Reliable discrimination of 10 ungulate species using high resolution melting analysis of Faecal DNA

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Ramón Laca, Ana ^a   Gleeson, Dianne ^b   Yockney, Ivor ^c   Perry, Michael ^d   Nugent, Graham ^c   Forsyth, David M ^e  

^a LANDCARE RESEARCH   (New Zealand)

^b UNIVERSITY OF CANBERRA   (Australia)

^c LANDCARE RESEARCH   (New Zealand)

^d LANDCARE RESEARCH   (New Zealand)

^e ARTHUR RYLAH INSTITUTE FOR ENVIRONMENTAL RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MITOCHONDRIAL DNA; RNA 12S;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DNA DEGRADATION; FEASIBILITY STUDY; FECES ANALYSIS; GENE AMPLIFICATION; GENOTYPE; HIGH RESOLUTION MELTING ANALYSIS; HIGH THROUGHPUT SCREENING; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE; SPECIES IDENTIFICATION; UNGULATE;

ANIMALS; ARTIODACTYLA; CYTOCHROMES B; DNA; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; FECES; MOLECULAR SEQUENCE DATA; NEW ZEALAND; NUCLEIC ACID DENATURATION; PRESERVATION, BIOLOGICAL; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL; SPECIES SPECIFICITY;

EID: 84898621353     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0092043     Document Type: Article

References (69)

1. Thompson WL, White GC, Gowan C (1998) Monitoring Vertebrate Populations. San Diego: Academic Press. 365 p.
2. Thompson WL (2004) Sampling rare or elusive species. Washington DC: Island Press. 429 p.
3. Mayle BA, Peace AJ, Gill RMA (1999) How many deer? A field guide to estimating deer population size. Edinburgh: Forestry Commission. 96 p.
4. Van Vliet N, Zundel S, Miquel C, Taberlet P, Nasi R (2008) Distinguishing dung from blue, red and yellow-backed duikers through noninvasive genetic techniques. Afr J Ecol 46: 411-417.
5. Yamashiro A, Yamashiro T, Baba M, Endo A, Kamada M (2010) Species identification based on the faecal DNA samples of the Japanese serow (Capricornis crispus). Conserv Genet Resources 2: 409-414.
6. Bowkett AE, Jones T, Laizzer RL, Plowman AB, Stevens JR (2013) Can molecular data validate morphometric identification of faecal pellets in Tanzanian forest antelope species? Conserv Genet Resources 5: 1095-1100.
7. Rutledge LY, Holloway JJ, Patterson BR, White BN (2009) An improved field method to obtain DNA for individual identification from wolf scat. J Wildl Manage 73: 1430-1435.
8. Perry GH, Marioni JC, Melsted P, Gilad Y (2010) Genomic-scale capture and sequencing of endogenous DNA from feces. Mol Ecol 19: 5332-5344.
9. Brinkman T, Schwartz M, Person D, Pilgrim K, Hundertmark K (2011) Effects of time and rainfall on PCR success using DNA extracted from deer fecal pellets. Conserv Genet 11: 1547-1552.
10. DeMay SM, Becker PA, Eidson CA, Rachlow JL, Johnson TR, et al. (2013) Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit. Mol Ecol Resources 13: 654-662.
11. Roques S, Adrados B, Chavez C, Keller C, Magnusson WE, et al. (2011) Identification of Neotropical felid faeces using RCP-PCR. Mol Ecol Resources 11: 171-175.
12. Wadley JJ, Austin JJ, Fordham DA (2013) Rapid species identification of eight sympatric northern Australian macropods from faecal-pellet DNA. Wildl Res 40: 241-249.
13. Forsyth DM, Duncan RP (2001) Propagule size and the relative success of exotic ungulate and bird introductions to New Zealand. Am Nat 157: 583-595. (Pubitemid 32546074)
14. Fraser KW, Cone JM, Whitford EJ (2000) A revision of the established ranges and new populations of 11 introduced ungulate species in New Zealand. J R Soc N Z 30: 419-437. (Pubitemid 32177403)
15. King CM (2005) The Handbook of New Zealand Mammals. Melbourne: Oxford University Press. 610 p.
16. Challies C (1985) Establishment, control, and commercial exploitation of wild deer in New Zealand. Royal Society of New Zealand Bulletin 22: 23-36.
17. Veblen TT, Stewart GH (1982) The effects of introduced wild animals on New Zealand forests. Ann Assoc Am Geogr 72: 372-397.
18. Stewart GH, Burrows LE (1989) The impact of white-tailed deer Odocoileus virginianus on regeneration in the coastal forests of Stewart Island, New Zealand. Biol Conserv 49: 275-293. (Pubitemid 20420297)
19. Coomes DA, Allen RB, Forsyth DM, Lee WG (2003) Factors preventing the recovery of New Zealand forests following control of invasive deer. Conserv Biol 17: 450-459. (Pubitemid 37084060)
20. Caughley G (1983) The deer wars: the story of deer in New Zealand. Auckland: Heinemann. 187 p.
21. Harris LH (2002) The deer menace. A history of government pest control operations, 1930-1987. Wellington, New Zealand: L.H. Harris. 192 p.
22. Riney T (1957) The use of faeces counts in studies of several free-ranging mammals in New Zealand. New Zealand Journal of Science and Technology 38: 507-532.
23. Forsyth DM, Thomson C, Hartley LJ, MacKenzie DI, Price R, et al. (2011) Long-term changes in the relative abundances of introduced deer in New Zealand estimated from faecal pellet frequencies. N Z J Zool 38: 237-249.
24. Murphy MA, Kendall KC, Robinson A, Waits LP (2007) The impact of time and field conditions on brown bear (Ursus arctos) faecal DNA amplification. Conserv Genet 8: 1219-1224. (Pubitemid 47174989)
25. Deagle BE, Eveson JP, Jarman SN (2006) Quantification of damage in DNA recovered from highly degraded samples - a case study on DNA in faeces. Front Zool 3: 11 10.1186/1742-9994-3-11.
26. Faria PJ, Kavembe GD, Jung'a JO, Kimwele CN, Estes LD, et al. (2011) The use of non-invasive molecular techniques to confirm the presence of mountain bongo Tragelaphus eurycerus isaaci populations in Kenya and preliminary inference of their mitochondrial genetic variation. Conserv Genet 12: 745-751.
27. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ (2003) Highresolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 49: 853-860. (Pubitemid 36623462)
28. Vossen RHAM, Aten E, Roos A, den Dunnen JT (2009) High-Resolution Melting Analysis (HRMA)-More than just sequence variant screening. Hum Mutat 30: 860-866.
29. Reed GH, Kent JO, Wittwer CT (2007) High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8: 597-608. (Pubitemid 46939585)
30. Erali M, Wittwer CT (2010) High resolution melting analysis for gene scanning. Methods 50: 250-261.
31. Cheng J-C, Huang C-L, Lin C-C, Chen C-C, Chang Y-C, et al. (2006) Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR. Clin Chem 52: 1997-2004. (Pubitemid 44658199)
32. Morgan JAT, Welch DJ, Harry AV, Street R, Broderick D, et al. (2011) A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis. Mol Ecol Resources 11: 813-819.
33. Montgomery JL, Sanford LN, Wittwer CT (2010) High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 10: 219-240.
34. Sakaridis I, Ganopoulos I, Argiriou A, Tsaftaris A (2013) A fast and accurate method for controlling the correct labeling of products containing buffalo meat using High Resolution Melting (HRM) analysis. Meat Sci 94: 84-88.
35. Nugent G (2005) Wapiti. In: King CM, editor. The Handbook of New Zealand Mammals. Melbourne: Oxford University Press. pp. 420-428.
36. Longmire JL, Maltbie M, Baker RJ (1997) Use of ''lysis buffer'' in DNA isolation and its implications for museum collections. Occasional Papers Museum of Texas Tech University 163.
37. Douzery E, Catzeflis FM (1995) Molecular evolution of the mitochondrial 12S rRNA in Ungulata (mammalia). J Mol Evol 41: 622-636.
38. Li B, Bai S-y, Xu Y-c, Zhang W, Ma J-z (2006) Identification of sika deer and red deer using partial cytochrome b and 12s ribosomal RNA genes. Journal of Forestry Research 17: 160-162.
39. Dwight Z, Palais R, Wittwer CT (2011) uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application. Bioinformatics 27: 1019-1020.
40. Granados-Cifuentes C, Rodriguez-Lanetty M (2011) The use of high-resolution melting analysis for genotyping Symbiodinium strains: a sensitive and fast approach. Mol Ecol Resources 11: 394-399.
41. Reja V, Kwok A, Stone G, Yang LS, Missel A, et al. (2010) ScreenClust: Advanced statistical software for supervised and unsupervised high resolution melting (HRM) analysis. Methods 50: S10-S14.
42. Forsyth DM (2005) Protocol for estimating changes in the relative abundance of deer in New Zealand forests using the Faecal Pellet Index (FPI). http://www. doc.govt.nz//documents/conservation/threats-and-impacts/animal- pests/fpiprotocol. pdf. Accessed 22 January 2014.
43. Forsyth DM, Barker RJ, Morriss G, Scroggie MP (2007) Modeling the relationship between fecal pellet indices and deer density. J Wildl Manage 71: 964-970.
44. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55: 611-622.
45. Kuwayama R, Ozawa T (2000) Phylogenetic relationships among European red deer, wapiti, and sika deer inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 15: 115-123. (Pubitemid 30308745)
46. Conover MR (1997) Monetary and intangible valuation of deer in the United States. Wildl Soc Bull 25: 298-305. (Pubitemid 27383574)
47. Côté SD, Rooney TP, Tremblay J-P, Dussault C, Waller DM (2004) Ecological impacts of deer overabundance. Annu Rev Ecol Evol Syst: 113-147. (Pubitemid 40059716)
48. Gormley AM, Forsyth DM, Griffioen P, Woodford L, Lindeman M, et al. (2011) Using presence-only and presence-absence data to estimate the current and potential distributions of established invasive species. J Appl Ecol 48: 25-34.
49. Forsyth DM, Ramsey DSL, Veltman CJ, Allen RB, Allen WJ, et al. (2013) When deer must die: large uncertainty surrounds changes in deer abundance achieved by helicopter- and ground-based hunting in New Zealand forests. Wildl Res 40: 447-458.
50. Girish PS, Anjaneyulu ASR, Viswas KN, Shivakumar BM, Anand M, et al. (2005) Meat species identification by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of mitochondrial 12S rRNA gene. Meat Sci 70: 107-112. (Pubitemid 40274779)
51. Fajardo V, González I, López-Calleja I, Mart́n I, Hernández PE, et al. (2006) PCR-RFLP authentication of meats from red deer (Cervus elaphus), fallow deer (Dama dama), roe deer (Capreolus capreolus), cattle (Bos taurus), sheep (Ovis aries), and goat (Capra hircus). J Agric Food Chem 54: 1144-1150. (Pubitemid 43374203)
52. Fajardo V, González I, Rojas M, Garća T, Mart́n R (2010) A review of current PCR-based methodologies for the authentication of meats from game animal species. Trends Food Sci Technol 21: 408-421.
53. Berry O, Sarre SD (2007) Gel-free species identification using melt-curve analysis. Mol Ecol Notes 7: 1-4. (Pubitemid 46046569)
54. Davidson MM (1973) Characteristics, liberation and dispersal of sika deer (Cervus nippon) in New Zealand. New Zealand Journal of Forestry Science 3: 153-180.
55. Groves CP, Grubb P (1987) Relationships of living deer. In: Wemmer CM, editor. Biology and Management of the Cervidae. Washington DC: Smithsonian Institution Press. pp. 21-59.
56. Goodman SJ, Barton NH, Swanson G, Abernethy K, Pemberton JM (1999) Introgression through rare hybridization: a genetic study of a hybrid zone between red and sika deer (Genus Cervus) in Argyll, Scotland. Genetics 152: 355-371. (Pubitemid 29222539)
57. Diaz A, Hughes S, Putman R, Mogg R, Bond JM (2006) A genetic study of sika (Cervus nippon) in the New Forest and in the Purbeck region, southern England: is there evidence of recent or past hybridization with red deer (Cervus elaphus)? J Zool 270: 227-235. (Pubitemid 44394064)
58. McDevitt AD, Edwards CJ, O'Toole P, O'Sullivan P, O'Reilly C, et al. (2009) Genetic structure of, and hybridisation between, red (Cervus elaphus) and sika (Cervus nippon) deer in Ireland. Mammalian Biology - Zeitschrift für Säugetierkunde 74: 263-273.
59. Senn HV, Pemberton JM (2009) Variable extent of hybridization between invasive sika (Cervus nippon) and native red deer (C. elaphus) in a small geographical area. Mol Ecol 18: 862-876.
60. Allen RB, Wright EF, MacLeod CJ, Bellingham PJ, Forsyth DM, et al. (2009) Designing an inventory and monitoring programme for the Department of Conservation's natural heritage management system. Prepared for Department of Conservation, Wellington, New Zealand: Landcare Research. 229 p.
61. Fajardo V, González I, Mart?́n I, Rojas M, Hernández PE, et al. (2008) Realtime PCR for detection and quantification of red deer (Cervus elaphus), fallow deer (Dama dama), and roe deer (Capreolus capreolus) in meat mixtures. Meat Sci 79: 289-298. (Pubitemid 351400526)
62. Shackell GH (2008) Traceability in the meat industry - the farm to plate continuum. Int J Food Sci Tech 43: 2134-2142.
63. Lorenzini R (2005) DNA forensics and the poaching of wildlife in Italy: A case study. Forensic Sci Int 153: 218-221. (Pubitemid 41219677)
64. Nichols R, Königsson H, Danell K, Spong G (2012) Browsed twig environmental DNA: diagnostic PCR to identify ungulate species. Mol Ecol Resources 12: 983-989.
65. 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 Biotechnol 3: 294-299.
66. Ramón-Laca A, Linacre AMT, Gleeson DM, Tobe SS (2013) Identification multiplex assay of 19 terrestrial mammal species present in New Zealand. Electrophoresis 34: 3370-3376.
67. Simon C, Frati F, Beckenbach A, Crespi B, Liu H, et al. (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann Entomol Soc Am 87: 651-701.
68. Tobe SS, Linacre AMT (2008) A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochrome b gene. Electrophoresis 29: 340-347. (Pubitemid 351201508)
69. Wada K, Okumura K, Nishibori M, Kikkawa Y, Yokohama M (2010) The complete mitochondrial genome of the domestic red deer (Cervus elaphus) of New Zealand and its phylogenic position within the family Cervidae. Anim Sci J 81: 551-557.