Phylogenetic comparative biology • In phylogenetic comparative biology we use the comparative data of species & a phylogeny to make inferences about evolutionary process and history. • Reconstructing the ancestral phenotypes of extinct hypothetical ancestral species continues to be a major goal of phylogenetic comparative analysis. Ancestral state reconstruction • In ancestral character reconstruction our goal is to estimate the ancestral condition of phenotypic traits – usually at internal nodes. • Ideally, we should also obtain a measurement of the uncertainty associated with our ancestral state estimate. Why do we want to reconstruct ancestral states? • We have a data set of body size in Anolis lizards of the Caribbean, and we are interested in the ancestral value of one or multiple nodes in the tree. Anolis occultus Anolis cuvieri Why do we want to reconstruct ancestral states? • We have digit number in Lerista skinks & we are interested in the ancestral state at the root or the number of times digits have been lost in the group. Disclaimer • I’m not going to cover all methods of ancestral character reconstruction – in part because many have been proposed & so doing would be tedious. • I’m going to concentrate on “statistical” methods for ancestral character reconstruction . • I define this as including methods with an explicit underlying model (i.e., “model-based”); and for which we can compute a measure of our confidence in our inference to compare against alternative scenarios. Ancestral state reconstruction • The first step in ancestral character estimation involves identifying the type of data we are interested in analyzing. • For instance, we might have data measured on a continuous scale (“continuous characters”) or discrete characters (qualitative features or characteristics that we count). • The distinction between continuous & discrete characters is not always straightforward. • For instance: Drosophila bristle number; scale counts on the midline; etc. Ancestral state reconstruction • We need to think not only about the character but also about the model that’s appropriate to our data. • For instance, whether or character is meristic or metric – is it more appropriate to think that it evolves by Brownian evolution (wandering up & down gradually through time); or via (more or less) instantaneous leaps between state. Brownian motion • Remember Brownian motion? • Brownian motion is a continuous-time stochastic process. • The expected distribution of the phenotypic trait data at the tips the tree is multivariate normal. Brownian motion (on a phylogeny)