Loading…
A probabilistic model for designing and assessing the performance of eDNA sampling protocols
Environmental DNA (eDNA) sampling, the detection of species‐specific genetic material in water samples, is an emerging tool for monitoring aquatic invasive species. Optimizing eDNA sampling protocols can be challenging because there is imperfect understanding of how each step of the protocol influen...
Saved in:
Published in: | Molecular ecology resources 2020-03, Vol.20 (2), p.404-414 |
---|---|
Main Authors: | , , , , , , , |
Format: | Article |
Language: | English |
Subjects: | |
Citations: | Items that this one cites Items that cite this one |
Online Access: | Get full text |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
cited_by | cdi_FETCH-LOGICAL-c3713-1d15fc6df86059a60654eda4cc110f0cf92258f3a14a2c4ead4327673cc4a7403 |
---|---|
cites | cdi_FETCH-LOGICAL-c3713-1d15fc6df86059a60654eda4cc110f0cf92258f3a14a2c4ead4327673cc4a7403 |
container_end_page | 414 |
container_issue | 2 |
container_start_page | 404 |
container_title | Molecular ecology resources |
container_volume | 20 |
creator | Song, Jeffery W. Schultz, Martin T. Casman, Elizabeth A. Bockrath, Katherine D. Mize, Erica Monroe, Emy M. Tuttle‐Lau, Maren Small, Mitchell J. |
description | Environmental DNA (eDNA) sampling, the detection of species‐specific genetic material in water samples, is an emerging tool for monitoring aquatic invasive species. Optimizing eDNA sampling protocols can be challenging because there is imperfect understanding of how each step of the protocol influences its sensitivity. This paper develops a probabilistic model that characterizes each step of an eDNA sampling protocol to evaluate the protocol's overall detection sensitivity for one sample. The model is then applied to analyse how changes over time made to the eDNA sampling protocol to detect bighead (BH) and silver carp (SC) eDNA have influenced its sensitivity, and hence interpretation of the results. The model shows that changes to the protocol have caused the sensitivity of the protocol to fluctuate. A more efficient extraction method in 2013, new species‐specific markers with a qPCR assay in 2014, and a more efficient capture method in 2015 have improved the sensitivity, while switching to a larger elution volume in 2013 and a smaller sample volume in 2015 have reduced the sensitivity. Overall, the sensitivity of the current protocol is higher for BH eDNA detection and SC eDNA detection compared to the original protocol used from 2009 to 2012. The paper shows how this model of eDNA sampling can be used to evaluate the effect of proposed changes in an eDNA sampling and analysis protocol on the sensitivity of that protocol to help researchers optimize their design. |
doi_str_mv | 10.1111/1755-0998.13113 |
format | article |
fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_journals_2366245616</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2366245616</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3713-1d15fc6df86059a60654eda4cc110f0cf92258f3a14a2c4ead4327673cc4a7403</originalsourceid><addsrcrecordid>eNqFkElLAzEYQIMotlbP3iTgedrsmTmWWheo9aLgQQhpljpllppMkf57Z5zaq7lk4eV98AC4xmiM2zXBkvMEZVk6xhRjegKGx5fT4zl9H4CLGDcICZRJdg4GFAspCSFD8DGF21Cv9Cov8tjkBpa1dQX0dYDWxXxd5dUa6spCHaOLsbs1nw5uXWiRUlfGwdpDd7ecwqjLbdEBrbCpTV3ES3DmdRHd1WEfgbf7-evsMVm8PDzNpovEUIlpgi3m3gjrU4F4pgUSnDmrmTEYI4-MzwjhqacaM00Mc9oySqSQ1BimJUN0BG57bzv5a-diozb1LlTtSEWoEIRxgUVLTXrKhDrG4LzahrzUYa8wUl1N1fVSXTv1W7P9cXPw7lals0f-L18L8B74zgu3_8-nnufLXvwDPF1-eg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2366245616</pqid></control><display><type>article</type><title>A probabilistic model for designing and assessing the performance of eDNA sampling protocols</title><source>Wiley</source><creator>Song, Jeffery W. ; Schultz, Martin T. ; Casman, Elizabeth A. ; Bockrath, Katherine D. ; Mize, Erica ; Monroe, Emy M. ; Tuttle‐Lau, Maren ; Small, Mitchell J.