scholarly journals MASCOT: Parameter and state inference under the marginal structured coalescent approximation

2017 ◽  
Author(s):  
Nicola F. Müller ◽  
David A. Rasmussen ◽  
Tanja Stadler
Keyword(s):  
Migration Rate ◽  
Sequence Data ◽  
Source Code ◽  
Large Datasets ◽  
Population Size Estimates ◽  
Integration Techniques ◽  
Structured Coalescent ◽  
And Migration ◽  
State Inference ◽  
Size Estimates

AbstractMotivationThe structured coalescent is widely applied to study demography within and migration between sub-populations from genetic sequence data. Current methods are either exact but too computationally inefficient to analyse large datasets with many states, or make strong approximations leading to severe biases in inference. We recently introduced an approximation based on weaker assumptions to the structured coalescent enabling the analysis of larger datasets with many different states. We showed that our approximation provides unbiased migration rate and population size estimates across a wide parameter range.ResultsWe here extend this approach by providing a new algorithm to calculate the probability of the state of internal nodes that includes the information from the full phylogenetic tree. We show that this algorithm is able to increase the probability attributed to the true node states. Furthermore we use improved integration techniques, such that our method is now able to analyse larger datasets, including a H3N2 dataset with 433 sequences sampled from 5 different locations.AvailabilityThe here presented methods are combined into the BEAST2 package MASCOT, the Marginal Approximation of the Structured COalescenT. This package can be downloaded via the BEAUti package manager. The source code is available at https://github.com/nicfel/Mascot.git.

scholarly journals Joint inference of migration and reassortment patterns for viruses with segment genomes

2021 ◽  
Author(s):  
Ugnė Stolz ◽  
Nicola Felix Müller ◽  
Tanja Stadler ◽  
Timothy Glenn Vaughan
Keyword(s):  
Influenza A ◽  
Genetic Recombination ◽  
Sequence Data ◽  
Avian Host ◽  
Sequencing Data ◽  
Effective Population ◽  
New Model ◽  
Joint Inference ◽  
Structured Coalescent ◽  
And Migration

The structured coalescent allows inferring migration patterns between viral sub-populations from genetic sequence data. However, these analyses typically assume that no genetic recombination process impacted the sequence evolution of pathogens. For segmented viruses, such as influenza, that can undergo reassortment this assumption is broken. Reassortment reshuffles the segments of different parent lineages upon a coinfection event, which means that the shared history of viruses has to be represented by a network instead of a tree. Therefore, full genome analyses of such viruses is complex or even impossible. While this problem has been addressed for unstructured populations, it is still impossible to account for population structure, such as induced by different host populations, while also accounting for reassortment% at the same time. We address this by extending the structured coalescent to account for reassortment and present a framework for investigating possible ties between reassortment and migration (host jump) events. This method can accurately estimate sub-population dependent effective populations sizes, reassortment and migration rates from simulated data. Additionally, we apply the new model to avian influenza A/H5N1 sequences, sampled from two avian host types, Anseriformes and Galliformes. We contrast our results with a structured coalescent without reassortment inference, which assumes independently evolving segments. This reveals that taking into account segment reassortment and using sequencing data from several viral segments for joint phylodynamic inference leads to different estimates for effective population sizes, migration and clock rates. This new model is implemented as the Structured Coalescent with Reassortment (SCoRe) package for BEAST 2.5 and is available at https://github.com/jugne/SCORE.

scholarly journals The Structured Coalescent and its Approximations

2016 ◽  
Author(s):  
Nicola F. Müller ◽  
David A. Rasmussen ◽  
Tanja Stadler
Keyword(s):  
Sequence Data ◽  
Large Datasets ◽  
Approximate Methods ◽  
Exact Numerical Solution ◽  
Migration Rates ◽  
Geographic Spread ◽  
Occurrence Data ◽  
Migration History ◽  
History Of ◽  
Structured Coalescent

Phylogenetics can be used to elucidate the movement of genes between populations of organisms, using phylogeographic methods. This has been widely done to quantify pathogen movement between different host populations, the migration history of humans, and the geographic spread of languages or the gene flow between species using the location or state of samples alongside sequence data. Phylogenies therefore offer insights into migration processes not available from classic epidemiological or occurrence data alone. Phylogeographic methods have however several known shortcomings. In particular, one of the most widely used methods treats migration the same as mutation, and therefore does not incorporate information about population demography. This may lead to severe biases in estimated migration rates for datasets where sampling is biased across populations. The structured coalescent on the other hand allows us to coherently model the migration and coalescent process, but current implementations struggle with complex datasets due to the need to infer ancestral migration histories. Thus, approximations to the structured coalescent, which integrate over all ancestral migration histories, have been developed. However, the validity and robustness of these approximations remain unclear. We present an exact numerical solution to the structured coalescent that does not require the inference of migration histories. While this solution is computationally unfeasible for large datasets, it clarifies the assumptions of previously developed approximate methods and allows us to provide an improved approximation to the structured coalescent. We have implemented these methods in BEAST2, and we show how these methods compare under different scenarios.

