Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera)

Molecular Ecology Resources

Volumn 14, Issue 3, 2014, Pages 606-615

  Heintzman, Peter D ^a,c   Elias, Scott A ^a   Moore, Karen ^b   Paszkiewicz, Konrad ^b   Barnes, Ian ^a,d  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY OF EXETER   (United Kingdom)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

Ancient DNA; Coleoptera; DNA preservation; Metagenomics; Museum DNA; Shotgun sequencing

Indexed keywords

AMARA ALPINA; CARABIDAE; COLEOPTERA; HEXAPODA; SPIROPLASMA; WOLBACHIA;

DNA; MITOCHONDRIAL DNA;

ANIMAL; BEETLE; CLASSIFICATION; DNA CONTAMINATION; DNA SEQUENCE; GENETICS; INFORMATION CENTER; MOLECULAR GENETICS; PHYLOGENY; PRESERVATION;

ANIMALS; BEETLES; DNA; DNA CONTAMINATION; DNA, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; MUSEUMS; PHYLOGENY; PRESERVATION, BIOLOGICAL; SEQUENCE ANALYSIS, DNA;

EID: 84898544120     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12205     Document Type: Article

References (75)

1. Allentoft ME, Collins M, Harker D et al. (2012) The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society of London Series B-Biological Sciences, 279, 4724-4733.
2. Andersen JC, Mills NJ (2012) DNA extraction from museum specimens of parasitic hymenoptera. PLoS ONE, 7, e45549.
3. Arino AH (2010) Approaches to estimating the universe of natural history collections data. Biodiversity Informatics, 7, 81-92.
4. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A (2002) Dynamics of Pleistocene population extinctions in Beringian brown bears. Science, 295, 2267-2270.
5. Barnes I, Shapiro B, Lister A et al. (2007) Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Current Biology, 17, 1072-1075.
6. Bennike O, Björck S, Böcher J, Walker IR (2000) The Quaternary arthropod fauna of Greenland: a review with new data. Bulletin of the Geological Society of Denmark, 47, 111-134.
7. Binladen J, Wiuf C, Gilbert MTP et al. (2006) Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics, 172, 733-741.
8. Blankenberg D, Gordon A, Von Kuster G et al. (2010) Manipulation of FASTQ data with Galaxy. Bioinformatics, 26, 1783-1785.
9. Brace S, Barnes I, Powell A et al. (2012) Population history of the Hispaniolan hutia Plagiodontia aedium (Rodentia: Capromyidae): testing the model of ancient differentiation on a geotectonically complex Caribbean island. Molecular Ecology, 21, 2239-2253.
10. Campos PF, Kristensen T, Orlando L et al. (2010a) Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene. Molecular Ecology, 19, 4863-4875.
11. Campos PF, Willerslev E, Sher A et al. (2010b) Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proceedings of the National Academy of Sciences of the United States of America, 107, 5675-5680.
12. Castalanelli MA, Severtson DL, Brumley CJ et al. (2010) A rapid non-destructive DNA extraction method for insects and other arthropods. Journal of Asia-Pacific Entomology, 13, 243-248.
13. Coope GR (2004) Several million years of stability among insect species because of, or in spite of, Ice Age climatic instability? Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 359, 209-214.
14. Cooper A, Poinar HN (2000) Ancient DNA: do it right or not at all. Science, 289, 1139.
15. Darcy JL, Lynch RC, King AJ, Robeson MS, Schmidt SK (2011) Global distribution of Polaromonas phylotypes-evidence for a highly successful dispersal capacity. PLoS ONE, 6, e23742.
16. Dillon N, Austin AD, Bartowsky E (1996) Comparison of preservation techniques for DNA extraction from hymenopterous insects. Insect Molecular Biology, 5, 21-24.
17. Doughari HJ, Ndakidemi PA, Human IS, Benade S (2011) The ecology, biology and pathogenesis of Acinetobacter spp.: an overview. Microbes and Environments, 26, 101-112.
18. Duron O, Bouchon D, Boutin S et al. (2008) The diversity of reproductive parasites among arthropods: Wolbachia do not walk alone. BMC Biology, 6, 27.
19. Elias SA (1994) Quaternary Insects and Their Environments. Smithsonian Institute, Washington, District of Columbia.
