Assembling the Tree of Life

Research Projects

   “The Deep Scaly Project: Resolving Higher Level Squamate Phylogeny Using Genomic and Morphological Approaches”: T. Reeder PI (San Diego St. Univ.), Co-PIs (by institutional alphabetical order): J.W. Sites, Jr. (BYU), O. Rieppel (Field Mus. Nat. Hist.), M. Kearney (NSF), J. Wiens (Stony Brook Univ.), J. Maisano (Univ. Texas – Austin), and J. Gauthier (Yale Univ.). For more information see
With more than 8,400 species, squamate reptiles are the second largest group of vertebrates after birds. Many critical questions in squamate evolution remain unresolved, such as identification of the most primitive cladee of squamates, the origin of the strange amphisbaenians (“worm lizards’), the origin of snakes, and the relationships of venomous snakes to other snake lineages. A team of seven investigators from diverse institutions is collaborating to resolve deep-history relationships within the Squamata, and will include multiple data sets. Anatomical data from living and fossil forms (~ 670 characters) will be combined with DNA sequences from ~ 50 single-copy, protein-coding, nuclear genes for 153 living squamate species – chosen to represent all recognized families and subfamilies of the group. Anatomical data are obtained from the same individuals as those used for DNA studies, along with ~ 60 key fossil taxa, using traditional methods and new high resolution X-ray scanning techniques. These CT scans can be resliced and rendered in three dimensions to produce cutaway animations that allow visualization of many internal characters with uncommon clarity (see: DNA data are generated by incorporating new tools and databases from recent vertebrate genome projects, and computer modeling will be used to determine how data from molecular and fossil studies can best be combined to reconstruct evolutionary trees. Postdoctoral researchers and students (graduate and undergraduate) have been involved in nearly every aspect of the project, and many of the nuclear genes identified for this project have been successfully applied to other taxa in unrelated studies. Although formal NSF support for this project has ended, some synthesis papers are emerging, and the larger data sets will continue to be published as more synthesis is achieved. We anticipate that the data and products produced will continue to contribute to many of our other evolutionary studies of squamates.