DNA extraction and amplification methods for ephippial cases of Daphnia resting eggs in lake sediments: a novel approach for reconstructing zooplankton population structure from the past
This study describes a method of DNA extraction and amplification for ephippial cases of Daphnia resting eggs from lake sediment. Recent studies have reconstructed succession records of Daphnia species by genetically analyzing Daphnia resting eggs stored in lake sediments and revealed changes in dominant Daphnia species that correspond well with environmental changes. However, this approach is not applicable to lakes where most of the resting eggs in the sediment have already hatched out. We modified conventional methods for DNA extraction and amplification to enable genetic analyses of the ephippial case that envelops and protects the resting eggs, and we compared the performance of the modified method to the conventional one. We confirmed that we could efficiently analyze the sequences of the ephippial cases collected in a sediment core using our modified method. It enables us to reconstruct changes in genetic structure of Daphnia populations regardless of hatching rates of the resting eggs.
KeywordsPaleolimnology Daphnia Resting eggs Ephippia DNA extraction
This study was supported, in whole or in part, by the Environmental Research & Technology Development Fund (D-1002) from the Ministry of the Environment of Japan, a Global COE Research Grant (Tohoku University Ecosystem Adaptability), and a Grant-in-Aid for Scientific Research (B) (22370007) and Young Scientists (B) (22770076) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan. We thank Marcia Kyle for kind review of our manuscript before submitting it.
- Benzie JAH (2005) Cladocera: the genus Daphnia (including Daphniopsis) (Anomopoda: Daphniidae). Guides to the identification of the microinvertebrates of the conntinental waters of the world, vol 21. Kenobi Productions, GhentGoogle Scholar
- Caceres C (1998) Interspecific variation in the abundance, production, and emergence of Daphnia diapausing eggs. Ecology 79:1699–1710Google Scholar
- Tsugeki NK, Urabe J (2009) Paleolimnological approach as a tool for reconstructing lake ecosystems in the past (in Japanese). Seibutsu no Kagaku Iden 63:66–72Google Scholar
- Willerslev E, Cappellini E, Boomsma W, Nielsen R, Hebsgaard MB, Brand TB, Hofreiter M, Bunce M, Poinar HN, Dahl-Jensen D, Johnsen S, Steffensen JP, Bennike O, Schwenninger J-L, Nathan R, Armitage S, de Hoog C-J, Alfimov V, Christl M, Beer J, Muscheler R, Barker J, Sharp M, Penkman KEH, Haile J, Taberlet P, Gilbert MTP, Casoli A, Campani E, Collins MJ (2007) Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 317:111–114PubMedCrossRefGoogle Scholar