Dung, Dirt & DNA: unearthing past and present biodiversity using environmental DNA metabarcoding
The rapid loss of biodiversity highlights the urgency of large-scale biodiversity monitoring for conservation, as well as the importance of understanding biodiversity in all its dimensions, especially in light of environmental change. In order to understand the causes of these changes in biodiversit...
Published in: | Environmental DNA |
---|---|
Main Author: | |
Format: | Doctoral or Postdoctoral Thesis |
Language: | English |
Published: |
Series of dissertations submitted to the Faculty of Mathematics and Natural Sciences, University of Oslo
2021
|
Subjects: | |
Online Access: | http://hdl.handle.net/10852/89875 http://urn.nb.no/URN:NBN:no-92479 |
id |
ftoslouniv:oai:www.duo.uio.no:10852/89875 |
---|---|
record_format |
openpolar |
institution |
Open Polar |
collection |
Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
op_collection_id |
ftoslouniv |
language |
English |
description |
The rapid loss of biodiversity highlights the urgency of large-scale biodiversity monitoring for conservation, as well as the importance of understanding biodiversity in all its dimensions, especially in light of environmental change. In order to understand the causes of these changes in biodiversity, we need to track them over time, either through continued biomonitoring, or through reconstructions of past changes. Trace DNA in environmental samples such as sediments and faeces, allows for the detection of species and biodiversity monitoring without the need to sight or sample the actual organisms. This is not only useful for conservation purposes, but also for the detection of species in palaeo records, such as those presented by lakes, caves, and permafrost. Particularly eDNA metabarcoding, a tool for the simultaneous identification of many organisms in an environmental sample, is a useful tool that can provide a window to the biological past. With initial technological issues involved in these methods largely worked out, and many guides are being published on how to apply them (including chapter 1), the field of eDNA metabarcoding can now move towards enhancing the interpretation of the resulting data. This is especially complex in interdisciplinary contexts and testing of its application to a range of topics and contexts is therefore needed. By applying these methods to faecal and sediment samples, this thesis provides insight into its applications through the biomonitoring of herbivores in a wildlife reserve in India (chapter 2), reconstructing the diets and habitats of extinct and extant megafauna (chapter 3), the untangling of human-environment interactions (chapter 4) and the assessment of DNA metabarcoding for reconstructing prehistoric human plant use (chapter 5). In interdisciplinary collaborations such as many of these chapters, good communication is very important. Environmental DNA metabarcoding, combined with statistical approaches as well as clear visualisation of the obtained results, such as ... |
format |
Doctoral or Postdoctoral Thesis |
author |
ter Schure, Anneke |
spellingShingle |
ter Schure, Anneke Dung, Dirt & DNA: unearthing past and present biodiversity using environmental DNA metabarcoding |
author_facet |
ter Schure, Anneke |
author_sort |
ter Schure, Anneke |
title |
Dung, Dirt & DNA: unearthing past and present biodiversity using environmental DNA metabarcoding |
title_short |
Dung, Dirt & DNA: unearthing past and present biodiversity using environmental DNA metabarcoding |
title_full |
Dung, Dirt & DNA: unearthing past and present biodiversity using environmental DNA metabarcoding |
title_fullStr |
Dung, Dirt & DNA: unearthing past and present biodiversity using environmental DNA metabarcoding |
title_full_unstemmed |
Dung, Dirt & DNA: unearthing past and present biodiversity using environmental DNA metabarcoding |
title_sort |
dung, dirt & dna: unearthing past and present biodiversity using environmental dna metabarcoding |
publisher |