</creator><creatorcontrib>Song, Jeffery W. ; Schultz, Martin T. ; Casman, Elizabeth A. ; Bockrath, Katherine D. ; Mize, Erica ; Monroe, Emy M. ; Tuttle‐Lau, Maren ; Small, Mitchell J.</creatorcontrib><description>Environmental DNA (eDNA) sampling, the detection of species‐specific genetic material in water samples, is an emerging tool for monitoring aquatic invasive species. Optimizing eDNA sampling protocols can be challenging because there is imperfect understanding of how each step of the protocol influences its sensitivity. This paper develops a probabilistic model that characterizes each step of an eDNA sampling protocol to evaluate the protocol's overall detection sensitivity for one sample. The model is then applied to analyse how changes over time made to the eDNA sampling protocol to detect bighead (BH) and silver carp (SC) eDNA have influenced its sensitivity, and hence interpretation of the results. The model shows that changes to the protocol have caused the sensitivity of the protocol to fluctuate. A more efficient extraction method in 2013, new species‐specific markers with a qPCR assay in 2014, and a more efficient capture method in 2015 have improved the sensitivity, while switching to a larger elution volume in 2013 and a smaller sample volume in 2015 have reduced the sensitivity. Overall, the sensitivity of the current protocol is higher for BH eDNA detection and SC eDNA detection compared to the original protocol used from 2009 to 2012. The paper shows how this model of eDNA sampling can be used to evaluate the effect of proposed changes in an eDNA sampling and analysis protocol on the sensitivity of that protocol to help researchers optimize their design.</description><identifier>ISSN: 1755-098X</identifier><identifier>EISSN: 1755-0998</identifier><identifier>DOI: 10.1111/1755-0998.13113</identifier><identifier>PMID: 31677222</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Carp ; Deoxyribonucleic acid ; Design optimization ; detection sensitivity ; DNA ; Elution ; Environmental DNA ; Introduced species ; Invasive species ; New species ; Probabilistic models ; Probability theory ; Protocol ; Sampling ; sampling protocol ; Sensitivity analysis ; Water analysis ; Water sampling</subject><ispartof>Molecular ecology resources, 2020-03, Vol.20 (2), p.404-414</ispartof><rights>2019 John Wiley & Sons Ltd</rights><rights>2019 John Wiley & Sons Ltd.</rights><rights>Copyright © 2020 John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3713-1d15fc6df86059a60654eda4cc110f0cf92258f3a14a2c4ead4327673cc4a7403</citedby><cites>FETCH-LOGICAL-c3713-1d15fc6df86059a60654eda4cc110f0cf92258f3a14a2c4ead4327673cc4a7403</cites><orcidid>0000-0002-0964-8888</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31677222$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Song, Jeffery W.</creatorcontrib><creatorcontrib>Schultz, Martin T.</creatorcontrib><creatorcontrib>Casman, Elizabeth A.</creatorcontrib><creatorcontrib>Bockrath, Katherine D.</creatorcontrib><creatorcontrib>Mize, Erica</creatorcontrib><creatorcontrib>Monroe, Emy M.</creatorcontrib><creatorcontrib>Tuttle‐Lau, Maren</creatorcontrib><creatorcontrib>Small, Mitchell J.</creatorcontrib><title>A probabilistic model for designing and assessing the performance of eDNA sampling protocols</title><title>Molecular ecology resources</title><addtitle>Mol Ecol Resour</addtitle><description>Environmental DNA (eDNA) sampling, the detection of species‐specific genetic material in water samples, is an emerging tool for monitoring aquatic invasive species. Optimizing eDNA sampling protocols can be challenging because there is imperfect understanding of how each step of the protocol influences its sensitivity. This paper develops a probabilistic model that characterizes each step of an eDNA sampling protocol to evaluate the protocol's overall detection sensitivity for one sample. The model is then applied to analyse how changes over time made to the eDNA sampling protocol to detect bighead (BH) and silver carp (SC) eDNA have influenced its sensitivity, and hence interpretation of the results. The model shows that changes to the protocol have caused the sensitivity of the protocol to fluctuate. A more efficient extraction method in 2013, new species‐specific markers with a qPCR assay in 2014, and a more efficient capture method in 2015 have improved the sensitivity, while switching to a larger elution volume in 2013 and a smaller sample volume in 2015 have reduced the sensitivity. Overall, the sensitivity of the current protocol is higher for BH eDNA detection and SC eDNA detection compared to the original protocol used from 2009 to 2012. The paper shows how this model of eDNA sampling can be used to evaluate the effect of proposed changes in an eDNA sampling and analysis protocol on the sensitivity of that protocol to help researchers optimize their design.</description><subject>Carp</subject><subject>Deoxyribonucleic acid</subject><subject>Design optimization</subject><subject>detection sensitivity</subject><subject>DNA</subject><subject>Elution</subject><subject>Environmental DNA</subject><subject>Introduced species</subject><subject>Invasive species</subject><subject>New species</subject><subject>Probabilistic models</subject><subject>Probability theory</subject><subject>Protocol</subject><subject>Sampling</subject><subject>sampling protocol</subject><subject>Sensitivity analysis</subject><subject>Water analysis</subject><subject>Water sampling</subject><issn>1755-098X</issn><issn>1755-0998</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNqFkElLAzEYQIMotlbP3iTgedrsmTmWWheo9aLgQQhpljpllppMkf57Z5zaq7lk4eV98AC4xmiM2zXBkvMEZVk6xhRjegKGx5fT4zl9H4CLGDcICZRJdg4GFAspCSFD8DGF21Cv9Cov8tjkBpa1dQX0dYDWxXxd5dUa6spCHaOLsbs1nw5uXWiRUlfGwdpDd7ecwqjLbdEBrbCpTV3ES3DmdRHd1WEfgbf7-evsMVm8PDzNpovEUIlpgi3m3gjrU4F4pgUSnDmrmTEYI4-MzwjhqacaM00Mc9oySqSQ1BimJUN0BG57bzv5a-diozb1LlTtSEWoEIRxgUVLTXrKhDrG4LzahrzUYa8wUl1N1fVSXTv1W7P9cXPw7lals0f-L18L8B74zgu3_8-nnufLXvwDPF1-eg</recordid><startdate>202003</startdate><enddate>202003</enddate><creator>Song, Jeffery W.</creator><creator>Schultz, Martin T.</creator><creator>Casman, Elizabeth A.</creator><creator>Bockrath, Katherine D.</creator><creator>Mize, Erica</creator><creator>Monroe, Emy M.</creator><creator>Tuttle‐Lau, Maren</creator><creator>Small, Mitchell J.</creator><general>Wiley Subscription Services, Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SN</scope><scope>7SS</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><orcidid>https://orcid.org/0000-0002-0964-8888</orcidid></search><sort><creationdate>202003</creationdate><title>A probabilistic model for designing and assessing the performance of eDNA sampling protocols</title><author>Song, Jeffery W. ; Schultz, Martin T. ; Casman, Elizabeth A. ; Bockrath, Katherine D. ; Mize, Erica ; Monroe, Emy M. ; Tuttle‐Lau, Maren ; Small, Mitchell J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3713-1d15fc6df86059a60654eda4cc110f0cf92258f3a14a2c4ead4327673cc4a7403</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Carp</topic><topic>Deoxyribonucleic acid</topic><topic>Design optimization</topic><topic>detection sensitivity</topic><topic>DNA</topic><topic>Elution</topic><topic>Environmental DNA</topic><topic>Introduced species</topic><topic>Invasive species</topic><topic>New species</topic><topic>Probabilistic models</topic><topic>Probability theory</topic><topic>Protocol</topic><topic>Sampling</topic><topic>sampling protocol</topic><topic>Sensitivity analysis</topic><topic>Water analysis</topic><topic>Water sampling</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Song, Jeffery W.</creatorcontrib><creatorcontrib>Schultz, Martin T.</creatorcontrib><creatorcontrib>Casman, Elizabeth A.</creatorcontrib><creatorcontrib>Bockrath, Katherine D.</creatorcontrib><creatorcontrib>Mize, Erica</creatorcontrib><creatorcontrib>Monroe, Emy M.