Estimating the population size of people who inject drugs in Ho Chi Minh City, Vietnam: A two-survey capture-recapture exercise (Preprint)

2019 ◽  
Author(s):  
Abu Abdul-Quader
Keyword(s):  
Population Size ◽  
Illicit Drugs ◽  
People Who Inject Drugs ◽  
Care Service ◽  
Ho Chi Minh City ◽  
Size Estimation ◽  
Population Size Estimates ◽  
Capture Recapture ◽  
The City ◽  
Size Estimates

BACKGROUND Population size estimation of people who inject drugs (PWID) in Ho Chi Minh City (HCMC), Vietnam relied on the UNAIDS Estimation and Projection Package and reports from the city police department. The two estimates vary widely. OBJECTIVE To estimate the population size of people who inject drugs in Ho Chi Minh City, Vietnam METHODS Using Respondent-driven sampling (RDS), we implemented two-source capture-recapture method to estimate the population size of PWID in HCMC in 2017 in 7 out of 24 districts. The study included men or women aged at least 18 years who reported injecting illicit drugs in the last 90 days and who had lived in the city the past six months. We calculated two sets of size estimates, the first assumed that all participants in each survey round resided in the district where the survey was conducted, the second, used the district of residence as reported by the participant. District estimates were summed to obtain an aggregate estimate for the seven districts. To calculate the city total, we weighted the population size estimates for each district by the inverse of the stratum specific sampling probabilities. RESULTS The first estimate resulted in a population size of 19,155 (95% CI: 17,006–25,039). The second one generated a smaller population size estimate of 12,867 (95% CI: 11,312–17,393). CONCLUSIONS The two-survey capture-recapture exercise provided two disparate estimates of PWID in HCMC. For planning HIV prevention and care service needs among PWID in HCMC, both estimates may need to be taken into consideration together with size estimates from other sources.

scholarly journals Microsatellite Development and First Population Size Estimates for the Groundwater Isopod Proasellus walteri

PLoS ONE ◽  
2013 ◽  
Vol 8 (9) ◽  
pp. e76213 ◽  
Author(s):  
Cécile Capderrey ◽  
Bernard Kaufmann ◽  
Pauline Jean ◽  
Florian Malard ◽  
Lara Konecny-Dupré ◽  
...  
Keyword(s):  
Population Size ◽  
Microsatellite Development ◽  
Population Size Estimates ◽  
Size Estimates

Estimation of Catchabilities and Population Sizes of Lobsters

1963 ◽  
Vol 20 (1) ◽  
pp. 59-88 ◽  
Author(s):  
J. E. Paloheimo
Keyword(s):  
Environmental Factors ◽  
Population Size ◽  
Atlantic Coast ◽  
Temperature Data ◽  
New Method ◽  
Bottom Temperature ◽  
Population Size Estimates ◽  
Population Sizes ◽  
Estimate Population Size ◽  
Size Estimates

Techniques of estimating population size, level of fishing, and the degree of dependence of fishing success on environmental factors are examined on the basis of tagging, catch and effort data. A new method is developed to estimate population size from catch, effort, and temperature data when the catchability varies with temperature.The methods of estimation discussed are applied to data collected from a number of lobster fisheries on Canada's Atlantic coast. Analysis confirms a relationship between the catchability of lobsters and bottom temperature. Differences in this relationship are found between areas and between tagged and untagged lobsters within areas. It is suggested that these differences are attributable to the differences in densities as well as to aggregations of lobsters and fishing. The effect of these aggregations on population size estimates is considered.Calculated average catchabilities at comparable temperatures are different for different areas. These differences are correlated with the numbers of trap hauls per day per square miles fished. It is suggested that the differences in the catchabilities might be due to interactions between units of gear not predicted by the customary relationship between catch and effort.

scholarly journals Estimating population size of the cave shrimp Troglocaris anophthalmus (Crustacea, Decapoda, Caridea) using mark–release–recapture data

