DOI: 10.5061/dryad.xsj3tx99b
title: Comparative analyses of phenotypic sequences using phylogenetic trees

description: 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.
description: 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
  
description: September, 2019<br> Daniel Caetano and Jeremy
 Beaulieu<br> University of Arkansas<br> Department of
 Biological Sciences This is the repository for our
 publication "Comparative analyses of phenotypic sequences using
 phylogenetic trees". The repository is divided into directories with
 the correspondent information and data. /data: Has the
 song sequences in raw format and time rescaled formats. Also divided in
 complete sequences (the 5s recording interval) and song bouts. There are
 two types of song bouts - long silence bouts and short silence bouts. The
 difference is that short silence bouts consider only half of the
 interchirp silence intervals and the long bouts consider the whole
 interchirp silence interval. Short bouts were introduced by the suggestion
 of the reviewers. See main text and supplementary material for more
 information. /empirical_analysis: Has the scripts and
 results for the sequence alignment and model fit to the data. These are
 subdivided into treatments following the same rationale described on the
 manuscript. /manuscript_figures: Information for the
 figures used in the main text of the manuscript.
 /phylogeny: Has the molecular alignment, BEAST xml files and the
 MCC tree used in this study. /simulations: The scripts
 and results for simulations. /tutorial_analyses: An
 script showing how to use the resources of the R package.
 ###########################################
 The software used to conduct the analyses is available on
 github. We used an machine with Ubuntu Linux version
 18.04.2 LTS The programming language was: R version
 3.6.0 (2019-04-26) -- "Planting of a Tree"
 The link to the package repository:
 https://github.com/Caetanods/CorrSeq You can install
 the package from the github repository using the function:<br>
 devtools::install_github("Caetanods/CorrSeq")
 Dependencies of the package (as of Sept, 2019):
 Rcpp::sourceCpp<br> ape::Ntip<br>
 ape::reorder.phylo<br> expm::expm<br> nloptr::nloptr<br>
 pbivnorm::pbivnorm
 ########################################### If
 reusing this data, please cite: 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.