Advertisement

Biodiversity Genomics: Monitoring Restoration Efforts Using DNA Barcoding and Environmental DNA

  • Ian D. HoggEmail author
  • Jonathan C. Banks
  • Steve M. Woods
Chapter

Abstract

We review recent advances in the use of molecular techniques as they apply to monitoring restoration efforts in lakes. Using DNA sequence data, biodiversity can now be assessed to levels previously unattainable using traditional, morphological assessments. In particular, DNA barcoding, the use of small standardised fragments of DNA, has become an increasingly widespread and common approach to identify species. Global initiatives such as the International Barcode of Life (iBOL) have coordinated these efforts and facilitated publically accessible reference databases such as the Barcode of Life Datasystems (BOLD). Such databases can be used for routine identification of specimens as well as for the assessment of community composition and monitoring of changes over time. Through the application of Next Generation Sequencing techniques, multiple samples can be run simultaneously (metabarcoding), greatly automating and streamlining the monitoring process. Reference databases can also be applied to environmental DNA (DNA that is shed into the environment by plants and animals). Here, species can be identified “sight unseen” through analyses of environmental samples (e.g. water, sediment). This latter method has proven useful for the monitoring of exotic fish species, particularly following eradication efforts. Ongoing developments in sequencing technology are likely to further enhance the utility of molecular techniques for assessing and monitoring restoration efforts in New Zealand.

Keywords

DNA barcoding Barcode of life datasystems Genetic characterisation of fauna eDNA International barcode of life 

