The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data1

Genome

Volumn 59, Issue 11, 2016, Pages 981-990

  Clare, Elizabeth L ^a   Chain, Frédéric J J ^b   Littlefair, Joanne E ^a   Cristescu, Melania E ^b  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

DNA barcoding; Ecological simulations; EDNA; Metabarcoding; MOTU

Indexed keywords

CYTOCHROME C OXIDASE;

BIODIVERSITY; BIOLOGY; DNA BARCODING; ECOLOGY; ECOSYSTEM; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

BIODIVERSITY; COMPUTATIONAL BIOLOGY; DNA BARCODING, TAXONOMIC; ECOLOGY; ECOSYSTEM; ELECTRON TRANSPORT COMPLEX IV; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING;

EID: 84994517747     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/gen-2015-0184     Document Type: Article

References (28)

1. Adamowicz S.J. 2015. International Barcode of Life: Evolution of a global research community. Genome, 58 (5): 151-162. 10.1139/gen-2015-0094. 26444714.
2. Bohmann K. Evans A. Gilbert M.T.P. Carvalho G.R. Creer S. Knapp M. et al 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol. Evol. 29 (6): 358-367. 10.1016/j.tree.2014.04.003. 24821515.
3. Brown D.S. Burger R. Cole N. Vencatasamy D. Clare E.L. Montazam A. Symondson W.O.C. 2014. Dietary competition between the alien Asian musk shrew (Suncus murinus) and a reintroduced population of Telfair's skink (Leiolopisma telfairii). Mol. Ecol. 23: 3695-3705. 10.1111/mec.12445. 24033506.
4. Brown E.A. Chain F.J.J. Crease T.J. MacIsaac H.J. Cristescu M.E. 2015. Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? Ecol. Evol. 5 (11): 2234-2251. 10.1002/ece3.1485. 26078859.
5. Caporaso G. Kuczynski J. Stombaugh J. Bittinger K. Bushman F. Costello E. et al 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods, 7 (5): 335-336. 10.1038/nmeth.f.303. 20383131.
6. Clare E.L. 2014. Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications. Evol. Appl. 7: 1144-1157. 10.1111/eva.12225. 25553074.
7. Crawley M.J. 2012. The R Book, 2nd Edition. Wiley-Blackwell. ISBN-10: 0470973927.
8. Cristescu M.E. 2014. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends Ecol. Evol. 29 (10): 566-571. 10.1016/j.tree.2014.08.001. 25175416.
9. Edgar R.C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26 (19): 2460-2461. 10.1093/bioinformatics/btq461.
10. Edgar R.C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods, 10 (10): 996-998. 10.1038/nmeth.2604. 23955772.
11. Floyd R. Abebe E. Papert A. Blaxter M. 2002. Molecular barcodes for soil nematode identification. Mol. Ecol. 11 (4): 839-850. 10.1046/j.1365-294X.2002.01485.x. 11972769.
12. Flynn J.M. Brown E.A. Chain F.J.J. MacIsaac H.J. Cristescu M.E. 2015. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods. Ecol. Evol. 5 (11): 2252-2266. 10.1002/ece3.1497. 26078860.
13. Hajibabaei M. Janzen D.H. Burns J.M. Hallwachs W. Hebert P.D.N. 2006. DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl. Acad. Sci. U.S.A.; 103: 968-971. 10.1073/pnas.0510466103.
14. Hebert P.D.N. Cywinska A. Ball S.L. DeWaard J.R. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. B Biol. Sci. 270 (1512): 313-321. 10.1098/rspb.2002.2218.
15. Jones M. Ghoorah A. Blaxter M. 2011. jMOTU and Taxonerator: turning DNA barcode sequences into annotated operational taxonomic units. PLoS ONE, 6 (4): e19259. 10.1371/journal.pone.0019259. 21541350.
16. Kunin V. Engelbrektson A. Ochman H. Hugenholtz P. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12 (1): 118-123. 10.1111/j.1462-2920.2009.02051.x. 19725865.
17. Mahé F. Rognes T. Quince C. de Vargas C. Dunthorn M. 2014. Swarm: robust and fast clustering method for amplicon-based studies. PeerJ, 2: e593. 10.7717/peerj.593. 25276506.
18. Meyer C.P. Paulay G. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS Biol. 3: 2229-2238. 10.1371/journal.pbio.0030422. 16336051.
19. Pianka E.R. 1973. The structure of lizard communities. Annu. Rev. Ecol. Syst. 4: 53-74. 10.1146/annurev.es.04.110173.000413.
20. Pompanon F. Deagle B.E. Symondson W.O.C. Brown D.S. Jarman S.N. Taberlet P. 2012. Who is eating what: diet assessment using next generation sequencing. Mol. Ecol. 21: 1931-1950. 10.1111/j.1365-294X.2011.05403.x. 22171763.
21. R Core Team. 2015. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available from http://www.R-project.org/.
22. Ratnasingham S. Hebert P.D.N. 2013. A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE, 8 (7): e66213. 10.1371/journal.pone.0066213. 23861743.
23. Razgour O. Clare E.L. Zeale M.R.K. Hanmer J. Schnell I.B. Rasmussen M. et al 2011. High-throughput sequencing offers insight into mechanisms of resource partitioning in cryptic bat species. Ecol. Evol. 1 (4): 556-570. 10.1002/ece3.49. 22393522.
24. Salinas-Ramos V.B. Herrera Montalvo L.G. León-Regagnon V. Arrizabalaga-Escudero A. Clare E.L. 2015. Dietary overlap and seasonality in three species of mormoopid bats from a tropical dry forest. Mol. Ecol. 24 (20): 5296-5307. 10.1111/mec.13386. 26369564.
25. Schirmer M. Ijaz U.Z. D'Amore R. Hall N. Sloan W.T. Quince C. 2015. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 43: e37. 10.1093/nar/gku1341.
26. Trontelj P. Fišer C. 2009. Cryptic species diversity should not be trivialised. Syst. Biodivers. 7 (01): 1-3. 10.1017/S1477200008002909.
27. Yang C.X. Ji Y.Q. Wang X.Y. Yang C.Y. Yu D.W. 2013. Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity. Sci. China Life Sci. 56 (1): 73-81. 10.1007/s11427-012-4423-7. 23269552.
28. Zhan A. Hulák M. Sylvester F. Huang X. Adebayo A.A. Abbott C.L. et al 2013. High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods Ecol. Evol. 4 (6): 558-565. 10.1111/2041-210X.12037.