Unifying Phylogenetic Birth–Death Models in Epidemiology and Macroevolution
| Autor: | Jeffrey B. Joy, Ailene MacPherson, Angela McLaughlin, Stilianos Louca, Matthew W. Pennell |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
Likelihood Functions 0303 health sciences Theoretical computer science Phylogenetic tree Unification Process (engineering) Stochastic process Sampling (statistics) Macroevolution Biology Models Biological 010603 evolutionary biology 01 natural sciences 03 medical and health sciences Range (mathematics) Genetics Statistical inference Phylogeny Ecology Evolution Behavior and Systematics 030304 developmental biology |
| Zdroj: | Systematic Biology. 71:172-189 |
| ISSN: | 1076-836X 1063-5157 |
| DOI: | 10.1093/sysbio/syab049 |
| Popis: | Birth–death stochastic processes are the foundations of many phylogenetic models and are widely used to make inferences about epidemiological and macroevolutionary dynamics. There are a large number of birth–death model variants that have been developed; these impose different assumptions about the temporal dynamics of the parameters and about the sampling process. As each of these variants was individually derived, it has been difficult to understand the relationships between them as well as their precise biological and mathematical assumptions. Without a common mathematical foundation, deriving new models is nontrivial. Here, we unify these models into a single framework, prove that many previously developed epidemiological and macroevolutionary models are all special cases of a more general model, and illustrate the connections between these variants. This unification includes both models where the process is the same for all lineages and those in which it varies across types. We also outline a straightforward procedure for deriving likelihood functions for arbitrarily complex birth–death(-sampling) models that will hopefully allow researchers to explore a wider array of scenarios than was previously possible. By rederiving existing single-type birth–death sampling models, we clarify and synthesize the range of explicit and implicit assumptions made by these models. [Birth–death processes; epidemiology; macroevolution; phylogenetics; statistical inference.] |
| Databáze: | OpenAIRE |
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