References

  1. Armstrong K, Ball S (2005) DNA barcodes for biosecurity: invasive species identification. Philos Trans R Soc Lond B Biol Sci 360:1813–1823PubMedPubMedCentralCrossRefGoogle Scholar
  2. Auckland Regional Council (2005) Assessment of trophic state change in selected lakes of the Auckland Region based on rotifer assemblages. Technical Publication 269:31 Auckland Regional Council, Auckland, New ZealandGoogle Scholar
  3. Baird DJ, Hajibabaei M (2012) Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next–generation DNA sequencing. Mol Ecol 21:2039–2044PubMedCrossRefPubMedCentralGoogle Scholar
  4. Banks JC, Hogg ID, Cary SC (2009) The phylogeography of Adelie penguin faecal bacteria. Environ Microbiol 11:577–588PubMedCrossRefPubMedCentralGoogle Scholar
  5. Banks JC, Demetras NJ, Hogg ID, Knox MA, West DW (2016) Monitoring brown trout (Salmo trutta) eradication in a wildlife sanctuary using environmental DNA. N Z Nat Sci 41:1–13Google Scholar
  6. Bianchi F, Acri F, Aubry FB, Berton A, Boldrin A, Camatti E, Cassin D, Comaschi A (2003) Can plankton communities be considered as bio-indicators of water quality in the Lagoon of Venice? Mar Pollut Bull 46:964–971PubMedCrossRefPubMedCentralGoogle Scholar
  7. Biggs J, Ewald N, Valentini A, Gaboriaud C, Dejean T, Griffiths RA, Foster J, Wilkinson JW, Arnell A, Brotherton P, Williams P, Dunn F (2015) Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biol Conserv 183:19–28CrossRefGoogle Scholar
  8. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 27:233–243PubMedPubMedCentralCrossRefGoogle Scholar
  9. Bongers T (1990) The maturity index: an ecological measure of environmental disturbance based on nematode species composition. Oecologia 83:14–19PubMedCrossRefPubMedCentralGoogle Scholar
  10. Burns NM, Rutherford JC, Clayton JS (1999) A monitoring and classification system for New Zealand lakes and reservoirs. Lake Reservoir Manage 15:255–271CrossRefGoogle Scholar
  11. Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336PubMedPubMedCentralCrossRefGoogle Scholar
  12. Chapman MA, Lewis MH, Winterbourn MJ (2011) Guide to the freshwater Crustacea of New Zealand. New Zealand Freshwater Sciences Society, Wellington, New ZealandGoogle Scholar
  13. Civade R, Dejean T, Valentini A et al (2016) Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system. PLoS One 11:e0157366PubMedPubMedCentralCrossRefGoogle Scholar
  14. Cline J, Braman JC, Hogrefe HH (1996) PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res 24:3546–3551PubMedPubMedCentralCrossRefGoogle Scholar
  15. Cristescu ME (2015) Genetic reconstructions of invasion history. Mol Ecol 24:2212–2225PubMedCrossRefPubMedCentralGoogle Scholar
  16. Darling JA, Mahon AR (2011) From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environ Res 111:978–988PubMedCrossRefPubMedCentralGoogle Scholar
  17. Deagle BE, Thomas AC, Shaffer AK, Trites AW, Jarman SN (2013) Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? Mol Ecol Resour 13:620–633PubMedCrossRefPubMedCentralGoogle Scholar
  18. Deiner K, Walser J-C, Mächler E, Altermatt F (2015) Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol Conserv 183:53–63CrossRefGoogle Scholar
  19. Dejean T, Valentini A, Duparc A, Pellier-Cuit S, Pompanon F, Teberlet P, Miaud C (2011) Persistence of environmental DNA in freshwater ecosystems. PLoS One 6:e23398PubMedPubMedCentralCrossRefGoogle Scholar
  20. Dejean T, Valentini A, Miquel C, Taberlet P, Bellemain E, Miaud C (2012) Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. J Appl Ecol 49:953–959CrossRefGoogle Scholar
  21. Diggle J, Patil J, Wisniewski C (2012) A manual for carp control: the Tasmanian model. Invasive Animals CRC, New Norfolk, TAS, AustraliaGoogle Scholar
  22. Dowle E, Pochon X, Banks J, Shearer K, Wood SA (2016) Targeted gene enrichment and high throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates. Mol Ecol Resour 16(5):1240–1254PubMedCrossRefPubMedCentralGoogle Scholar
  23. Duggan IC (2007) An assessment of the water quality of ten Waikato lakes based on zooplankton community composition. CBER Contract Report No. 60, Prepared for Environment Waikato, Centre for Biodiversity and Ecology Research, University of Waikato, Hamilton, New ZealandGoogle Scholar
  24. Duggan IC, Green JD, Shiel RJ (2001a) Distribution of rotifers in North Island, New Zealand, and their potential use as bioindicators of lake trophic state. Hydrobiologia 446–447:155–164CrossRefGoogle Scholar
