Similar protocols

Pipeline publication

[…] f taxa may alter the precise nature of the quantified shape variation, its magnitude in each dataset is maximised., It is widely recognised that the interrelatedness of data points in biological datasets violates assumptions of traditional statistical methods – and can lead to elevated Type I errors . For this reason, phylogenetic comparative methods were favoured over ahistorical tests. All statistical analyses were conducted in R 2.13.1 (CRAN Project, . R FAQ. Available: http://cran.r-project.org/doc/FAQ/R-FAQ.html. Accessed 13 April 2012) using the ape , geiger (CRAN - Package geiger. Available: http://cran.r-project.org/web/packages/geiger/index.html. Accessed 13 April 2012), picante , phytools (CRAN - Package phytools. Available: http://CRAN.R-project.org/package=phytools. Accessed 13 April 2012) and adephylo packages., A composite phylogenetic tree () for use with PCMs was constructed in Mesquite 2.75 (Mesquite. Available: http://mesquiteproject.org. Accessed 13 April 2012). The topology was based at an ordinal level on the mitochondrial study of Hackett et al. , which has recently received support from the retroposon analysis of Suh et al. . Additional phylogenetic studies were consulted to resolve the intra-ordinal relationships not sampled by : Barker et al. for Passeriformes, Livezey for Charadriiformes, and Lerner and Mindell for Falconiformes and Accipitriformes. The topology for our Mesozoic bird dataset was derived from the recent cladistic analysis of O'Connor et al. , while non-avian theropod relationships follow Turner et al. ., Because of the composite nature […]

Pipeline specifications

Software tools Phytools, adephylo, Mesquite