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The multifurcating skyline plot
- Source :
- Virus Evolution, Virus Evolution, 2019, ⟨10.1093/ve/vez031⟩, Virus Evolution, Oxford University Press, 2019, ⟨10.1093/ve/vez031⟩
- Publication Year :
- 2019
- Publisher :
- HAL CCSD, 2019.
-
Abstract
- A variety of methods based on coalescent theory have been developed to infer demographic history from gene sequences sampled from natural populations. The “skyline plot” and related approaches are commonly employed as exible prior distributions for phylogenetic trees in the Bayesian analysis of pathogen gene sequences. In this work we extend the classic and generalised skyline plot methods to phylogenies that contain one or more multifurcations (i.e.hard polytomies). We use the theory of Λ-coalescents (specifically, Beta(2α,α)-coalescents) to develop the “multifurcating skyline plot”, which estimates a piecewise constant function of effective population size through time, conditional on a time-scaled multifurcating phylogeny. We implement a smoothing procedure and extend the method to serially-sampled (heterochronous) data, but we do not address here the problem of estimating trees with multifurcations from gene sequence alignments. We validate our estimator on simulated data using maximum likelihood and find that parameters of the Beta(2α,α)-coalescent process can be estimated accurately. Lastly we apply the multifurcating skyline plot to a molecular clock phylogeny of 1,610 Ebola virus sequences from the 2014-2016 West African outbreak. We artificially collapse short branches in this empirical phylogeny in order to mimic different levels of multifurcation and show that variance in the reproductive success of the pathogen through time can be estimated by combining the skyline plot with epidemiological case count data.
- Subjects :
- MESH: phylodynamics
MESH: phylogenetics
[SDV]Life Sciences [q-bio]
Bayesian probability
computer.software_genre
01 natural sciences
Microbiology
Plot (graphics)
Coalescent theory
010104 statistics & probability
03 medical and health sciences
Virology
MESH: maximum likelihood
Statistics
Quantitative Biology::Populations and Evolution
[INFO]Computer Science [cs]
MESH: coalescent
maximum likelihood
0101 mathematics
[MATH]Mathematics [math]
030304 developmental biology
Mathematics
Skyline
0303 health sciences
Degree (graph theory)
Phylogenetic tree
030306 microbiology
MESH: multifurcating
Estimator
coalescent
phylodynamics
3. Good health
phylogenetics
Piecewise
multifurcating
Data mining
Erratum
Algorithm
computer
Smoothing
Research Article
Count data
Subjects
Details
- Language :
- English
- ISSN :
- 20571577
- Database :
- OpenAIRE
- Journal :
- Virus Evolution, Virus Evolution, 2019, ⟨10.1093/ve/vez031⟩, Virus Evolution, Oxford University Press, 2019, ⟨10.1093/ve/vez031⟩
- Accession number :
- edsair.doi.dedup.....c1bae66d8617ae98eed94312fbed4366