  25. Duggan IC, Green JD, Thomasson K (2001b) Do rotifers have potential as bioindicators of lake trophic state? Verh Internat Verein Limnol 27:3497–3502Google Scholar
  26. Duggan IC, Robinson KV, Burns CW, Banks JC, Hogg ID (2012) Identifying invertebrate invasions using morphological and molecular analyses: North American Daphnia ‘pulex’ in New Zealand fresh waters. Aquat Invasions 7:585–590CrossRefGoogle Scholar
  27. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998PubMedCrossRefPubMedCentralGoogle Scholar
  28. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200PubMedPubMedCentralCrossRefGoogle Scholar
  29. Environmental Protection Agency (2014) http://www.epa.gov/greatlakes/basicinfo.html. Accessed 3 Sept 2018
  30. Evans NT, Olds BP, Renshaw MA, Turner CR, Li Y, Jerde CL, Mahon AR, Pfrender ME, Lamberti GA, Lodge DM (2016) Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol Ecol Resour 16:29–41PubMedCrossRefPubMedCentralGoogle Scholar
  31. Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4:423–425PubMedPubMedCentralCrossRefGoogle Scholar
  32. Ficetola GF, Pansu J, Bonin A, Coissac E, Giguet-Covex C, De Barba M, Gielly L, Lopes CM, Boyer F (2015) Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Mol Ecol Resour 15:543–556PubMedCrossRefGoogle Scholar
  33. Field KG, Samadpour M (2007) Fecal source tracking, the indicator paradigm, and managing water quality. Water Res 41:3517–3538PubMedCrossRefPubMedCentralGoogle Scholar
  34. Furlan E, Gleeson D (2017) Improving reliability in environmental DNA detection surveys through enhanced quality control. Mar Freshw Res 68:388–395CrossRefGoogle Scholar
  35. Furlan E, Gleeson D, Hardy C, Duncan RP (2015) A framework for estimating the sensitivity of eDNA detection. Mol Ecol Resour 16:641–654PubMedCrossRefPubMedCentralGoogle Scholar
  36. Goldberg CS, Pilliod DS, Arkle RS, Waits LP (2011) Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PLoS One 6:e22746PubMedPubMedCentralCrossRefGoogle Scholar
  37. Goldberg CS, Sepulveda A, Ray A, Baumgardt J, Waits LP (2013) Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshw Sci 32:792–800CrossRefGoogle Scholar
  38. Griffin DW, Lipp EK, McLaughlin MR, Rose JB (2001) Marine recreation and public health microbiology: quest for the ideal indicator. Bioscience 51:817–826CrossRefGoogle Scholar
  39. Gu W, Swihart RK (2004) Absent or undetected? Effects of non-detection of species occurrence on wildlife–habitat models. Biol Conserv 116:195–203CrossRefGoogle Scholar
  40. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ; Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504PubMedCrossRefPubMedCentralGoogle Scholar
  41. Hajibabaei M, Shokralla S, Zhou X, Singer GA, Baird DJ (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One 6:e17497PubMedPubMedCentralCrossRefGoogle Scholar
  42. Hänfling B, Handley L, Read DS, Hahn C, Li J, Nichols P, Blackman RC, Oliver A, Winfield IJ (2016) Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Mol Ecol 25:3101–3119PubMedCrossRefPubMedCentralGoogle Scholar
  43. Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003a) Biological identifications through DNA barcodes. Proc Biol Sci 270:313–321PubMedPubMedCentralCrossRefGoogle Scholar
  44. Hebert PDN, Ratnasingham S, de Waard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci 270(Suppl 1):S96–S99PubMedPubMedCentralGoogle Scholar
  45. Hicks BJ, Watson NRN (1985) Seasonal changes in abundance of brown trout (Salmo trutta) and rainbow trout (S. gairdnerii) assessed by drift diving in the Rangitikei River, New Zealand. N Z J Mar Freshw Res 19:1–10CrossRefGoogle Scholar
  46. Hicks BJ, Brijs J, Daniel A, Morgan DKJ, Ling N (2015) Biomass estimation of invasive fish. In: Collier KJ, Gainger NPJ (eds) New Zealand invasive fish management handbook. The University of Waikato, Hamilton, New Zealand, pp 116–122Google Scholar
  47. Hofreiter M, Mead JI, Martin P, Poinar HN (2003) Molecular caving. Curr Biol 13:R693–R695PubMedCrossRefPubMedCentralGoogle Scholar
  48. Hogg ID, Larose C, de Lafontaine Y, Doe KG (1998) Genetic evidence for a Hyalella species complex within the Great Lakes-St. Lawrence River drainage basin: implications for ecotoxicology and conservation biology. Can J Zool 76:1134–1152CrossRefGoogle Scholar
  49. Hogg ID, Stevens MI, Schnabel KE, Chapman MA (2006) Deeply divergent lineages among populations of the widespread New Zealand amphipod Paracalliope fluviatilis revealed using allozyme and mitochondrial DNA analyses. Freshw Biol 51:236–248CrossRefGoogle Scholar
