Stochastic Models in Phylogenetic Comparative Methods: Analytical Properties and Parameter Estimation
Doctoral thesis, 2013
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to include uncertainty and measurement error in the phylogeny as well as the measured traits. This thesis addresses all these three issues. First, by investigating the effects of correlated measurement errors on a phylogenetic regression. Second, by developing a multivariate Ornstein-Uhlenbeck model combined with a maximum-likelihood estimation package in R. This model allows, uniquely, a direct way of testing adaptive coevolution. Third, accounting for the often substantial phylogenetic uncertainty in comparative studies requires an explicit model for the tree. Based on recently developed conditioned branching processes, with Brownian and Ornstein-Uhlenbeck evolution on top, expected species similarities are derived, together with phylogenetic confidence intervals for the optimal trait value. Finally, inspired by these developments, the phylogenetic framework is illustrated by an exploration of questions concerning “time since hybridization”, the distribution of which proves to be asymptotically exponential.
Macroevolution
Adaptation
General Linear Model
Branching diffusion
Hybridization
Adaptation
Optimality
Phylogenetic uncertainty
Measurement error
Birth-death process
Conditioned branching process
Evolution
Ornstein-Uhlenbeck process
Phyletic gradualism
Multivariate phylogenetic comparative method
Brownian motions
Phylogenetic inertia
Yule tree
Punctuated equilibrium
Fredagen den 18 oktober 2013, kl. 13.15, Hörsal Pascal, Mathematical Sciences, Chalmers Tvärgata 3
Author
Krzysztof Bartoszek
Chalmers, Mathematical Sciences
University of Gothenburg
Subject Categories (SSIF 2011)
Mathematics
ISBN
978-91-628-8746-9
Fredagen den 18 oktober 2013, kl. 13.15, Hörsal Pascal, Mathematical Sciences, Chalmers Tvärgata 3