Isolation, amplification, and identification of ancient copepod DNA from lake sediments

Species identification of copepods in lake sediments is often difficult because their remains lack diagnostic features. It is therefore not easy to track changes in copepod biodiversity in lakes through time. We report a method for the isolation, amplification, and identification of copepod DNA from whole lake sediments formed in the early Holocene to the present. The method, which involves amplification of a short (~300 base pair) DNA sequence that varies between copepod species, provides a new approach to the study of copepod paleobiodiversity. Successful amplification of copepod DNA was possible in samples as old as 9950 calibrated 14C y BP. Attempts failed to recover DNA from a sediment sample ca 65,000 years old. In most cases the species identified in the sediments matched those of extant lake populations, but analysis of early-mid Holocene sediments from one lake revealed a species that is not present today. We were able to recover copepod DNA from core samples stored at –20° C, at 4° C, and preserved with polyethyleneglycol. *Corresponding author e-mail address: [email protected] Acknowledgments This work was funded by a grant from the Institutional Research Grants Scheme of the University of Tasmania. Field work was supported by an ARC Discovery grant to J.A.E.G. and K.M.S. (DP0342815) and a grant from the Australian Science Advisory Committee (Project 2348). Further funding was provided by the Australian Institute for Nuclear Science and Engineering (grants 04057 and 05063) for determination of the radiocarbon age of sediments to J.A.E.G. and K.M.S., and through a grant from the Trans-Antarctic Association to K.M.S. We thank Dr. A. Quesada (Universidad Autonoma de Madrid, Spain) for supplying us the core from Limnopolar Lake (project REN2000-0435-ANT, funded by the Ministerio de Ciencia y Tecnología, Spain), Dr. R. Zale (Umeå Universitet, Sweden) for supplying the material from Lake Boeckella, and Dr. D. Hodgson (British Antarctic Survey, Cambridge, UK) for supplying sediment from Lake Reid. The comments of three reviewers—Professor Nelson G. Hairston Jr, Dr. Ryan A. Thum, and Dr. Marco J. L. Coolen— improved the manuscript. Limnol. Oceanogr.: Methods 3, 2005, 533–542 © 2005, by the American Society of Limnology and Oceanography, Inc. LIMNOLOGY and OCEANOGRAPHY: METHODS