Series of dissertations submitted to the Faculty of Mathematics and Natural Sciences, University of Oslo |
publishDate |
2021 |
url |
http://hdl.handle.net/10852/89875 http://urn.nb.no/URN:NBN:no-92479 |
genre |
permafrost |
genre_facet |
permafrost |
op_relation |
Paper I / Chapter 1 ter Schure, Anneke TM, et al. "aDNA from sediments" Chapter 8 in: de Boer H, Rydmark MO, Verstraete B, Gravendeel B (Eds) Molecular identification of plants: from sequence to species. Advanced Books. An author version is included in the thesis. The published version is available at: https://doi.org/10.3897/ab.e98875 Paper II / Chapter 2 ter Schure, Anneke TM, et al. "eDNA metabarcoding reveals dietary niche overlap among herbivores in an Indian wildlife sanctuary." Environmental DNA 3.3 (2021): 681-696. An author version is included in the thesis. The published version is available at: https://doi.org/10.1002/edn3.168 Paper III / Chapter 3 Polling, Marcel, et al. "Multiproxy analysis of permafrost preserved faeces provides an unprecedented insight into the diets and habitats of extinct and extant megafauna." Quaternary Science Reviews 267 (2021): 107084. An author version is included in the thesis. The published version is available at: https://doi.org/10.1016/j.quascirev.2021.107084 Paper IV / Chapter 4 ter Schure, Anneke Theresia Maria, et al. "Anthropogenic and environmental drivers of vegetation change in southeastern Norway during the Holocene." Quaternary Science Reviews 270 (2021): 107175. An author version is included in the thesis. The published version is available at: https://doi.org/10.1016/j.quascirev.2021.107175 Paper V / Chapter 5 ter Schure, Anneke Theresia Maria, et al. "SedaDNA metabarcoding as a tool for assessing prehistoric plant use at Upper Palaeolithic cave site Aghitu-3, Armenia". Manuscript. Published as: Sedimentary ancient DNA metabarcoding as a tool for assessing prehistoric plant use at the Upper Paleolithic cave site Aghitu-3, Armenia. Journal of Human Evolution, 2022, 172:103258. DOI:10.1016/j.jhevol.2022.103258. An author version is included in the thesis. The published version is available at: https://doi.org/10.1016/j.jhevol.2022.103258 https://doi.org/10.1002/edn3.168 https://doi.org/10.1016/j.quascirev.2021.107084 https://doi.org/10.1016/j.quascirev.2021.107175 https://doi.org/10.3897/ab.e98875 https://doi.org/10.1016/j.jhevol.2022.103258 http://urn.nb.no/URN:NBN:no-92479 http://hdl.handle.net/10852/89875 1957737 230 URN:NBN:no-92479 Fulltext https://www.duo.uio.no/bitstream/handle/10852/89875/5/phd-ter-schure-duo.pdf |
op_doi |
https://doi.org/10.3897/ab.e98875 https://doi.org/10.1002/edn3.168 https://doi.org/10.1016/j.quascirev.2021.107084 https://doi.org/10.1016/j.quascirev.2021.107175 https://doi.org/10.1016/j.jhevol.2022.103258 |
container_title |
Environmental DNA |
container_volume |
3 |
container_issue |
3 |
container_start_page |
681 |
op_container_end_page |
696 |
_version_ |
1766166764652068864 |
spelling |
ftoslouniv:oai:www.duo.uio.no:10852/89875 2023-05-15T17:58:12+02:00 Dung, Dirt & DNA: unearthing past and present biodiversity using environmental DNA metabarcoding ter Schure, Anneke 2021-11-23T12:19:14Z http://hdl.handle.net/10852/89875 http://urn.nb.no/URN:NBN:no-92479 EN eng Series of dissertations submitted to the Faculty of Mathematics and Natural Sciences, University of Oslo Paper I / Chapter 1 ter Schure, Anneke TM, et al. "aDNA from sediments" Chapter 8 in: de Boer H, Rydmark MO, Verstraete B, Gravendeel B (Eds) Molecular identification of plants: from sequence to species. Advanced Books. An author version is included in the thesis. The published version is available at: https://doi.org/10.3897/ab.e98875 Paper II / Chapter 2 ter Schure, Anneke TM, et al. "eDNA metabarcoding reveals dietary niche overlap among herbivores in an Indian wildlife sanctuary." Environmental DNA 3.3 (2021): 681-696. An author version is included in the thesis. The published version is available at: https://doi.org/10.1002/edn3.168 Paper III / Chapter 3 Polling, Marcel, et al. "Multiproxy analysis of permafrost preserved faeces provides an unprecedented insight into the diets and habitats of extinct and extant megafauna." Quaternary Science Reviews 267 (2021): 107084. An author version is included in the thesis. The published version is available at: https://doi.org/10.1016/j.quascirev.2021.107084 Paper IV / Chapter 4 ter Schure, Anneke Theresia Maria, et al. "Anthropogenic and environmental drivers of vegetation change in southeastern Norway during the Holocene." Quaternary Science Reviews 270 (2021): 107175. An author version is included in the thesis. The published version is available at: https://doi.org/10.1016/j.quascirev.2021.107175 Paper V / Chapter 5 ter Schure, Anneke Theresia Maria, et al. "SedaDNA metabarcoding as a tool for assessing prehistoric plant use at Upper Palaeolithic cave site Aghitu-3, Armenia". Manuscript. Published as: Sedimentary ancient DNA metabarcoding as a tool for assessing prehistoric plant use at the Upper Paleolithic cave site Aghitu-3, Armenia. Journal of Human Evolution, 2022, 172:103258. DOI:10.1016/j.jhevol.2022.103258. An author version is included in the thesis. The published version is available at: https://doi.org/10.1016/j.jhevol.2022.103258 https://doi.org/10.1002/edn3.168 https://doi.org/10.1016/j.quascirev.2021.107084 https://doi.org/10.1016/j.quascirev.2021.107175 https://doi.org/10.3897/ab.e98875 https://doi.org/10.1016/j.jhevol.2022.103258 http://urn.nb.no/URN:NBN:no-92479 http://hdl.handle.net/10852/89875 1957737 230 URN:NBN:no-92479 Fulltext https://www.duo.uio.no/bitstream/handle/10852/89875/5/phd-ter-schure-duo.pdf Doctoral thesis Doktoravhandling 2021 ftoslouniv https://doi.org/10.3897/ab.e98875 https://doi.org/10.1002/edn3.168 https://doi.org/10.1016/j.quascirev.2021.107084 https://doi.org/10.1016/j.quascirev.2021.107175 https://doi.org/10.1016/j.jhevol.2022.103258 2023-02-08T23:36:24Z The rapid loss of biodiversity highlights the urgency of large-scale biodiversity monitoring for conservation, as well as the importance of understanding biodiversity in all its dimensions, especially in light of environmental change. In order to understand the causes of these changes in biodiversity, we need to track them over time, either through continued biomonitoring, or through reconstructions of past changes. Trace DNA in environmental samples such as sediments and faeces, allows for the detection of species and biodiversity monitoring without the need to sight or sample the actual organisms. This is not only useful for conservation purposes, but also for the detection of species in palaeo records, such as those presented by lakes, caves, and permafrost. Particularly eDNA metabarcoding, a tool for the simultaneous identification of many organisms in an environmental sample, is a useful tool that can provide a window to the biological past. With initial technological issues involved in these methods largely worked out, and many guides are being published on how to apply them (including chapter 1), the field of eDNA metabarcoding can now move towards enhancing the interpretation of the resulting data. This is especially complex in interdisciplinary contexts and testing of its application to a range of topics and contexts is therefore needed. By applying these methods to faecal and sediment samples, this thesis provides insight into its applications through the biomonitoring of herbivores in a wildlife reserve in India (chapter 2), reconstructing the diets and habitats of extinct and extant megafauna (chapter 3), the untangling of human-environment interactions (chapter 4) and the assessment of DNA metabarcoding for reconstructing prehistoric human plant use (chapter 5). In interdisciplinary collaborations such as many of these chapters, good communication is very important. Environmental DNA metabarcoding, combined with statistical approaches as well as clear visualisation of the obtained results, such as ... Doctoral or Postdoctoral Thesis permafrost Universitet i Oslo: Digitale utgivelser ved UiO (DUO) Environmental DNA 3 3 681 696 |