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The Fossilized Birth-Death Process: A Coherent Model of Fossil Calibration for Divergence Time Estimation
Tracy A. Heath, John P. Huelsenbeck, Tanja Stadler
Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover p…
Macro-evolutionary models and coalescent point processes: The shape and probability of reconstructed phylogenies
Amaury Lambert, Tanja Stadler
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such…
Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model
Denise Kühnert, Tanja Stadler, Timothy G. Vaughan +1
The evolution of RNA viruses such as HIV, Hepatitis C and Influenza virus occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we dev…
Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics
Amaury Lambert, Helen K. Alexander, Tanja Stadler
The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting…