Chapter 11
Phylodynamics
Samuel ALIZON,
Samuel ALIZON
MIVEGEC, IRD, CNRS, Université de Montpellier, France
CIRB, CNRS, INSERM, Collège de France, Paris, France
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Samuel ALIZON,
Samuel ALIZON
MIVEGEC, IRD, CNRS, Université de Montpellier, France
CIRB, CNRS, INSERM, Collège de France, Paris, France
Search for more papers by this author
Gilles Didier,
Stéphane Guindon,
Gilles Didier
Search for more papers by this authorStéphane Guindon
Search for more papers by this author
Book Author(s):Gilles Didier,
Stéphane Guindon,
Gilles Didier
Search for more papers by this authorStéphane Guindon
Search for more papers by this author
First published: 12 April 2024
Summary
The reconciliation between ecology and evolution had been particularly built on inevitably limited phenotypic data. Phylodynamics is primarily based on neutral evolution, which allows it to easily exploit a lot of genetic sequence data. This chapter briefly reviews the technical developments that contributed to the development of phylodynamics. It presents infection phylogenies and their initial, almost purely illustrative use, which is still the major one. Phylogenetic analyses have been possible for a long time, but were initially limited by the availability of biological data and by the computing power that could be dedicated. The chapter also presents the spatial analyses or, more generally, in heterogeneous environment that can be performed. It discusses more recent extensions coupling infection phenotypes to sequence data. The combination of phylogeny and life history traits is very similar to phylogeography. Phylogeography is an old discipline whose statistical methods were well developed before the advent of phylodynamics.
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