Effect of species neutral genetic diversity on protein divergence parameters.

<p>Each dot is for one species pair. Blue: vertebrates; green: invertebrates. a: non-adaptive rate; b: non-synonymous/synonymous ratio; c: adaptive rate; d: proportion of adaptive non-synonymous substitutions. X-axis: focal species synonymous heterozygosity.</p

Effect of the underlying DFE model on estimators of α.

<p>Each dot is for a species pair. X-axis: estimated α under the Gamma model. Y-axis: estimated α under the Neutral (black), GammaExpo (blue) and ScaledBeta models (red). Dotted red line: (y = x) line. Closed circles indicate species pairs for which the considered model obtained the highest AIC.</p

Effect of gene GC-content and expression level on estimates of α.

<p>Only the 26 species for which at least seven individuals have been sampled are considered here.</p

Distributions of α and ω_a split by taxa.

<p>Ma: mammals; Sa: sauropsids; Ar: arthropods; Mo: molluscs; Ec: echinoderms; Ot: others</p

Scornavacca_SuppFig

Supplementary figures, Scornavacca & Galtie

Dataset Nabholz Glémin Galtier 2008

This is the dataset used in : Nabholz B, Glémin S, Galtier N. 2008. Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis. Mol. Biol. Evol 25:120–130. 0 or NA indicates missing data. Life-history traits are from AnAge database (http://genomics.senescence.info/species/) De Magalhães JP, Costa J. 2009. A database of vertebrate longevity records and their relation to other life-history traits. J. Evol. Biol. 22:1770–1774. mass : body mass in gram longevity : maximum longevity in Years metabolism : Basal metabolic rate in W maturity_F : Female sexual maturity in day maturity_M : Male sexual maturity in day gestation : Gestation in day Rate : Substitution rate (subst/site/MA) estimated with Cytochrome b third codon position

Table_S1 - Datasets

Datasets used in the main statistical analyses of the study. Details of column headings : gene : Ensembl accession number (human); Species; labs : Species+Chromosome; chrMark : X or Autosomes; chr : Chromosome number; dN : Number of nonsynonymous substitutions; dS: Number of synonymous substitutions , dNdS : ratio of dN/dS; RPKM : Expression level in Reads Per Kilobase per Million sequenced Reads; Tau : Expression specificity, GC3 : GC content of the third codon positio

completeMito_phyloBayes.tr

Cetartiodactyla phylogenetic tree obtained from PhyloBayes (CAT GTR Gamma 4 model). Branch lengths are given in number of substitutions per nucleotide site