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

Limnology

Volumn 13, Issue 3, 2012, Pages 261-267

  Ishida, Seiji ^a   Ohtsuki, Hajime ^a   Awano, Tamotsu ^a   Tsugeki, Narumi K ^b   Makino, Wataru ^a   Suyama, Yoshihisa ^a   Urabe, Jotaro ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b EHIME UNIVERSITY   (Japan)

Author keywords

Daphnia; DNA extraction; Ephippia; Paleolimnology; Resting eggs

Indexed keywords

AMPLIFICATION; DNA; EGG; ENVIRONMENTAL CHANGE; EXTRACTION METHOD; GENETIC ANALYSIS; GENETIC STRUCTURE; HATCHING; LACUSTRINE DEPOSIT; PALEOLIMNOLOGY; POPULATION GENETICS; POPULATION STRUCTURE; SEDIMENT CORE; ZOOPLANKTON;

DAPHNIA;

EID: 84869140380     PISSN: 14398621     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10201-012-0380-x     Document Type: Article

References (35)

1. Alasaad S, Rossi L, Maione S, Sartore S, Soriguer RC, Pérez JM, Rasero R, Zhu XQ, Soglia D (2008) HotSHOT Plus ThermalSHOCK, a new and efficient technique for preparation of PCR-quality mite genomic DNA. Parasitol Res 103: 1455-1457.
2. Allen MR (2010) Genetic and environmental factors influence survival and hatching of diapausing eggs. Limnol Oceanogr 55: 549-559.
3. Appleby PG, Oldfield F (1978) The calculation of lead-210 dates assuming a constant rate of supply of unsupported 210Pb to the sediment. Catena 5: 1-8.
4. 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, Ghent.
5. Brede N, Sandrock C, Straile D, Spaak P, Jankowski T, Streit B, Schwenk K (2009) The impact of human-made ecological changes on the genetic architecture of Daphnia species. Proc Natl Acad Sci USA 106: 4758-4763.
6. Caceres C (1998) Interspecific variation in the abundance, production, and emergence of Daphnia diapausing eggs. Ecology 79: 1699-1710.
7. Caceres CE, Tessier AJ (2003) How long to rest: the ecology of optimal dormancy and environmental constraint. Ecology 84: 1189-1198.
8. Cousyn C, De Meester L, Colbourne JK, Brendonck L, Verschuren D, Volckaert F (2001) Rapid, local adaptation of zooplankton behavior to changes in predation pressure in the absence of neutral genetic changes. Proc Natl Acad Sci USA 98: 6256-6260.
9. Decaestecker E, Gaba S, Raeymaekers JAM, Stoks R, van Kerckhoven L, Ebert D, De Meester L (2007) Host-parasite 'Red Queen' dynamics archived in pond sediment. Nature 450: 870-873. doi: 10. 1038/nature06291.
10. Faustová M, Petrusek A, Černý M (2004) Status of Daphnia resting egg banks in Bohemian forest lakes affected by acidification. Hydrobiologia 526: 23-31.
11. Hairston NG, Lampert W, Caceres CE, Holtmeier CL, Weider LJ, Gaedke U, Fischer JM, Fox JA, Post DM (1999) Lake ecosystems-rapid evolution revealed by dormant eggs. Nature 401: 446-446.
12. Hairston NG, Holtmeier CL, Lampert W, Weider LJ, Post DM, Fischer JM, Cáceres CE, Fox JA, Gaedke U (2001) Natural selection for grazer resistance to toxic cyanobacteria: evolution of phenotypic plasticity? Evolution 55: 2203-2214.
13. Hofreiter M, Mead JI, Martin P, Poinar HN (2003) Molecular caving. Curr Biol 13: R693-R695.
14. Ishida S, Kotov A, Taylor D (2006) A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887. Zool J Linn Soc 146: 385-405.
15. Jankowski T, Straile D (2003) A comparison of egg-bank and long-term plankton dynamics of two Daphnia species, D. hyalina and D. galeata: potentials and limits of reconstruction. Limnol Oceanogr 48: 1948-1955.