20. Elias SA (2010) Advances in Quaternary Entomology. Elsevier, Oxford, UK.
21. Elias SA, Berman D, Alfimov A (2000) Late Pleistocene beetle faunas of Beringia: where east met west. Journal of Biogeography, 27, 1349-1363.
22. Faulds K, Smith WE, Graham D (2004) Evaluation of surface-enhanced resonance Raman scattering for quantitative DNA analysis. Analytical Chemistry, 76, 412-417.
23. Gibson CM, Kao RH, Blevins KK, Travers PD (2012) Integrative taxonomy for continental-scale terrestrial insect observations. PLoS ONE, 7, e37528.
24. Gilbert MTP, Bandelt HJ, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends in Ecology and Evolution, 20, 541-544.
25. Gilbert MTP, Moore W, Melchior L, Worobey M (2007a) DNA extraction from dry museum beetles without conferring external morphological damage. PLoS ONE, 2, e272.
26. Gilbert MTP, Tomsho LP, Rendulic S et al. (2007b) Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science, 317, 1927-1930.
27. Gilbert MTP, Kivisild T, Gronnow B et al. (2008) Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science, 320, 1787-1789.
28. Goecks J, Nekrutenko A, Taylor J, Team G (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11, 1-13.
29. Goldstein PZ, Desalle R (2003) Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens. Molecular Ecology, 12, 1993-1998.
30. Grove SJ, Stork NE (2000) An inordinate fondness for beetles. Invertebrate Taxonomy, 14, 733-739.
31. Gullan PJ, Cranston PS (2010) The Insects: An Outline of Entomology, 4th edn. Wiley-Blackwell, Chichester, UK.
32. Hansen AJ, Mitchell DL, Wiuf C et al. (2006) Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics, 173, 1175-1179.
33. Harper GL, Maclean N, Goulson D (2006) Analysis of museum specimens suggests extreme genetic drift in the adonis blue butterfly (Polyommatus bellargus). Biological Journal of the Linnean Society, 88, 447-452.
34. Hartley CJ, Newcomb RD, Russell RJ et al. (2006) Amplification of DNA from preserved specimens shows blowflies were preadapted for the rapid evolution of insecticide resistance. Proceedings of the National Academy of Sciences of the United States of America, 103, 8757-8762.
35. Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S (2001) Ancient DNA. Nature Reviews Genetics, 2, 353-359.
36. van Houdt JK, Breman FC, Virgilio M, de Meyer M (2010) Recovering full DNA barcodes from natural history collections of Tephritid fruitflies (Tephritidae, Diptera) using mini barcodes. Molecular Ecology Resources, 10, 459-465.
37. Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Research, 21, 1552-1560.
38. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Applied and Environmental Microbiology, 72, 1719-1728.
39. Keeling CI, Yuen MM, Liao NY et al. (2013) Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biology, 14, R27.
40. King GA, Gilbert MTP, Willerslev E, Collins MJ, Kenward H (2009) Recovery of DNA from archaeological insect remains: first results, problems and potential. Journal of Archaeological Science, 36, 1179-1183.
41. Kircher M (2012) Analysis of high-throughput ancient DNA sequencing data. In: Ancient DNA: Methods and Protocols, Methods in Molecular Biology (eds Shapiro B & Hofreiter M), pp. 197-228. Springer, New York.
42. Klasson L, Westberg J, Sapountzis P et al. (2009) The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans. Proceedings of the National Academy of Sciences of the United States of America, 106, 5725-5730.
43. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357-359.
44. Laub MT, Shapiro L, McAdams HH (2007) Systems biology of Caulobacter. Annual Review of Genetics, 41, 429-441.
45. Lindahl T (1993) Instability and Decay of the Primary Structure of DNA. Nature, 362, 709-715.
46. Lindqvist C, Schuster SC, Sun Y et al. (2010) Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proceedings of the National Academy of Sciences of the United States of America, 107, 5053-5057.
47. Mack L (2008) Investigating mitochondrial DNA phylogenies of Arctic and European beetle taxa. MSc thesis, Mainz University.
