Trees

Chemical tagging of stellar debris from disrupted open clusters and associations underpins the science cases for next-generation multi-object spectroscopic surveys. As part of the Galactic Archaeology project TraCD (Tracking Cluster Debris), a preliminary attempt at reconstructing the birth clouds of now phase-mixed thin disk debris is undertaken using a parametric minimum spanning tree (MST) approach. Empirically-motivated chemical abundance pattern uncertainties (for a 10-dimensional chemistry-space) are applied to NBODY6-realised stellar associations dissolved into a background sea of field stars, all evolving in a Milky Way potential. We demonstrate that significant population reconstruction degeneracies appear when the abundance uncertainties approach 0.1 dex and the parameterised MST approach is employed; more sophisticated methodologies will be required to ameliorate these degeneracies

Security-oriented infrastructures for social simulation

The JISC-funded National e-Infrastructure for Social Simulation (NeISS) project aims to develop and provide new services to social scientists and public/private sector policymakers interested in “what-if” questions that have an impact upon society and can be tackled through social simulation. For the first what-if question, a traffic simulation modelling how congestion will affect routes within a city or region projected across a time-span of decades has been identified. This paper describes the work that has been done in implementing a secure, user-oriented environment that provides seamless access to relevant nationally significant data sets such as the 2001 Census and demographic transition statistics from the British Household Panel Survey (BHPS) , and a Population Reconstruction Model (PRM) simulator, which simulates a population of individuals or households based upon these data sets

Galactic Archaeology and Minimum Spanning Trees

Chemical tagging of stellar debris from disrupted open clusters and associations underpins the science cases for next-generation multi-object spectroscopic surveys. As part of the Galactic Archaeology project TraCD (Tracking Cluster Debris), a preliminary attempt at reconstructing the birth clouds of now phase-mixed thin disk debris is undertaken using a parametric minimum spanning tree (MST) approach. Empirically-motivated chemical abundance pattern uncertainties (for a 10-dimensional chemistry-space) are applied to NBODY6-realised stellar associations dissolved into a background sea of field stars, all evolving in a Milky Way potential. We demonstrate that significant population reconstruction degeneracies appear when the abundance uncertainties approach 0.1 dex and the parameterised MST approach is employed; more sophisticated methodologies will be required to ameliorate these degeneracies.Comment: To appear in "Multi-Object Spectroscopy in the Next Decade: Big Questions, Large Surveys and Wide Fields"; Held: Santa Cruz de La Palma, Canary Islands, Spain, 2-6 Mar 2015; ed. I Skillen & S. Trager; ASP Conference Series (Figures now optimised for B&W printing

All-optical reconstruction of atomic ground-state population

The population distribution within the ground-state of an atomic ensemble is of large significance in a variety of quantum optics processes. We present a method to reconstruct the detailed population distribution from a set of absorption measurements with various frequencies and polarizations, by utilizing the differences between the dipole matrix elements of the probed transitions. The technique is experimentally implemented on a thermal rubidium vapor, demonstrating a population-based analysis in two optical pumping examples. The results are used to verify and calibrate an elaborated numerical model, and the limitations of the reconstruction scheme which result from the symmetry properties of the dipole matrix elements are discussed.Comment: 6 pages, 4 figure

Viral population estimation using pyrosequencing

The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing technologies (pyrosequencing) can be used for quantifying this diversity by ultra-deep sequencing of virus samples. We present computational methods for the analysis of such sequence data and apply these techniques to pyrosequencing data obtained from HIV populations within patients harboring drug resistant virus strains. Our main result is the estimation of the population structure of the sample from the pyrosequencing reads. This inference is based on a statistical approach to error correction, followed by a combinatorial algorithm for constructing a minimal set of haplotypes that explain the data. Using this set of explaining haplotypes, we apply a statistical model to infer the frequencies of the haplotypes in the population via an EM algorithm. We demonstrate that pyrosequencing reads allow for effective population reconstruction by extensive simulations and by comparison to 165 sequences obtained directly from clonal sequencing of four independent, diverse HIV populations. Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies.Comment: 23 pages, 13 figure

Statistical Population Reconstruction Using Wings from Harvested Northern Bobwhites Can Inform Management

Despite the widespread collection wings from harvested northern bobwhite (Colinus virginianus) by state wildlife agencies and private entities, age-at-harvest information has been largely underutilized for guiding management decisions for this species. Statistical population reconstruction (SPR) techniques can use age-at-harvest information and provide a valuable tool for monitoring trends and the status of bobwhite (and other game bird) populations. However, SPR has not been applied to bobwhite. We evaluated the utility of statistical population reconstruction models, which have been applied successfully to other species (e.g., elk, Cervus elaphus; blacktailed deer, Odocoilues hemonius; and greater sage-grouse, Centrocercus urophasianus), to reconstruct annual abundance and demographic attributes for a bobwhite population in southwest Georgia. During 1998 – 2016, we collected wings from harvested birds (n = 17,448; nannual = 969 ± 104) in conjunction with survival information from mark-recapture. We derived independent estimates of fall abundance from the same site using covey call counts and a standardized measure of hunting success (coveys moved per hour). SPR models suggested that population change was stable (λ = 1.00; CV = 0.19) compared to moderate population growth (λ = 1.05; CV = 0.29) indicated by the covey call quadrat method. Abundance estimates from SPR and covey call counts were moderately correlated (r = 0.48) with only 3 out 18 years statistically different. Abundance estimates from SPR and hunting success (coveys moved per hour) was highly correlated (r = 0.86). SPR provides valid, conservative abundance estimates for bobwhite age-at-harvest data. Therefore, we endorse the use of SPR for bobwhites where age-at-harvest, hunter effort and another source of auxiliary data are readily available. As such, given that the collection of harvested wings is simple and low cost, we recommend managers and state agencies consider incorporating this technique into their management program

Comparison of Statistical Population Reconstruction Using Full and Pooled Adult Age-Class Data

BACKGROUND: Age-at-harvest data are among the most commonly collected, yet neglected, demographic data gathered by wildlife agencies. Statistical population construction techniques can use this information to estimate the abundance of wild populations over wide geographic areas and concurrently estimate recruitment, harvest, and natural survival rates. Although current reconstruction techniques use full age-class data (0.5, 1.5, 2.5, 3.5, … years), it is not always possible to determine an animal's age due to inaccuracy of the methods, expense, and logistics of sample collection. The ability to inventory wild populations would be greatly expanded if pooled adult age-class data (e.g., 0.5, 1.5, 2.5+ years) could be successfully used in statistical population reconstruction. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the performance of statistical population reconstruction models developed to analyze full age-class and pooled adult age-class data. We performed Monte Carlo simulations using a stochastic version of a Leslie matrix model, which generated data over a wide range of abundance levels, harvest rates, and natural survival probabilities, representing medium-to-big game species. Results of full age-class and pooled adult age-class population reconstructions were compared for accuracy and precision. No discernible difference in accuracy was detected, but precision was slightly reduced when using the pooled adult age-class reconstruction. On average, the coefficient of variation (i.e., SE(θ)/θ) increased by 0.059 when the adult age-class data were pooled prior to analyses. The analyses and maximum likelihood model for pooled adult age-class reconstruction are illustrated for a black-tailed deer (Odocoileus hemionus) population in Washington State. CONCLUSIONS/SIGNIFICANCE: Inventorying wild populations is one of the greatest challenges of wildlife agencies. These new statistical population reconstruction models should expand the demographic capabilities of wildlife agencies that have already collected pooled adult age-class data or are seeking a cost-effective method for monitoring the status and trends of our wild resources