Low Mitochondrial DNA Variation Among American Alligators and a Novel Non-Coding Region in Crocodilians TRAVIS C. GLENN, 1,2 n JOSEPH L. STATON, 3 ALEX T. VU, 1 LISA M. DAVIS, 1,2 JAIME R. ALVARADO BREMER, 1 WALTER E. RHODES, 4 I. LEHR BRISBIN, JR., 2 and ROGER H. SAWYER 1 1 Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 2 Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina 29802 3 Belle W. Baruch Institute for Marine and Coastal Research, University of South Carolina, Columbia, South Carolina 29208 4 South Carolina Department of Natural Resources, Dennis Wildlife Research Center, Bonneau, South Carolina 29431 ABSTRACT We analyzed 1317–1823 base pairs (bp) of mitochondrial DNA sequence beginning in the 5’ end of cytochrome b (cyt b) and ending in the central domain of the control region for 25 American alligators (Alligator mississippiensis) and compared these to a homologous sequence from a Chinese alligator (A. sinensis). Both species share a non-coding spacer between cyt b and tRNA Thr . Chinese alligator cyt b differs from that of the American alligator by 17.5% at the nucleotide level and 13.8% for inferred amino acids, which is consistent with their presumed ancient divergence. Only two cyt b haplotypes were detected among the 25 American alligators (693–1199 bp surveyed), with one haplotype shared among 24 individuals. One alligator from Mississippi differed from all other alligators by a single silent substitution. The control region contained only slightly more variation among the 25 American alligators, with two variable positions (624 bp surveyed), yielding three haplotypes with 22, two, and one individuals in each of these groups. Previous genetic studies examining allozymes and the proportion of variable microsatellite DNA loci also found low levels of genetic diversity in American alligators. However, in contrast with allozymes, microsatellites, and morphology, the mtDNA data shows no evidence of differentiation among populations from the extremes of the species range. These results suggest that American alligators underwent a severe population bottleneck in the late Pleistocene, resulting in nearly homogenous mtDNA among all American alligators today. J. Exp. Zool. (Mol. Dev. Evol.) 294:312–324, 2002. r 2002 Wiley-Liss, Inc. DNA studies allow new insights into the genetic relationships and evolutionary history of species. Analysis of orthologous DNA sequences among species can provide information about phyloge- netic relationships, whereas comparisons of DNA within species can furnish information about phylogeography, population structure, and popu- lation history (Avise, ’94). Mitochondrial DNA (mtDNA) is an especially useful portion of the genome to investigate because it is maternally inherited, and thus reveals patterns of female philopatry as well as revealing population differ- entiation more quickly than nuclear DNA (Avise, ’94; Moore, ’95; Parker et al., ’98). Different portions of the mtDNA genome can be used for comparison at different hierarchical levels because of mutational rate differences along the molecule (Brown, ’83; Parker et al., ’98). Coding regions are often used in interspecific phylogenetic investigations, whereas noncoding portions of the mtDNA (usually non-conserved portions of the control region; i.e., domain I and domain III cf. Jaime R. Alvarado Bremer’s present address: Department of Marine Biology, Texas A&M University, 5007 Ave U., Galveston, Texas 77551 Grant sponsors: US Department of Energy; Grant numbers: DE- FG02-97EW09999 and DE-FC09-96SR18546; Grant sponsor: Univer- sity of South Carolina Research and Development; Grant number: 96-E125; Grant sponsor: Savannah River Ecology Lab; Grant number: 96-F111. n Correspondence to: Travis C. Glenn, Savannah River Ecology Lab, PO Drawer E, Aiken, SC 29802. E-mail: Travis.Glenn@sc.edu Received 13 December 2001; Accepted 13 September 2002 Published online in Wiley InterScience (www.interscience.wiley. com). DOI: 10.1002/jez.10206 r 2002 WILEY-LISS, INC. JOURNAL OF EXPERIMENTAL ZOOLOGY (MOL DEV EVOL) 294:312–324 (2002)