</creatorcontrib><creatorcontrib>Tuttle‐Lau, Maren</creatorcontrib><creatorcontrib>Small, Mitchell J.</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Molecular ecology resources</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Song, Jeffery W.</au><au>Schultz, Martin T.</au><au>Casman, Elizabeth A.</au><au>Bockrath, Katherine D.</au><au>Mize, Erica</au><au>Monroe, Emy M.</au><au>Tuttle‐Lau, Maren</au><au>Small, Mitchell J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A probabilistic model for designing and assessing the performance of eDNA sampling protocols</atitle><jtitle>Molecular ecology resources</jtitle><addtitle>Mol Ecol Resour</addtitle><date>2020-03</date><risdate>2020</risdate><volume>20</volume><issue>2</issue><spage>404</spage><epage>414</epage><pages>404-414</pages><issn>1755-098X</issn><eissn>1755-0998</eissn><abstract>Environmental DNA (eDNA) sampling, the detection of species‐specific genetic material in water samples, is an emerging tool for monitoring aquatic invasive species. Optimizing eDNA sampling protocols can be challenging because there is imperfect understanding of how each step of the protocol influences its sensitivity. This paper develops a probabilistic model that characterizes each step of an eDNA sampling protocol to evaluate the protocol's overall detection sensitivity for one sample. The model is then applied to analyse how changes over time made to the eDNA sampling protocol to detect bighead (BH) and silver carp (SC) eDNA have influenced its sensitivity, and hence interpretation of the results. The model shows that changes to the protocol have caused the sensitivity of the protocol to fluctuate. A more efficient extraction method in 2013, new species‐specific markers with a qPCR assay in 2014, and a more efficient capture method in 2015 have improved the sensitivity, while switching to a larger elution volume in 2013 and a smaller sample volume in 2015 have reduced the sensitivity. Overall, the sensitivity of the current protocol is higher for BH eDNA detection and SC eDNA detection compared to the original protocol used from 2009 to 2012. The paper shows how this model of eDNA sampling can be used to evaluate the effect of proposed changes in an eDNA sampling and analysis protocol on the sensitivity of that protocol to help researchers optimize their design.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>31677222</pmid><doi>10.1111/1755-0998.13113</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-0964-8888</orcidid></addata></record> |
fulltext | fulltext |
identifier | ISSN: 1755-098X |
ispartof | Molecular ecology resources, 2020-03, Vol.20 (2), p.404-414 |
issn | 1755-098X 1755-0998 |
language | eng |
recordid | cdi_proquest_journals_2366245616 |
source | Wiley |
subjects | Carp Deoxyribonucleic acid Design optimization detection sensitivity DNA Elution Environmental DNA Introduced species Invasive species New species Probabilistic models Probability theory Protocol Sampling sampling protocol Sensitivity analysis Water analysis Water sampling |
title | A probabilistic model for designing and assessing the performance of eDNA sampling protocols |
url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T09%3A42%3A52IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=A%20probabilistic%20model%20for%20designing%20and%20assessing%20the%20performance%20of%20eDNA%20sampling%20protocols&rft.jtitle=Molecular%20ecology%20resources&rft.au=Song,%20Jeffery%20W.&rft.date=2020-03&rft.volume=20&rft.issue=2&rft.spage=404&rft.epage=414&rft.pages=404-414&rft.issn=1755-098X&rft.eissn=1755-0998&rft_id=info:doi/10.1111/1755-0998.13113&rft_dat=%3Cproquest_cross%3E2366245616%3C/proquest_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c3713-1d15fc6df86059a60654eda4cc110f0cf92258f3a14a2c4ead4327673cc4a7403%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2366245616&rft_id=info:pmid/31677222&rfr_iscdi=true |