2015 ◽  
Vol 38 (1) ◽  
pp. 77-86
Author(s):  
J. Jugovic ◽  
◽  
E. Praprotnik ◽  
E. V. Buzan ◽  
M. Luznik ◽  
...  
Keyword(s):  
Population Size ◽  
Aquatic Invertebrates ◽  
Anthropogenic Activities ◽  
Age Distribution ◽  
Mark Release Recapture ◽  
Population Size Estimates ◽  
Cave Ecosystems ◽  
Size Estimates ◽  
Abundant Population ◽  
Population Numbers

Population size estimates are lacking for many small cave–dwelling aquatic invertebrates that are vulnerable to groundwater contamination from anthropogenic activities. Here we estimated the population size of freshwater shrimp Troglocaris anophthalmus sontica (Crustacea, Decapoda, Caridea) based on mark–release–recapture techniques. The subspecies was investigated in Vipavska jama (Vipava cave), Slovenia, with estimates of sex ratio and age distribution. A high abundance of shrimps was found even after considering the lower limit of the confidence intervals. However, we found no evidence of differences in shrimp abundances between summer and winter. The population was dominated by females. Ease of capture and abundant population numbers indicate that these cave shrimps may be useful as a bioindicator in cave ecosystems.

scholarly journals Unbiased estimation of linkage disequilibrium from unphased data

2019 ◽  
Author(s):  
Aaron P. Ragsdale ◽  
Simon Gravel
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Evolutionary History ◽  
Unbiased Estimation ◽  
Sequencing Data ◽  
Unbiased Estimators ◽  
Population Size Estimates ◽  
Wide Range ◽  
The Common ◽  
Size Estimates

AbstractLinkage disequilibrium is used to infer evolutionary history and to identify regions under selection or associated with a given trait. In each case, we require accurate estimates of linkage disequilibrium from sequencing data. Unphased data presents a challenge because the co-occurrence of alleles at different loci is ambiguous. Commonly used estimators for the common statistics r2 and D2 exhibit large and variable upward biases that complicate interpretation and comparison across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, including D2, for both single and multiple randomly mating populations. These provide accurate estimates over three orders of magnitude in LD. We also use these estimators to construct an estimator for r2 that is less biased than commonly used estimators, but nevertheless argue for using rather than r2 for population size estimates.

scholarly journals Software Application Profile: The Anchored Multiplier calculator—a Bayesian tool to synthesize population size estimates

2019 ◽  
Vol 48 (6) ◽  
pp. 1744-1749
Author(s):  
Paul D Wesson ◽  
Willi McFarland ◽  
Cong Charlie Qin ◽  
Ali Mirzazadeh
Keyword(s):  
Population Size ◽  
Web Application ◽  
Probability Distributions ◽  
Public Health Research ◽  
Forest Plot ◽  
Hidden Populations ◽  
Software Application ◽  
Posterior Probability Distribution ◽  
Population Size Estimates ◽  
Size Estimates

Abstract Estimating the number of people in hidden populations is needed for public health research, yet available methods produce highly variable and uncertain results. The Anchored Multiplier calculator uses a Bayesian framework to synthesize multiple population size estimates to generate a consensus estimate. Users submit point estimates and lower/upper bounds which are converted to beta probability distributions and combined to form a single posterior probability distribution. The Anchored Multiplier calculator is available as a web browser-based application. The software allows for unlimited empirical population size estimates to be submitted and combined according to Bayes Theorem to form a single estimate. The software returns output as a forest plot (to visually compare data inputs and the final Anchored Multiplier estimate) and a table that displays results as population percentages and counts. The web application ‘Anchored Multiplier Calculator’ is free software and is available at [http://globalhealthsciences.ucsf.edu/resources/tools] or directly at [http://anchoredmultiplier.ucsf.edu/].

scholarly journals RS CVn STARS: Photospheric Phenomena and Rotation

1983 ◽  
Vol 71 ◽  
pp. 343-361
Author(s):  
S. Catalano
Keyword(s):  
Migration Rate ◽  
Orbital Motion ◽  
Rotation Period ◽  
Maximum Amplitude ◽  
Activity Level ◽  
Period 2 ◽  
Rs Cvn Stars ◽  
Activity Cycles ◽  
And Migration ◽  
Wave Migration

ABSTRACTThis review presents a summary of observed photospheric phenomena on RS CVn stars: the amplitude, shape, evolution and migration rate of the photometric wave in relation to the rotational and orbital motion.The main points considered are: 1) the activity level (maximum amplitude, short and long timescale variability) versus rotation period; 2) the activity cycles as inferred from changes in the wave migration rate and direction and from the variation of its amplitude; 3) the detection of differential rotation; 4) the connection between the orbital period variation and activity.

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