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...ompared with the Kass and Raftery table (Kass and Raftery 1995). The CAT and CAT-GTR were tested against homogeneous models in PhyloBayes v3.2 (Lartillot et al. 2009) using Bayesian Cross Validation (=-=Stone 1974-=-), which is implemented in PhyloBayes v3.2 (Lartillot et al. 2009). Cross Validation was calculated by splitting the data set into two unequal parts, the learning set and the test set. The parameters ...

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...ere are substantial variations in both mutational rate and nucleotide composition (Li et al. 1987; Romiguier et al. 2010). The observed heterogeneity can be influenced by many factors including diet (=-=Yang 1998-=-), disease (Usanga and Luzzatto 1985), and intense sexual selection (Dorus et al. 2004). Variations in body size, longevity, metabolic rate, and germ-line generation time across species have also been...

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...eneity across the data set, and so we applied profile mixture model CAT to the data. BF comparisons were not employed to test the fit of the CAT model as they were not implemented in PhyloBayes v3.2 (=-=Lartillot et al. 2009-=-), instead we used 10-fold Bayesian cross validation. The fit of data set heterogeneous models CAT and CAT-GTR were compared against the fit of homogeneous models 1GTR+ 1C+ I+ 4 and 1JTT+ I+ 4. Resu...

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...e than nuclear proteincoding genes, making them less appropriate for resolving deep nodes on a phylogeny. In addition, DNA sequences are more prone to mutational saturation than amino acid data sets (=-=Kosiol et al. 2007-=-) and might be more strongly affected by biases related to lineage-specific codon usage preferences (Rota-Stabelli et al. 2013). To fully address the root of the placental mammals, evolutionary models...

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...on, evolutionary models, placental root, heterogeneous modeling. Introduction There are conflicting views over the root of the placental mammal phylogeny (Meredith et al. 2011; McCormack et al. 2012; =-=Song et al. 2012-=-; O’Leary et al. 2013). The conflict is largely due to the impact of compressed cladogenesis, a phenomenon shown to have a major negative impact on the resolution of the metazoan phylogeny for example...

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...endent data sets and independent analyses is highly desirable. The Atlantogenata hypothesis is being recovered with greater frequency in mammal phylogenetic analyses (Madsen et al. 2001; Scally 2001; =-=Hudelot et al. 2003-=-; van Rheede et al. 2006; Nishihara et al. 2007; Hallstrom et al. 2007; Wildman et al. 2007; Hallstrom and Janke 2008; Prasad et al. 2008; Song et al. 2012). Here, we have shown that when better fitti...

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...ion (Li et al. 1987; Romiguier et al. 2010). The observed heterogeneity can be influenced by many factors including diet (Yang 1998), disease (Usanga and Luzzatto 1985), and intense sexual selection (=-=Dorus et al. 2004-=-). Variations in body size, longevity, metabolic rate, and germ-line generation time across species have also been shown to affect the rate of mutation (Peto et al. 1975; Martin and Palumbi 1993; Blei...

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...highly desirable. The Atlantogenata hypothesis is being recovered with greater frequency in mammal phylogenetic analyses (Madsen et al. 2001; Scally 2001; Hudelot et al. 2003; van Rheede et al. 2006; =-=Nishihara et al. 2007-=-; Hallstrom et al. 2007; Wildman et al. 2007; Hallstrom and Janke 2008; Prasad et al. 2008; Song et al. 2012). Here, we have shown that when better fitting models are used support for the Atlantogenat...

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...to account and as such cannot 2153 Rooting the Placental Mammal Phylogeny . doi:10.1093/molbev/mst117 MBE accommodate individual lineages that may deviate from the average compositional distribution (=-=Rzhetsky and Nei 1995-=-). Therefore, we applied a second test for compositional homogeneity that is a tree and model-based composition test (Foster 2004). We generated 100 simulated data sets based on the given model, phylo...

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...ertain Superorders (e.g., Laurasiatheria), is due in no small part to incorrect ortholog identification (Philippe et al. 2011), long branch attraction (LBA) (Heath et al. 2008), saturation of signal (=-=Moreira and Philippe 2000-=-), compositional bias (Foster and Hickey 1999), evolutionary rate variation between lineages and between different characters in a data set (Li et al. 1987), and model misspecification (Philippe et al...

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...and intense sexual selection (Dorus et al. 2004). Variations in body size, longevity, metabolic rate, and germ-line generation time across species have also been shown to affect the rate of mutation (=-=Peto et al. 1975-=-; Martin and Palumbi 1993; Bleiweiss 1998; Leroi et al. 2003; de Magalhaes and Costa 2009; Caulin and Maley 2011). Smaller, shorter-lived mammals with high metabolic rates and short germ-line generati...

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...2004). Variations in body size, longevity, metabolic rate, and germ-line generation time across species have also been shown to affect the rate of mutation (Peto et al. 1975; Martin and Palumbi 1993; =-=Bleiweiss 1998-=-; Leroi et al. 2003; de Magalhaes and Costa 2009; Caulin and Maley 2011). Smaller, shorter-lived mammals with high metabolic rates and short germ-line generation times accumulate mutations at a higher...

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...DNA sequences are more prone to mutational saturation than amino acid data sets (Kosiol et al. 2007) and might be more strongly affected by biases related to lineage-specific codon usage preferences (=-=Rota-Stabelli et al. 2013-=-). To fully address the root of the placental mammals, evolutionary models that account for heterogeneity in both composition and the rate of mutational change (i.e., exchange rate) across the tree an...

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... et al. 2003; de Magalhaes and Costa 2009; Caulin and Maley 2011). Smaller, shorter-lived mammals with high metabolic rates and short germ-line generation times accumulate mutations at a higher rate (=-=Li et al. 1996-=-). With such variation in mutational rate across lineages, these data are also likely to suffer the effects of LBA. Holton and Pisani (2010) have shown that LBA has led to the incorrect resolution of ...