Thông tin tài nguyên

Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA

pmc-PMC7082047.pdf · Phiên bản 1 · 17 trang

18
Bản gốc
Trang 14 · Đoạn 32Vị trí nguồn

Funding acquisition: Mehrdad Hajibabaei. Methodology: Beverly McClenaghan. Supervision: Mehrdad Hajibabaei. Validation: Zacchaeus G. Compson. Writing – original draft: Beverly McClenaghan. Writing – review & editing: Zacchaeus G. Compson, Mehrdad Hajibabaei. References 1. Deiner K, Bik HM, Ma¨ chler E, Seymour M, Lacoursière-Roussel A, Altermatt F, et al. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol Ecol. 2017; 26: 5872–5895. https://doi.org/10.1111/mec.14350 PMID: 28921802 2. Thomsen PF, Willerslev E. Environmental DNA–An emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv. 2015; 183: 4–18. https://doi.org/10.1016/j.biocon.2014.11.019 3. Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, et al. Environmental DNA for wild- life biology and biodiversity monitoring. Trends Ecol Evol. 2014; 29: 358–367. https://doi.org/10.1016/j. tree.2014.04.003 PMID: 24821515 4. Jeunen G, Knapp M, Spencer HG, Lamare MD, Taylor HR, Stat M, et al. Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water move- ment. Mol Ecol Resour. 2019; 19: 426–438. https://doi.org/10.1111/1755-0998.12982 PMID: 30576077 5. Singer GAC, Fahner NA, Barnes JG, McCarthy A, Hajibabaei M. Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater. Sci Rep. 2019; 9: 5991. https://doi.org/10.1038/s41598-019-42455-9 PMID: 30979963

Trang 14 · Đoạn 33Vị trí nguồn

6. Stat M, Huggett MJ, Bernasconi R, DiBattista JD, Berry TE, Newman SJ, et al. Ecosystem biomonitor- ing with eDNA: metabarcoding across the tree of life in a tropical marine environment. Sci Rep. 2017; 7: 12240. https://doi.org/10.1038/s41598-017-12501-5 PMID: 28947818 7. Baird DJ, Hajibabaei M. Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Mol Ecol. 2012; 21: 2039–2044. https://doi.org/10.1111/j.1365- 294x.2012.05519.x PMID: 22590728 8. Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, et al. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol Ecol. 2016; 25: 929–942. https://doi. org/10.1111/mec.13428 PMID: 26479867 9. Ke´ ry M, Schmidt B. Imperfect detection and its consequences for monitoring for conservation. Commu- nity Ecol. 2008; 9: 207–216. https://doi.org/10.1556/ComEc.9.2008.2.10 10. Dorazio RM, Royle JA, So¨ derstro¨m B, Glimska¨ r A. Estimating species richness and accumulation by modeling species occurence and detectability. Ecology. 2006; 87: 842–854. https://doi.org/10.1890/ 0012-9658(2006)87[842:esraab]2.0.co;2 PMID: 16676528 11. Guillera-Arroita G, Lahoz-Monfort JJ, MacKenzie DI, Wintle BA, McCarthy MA. Ignoring imperfect detection in biological surveys is dangerous: A response to ‘Fitting and interpreting occupancy models”.’ White EP, editor. PLoS ONE. 2014; 9: e99571. https://doi.org/10.1371/journal.pone.0099571 PMID: 25075615

Trang 14 · Đoạn 34Vị trí nguồn

12. Evans NT, Shirey PD, Wieringa JG, Mahon AR, Lamberti GA. Comparative cost and effort of fish distri- bution detection via environmental DNA analysis and electrofishing. Fisheries. 2017; 42: 90–99. https:// doi.org/10.1080/03632415.2017.1276329 13. Freeland J. The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA (eDNA). Genome. 2017; 60: 358–374. https://doi.org/10.1139/gen-2016-0100 PMID: 28177833 14. Smith DP, Peay KG. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. Kellogg CA, editor. PLoS ONE. 2014; 9: e90234. https://doi.org/10.1371/ journal.pone.0090234 PMID: 24587293 15. Ficetola GF, Pansu J, Bonin A, Coissac E, Giguet-Covex C, De Barba M, et al. Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Mol Ecol Resour. 2015; 15: 543–556. https://doi.org/10.1111/1755-0998.12338 PMID: 25327646 16. Campos-Cerqueira M, Aide TM. Improving distribution data of threatened species by combining acous- tic monitoring and occupancy modelling. Jones K, editor. Methods Ecol Evol. 2016; 7: 1340–1348. https://doi.org/10.1111/2041-210X.12599 PLOS ONE Multi-species occupancy models for metabarcoding PLOS ONE | https://doi.org/10.1371/journal.pone.0224119 March 19, 2020 14 / 17