  50. Jerde CL, Mahon AR, Chadderton WL, Lodge DM (2011) “Sight-unseen” detection of rare aquatic species using environmental DNA. Conserv Lett 4:150–157CrossRefGoogle Scholar
  51. Jerde CL, Chadderton WL, Mahon AR, Renshaw MA, Corush J, Budny ML, Mysorekar S, Lodge DM (2013) Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program. Can J Fish Aquat Sci 70:522–526CrossRefGoogle Scholar
  52. Laramie MB, Pilliod DS, Goldberg CS (2015) Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biol Conserv 183:29–37CrossRefGoogle Scholar
  53. Lear G, Lewis GD (2009) Impact of catchment land use on bacterial communities within stream biofilms. Ecol Indic 9:848–855CrossRefGoogle Scholar
  54. Lindeque PK, Parry HE, Harmer RA et al (2013) Next generation sequencing reveals the hidden diversity of zooplankton assemblages. PLoS One 8:e81327PubMedPubMedCentralCrossRefGoogle Scholar
  55. Lodge DM, Turner CR, Jerde CL, Barnes MA, Chadderton L, Egan SP, Feder JL, Mahon AR, Pfrender ME (2012) Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Mol Ecol 21:2555–2558PubMedPubMedCentralCrossRefGoogle Scholar
  56. Machida R, Hashiguchi Y, Nishida M, Nishida S (2009) Zooplankton diversity analysis through single-gene sequencing of a community sample. BMC Genomics 10:438PubMedPubMedCentralCrossRefGoogle Scholar
  57. Mahon AR, Jerde CL, Galaska M, Bergner JL, Chadderton WL, Lodge DM, Hunter ME, Nico LG (2013) Validation of eDNA surveillance sensitivity for detection of Asian carp in controlled and field experiments. PLoS One 8:e58316PubMedPubMedCentralCrossRefGoogle Scholar
  58. Mahon AR, Nathan LR, Jerde CL (2014) Meta-genomic surveillance of invasive species in the bait trade. Conserv Genet Resour 6:563–567CrossRefGoogle Scholar
  59. McDowall RM (2003) Impacts of introduced salmonids on native galaxiids in New Zealand upland streams: a new look at an old problem. Trans Am Fish Soc 132:229–238CrossRefGoogle Scholar
  60. McInerney PJ, Rees GN, Gawne B, Suter P, Watson G, Stoffels RJ (2016) Invasive willows drive instream community structure. Freshw Biol 61:1379–1391CrossRefGoogle Scholar
  61. McIntosh AR, McHugh PA, Dunn NR, Goodman J, Howard SW, Jellyman PG, O’Brien LK, Nyström P, Woodford DJ (2010) The impact of trout on galaxiid fishes in New Zealand. N Z J Ecol 34:195–206Google Scholar
  62. Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46CrossRefGoogle Scholar
  63. Mills EL, Leach JH, Carlton JT, Secor CL (1993) Exotic species in the Great Lakes: a history of biotic crises and anthropogenic introductions. J Great Lakes Res 19:1–54CrossRefGoogle Scholar
  64. Minamoto T, Yamanaka H, Takahara T, Honjo MN, Kawabata Z (2012) Surveillance of fish species composition using environmental DNA. Limnology 13:193–197CrossRefGoogle Scholar
  65. Moyer GR, Díaz-Ferguson E, Hill JE, Shea C (2014) Assessing environmental DNA detection in controlled lentic systems. PLoS One 9:e103767PubMedPubMedCentralCrossRefGoogle Scholar
  66. Murray DC, Bunce M, Cannell BL, Oliver R, Houston J, White NE, Barrero RA, Bellgard MI, Haile J (2011) DNA-based faecal dietary analysis: a comparison of qPCR and high throughput sequencing approaches. PLoS One 6:e2577Google Scholar
  67. Nathan LR, Jerde CL, Budny ML, Mahon AR (2014) The use of environmental DNA in invasive species surveillance of the Great Lakes commercial bait trade. Conserv Biol 29:430–439PubMedCrossRefPubMedCentralGoogle Scholar
  68. National Oceanic and Atmospheric Administration (2014) http://www.glerl.noaa.gov/pr/ourlakes/economy.html. Accessed 3 Dec 2014
  69. Nolte V, Pandey RV, Jost S, Medinger R, Ottenwälder B, Boenigk J, Schlötterer C (2010) Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Mol Ecol 19:2908–2915PubMedPubMedCentralCrossRefGoogle Scholar
  70. Olds BP, Jerde CL, Renshaw MA et al (2016) Estimating species richness using environmental DNA. Ecol Evol 6:4214–4226PubMedPubMedCentralCrossRefGoogle Scholar
  71. Porazinska DL, Sung WAY, Giblin-Davis RM, Thomas WK (2010) Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure. Mol Ecol Resour 10:666–676PubMedCrossRefGoogle Scholar
  72. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341PubMedPubMedCentralCrossRefGoogle Scholar
  73. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38PubMedPubMedCentralCrossRefGoogle Scholar
  74. Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of life data system (http://www.barcodinglife.org). Mol Ecol Notes 7:355–364
  75. Ratnasingham S, Hebert PDN (2013) A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS One 8:e66213PubMedPubMedCentralCrossRefGoogle Scholar
