This readme.txt file was generated on 2012-01-15 by Min Wang

Title of Dataset: Data and script for: The patterns and modes of the evolution of disparity in Mesozoic Birds. Proceedings of the Royal Society B

Min Wang1,2,*, Graeme T. Lloyd3,*, Chi Zhang1,2, and Zhonghe Zhou1,2
1 Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
2 CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
3 School of Earth & Environment, University of Leeds, Leeds, LS2 9JY, UK
Correspondence: wangmin@ivpp.ac.cn (M.W.), graemetlloyd@gmail.com (G.T.L.)

The data contains the raw measurements, discrete character matrix, R and MrBayes commands, used in comparative phylogenetic analyses of disparate morphologies of Mesozoic birds .
Data “limb length analysis”: R code perform comparative phylogenetic analysis of limb proportion of Mesozoic birds. 1) using length of the six appendicular limbs of Mesozoic birds in "limb proportion data.csv" to construct phylomorphospace of limb proportion after accounting for phylogeny and body mass; 2) disparity analyses using three commonly used disparity metrics: the sum of variances and ranges, and the median distance from centroids
Data “discrete character analysis”: This R code performs comparative phylogenetic analysis of the pattern and mode of morphological disparity of Mesozoic birds. Varing methods are used to scaled the phylogeny, including the minimal branch length (mbl), equal and tip-dated methods. 1) a distance matrix was constructed by calculating a morphological distance between each pair of taxa using the calculate_morphological_distances function. We chose the Maximum Observable Rescaled Distance (MORD) and the Generalised Euclidean Distance (GED) as the distance metrics, because they are more suitable to datasets containing fossils; the distance metrics were also calculated using the "HSJ" approach to account for inapplicable characters. All these different approaches can be applied by changing the Arguments in calculate_morphological_distances () and ordinate_cladistic_matrix (). These different methods produced essentially same results, and thus the mbl-scaled and MORD distance methods were detailed bellow, and corresponding results were present in figures. 2) First, we explore the pattern and mode of disparity of Mesozoic birds as a whole using three metrics (sum of variances and ranges, and median distance from centroids), and then conducted intergroup comparison; 3) A nonparametric multivariate analysis of variance (PERMANOVA) test was used to test whether the three avian groups were statistically separated in morphospace; 4) we subdivided the character matrix into six anatomical subregions (skull, vertebral column, pectoral girdle, forelimb, pelvis, and hindlimb), and conducted aforementioned comparative analyses to explore whether these subregions demonstrate different patterns; 5) finally, we performed the character exhaustion analyses.
Data “MrBayes tip dating”: MrBayes commands to perform tip-dating analysis of Mesozoic birds.