The multifurcating skyline plot
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 flexible prior distributions for phylogenetic trees in the Bayesian analysis of pa...
| Main Authors: | , |
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| Format: | Journal article |
| Language: | English |
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Oxford University Press
2019
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| _version_ | 1826275402562142208 |
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| author | Hoscheit, P Pybus, OG |
| author_facet | Hoscheit, P Pybus, OG |
| author_sort | Hoscheit, P |
| collection | OXFORD |
| description | 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 flexible prior distributions for phylogenetic trees in the Bayesian analysis of pathogen gene sequences. In this work we extend the classic and generalized skyline plot methods to phylogenies that contain one or more multifurcations (i.e. hard polytomies). We use the theory of Λ-coalescents (specifically, Beta(2-α,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(2-α,α) -coalescent process can be estimated accurately. Furthermore, we apply the multifurcating skyline plot to simulated trees generated by tracking transmissions in an individual-based model of epidemic superspreading. We find that high levels of superspreading are consistent with the high-variance assumptions underlying Λ-coalescents and that the estimated parameters of the Λ-coalescent model contain information about the degree of superspreading. |
| first_indexed | 2024-03-06T22:58:09Z |
| format | Journal article |
| id | oxford-uuid:612498ca-624f-450a-a1c9-4d18a1e84732 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T22:58:09Z |
| publishDate | 2019 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:612498ca-624f-450a-a1c9-4d18a1e847322022-03-26T17:57:53ZThe multifurcating skyline plotJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:612498ca-624f-450a-a1c9-4d18a1e84732EnglishSymplectic ElementsOxford University Press2019Hoscheit, PPybus, OGA 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 flexible prior distributions for phylogenetic trees in the Bayesian analysis of pathogen gene sequences. In this work we extend the classic and generalized skyline plot methods to phylogenies that contain one or more multifurcations (i.e. hard polytomies). We use the theory of Λ-coalescents (specifically, Beta(2-α,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(2-α,α) -coalescent process can be estimated accurately. Furthermore, we apply the multifurcating skyline plot to simulated trees generated by tracking transmissions in an individual-based model of epidemic superspreading. We find that high levels of superspreading are consistent with the high-variance assumptions underlying Λ-coalescents and that the estimated parameters of the Λ-coalescent model contain information about the degree of superspreading. |
| spellingShingle | Hoscheit, P Pybus, OG The multifurcating skyline plot |
| title | The multifurcating skyline plot |
| title_full | The multifurcating skyline plot |
| title_fullStr | The multifurcating skyline plot |
| title_full_unstemmed | The multifurcating skyline plot |
| title_short | The multifurcating skyline plot |
| title_sort | multifurcating skyline plot |
| work_keys_str_mv | AT hoscheitp themultifurcatingskylineplot AT pybusog themultifurcatingskylineplot AT hoscheitp multifurcatingskylineplot AT pybusog multifurcatingskylineplot |