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Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum.

ABSTRACT: Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no (or very low) inter-population gene flow and older splitting events with subsequent gene flow. Recently published methods to infer speciation parameters under the isolation-migration framework are based on summarizing polymorphism data at multiple loci in two species using the joint site-frequency spectrum (JSFS). We have developed two improvements of these methods based on a more extensive use of the JSFS classes of polymorphisms for species with high intra-locus recombination rates. First, using a likelihood based method, we demonstrate that taking into account low-frequency polymorphisms shared between species significantly improves the joint estimation of the divergence time and gene flow between species. Second, we introduce a local linear regression algorithm that considerably reduces the computational time and allows for the estimation of unequal rates of gene flow between species. We also investigate which summary statistics from the JSFS allow the greatest estimation accuracy for divergence time and migration rates for low (around 10) and high (around 100) numbers of loci. Focusing on cases with low numbers of loci and high intra-locus recombination rates we show that our methods for the estimation of divergence time and migration rates are more precise than existing approaches.

SUBMITTER: Tellier A

PROVIDER: S-EPMC3102651 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum.

Tellier Aurélien A Pfaffelhuber Peter P Haubold Bernhard B Naduvilezhath Lisha L Rose Laura E LE Städler Thomas T Stephan Wolfgang W Metzler Dirk D

PloS one 20110526 5

Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no (or very low) inter-population gene flow and older splitting events with subsequent gene flow. Recently published methods to infer speciation parameters under the isolation-migration framework are bas ...[more]

PMID: 21637331

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Project description:BackgroundDetermining the parameters of a mathematical model from quantitative measurements is the main bottleneck of modelling biological systems. Parameter values can be estimated from steady-state data or from dynamic data. The nature of suitable data for these two types of estimation is rather different. For instance, estimations of parameter values in pathway models, such as kinetic orders, rate constants, flux control coefficients or elasticities, from steady-state data are generally based on experiments that measure how a biochemical system responds to small perturbations around the steady state. In contrast, parameter estimation from dynamic data requires time series measurements for all dependent variables. Almost no literature has so far discussed the combined use of both steady-state and transient data for estimating parameter values of biochemical systems.ResultsIn this study we introduce a constrained optimization method for estimating parameter values of biochemical pathway models using steady-state information and transient measurements. The constraints are derived from the flux connectivity relationships of the system at the steady state. Two case studies demonstrate the estimation results with and without flux connectivity constraints. The unconstrained optimal estimates from dynamic data may fit the experiments well, but they do not necessarily maintain the connectivity relationships. As a consequence, individual fluxes may be misrepresented, which may cause problems in later extrapolations. By contrast, the constrained estimation accounting for flux connectivity information reduces this misrepresentation and thereby yields improved model parameters.ConclusionThe method combines transient metabolic profiles and steady-state information and leads to the formulation of an inverse parameter estimation task as a constrained optimization problem. Parameter estimation and model selection are simultaneously carried out on the constrained optimization problem and yield realistic model parameters that are more likely to hold up in extrapolations with the model.

Project description:BackgroundExcessive adipose visceral tissue (AVT) represents an independent risk factor for cardiometabolic alterations. The search continues for a highly valid marker for estimating visceral adiposity that is a simple and low cost tool able to screen individuals who are highly at risk of being viscerally obese. The aim of this study was to develop a predictive model for estimating AVT volume using anthropometric parameters.ObjectiveExcessive adipose visceral tissue (AVT) represents an independent risk factor for cardiometabolic alterations. The search continues for a highly valid marker for estimating visceral adiposity that is a simple and low cost tool able to screen individuals who are highly at risk of being viscerally obese. The aim of this study was to develop a predictive model for estimating AVT volume using anthropometric parameters.MethodsA cross-sectional study involving overweight individuals whose AVT was evaluated (using computed tomography-CT), along with the following anthropometric parameters: body mass index (BMI), abdominal circumference (AC), waist-to-hip ratio (WHpR), waist-to-height ratio (WHtR), sagittal diameter (SD), conicity index (CI), neck circumference (NC), neck-to-thigh ratio (NTR), waist-to-thigh ratio (WTR), and body adiposity index (BAI).Results109 individuals with an average age of 50.3±12.2 were evaluated. The predictive equation developed to estimate AVT in men was AVT = -1647.75 +2.43(AC) +594.74(WHpR) +883.40(CI) (R2 adjusted: 64.1%). For women, the model chosen was: AVT = -634.73 +1.49(Age) +8.34(SD) + 291.51(CI) + 6.92(NC) (R2 adjusted: 40.4%). The predictive ability of the equations developed in relation to AVT volume determined by CT was 66.9% and 46.2% for males and females, respectively (p<0.001).ConclusionsA quick and precise AVT estimate, especially for men, can be obtained using only AC, WHpR, and CI for men, and age, SD, CI, and NC for women. These equations can be used as a clinical and epidemiological tool for overweight individuals.

Project description:BackgroundThe National Institute for Health and Care Excellence recommends documenting all delirium episodes in the discharge summary using the term "delirium". Previous studies demonstrate poor delirium documentation rates in discharge summaries and no studies have assessed delirium documentation quality. The aim of this study was to determine the frequency and quality of delirium documentation in discharge summaries and explore differences between medical and surgical services.MethodsThis was a multi-center retrospective chart review. We included 110 patients aged ≥ 65 years identified to have delirium during their hospitalization using the Chart-based Delirium Identification Instrument (CHART-DEL). We assessed the frequency of any delirium documentation in discharge summaries, and more specifically, for the term "delirium". We evaluated the quality of delirium discharge documentation using the Joint Commission on Accreditation of Healthcare Organization's framework for quality discharge summaries. Comparisons were made between medical and surgical services. Secondary outcomes included assessing factors influencing the frequency of "delirium" being documented in the discharge summary.ResultsWe identified 110 patients with sufficient chart documentation to identify delirium and 80.9 % of patients had delirium documented in their discharge summary ("delirium" or other acceptable term). The specific term "delirium" was reported in 63.6 % of all delirious patients and more often by surgical than medical specialties (76.5 % vs. 52.5 %, p = 0.02). Documentation quality was significantly lower by surgical specialties in reporting delirium as a diagnosis (23.5 % vs. 57.6 %, p < 0.001), documenting delirium workup (23.4 % vs. 57.6 %, p = 0.001), etiology (43.3 % vs. 70.4 %, p = 0.03), treatment (36.7 % vs. 66.7 %, p = 0.02), medication changes (44.4 % vs. 100 %, p = 0.002) and follow-up (36.4 % vs. 88.2 %, p = 0.01).ConclusionsThe frequency of delirium documentation is higher than previously reported but remains subpar. Medical services document delirium with higher quality, but surgical specialties document the term "delirium" more frequently. The documentation of delirium in discharge summaries must improve to meet quality standards.

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Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum.

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Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum.

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