Comparative analyses of phenotypic sequences using phylogenetic trees

Phenotypic sequences are a type of multivariate trait organized structurally, such as teeth distributed along the dental arch, or temporally, such as the stages of an ontogenetic series. Unlike other multivariate traits, the elements of a phenotypic sequence are distributed along an ordered set, which allows for distinct evolutionary patterns between neighboring and distant positions. In fact, sequence traits share many characteristics with molecular sequences, although important distinctions pose challenges to current comparative methods. We implement an approach to estimate rates of trait evolution that explicitly incorporates the sequence organization of traits. We apply models to study the temporal pattern evolution of cricket calling songs. We test whether neighboring positions along a phenotypic sequence have correlated rates of evolution or if rate variation is independent of sequence position. Our results show that cricket song evolution is strongly autocorrelated and models perform well when used with sequence phenotypes even under small sample sizes. Our approach is flexible and can be applied to any multivariate trait with discrete units organized in a sequence-like structure.

Methods
Data was extracted from: Robillard, T., F. Legendre, L. Desutter-Grandcolas, and P. Grandcolas. 2006. Phylogenetic analysis and alignment of behavioral sequences by direct optimization. Cladistics 22:602–633.

Code to process the data is available on this repository.

Data was analyzed using custom software available at https://github.com/Caetanods/CorrSeq