Phylogenetic relationships and limb loss in sub-Saharan African scincine lizards (Squamata: Scincidae) Alison S. Whiting, a, * Aaron M. Bauer, b and Jack W. Sites Jr. a a Department of Integrative Biology and M.L. Bean Museum, Brigham Young University, Provo, UT 84602, USA b Department of Biology, Villanova University, Villanova, PA 19085, USA Received 30 August 2002; revised 17 February 2003 Abstract Skinks are the largest family of lizards and are found worldwide in a diversity of habitats. One of the larger and more poorly studied groups of skinks includes members of the subfamily Scincinae distributed in sub-Saharan Africa. Sub-Saharan African scincines are one of the many groups of lizards that show limb reduction and loss, and the genus Scelotes offers an excellent op- portunity to look at limb loss in a phylogenetic context. Phylogenetic relationships were reconstructed for a total of 52 taxa rep- resenting all subfamilies of skinks as well as other Autarchoglossan families using sequence from six gene regions including; 12S, 16S, and cytochrome b (mitochondrial), as well as a-Enolase, 18S, and C-mos (nuclear). The family Scincidae is recovered as monophyletic and is the sister taxon to a (Cordylidae + Xantusiidae) clade. Within skinks the subfamily Acontinae is monophyletic and sister group to all remaining skinks. There is no support for the monophyly of the subfamilies Lygosominae and Scincinae, but sub-Saharan African scincines + Feylinia form a well supported monophyletic group. The monophyly of Scelotes is confirmed, and support is found for two geographic groups within the genus. Reconstructions of ancestral states for limb and digital characters show limited support for the reversal or gain of both digits and limbs, but conservative interpretation of the results suggest that limb loss is common, occurring multiple times throughout evolutionary history, and is most likely not reversible. Ó 2003 Elsevier Science (USA). All rights reserved. Keywords: Scincidae; Scincinae; Scelotes; mtDNA; Nuclear genes; Phylogeny; Limb loss 1. Introduction With more than 1300 species, skinks comprise the largest family (Scincidae) of lizards, and include >25% of the worldÕs lizard diversity (Bauer, 1998). Greer (1970b) defined four subfamilies within skinks that are still widely used today. The Acontinae (18 spp.) and Feylininae (4 spp.) are small groups of completely limbless skinks restricted to Africa. The Lygosominae is the largest and most speciose subfamily and is distrib- uted worldwide, but with the majority of its diversity in Australia and Asia. Like the two small subfamilies, the monophyly of the Lygosominae has generally been ac- cepted on the basis of derived morphological features (Greer, 1970b, 1986; Griffith et al., 2000; but see Hutchinson, 1981). The Scincinae is also a large sub- family distributed throughout the Americas and Asia, but with its center of diversity in Africa. Greer (1970b) postulated that scincines were primitive, originated in Africa, and independently gave rise to the other three subfamilies. The recognized paraphyly of the Scincinae has long been an impediment to the resolution of higher order skink relationships. Recently, Greer and Shea (2000) described the shared occurrence of a derived head scale pattern (the ‘‘chalcidine’’ condition) characterizing all non-lygosomine skinks except Eumeces, Scincus, and Scincopus and Griffith et al. (2000) have proposed a fifth subfamily, the Eumecinae, in an attempt to identify monophyletic subgroups within the Scincinae sensu Greer (1970b). One of the most poorly studied groups of scincines consists of the seven genera occurring in sub-Saharan Africa. One of these, Chalcides, is chiefly Mediterranean in its distribution, and has been the subject of relatively Molecular Phylogenetics and Evolution 29 (2003) 582–598 MOLECULAR PHYLOGENETICS AND EVOLUTION www.elsevier.com/locate/ympev * Corresponding author. Fax: 1-801-422-0090. E-mail address: as77@email.byu.edu (A.S. Whiting). 1055-7903/$ - see front matter Ó 2003 Elsevier Science (USA). All rights reserved. doi:10.1016/S1055-7903(03)00142-8