48. Mandrioli M (2008) Insect collections and DNA analyses: how to manage collections? Museum Management and Curatorship, 23, 193-199.
49. McKenna DD, Farrell BD (2009) Beetles (Coleoptera). In: The Timetree of Life (eds Hedges SB & Kumar S), pp. 278-289. Oxford University Press, Oxford, UK.
50. Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protocols, 2010, pdb prot5448.
51. Miller W, Drautz DI, Ratan A et al. (2008) Sequencing the nuclear genome of the extinct woolly mammoth. Nature, 456, 387-390.
52. Miller W, Drautz DI, Janecka JE et al. (2009) The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research, 19, 213-220.
53. Milne I, Bayer M, Cardle L et al. (2010) Tablet-next generation sequence assembly visualization. Bioinformatics, 26, 401-402.
54. New TR (2007) Beetles and conservation. Journal of Insect Conservation, 11, 1-4.
55. Philippot L, Hallin S, Schloter M (2007) Ecology of denitrifying prokaryotes in agricultural soil. Advances in Agronomy, 96, 249-305.
56. Poinar HN, Schwarz C, Qi J et al. (2006) Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science, 311, 392-394.
57. Prufer K, Stenzel U, Hofreiter M et al. (2010) Computational challenges in the analysis of ancient DNA. Genome Biology, 11, R47.
58. Rasmussen M, Guo X, Wang Y et al. (2011) An Aboriginal Australian genome reveals separate human dispersals into Asia. Science, 334, 94-98.
59. Regassa LB, Gasparich GE (2006) Spiroplasmas: evolutionary relationships and biodiversity. Frontiers in Bioscience, 11, 2983-3002.
60. Reiss RA (2006) Ancient DNA from ice age insects: proceed with caution. Quaternary Science Reviews, 25, 1877-1893.
61. Reiss RA, Schwert DP, Ashworth AC (1995) Field preservation of Coleoptera for molecular genetic analyses. Environmental Entomology, 24, 716-719.
62. Richards S, Gibbs RA, Weinstock GM et al. (2008) The genome of the model beetle and pest Tribolium castaneum. Nature, 452, 949-955.
63. Rowe KC, Singhal S, Macmanes MD et al. (2011) Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Molecular Ecology Resources, 11, 1082-1092.
64. Rychlik W, Rychlik P (2005) Oligo: Primer Analysis Software. Molecular Biology Insights Inc, Cascade, Colorado, USA.
65. Schaefer H, Heibl C, Renner SS (2009) Gourds afloat: a dated phylogeny reveals an Asian origin of the gourd family (Cucurbitaceae) and numerous oversea dispersal events. Proceedings of the Royal Society of London Series B-Biological Sciences, 276, 843-851.
66. Schwarz C, Debruyne R, Kuch M et al. (2009) New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nucleic Acids Research, 37, 3215-3229.
67. Shapiro B, Cooper A (2003) Beringia as an Ice Age genetic museum. Quaternary Research, 60, 94-100.
68. Shapiro B, Drummond AJ, Rambaut A et al. (2004) Rise and fall of the Beringian steppe bison. Science, 306, 1561-1565.
69. Strange JP, Knoblett J, Griswold T (2009) DNA amplification from pin-mounted bumble bees (Bombus) in a museum collection: effects of fragment size and specimen age on successful PCR. Apidologie, 40, 134-139.
70. Thomsen PF, Elias S, Gilbert MT et al. (2009) Non-destructive sampling of ancient insect DNA. PLoS ONE, 4, e5048.
71. Tsangarasa K, Greenwood AD (2012) Museums and disease: using tissue archive and museum samples to study pathogens. Annals of Anatomy, 194, 58-73.
72. Ugelvig LV, Nielsen PS, Boomsma JJ, Nash DR (2011) Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion. BMC Evolutionary Biology, 11, 201.
73. Wandeler P, Hoeck PE, Keller LF (2007) Back to the future: museum specimens in population genetics. Trends in Ecology and Evolution, 22, 634-642.
74. Watts PC, Thompson DJ, Allen KA, Kemp SJ (2007) How useful is DNA extracted from the legs of archived insects for microsatellite-based population genetic analyses? Journal of Insect Conservation, 11, 195-198.
75. Willerslev E, Cappellini E, Boomsma W et al. (2007) Ancient biomolecules from deep ice cores reveal a forested Southern Greenland. Science, 317, 111-114.