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 (similar to 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 C-14 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 degrees C, at 4 degrees C, and preserved with polyethyleneglycol.