دورية أكاديمية
Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA.
العنوان: | Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA. |
---|---|
المؤلفون: | McClenaghan B; Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada., Compson ZG; Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada., Hajibabaei M; Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada.; Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.; Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada. |
المصدر: | PloS one [PLoS One] 2020 Mar 19; Vol. 15 (3), pp. e0224119. Date of Electronic Publication: 2020 Mar 19 (Print Publication: 2020). |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
اللغة: | English |
بيانات الدورية: | Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: San Francisco, CA : Public Library of Science |
مواضيع طبية MeSH: | Biodiversity* , DNA Barcoding, Taxonomic*, Aquatic Organisms/*genetics , DNA, Environmental/*genetics |
مستخلص: | Environmental DNA (eDNA) metabarcoding is an increasingly popular method for rapid biodiversity assessment. As with any ecological survey, false negatives can arise during sampling and, if unaccounted for, lead to biased results and potentially misdiagnosed environmental assessments. We developed a multi-scale, multi-species occupancy model for the analysis of community biodiversity data resulting from eDNA metabarcoding; this model accounts for imperfect detection and additional sources of environmental and experimental variation. We present methods for model assessment and model comparison and demonstrate how these tools improve the inferential power of eDNA metabarcoding data using a case study in a coastal, marine environment. Using occupancy models to account for factors often overlooked in the analysis of eDNA metabarcoding data will dramatically improve ecological inference, sampling design, and methodologies, empowering practitioners with an approach to wield the high-resolution biodiversity data of next-generation sequencing platforms. Competing Interests: B.M. and Z.G.C. are employees of eDNAtec Inc. and M.H. is the founder and Chief Scientific Officer of eDNAtec Inc. This does not alter our adherence to PLOS ONE policies on sharing data and materials. |
References: | PLoS One. 2014 Jul 30;9(7):e99571. (PMID: 25075615) Mol Ecol Resour. 2016 May;16(3):604-7. (PMID: 27062589) Sci Rep. 2019 Mar 5;9(1):3581. (PMID: 30837589) Ecology. 2006 Apr;87(4):842-54. (PMID: 16676528) Ecology. 2006 Apr;87(4):835-41. (PMID: 16676527) Mol Ecol. 2019 Jan;28(2):420-430. (PMID: 30408260) Integr Environ Assess Manag. 2019 Sep;15(5):760-771. (PMID: 30963692) Front Zool. 2013 Jun 14;10:34. (PMID: 23767809) J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712) Sci Rep. 2018 Mar 9;8(1):4226. (PMID: 29523803) Mol Ecol. 2012 Apr;21(8):2039-44. (PMID: 22590728) Sci Rep. 2019 Oct 17;9(1):14921. (PMID: 31624369) Nat Methods. 2016 Jul;13(7):581-3. (PMID: 27214047) Environ Manage. 2010 May;45(5):1223-30. (PMID: 20237922) Mol Ecol Resour. 2016 May;16(3):673-85. (PMID: 26558345) Sci Rep. 2015 Apr 17;5:9687. (PMID: 25884109) Ecology. 2016 Jul;97(7):1759-1770. (PMID: 27859174) Trends Ecol Evol. 2014 Jun;29(6):358-67. (PMID: 24821515) Mol Ecol Resour. 2015 May;15(3):543-56. (PMID: 25327646) Sci Rep. 2019 Apr 12;9(1):5991. (PMID: 30979963) Sci Rep. 2017 Sep 25;7(1):12240. (PMID: 28947818) PLoS One. 2015 Oct 21;10(10):e0138432. (PMID: 26488407) Philos Trans R Soc Lond B Biol Sci. 2016 Sep 5;371(1702):. (PMID: 27481783) Mol Ecol. 2016 Feb;25(4):929-42. (PMID: 26479867) Mol Ecol Resour. 2019 Mar;19(2):426-438. (PMID: 30576077) Mol Ecol. 2017 Nov;26(21):5872-5895. (PMID: 28921802) PLoS One. 2015 Apr 15;10(4):e0121655. (PMID: 25874630) Ecol Evol. 2018 Jul 13;8(16):7763-7777. (PMID: 30250661) Nucleic Acids Res. 2015 Dec 2;43(21):e143. (PMID: 26187991) Genome. 2017 Apr;60(4):358-374. (PMID: 28177833) Ecol Lett. 2013 Oct;16(10):1245-57. (PMID: 23910579) PLoS One. 2014 Feb 28;9(2):e90234. (PMID: 24587293) PLoS One. 2015 Jun 18;10(6):e0130874. (PMID: 26086250) Sci Rep. 2015 Oct 30;5:15894. (PMID: 26516098) |
المشرفين على المادة: | 0 (DNA, Environmental) |
تواريخ الأحداث: | Date Created: 20200320 Date Completed: 20200514 Latest Revision: 20211204 |
رمز التحديث: | 20221213 |
مُعرف محوري في PubMed: | PMC7082047 |
DOI: | 10.1371/journal.pone.0224119 |
PMID: | 32191699 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1932-6203 |
---|---|
DOI: | 10.1371/journal.pone.0224119 |