Finding copepod footprints: A protocol for molecular identification of diapausing eggs in lake sediments

Limnology

Volumn 14, Issue 3, 2013, Pages 269-282

  Makino, Wataru ^a   Ohtsuki, Hajime ^a   Urabe, Jotaro ^a  

^a TOHOKU UNIVERSITY   (Japan)

Author keywords

28S ribosomal DNA; Biodiversity; Calanoid copepods; Diapausing eggs; Japanese lakes; Molecular identification

Indexed keywords

BIODIVERSITY; CRUSTACEAN; DIAPAUSE; DNA; EGG DEVELOPMENT; FOOTPRINT; LACUSTRINE DEPOSIT; MOLECULAR ANALYSIS; PALEOLIMNOLOGY; POPULATION GENETICS;

JAPAN;

ACANTHODIAPTOMUS PACIFICUS; CALANOIDA; COPEPODA;

EID: 84881031923     PISSN: 14398621     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10201-013-0404-1     Document Type: Article

References (52)

1. Adamowicz SJ, Menu-Marque S, Halse SA, Topan JC, Zemlak TS, Hebert PDN, Witt JDS (2010) The evolutionary diversification of the Centropagidae (Crustacea, Calanoida): a history of habitat shifts. Mol Phylogenet Evol 55: 418-430.
2. Albert MR, Chen G, MacDonald GK, Vermaire JC, Bennett M, Gregory-Eaves I (2010) Phosphorus and land-use changes are significant drivers of cladoceran community composition and diversity: an analysis over spatial and temporal scales. Can J Fish Aquat Sci 67: 1262-1273.
3. Asmyhr MG, Cooper SJB (2012) Difficulties barcoding in the dark: the case of crustacean stygofauna from eastern Australia. Invertebr Syst 26: 583-591.
4. Auclair JC, Frenette JJ, Dodson J (1993) Zooplankton community structure in southwestern Québec lakes: the rôles of acidity and predation. J Plankton Res 15: 1103-1128.
5. Ban S (1992) Seasonal distribution, abundance and viability of dapause eggs of Eurytemora affinis (Copepoda: Calanoida) in the sediment of Lake Ohnuma, Hokkaido. Bull Plankton Soc Jpn 39: 41-48.
6. Ban S, Minoda T (1991) The effect of temperature on the development and hatching of diapausing and subitaneous eggs in Eurytemora affinis (Copepoda: Calanoida) in Lake Ohnuma, Hokkaido, Japan. Bull Plankton Soc Jpn Spec Vol: 299-308.
7. Ban S, Minoda T (1992) Hatching of diapause eggs of Eurytemora affinis (Copepoda: Calanoida) collected from lake-bottom sediments. J Crust Biol 12: 51-56.
8. Bennike O (1998) Fossil egg sacs of Diaptomus (Crustacea: Copepoda) in Late Quaternary lake sediments. J Paleolimnol 19: 77-79.
9. Bissett A, Gibson JAE, Jarman SN, Swadling KM, Cromer L (2005) Isolation, amplification, and identification of ancient copepod DNA from lake sediments. Limnol Oceanogr Methods 3: 533-542.
10. Blanco-Bercial L, Bradford-Grieve J, Bucklin A (2011) Molecular phylogeny of the Calanoida (Crustacea: Copepoda). Mol Phylogenet Evol 59: 103-113.
11. Briski E, Cristescu ME, Bailey SA, MacIssac HJ (2011) Use of DNA barcode to detect invertebrate invasive species from diapausing eggs. Biol Invasion 13: 1325-1340.
12. Brooks JL, Dodson SI (1965) Predation, body size, and composition of plankton: the effect of a marine planktivore on lake plankton illustrates theory of size, composition, and predation. Science 150: 28-35.
13. Bucklin A, Allen LD (2004) MtDNA sequencing from zooplankton after long-term preservation in buffered formalin. Mol Phylogenet Evol 30: 879-882.
14. Bucklin A, Steinke D, Blanco-Bercial L (2011) DNA barcoding of marine metazoa. Annu Rev Mar Sci 3: 471-508.
15. Carpenter SR, Kitchell JF (1985) Cascading trophic interactions and lake productivity. BioScience 35: 634-639.
16. Cepada GD, Blanco-Bercial L, Bucklin A, Beron CM, Vinas MD (2012) Molecular systematic of three species of Oithona (Copepoda, Cyclopoida) from the Atlantic Ocean: comparative analysis using 28S rDNA. PLoS ONE 7: e35861.
17. Chan EM, Derry AM, Watson LA, Arnott SE (2008) Variation in calanoid copepod resting egg abundance among lakes with different acidification histories. Hydrobiologia 614: 275-284.
18. Costa FO, deWaard FR, Boutillier F, Ratnasingham S, Dooh ST, Hajibabael M, Hebert PDN (2007) Biological identifications through DNA barcodes: the case of the Crustacea. Can J Fish Aquat Sci 64: 272-295.
19. De Stasio BT Jr (1989) The seed bank of a freshwater crustacean: copepodology for the plant ecologist. Ecology 70: 1377-1389.
20. deWaard JR, Hebert PDN, Humble LM (2011) A comprehensive DNA barcode library for the looper moss (Lepidoptera: Geometridae) of British Columbia, Canada. PLoS ONE 6: e18290.
21. Dussart BH, Defaye D (1983) Répertoire mondial des crustacés copépodes eaux intérieures. I. Calanoïdes. CNRS, Paris.
22. Dussart BH, Defaye D (1995) Copepoda. Introduction to the Copepoda. SPB Academic Publishing, Amsterdam.
23. Fell JW, Scorzetti G, Gonnell L, Graig S (2006) Biodiversity of micro-eukaryotes in Antarctic Dry Valley soils with < 5% soil moisture. Soil Biol Boichem 38: 3107-3119.
24. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotech 3: 294-299.
25. Frey DG (1964) Remains of animals in quaternary lake and bog sediments and their interpretation. Ergebn Limnol 2: 1-116.
26. Hairston N Jr, Olds EJ (1984) Population differences in the timing of diapause: adaptation in a spatially heterogeneous environment. Oecologia 61: 42-48.
27. Hairston N Jr, van Brunt RA, Kearns CM, Engstrom DR (1995) Age and survivorship of diapausing eggs in a sediment egg bank. Ecology 76: 1706-1711.
28. Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitefield JB, Hebert PDN (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Mol Ecol Notes 6: 959-964.
29. Hebert PDN, Cywinska A, Ball SL, deWaaard JR (2003a) Biological identifications through DNA barcodes. Proc R Soc Lond B 270: 313-321.
30. Hebert PDN, Ratnasingham S, deWaard DR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc London B 270(Suppl 1): S96-S99.
31. Hutchinson GE (1967) A treatise on limnology, vol. 2. Introduction to lake biology and the limnoplankton. John Wiley and Sons, New York.
32. Ishida S, Otsuki H, Awano T, Makino W, Suyama Y, Urabe J (2012) DNA extraction and amplification methods for ephippial carapace of Daphnia resting eggs in lake sediments: a novel approach for reconstructing zooplankton population structure from the past. Limnology 13: 261-267.
33. Jeppesen E, Jensen JP, Søndergaard M, Lauridsen T, Landkildehus F (2000) Trophic structure, species richness and biodiversity in Danish lakes: changes along a phosphorus gradient. Freshw Biol 45: 201-218.
34. Jeppesen E, Leavitt PR, De Meester L, Jensen JP (2001) Functional ecology and palaeolimnology: using cladoceran remains to reconstruct anthropogenic impact. Trends Ecol Evol 16: 191-198.
35. Kiesling TL, Wilkinson E, Rabalais J, Ortner PB, McCabe MM, Fell JW (2002) Rapid identification of adult and naupliar stages of copepods using DNA hybridization methodology. Mar Biotech 4: 30-39.
36. Kim S, Song K-H, Ree H-I, Kim W (2012) A DNA barcode library for Korean Chironomidae (Insecta: Diptera) and indexes for defining barcode gap. Mol Cells 33: 9-17.
37. Lampert W, Sommer U (1997) Limnoecology. The ecology of lakes and streams. Oxford University Press, Oxford.
38. Leavitt PR, Carpenter SR, Kitchell JF (1989) Whole-lake experiments: the annual records of fossil pigments and zooplankton. Limnol Oceanogr 34: 700-717.
39. Machida RJ, Tsuda A (2010) Dissimilarity of species and forms of planktonic Neocalanus copepod using mitochondrial COI, 12S, nuclear ITS, and 28S gene sequences. PLoS ONE 5: e10278.
40. Makino W, Tanabe AS (2009) Extreme population genetic differentiation and secondary contact in the freshwater copepod Acanthodiaptomus pacificus in the Japanese Archipelago. Mol Ecol 18: 3699-3713.
41. Makino W, Knox MA, Duggan IC (2010) Invasion, genetic variation and species identity of the calanoid copepod Sinodiaptomus valkanovi. Freshw Biol 55: 375-386.
42. Marrone F, Lo Brutto S, Hundsdoerfer AK, Arculeo M (2013) Overlooked cryptic endemism in copepods: systematics and natural history of the calanoid subgenus Occidodiaptomus Borutzky 1991 (Copepoda, Calanoida, Diaptomidae). Mol Phylogenet Evol 66: 190-202.
43. Meusnier I, Singer GAC, Landry J-F, Hickey DA, Hebert PDN, Hajibabaei M (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9: 214.
44. Mizuno T, Takahashi E (eds) (2000) An illustrated guide to freshwater zooplankton in Japan (in Japanese). Tokai University Press, Tokyo.
45. Montero-Pau J, Gómez A, Muños J (2008) Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing egg. Limnol Oceanogr Methods 6: 218-222.
46. Pace ML (1986) An empirical analysis of zooplankton community size structure across lake trophic gradients. Limnol Oceanogr 31: 45-55.
47. Parker BR, Wilhelm FM, Schindler DW (1996) Recovery of Hesperodiaptomus articus populations from diapausing eggs following elimination by stocked salmonids. Can J Zool 74: 1292-1297.
48. Schindler DW (1977) Evolution of phosphorus limitation in lakes. Science 195: 260-262.
49. Selden AP, Huys R, Stephenson MH, Heward AP, Taylor PN (2010) Crustaceans from bitumen clast in Carboniferous glacial diamictite extend fossil records of copepods. Nat Commun 1: 50.
50. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetic analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2371-2379.
51. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24: 4876-4882.
52. Xu Z-H, Wang G-Z, Mu Q, Wu L-S, Li S-J (2011) An approach to the study of copepod egg banks based on efficient DNA extraction from individual copepod eggs. Mar Biol Res 7: 592-598.