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...pport for highly partitioned modeling strategies, with 2ln(BF) values that are orders of magnitude above the recommended threshold (Mueller et al., 2004; Nylander et al., 2004; Brandley et al., 2005; =-=Castoe and Parkinson, 2006-=-). These results suggest that either Bayes factors have a high false-positive rate (they tend to support the inclusion of additional classes into analyses when it is unnecessary) or a great deal of he...

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...nary rate) for each potential data block have been used to guide the process of defining the optimal number of partitions for analysis (Mueller et al., 2004; Brandley et al., 2005; Poux et al., 2005; =-=Castoe and Parkinson, 2006-=-; McGuire et al., 2007; Nishihara et al., 2007). For example, using background information for protein-coding genes, the first plus second but not the third codon positions were grouped (Brandley et a...

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...pling of either viperines, or both viperines and crotalines. Causus is also generally regarded as a primitive viper, and has usually been placed either at the base of the Viperinae (Herrmann and Joger, 1995, 1997) or even as the sister group to all other viperids bar Azemiops (Groombridge, 1986). Moreover, it has often been classified in a separate subfamily, the Causinae (e.g., McDiarmid et al., 1999). Several studies have taken the basal position of Causus for granted and used the genus as an outgroup for analyses of the Viperinae (e.g., Lenk et al., 2001), or even the Viperidae as a whole (Castoe and Parkinson, 2006). However, others have found the evidence for viperine monophyly to the exclusion of Causus more ambiguous (Ashe and Marx, 1988; Cadle, 1992). In an analysis of nuclear and mitochondrial DNA sequences, Nagy et al. (2005) recovered this genus nested within the Viperinae, as the sister 446 W. Wüster et al. / Molecular Phylogenetics and Evolution 49 (2008) 445–459genus of Atheris, and viperine monophyly to the exclusion of Causus was contradicted by one strongly supported node. However, their analysis only included three viperines other than Causus and no crotalines, making the assessment of the ...

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...ystem for investigating historical patterns of Neotropical diversification. This large group of venomous snakes has a relatively well known phylogeny (Parkinson et al., 2002; Malhotra & Thorpe, 2004; =-=Castoe & Parkinson, 2006-=-) and an extensive fossil record in the USA (reviewed by Holman, 2000), and appears to have dispersed into the New World as a single lineage from Asia during the Miocene (Kraus et al., 1996; Parkinson...

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...as restricted to the comparison of a fixed number of alternative partitions in relatively modest data sets, often using Bayes factors (Bao et al., 2007; Brandley et al., 2005; Brown and Lemmon, 2007; =-=Castoe and Parkinson, 2006-=-; Fan et al., 2011; McGuire et al., 2007; Nylander et al., 2004; Pupko et al., 2002);but see Li et al. (2008). Opportunely, the release of PartitionFinder (Lanfear et al., 2012, 2014) made a big diffe...

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... (The Reptile Database, accessed March 2013; (Uetz and Etzold, 1996). Since Linnaeus described the first rattlesnake species (Linnaeus, 1758) they have become among the most studied group of reptiles (e.g. >2000 citations on PubMed). Multiple hypotheses concerning the systematic relationships of the rattlesnakes have beenproposed based on internal and external morphology (Brattstrom, 1964; Gloyd, 1940; Klauber, 1956, 1972), venom properties (Foote and MacMahon, 1977; Githens and George, 1931; Minton, 1956), immunological and electrophoretic data (Cadle, 1992; Minton, 1992) and molecular data (Castoe and Parkinson, 2006; Murphy et al., 2002; Parkinson, 1999, 2002). Despite substantial attention, a cohesive and well-supported phylogenetic hypothesis for the relationships among rattlesnake species remains absent, particularly at deeper nodes in the rattlesnake tree. Among published phylogenies there is much conflict between morphological and molecular-based analyses, and even among molecular-based estimates {Castoe, 2006 #91;Murphy, 2002 #72}. It is notable that the majority of molecular phylogenies that include rattlesnakes (e.g. Castoe and Parkinson, 2006; Lawing and Polly, 2011; Pyron et al., 2011) have rec...

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...dence that complex models of sequence evolution can extract additional phylogenetic signal from data, especially where saturation of base pair substitutions is commonplace (Castoe et al., 2004, 2005; =-=Castoe & Parkinson, 2006-=-). Therefore, we used different models of sequence evolution for biologically relevant partitions of our data. In the case of protein coding mitochondrial genes, the most relevant partitions are first...