  76. Rees HC, Maddison BC, Middleditch DJ, Patmore JRM, Gough KC (2014) The detection of aquatic animal species using environmental DNA—a review of eDNA as a survey tool in ecology. J Appl Ecol 51:1450–1459CrossRefGoogle Scholar
  77. Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541PubMedPubMedCentralCrossRefGoogle Scholar
  78. Schmidt BR, Kéry M, Ursenbacher S, Hyman OJ, Collins JP (2013) Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen. Methods Ecol Evol 4:646–653CrossRefGoogle Scholar
  79. Scott TM, Rose JB, Jenkins TM, Farrah SR, Lukasik J (2002) Microbial source tracking: current methodology and future directions. Appl Environ Microbiol 68:5796–5803PubMedPubMedCentralCrossRefGoogle Scholar
  80. Scriver M, Marinich A, Wilson C, Freeland J (2015) Development of species-specific environmental DNA (eDNA) markers for invasive aquatic plants. Aquat Bot 122:27–31CrossRefGoogle Scholar
  81. Sevilla RG, Diez A, Norén M et al (2007) Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes. Mol Ecol Notes 7:730–734CrossRefGoogle Scholar
  82. Shaw JL, Clarke ALJ, Wedderburn SD, Barnes TC, Weyricha LS, Cooper A (2016) Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biol Conserv 197:131–138CrossRefGoogle Scholar
  83. Sigsgaard EE, Carl H, Møller PR, Thomsen PF (2015) Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples. Biol Conserv 183:46–52CrossRefGoogle Scholar
  84. Spear SF, Groves JD, Williams LA, Waits LP (2015) Using environmental DNA methods to improve detectability in a hellbender (Cryptobranchus alleganiensis) monitoring program. Biol Conserv 183:38–45CrossRefGoogle Scholar
  85. Stark JD (1993) Performance of the macroinvertebrate community index: effects of sampling method, sample replication, water depth, current velocity, and substratum on index values. N Z J Mar Freshw Res 27:463–478CrossRefGoogle Scholar
  86. Stewart-Oaten A, Murdoch WW, Parker KR (1986) Environmental impact assessment: “Pseudoreplication” in time? Ecology 67:929–940CrossRefGoogle Scholar
  87. Takahara T, Minamoto T, Doi H (2015) Effects of sample processing on the detection rate of environmental DNA from the common carp (Cyprinus carpio). Biol Conserv 183:64–69CrossRefGoogle Scholar
  88. Thomsen PF, Willerslev E (2015) Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv 183:4–18CrossRefGoogle Scholar
  89. Thomsen P, Kielgast JOS, Iversen LL, Wiuf C, Rasmussen M, Gilbert MT, Orlando L, Willerslev E (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573PubMedCrossRefPubMedCentralGoogle Scholar
  90. Townsend CR (1996) Invasion biology and ecological impacts of brown trout Salmo trutta in New Zealand. Biol Conserv 78:13–22CrossRefGoogle Scholar
  91. Valentini A, Taberlet P, Miaud C et al (2016) Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol Ecol 25:929–942PubMedCrossRefPubMedCentralGoogle Scholar
  92. Wilcox TM, Mckelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS One 8:e59520PubMedPubMedCentralCrossRefGoogle Scholar
  93. Willerslev E, Cappellini E, Boomsma W et al (2007) Ancient biomolecules from deep ice cores reveal a forested Southern Greenland. Science 317:111–114PubMedPubMedCentralCrossRefGoogle Scholar
  94. Wilson IG (1997) Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63:3741–3751PubMedPubMedCentralGoogle Scholar
  95. Wittmann ME, Cooke RM, Rothlisberger JD, Rutherford ES, Zhang H, Mason DM, Lodge DM (2014) Use of structured expert judgment to forecast invasions by bighead and silver carp in Lake Erie. Conserv Biol 29:187–197PubMedCrossRefPubMedCentralGoogle Scholar
  96. Wood SA, Smith KF, Banks J, Tremblay L, Rhodes L, Mountfort D, Cary SC, Pochon X (2013) Molecular tools for environmental monitoring of New Zealand’s aquatic habitats: past, present and the future. N Z J Mar Freshw Res 47:90–119CrossRefGoogle Scholar
  97. Yoccoz NG, Nichols JD, Boulinier T (2001) Monitoring of biological diversity in space and time. Trends Ecol Evol 16:446–453CrossRefGoogle Scholar
  98. Yu DW, Ji Y, Emerson BC, Wang X, Ye C, Yang C, Ding Z (2012) Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol 3:613–623CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Ian D. Hogg
    • 1
    • 2
    Email author
  • Jonathan C. Banks
    • 3
  • Steve M. Woods
    • 1
  1. 1.School of Science, University of WaikatoHamiltonNew Zealand
  2. 2.Polar Knowledge CanadaCambridge BayCanada
  3. 3.Cawthron InstituteNelsonNew Zealand

Personalised recommendations