Ancestral Reconstruction: Theory & Practice

Ancestral reconstruction involves estimating the value or condition of a phenotypic trait or attribute at one or more internal nodes of a phylogenetic tree. Ancestral state reconstruction has long been among the most popular endeavors in phylogenetic comparative biology because it purports to offer researchers interested in trait evolution a window on the evolutionary past. Contemporary ancestral state reconstruction relies on explicit mathematical models for the evolutionary process of our traits. In the present section, I will outline ancestral state reconstruction for discretely-valued characters (such as qualitative or ordinal features), as well as for continuously-valued traits (such as numerical quantitative measures of morphology, behavior, or ecology). I will then proceed to briefly illustrate the application of ancestral character reconstruction to two different empirical datasets: feeding mode in centrarchid fishes; and body mass evolution in mammals. In spite of its popularity, ancestral character reconstruction includes some significant shortcomings. I will end by commenting on the general practice of ancestral state reconstruction and its limitations.