THE HIGHER-LEVEL RELATIONSHIPS OF ALETHINOPHIDIAN SNAKES INFERRED FROM SEVEN NUCLEAR AND MITOCHONDRIAL GENES

-Phylogenetic studies have defined two major groups of snakes, the Scolecophidia (ca. 340 species) and the Alethinophidia (ca. 2,640 sp.). Scolecophidians are burrowing snakes, whereas alethinophidians occupy a diversity of ecological niches. Here, we present new DNA-sequence data from several genes and analyze those together with available sequence data to examine the higher-level relationships of alethinophidian snakes, including boas and pythons. We find additional, significant support for a major split at the base of the evolutionary tree of alethinophidian snakes, between a South American clade (Anilius and Tropidophiidae) and all other species. Based on the fossil record and Earth history, we interpret this split as being the result of vicariance: the separation of South America and Africa in the mid-Cretaceous. We give the name Amerophidia to the South American clade and Afrophidia to the other clade. INTRODUCTION The order Squamata includes lizards (ca. 4770 species), snakes (ca. 3000 spp.) and amphisbaenians (ca. 170 spp.) (Uetz, 2006). According to recent molecular studies, the closest relatives of snakes are the anguimorphs and/or the iguanians. The presence of toxin-secreting oral glands is a shared derived character of this clade (named Toxicofera), demonstrating a single early origin of the venom system in squamates dating from the Jurassic (Fry et aI., 2005; Vidal and Hedges, 2005). Snakes are divided into two main groups. The fossorial scolecophidians (blindsnakes and threadsnakes, ca. 340 sp.) are small snakes with limited gape sizes that feed on small prey (mainly ants and termites) on a frequent basis. The alethinophidians (all other snakes, ca. 2640 sp.) are more ecologically diverse, and most species feed on relatively large prey, primarily vertebrates, on an infrequent basis (Cundall and Greene, 2000; Vidal and Hedges, 2002a). Among Alethinophidia, the caenophidians (advanced snakes, ca. 2470 sp.) widely use venom to subdue their prey, whereas the remaining alethinophidian snakes (ca. 170 sp.), which do not form a single (monophyletic) group, use constriction (secondarily lost by some fossorial species) (Greene and Burghardt, 1978; Greene, 1994; Vidal and Hedges, 2002a, b; Vidal and David, 2004). According to recent molecular studies (Vidal and Hedges, 2002a; Vidal and David, 2004), the alethinophidian snakes include the following lineages: IDepartment of Biology and Astrobiology Research Center, 208 . Mueller Lab, Pennsylvania State University, University Park, Pennsylvania 16802-5301, USA. 'VMS 602, Taxonomie et collections, Reptiles-Amphibiens, Departement Systematique et Evolution, Museum National d'Histoire Naturelle, 25 Rue Cuvier, Paris 75005, France. E-mail: nvidal@mnhn.fr 37, rue d'Arsonval, 75015 Paris, France Aniliidae (genus Anilius, 1 sp.), Tropidophiidae (genera Tropidophis and Trachyboa, 32 spp.), Boidae (genera Acrantophis, Boa, Candoia, Corallus, Epicrates, Eunectes, Sanzinia, Charina, Eryx, Gongylophis, Lichanura, Exiliboa, Ungaliophis, 49 spp.), Calabariidae (genus Calabaria, 1 sp.), Pythonidae (genera Aspidites, Antaresia, Apodora, Bothrochilus, Leiopython, Liasis, Morelia, Python, 33 spp.), Loxocemidae (genus Loxocemus, 1 sp.), Xenopeltidae (genus Xenopeltis, 2 spp.), Bolyeriidae (genera Bolyeria, Casarea, 2 spp.), Cylindrophiidae (genus Cylindrophis, 10 spp.), Anomochilidae (genus Anomochilus, 2 spp.), Uropeltidae (genera Brachyophidium, Melanophidium, Platyplectrurus, Plectrurus, Pseudotyphlops, Rhinophis, Teretrurus, Uropeltis, 47 spp.), Xenophidiidae (genus Xenophidion, 2 spp.) and advanced snakes (Caenophidia). Because no evidence supports the contention that boas and pythons form a monophyletic group, the study of their evolution and phylogeny must involve the study of all major clades of alethinophidian snakes. In this chapter we address the phylogeny of Alethinophidia, with emphasis on non-caenophidian taxa (including all boas and pythons), using DNA sequences obtained from seven nuclear and mitochondrial genes. This work builds upon a long history of research into snake classification, including landmark morphological studies such as those of Underwood (1967, 1976). However, our intent here is not to review the history of snake classification but rather to provide an update of the molecular evidence bearing on the higher-level relationships of the alethinophidians. Most of the data analyzed were collected in earlier published studies, although we present new data for a gene not previously analyzed (mitochondrial ND2), 13 new sequences of mitochondrial gene ND4, and one new sequence for the nuclear gene RAG 1. For recent 28 N Vidal, A. -S. Delmas, and S. B. Hedges I I Gongylophis colubrinus ~ '----Eryx miliaris 75/100 '------Candoia carinata