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

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Lake Restoration Handbook

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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.

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  1. Ian D. Hogg

    Present address: Polar Knowledge Canada, Cambridge Bay, NU, Canada

Authors and Affiliations

  1. School of Science, University of Waikato, Hamilton, New Zealand

    Ian D. Hogg & Steve M. Woods

  2. Cawthron Institute, Nelson, New Zealand

    Jonathan C. Banks

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Correspondence to Ian D. Hogg .

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Editors and Affiliations

  1. Australian Rivers Institute, Griffith University, Brisbane, Australia

    David P. Hamilton

  2. Environmental Research Institute, The University of Waikato, Hamilton, New Zealand

    Kevin J. Collier

  3. NIWA (National Institute of Water and Atmospheric Research), Hamilton, New Zealand

    John M. Quinn

  4. NIWA (National Institute of Water and Atmospheric Research), Christchurch, New Zealand

    Clive Howard-Williams

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Hogg, I.D., Banks, J.C., Woods, S.M. (2018). Biodiversity Genomics: Monitoring Restoration Efforts Using DNA Barcoding and Environmental DNA. In: Hamilton, D., Collier, K., Quinn, J., Howard-Williams, C. (eds) Lake Restoration Handbook. Springer, Cham. https://doi.org/10.1007/978-3-319-93043-5_12

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