16. Jeppesen E, Leavitt P, De Meester L, Jensen JP (2001) Functional ecology and palaeolimnology: using cladoceran remains to reconstruct anthropogenic impact. Trends Ecol Evol 16: 191-198.
17. Marková S, Černý M, Rees DJ, Stuchlík E (2006) Are they still viable? Physical conditions and abundance of Daphnia pulicaria resting eggs in sediment cores from lakes in the Tatra Mountains. Biologia 61: S135-S146.
18. Meeker ND, Hutchinson SA, Ho L, Trede NS (2007) Method for isolation of PCR-ready genomic DNA from zebrafish tissues. Biotechniques 43: 610-614.
19. Montero-Pau J, Gomez A, Munoz J (2008) Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs. Limnol Oceanogr Methods 6: 218-222.
20. Parducci L, Suyama Y, Lascoux M, Bennett KD (2005) Ancient DNA from pollen: a genetic record of population history in Scots pine. Mol Ecol 14: 2873-2882.
21. Petrusek A, Hobaek A, Nilssen JP, Skage M, Černý M, Brede N, Schwenk K (2008) A taxonomic reappraisal of the European Daphnia longispina complex (Crustacea, Cladocera, Anomopoda). Zool Scr 37: 507-519.
22. Rychlik W (2007) OLIGO 7 Primer Analysis Software. Methods Mol Biol 402: 35-60.
23. Schwartz SS, Hebert PDN (1987) Methods for the activation of the resting eggs of Daphnia. Freshwat Biol 17: 373-379.
24. Schwenk K, Posada D, Hebert PD (2000) Molecular systematics of European Hyalodaphnia: the role of contemporary hybridization in ancient species. Proc R Sci Lond B 267: 1833-1842.
25. Smol JP, Douglas MS (2007) From controversy to consensus: making the case for recent climate change in the Arctic using lake sediments. Front Ecol Environ 5: 466-474.
26. Suyama Y, Kawamuro K, Kinoshita I, Yoshimura K, Tsumura Y, Takahara H (1996) DNA sequence from a fossil pollen of Abies spp. from Pleistocene peat. Genes Genet Syst 71: 145-149.
27. Taylor DJ, Hebert PD (1993) Habitat-dependent hybrid parentage and differential introgression between neighboringly sympatric Daphnia species. Proc Natl Acad Sci USA 90: 7079-7083.
28. Taylor DJ, Hebert PD, Colbourne JK (1996) Phylogenetics and evolution of the Daphnia longispina group (Crustacea) based on 12S rDNA sequence and allozyme variation. Mol Phyl Evol 5: 495-510.
29. Truett GE, Heeger P, Mynatt RL, Truett AA, Walker JA, Warman ML (2000) Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and tris (HotSHOT). Biotechniques 29: 52-54.
30. Tsugeki NK, Urabe J (2009) Paleolimnological approach as a tool for reconstructing lake ecosystems in the past (in Japanese). Seibutsu no Kagaku Iden 63: 66-72.
31. Tsugeki N, Oda H, Urabe J (2003) Fluctuation of the zooplankton community in Lake Biwa during the 20th century: a paleolimnological analysis. Limnology 4: 101-107.
32. Tsugeki NK, Ishida S, Urabe J (2008) Sedimentary records of reduction in resting egg production of Daphnia galeata in Lake Biwa during the 20th century: a possible effect of winter warming. J Paleolimnol 42: 155-165.
33. Weider L, Lampert W, Wessels M, Colbourne J, Limburg P (1997) Long-term genetic shifts in a microcrustacean egg bank associated with anthropogenic changes in the Lake Constance ecosystem. Proc R Soc Lond Ser B Biol sci 264: 1613-1618.
34. Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300: 791-795.
35. 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: 111-114.