Welcome to the companion repository for the manuscript entitled Flight demand and environmental niche are associated with molecular evolutionary rates in a large avian radiation

by David A. Duchene, Paola A. Montoya, Santiago Claramunt, and Carlos D. Cadena.

This respository contains the DNA sequence alignments used in this study for each of the mitochondrial (mitochondrial_dna.fasta) and nuclear (nuclear_dna.fasta) data.

In addition, the repository contains a data file that can be read into R using the "load" function (pgls_data.Rdata). Use the following code in R to load the data:

library(caper)
load("path-to-repository/pgls_data.Rdata")

The following are the elements included:

Analyses of the association between flight habit and wing metrics

flight.score.data - data frame with data on the approximate flight habit score, wing loading, and hand-wing index.

furn.tree.genera - tree of genera of furnariidae extracted from the original phylogenetic study of the phylogenetics and diversification of furnariidae (Derryberry et al. 2011, Evolution, 65(10), 2973-2986).

models.flight.score - list containing two pgls regression objects examining the association among the flight habit score and each of wing loading and hand-wing index, respectively.

Analyses of the association between molecular evolutionary rates and wing metrics and environmental energy

table.mitochondrial - the data frame with mitochondrial molecular evolutionary rate estimates, wing loading, hand-wing index, and environmental energy for each of the species for which these data were available.

table.nuclear - as table.mitochondrial but including nuclear molecular evolutionary rate estimates.

furn.tree.mitochondrial - the time-tree taken from the original phylogenetic study and used for regression analyses, pruned to contain the data for which mitochondrial molecular rates could be estamated with confidence.

furn.tree.nuclear - as furn.tree.mitochondrial but including the taxa for which nuclear molecular rates could be estimated with confidence.

models.wl - list containing two elements for each of mitochondiral data and nuclear data. In each, three pgls regression models can be found, one for each of dN, dS, and dN/dS. All models include wing loading in the explanatory variables.

models.hwi - as models.wl but including the hand-wing index in the explanatory variables.

For enquiries contact David A. Duchene (david.duchene@anu.edu.au; david.duchene@sund.ku.dk).