General information
The EMBL reptile database

Herpetology: An Introductory Biology of Amphibians and Reptiles, Second Edition (Hardcover)
by George R. Zug, Laurie J. Vitt, Janalee P. Caldwell

Turtles of the World (World Biodiversity Database CD-ROM Series) (CD-ROM)
by C.H. Ernst, R.G.M. Altenburg, R.W. Babour

Phylogenetics of reptiles
Townsend TM, Larson A, Louis E, et al.
Molecular phylogenetics of Squamata: The position of snakes, Amphisbaenians, and Dibamids, and the root of the Squamate tree.
SYSTEMATIC BIOLOGY 53 (5): 735-757 OCT 2004

Kumazawa Y, Nishida M.
Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: Statistical evidence for Archosaurian affinity of turtles.
MOLECULAR BIOLOGY AND EVOLUTION 16 (6): 784-792 JUN 1999.

KUMAZAWA Y, NISHIDA M. VARIATIONS IN MITOCHONDRIAL TRANSFER-RNA GENE ORGANIZATION OF REPTILES AS PHYLOGENETIC MARKERS. MOLECULAR BIOLOGY AND EVOLUTION 12 (5): 759-772 SEP 1995

Divergence time estimation of reptiles
Jones ME, Anderson CL, Hipsley CA, Muller J, Evans SE, Schoch RR 2013.
Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara). BMC Evolutionary Biology 13: 208. doi: 10.1186/1471-2148-13-208

Kumazawa Y. 2007.
Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations.
Gene. 388: 19-26.

Pereira SL, Baker AJ. 2006.
A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock.
MOLECULAR BIOLOGY AND EVOLUTION 23: 1731-1740.

Wiens JJ, Brandley MC, Reeder TW
Why does a trait evolve multiple times within a clade? Repeated evolution of snakelike body form in squamate reptiles
EVOLUTION 60 (1): 123-141 JAN 2006

Phylogenetics of snakes
Dong S, Kumazawa Y.
Complete mitochondrial DNA sequences of six snakes: Phylogenetic relationships and molecular evolution of genomic features.
JOURNAL OF MOLECULAR EVOLUTION 61 (1): 12-22 JUL 2005

Kumazawa Y.
Mitochondrial DNA sequences of five squamates: Phylogenetic affiliation of snakes.
DNA RESEARCH 11 (2): 137-144 APR 30 2004.

Vidal N, David P.
New insights into the early history of snakes inferred from two nuclear genes.
MOLECULAR PHYLOGENETICS AND EVOLUTION 31 (2): 783-787 MAY 2004

Kelly CMR, Barker NP, Villet MH.
Phylogenetics of advanced snakes (Caenophidia) based on four mitochondrial genes.
SYSTEMATIC BIOLOGY 52 (4): 439-459 AUG 2003

Kumazawa Y, Ota H, Nishida M, et al.
The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions.
GENETICS 150 (1): 313-329 SEP 1998

Phylogenetics of turtle
Sasaki T, Yasukawa Y, Takahashi K, et al.
Extensive morphological convergence and rapid radiation in the evolutionary history of the family Geoemydidae (old world pond turtles) revealed by SINE insertion analysis
SYSTEMATIC BIOLOGY 55 (6): 912-927 DEC 2006

Parham JF, Feldman CR, Boore JL.
The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA.
BMC EVOLUTIONARY BIOLOGY 6: Art. No. 11 FEB 7 2006

Iwabe N, Hara Y, Kumazawa Y, et al.
Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins.
MOLECULAR BIOLOGY AND EVOLUTION 22 (4): 810-813 APR 2005

Cao Y, Sorenson MD, Kumazawa Y, et al.
Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes.
GENE 259 (1-2): 139-148 Sp. Iss. SI DEC 23 2000

Divergence time estimation of turtles
Near TJ, Meylan PA, Shaffer HB
Assessing concordance of fossil calibration points in molecular clock studies: An example using turtles
AMERICAN NATURALIST 165 (2): 137-146 FEB 2005

Phylogenetics of lizards
Amer SAM, Kumazawa Y.
Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 85 (2): 247-260 JUN 2005.

Amer SAM, Kumazawa Y.
Mitochondrial genome of Pogona vitticepes (Reptilia; Agamidae): control region duplication and the origin of Australasian agamids.
GENE 346: 249-256 FEB 14 2005

Phylogenetic and divergence time estimation of crocodiles
Janke A, Gullberg A, Hughes S, et al.
Mitogenomic analyses place the gharial (Gavialis gangeticus) on the crocodile tree and provide Pre-K/T divergence times for most crocodilians
JOURNAL OF MOLECULAR EVOLUTION 61 (5): 620-626 NOV 2005