Histories Arman Bilge Lexington High School Lexington, Massachusetts November 9, 2013 x Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Approach to Coevolution Molecular Evolution Felsenstein (1981) Population Genetics Kingman (1982) Gene Evolution Arvestad et al. (2003) Biogeography Lemey et al. (2009, 2010) Speciation Yang & Rannala (2010) Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Approach to Coevolution Molecular Evolution Felsenstein (1981) Population Genetics Kingman (1982) Gene Evolution Arvestad et al. (2003) Biogeography Lemey et al. (2009, 2010) Speciation Yang & Rannala (2010) Coevolution? Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Coevolution probability of reconstruction P H, S, R | D H = host tree, S = symbiont tree, R = reconciliation, θ = coevolutionary rates, D, dH, dS = sequence data Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Coevolution probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ H = host tree, S = symbiont tree, R = reconciliation, θ = coevolutionary rates, D, dH, dS = sequence data Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Coevolution probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ Likelihood P dH, dS | H, S, R, θ = P dH | H, S, R, θ P dS | H, S, R, θ H = host tree, S = symbiont tree, R = reconciliation, θ = coevolutionary rates, D, dH, dS = sequence data Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Coevolution probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ Likelihood P dH, dS | H, S, R, θ = P dH | H, S, R, θ P dS | H, S, R, θ = P dH | H tree likelihood P dS | S tree likelihood H = host tree, S = symbiont tree, R = reconciliation, θ = coevolutionary rates, D, dH, dS = sequence data Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Coevolution probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ Prior P (H, S, R, θ) = P S | H, R, θ P (H, R, θ) H = host tree, S = symbiont tree, R = reconciliation, θ = coevolutionary rates, D, dH, dS = sequence data Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Coevolution probability of reconstruction P H, S, R | D ∝ θ likelihood P dH, dS | H, S, R, θ prior P (H, S, R, θ) dθ Prior P (H, S, R, θ) = P S | H, R, θ P (H, R, θ) = P S | H, R, θ ? P (H) P (R) P (θ) existing/trivial priors H = host tree, S = symbiont tree, R = reconciliation, θ = coevolutionary rates, D, dH, dS = sequence data Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Prior, P S | H, R, θ Cannot be calculated easily because of inﬁnite permutations of unobserved events Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Prior, P S | H, R, θ Cannot be calculated easily because of inﬁnite permutations of unobserved events Approximation by considering only observed events Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Prior, P S | H, R, θ Cannot be calculated easily because of inﬁnite permutations of unobserved events Approximation by considering only observed events Observation of duplication, host-switch, and loss events are modeled as independent Poisson processes Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Prior, P S | H, R, θ Cannot be calculated easily because of inﬁnite permutations of unobserved events Approximation by considering only observed events Observation of duplication, host-switch, and loss events are modeled as independent Poisson processes Cospeciation assumed to occur whenever host speciates Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Prior, P S | H, R, θ Cannot be calculated easily because of inﬁnite permutations of unobserved events Approximation by considering only observed events Observation of duplication, host-switch, and loss events are modeled as independent Poisson processes Cospeciation assumed to occur whenever host speciates For each ancestral symbiont, algorithm identiﬁes between 7 situations to calculate probability of observation Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Prior, P S | H, R, θ Cannot be calculated easily because of inﬁnite permutations of unobserved events Approximation by considering only observed events Observation of duplication, host-switch, and loss events are modeled as independent Poisson processes Cospeciation assumed to occur whenever host speciates For each ancestral symbiont, algorithm identiﬁes between 7 situations to calculate probability of observation Any uncertainties are integrated out Bayesian Reconstruction of Coevolutionary Histories Lexington High School
of a reconstruction cannot be determined analytically, so approximated using Markov chain Monte Carlo Bayesian Reconstruction of Coevolutionary Histories Lexington High School
of a reconstruction cannot be determined analytically, so approximated using Markov chain Monte Carlo Algorithm implemented as a Java plug-in for BEAST, an existing program for evolutionary analysis via Bayesian MCMC Bayesian Reconstruction of Coevolutionary Histories Lexington High School
of a reconstruction cannot be determined analytically, so approximated using Markov chain Monte Carlo Algorithm implemented as a Java plug-in for BEAST, an existing program for evolutionary analysis via Bayesian MCMC All parameters estimated simultaneously, including host tree, symbiont tree, and the reconciliation between them Bayesian Reconstruction of Coevolutionary Histories Lexington High School
for the probability of a coevolutionary reconstruction Developed an algorithm to approximate the probability of symbiont tree for a reconstruction Bayesian Reconstruction of Coevolutionary Histories Lexington High School
for the probability of a coevolutionary reconstruction Developed an algorithm to approximate the probability of symbiont tree for a reconstruction Implemented the algorithm in a popular, widely-used phylogenetics program Bayesian Reconstruction of Coevolutionary Histories Lexington High School
real datasets Model for preferential host-switching Integration with other evolutionary models (e.g., biogeography) Bayesian Reconstruction of Coevolutionary Histories Lexington High School
real datasets Model for preferential host-switching Integration with other evolutionary models (e.g., biogeography) Hypothesis-testing of coevolutionary theories Bayesian Reconstruction of Coevolutionary Histories Lexington High School
Jessica Wu, Rachel Sealfon, and Prof. Mukul Bansal Andrew Brownjohn, Jon Sanders, Prof. Ran Libeskind-Hadas, Hayden Metsky, and Prof. Manolis Kellis, for their support Dr. Susan Oﬀner, for inspiring me My family Siemens Foundation University of Notre Dame Bayesian Reconstruction of Coevolutionary Histories Lexington High School
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