A new way to contemplate darwin’s tangled bank: How DNA barcodes are reconnecting biodiversity science and biomonitoring

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 371, Issue 1702, 2016, Pages

  Hajibabaei, Mehrdad ^a   Baird, Donald J ^b   Fahner, Nicole A ^a   Beiko, Robert ^c   Brian Golding, G ^d  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITY OF NEW BRUNSWICK   (Canada)

^c DALHOUSIE UNIVERSITY   (Canada)

^d MCMASTER UNIVERSITY   (Canada)

Author keywords

Biodiversity; DNA barcoding; Environment; Genomics; Phylogenetics; Taxonomy

Indexed keywords

BIODIVERSITY; BIOINFORMATICS; BIOMONITORING; DNA; ECOSYSTEM APPROACH; ENVIRONMENTAL ASSESSMENT; GENETIC ANALYSIS; GENOMICS; PHYLOGENETICS; TAXONOMY;

BIODIVERSITY; BIOLOGY; DNA BARCODING; ENVIRONMENTAL MONITORING; ENVIRONMENTAL PROTECTION; PROCEDURES;

BIODIVERSITY; COMPUTATIONAL BIOLOGY; CONSERVATION OF NATURAL RESOURCES; DNA BARCODING, TAXONOMIC; ENVIRONMENTAL MONITORING;

EID: 84982859351     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2015.0330     Document Type: Article

References (72)

1. Darwin C. 1859. On the origin of species. London, UK: John Murray.
2. Wilson EO. 1997 Introduction. In Biodiversity II: understanding and protecting our biological resources, pp. 1-3. Washington, DC: Joseph Henry Press.
3. De Queiroz K. 2007 Species concepts and species delimitation. Syst Biol. 56, 879-886. (doi:10.1080/ 10635150701701083)
4. Doolittle WF. 1999 Phylogenetic classification and the universal tree. Science 284, 2124-2129. (doi:10.1126/science.284.5423.2124)
5. Lenat DR, Resh VH. 2001 Taxonomy and stream ecology—the benefits of genus-and specieslevel identifications. J. N. Am. Benthol. Soc. 20, 287-298. (doi:10.2307/1468323)
6. Sweeney BW, Battle JM, Jackson JK, Dapkey T. 2011 Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality? J. N. Am. Benthol. Soc. 30, 195-216. (doi:10.1899/10-016.1)
7. Bonada N, Prat N, Resh VH, Statzner B. 2006 Developments in aquatic insect biomonitoring: a comparative analysis of recent approaches. Annu. Rev. Entomol. 51, 495-523. (doi:10.1146/annurev. ento.51.110104.151124)
8. Gray C et al. 2014 FORUM: ecological networks: the missing links in biomonitoring science. J. Appl. Ecol. 51, 1444-1449. (doi:10.1111/1365-2664.12300)
9. Barlow J et al. 2007 Quantifying the biodiversity value of tropical primary, secondary, and plantation forests. Proc. Natl Acad. Sci. USA 104, 18555-18560. (doi:10.1073/pnas.0703333104)
10. Gardner TA et al. 2008 The cost-effectiveness of biodiversity surveys in tropical forests. Ecol. Lett. 11, 139-150. (doi:10.1111/j.1461-0248.2007. 01133.x)
11. de Carvalho MR et al. 2007 Taxonomic impediment or impediment to taxonomy? A commentary on systematics and the cybertaxonomic-automation paradigm. Evol. Biol. 34, 140-143. (doi:10.1007/ s11692-007-9011-6)
12. Hinchliff CE et al. 2015 Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proc. Natl Acad. Sci. USA 112, 12764-12769. (doi:10. 1073/pnas.1423041112)
13. Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AGB, Roger AJ. 2009 Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic ‘supergroups’. Proc. Natl Acad. Sci. USA 106, 3859-3864. (doi:10.1073/pnas.0807880106)
14. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA. 2007 DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 23, 167-172. (doi:10.1016/ j.tig.2007.02.001)
15. Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003 Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270, 313-321. (doi:10.1098/ rspb.2002.2218)
16. Hebert PDN, Hollingsworth PM, Hajibabaei M. 2016 From writing to reading the encyclopedia of life. Phil. Trans. R. Soc. B 371, 20150321. (doi:10.1098/ rstb.2015.0321)
17. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. 2004 Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl Acad. Sci. USA 101, 14812-14817. (doi:10.1073/ pnas.0406166101)
18. Orlofske JM, Baird DJ. 2014 A geometric morphometric approach to establish body-shape trait criteria for aquatic insects. Freshw. Sci. 33, 978-994. (doi:10.1086/676912)
19. Pilgrim EM, Jackson SA, Swenson S, Turcsanyi I, Friedman E, Weigt L, Bagley MJ. 2011 Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls. J. N. Am. Benthol. Soc. 30, 217-231. (doi:10.1899/ 10-012.1)
20. Stein ED, White BP, Mazor RD, Jackson JK, Battle JM, Miller PE, Pilgrim EM, Sweeney BW. 2014 Does DNA barcoding improve performance of traditional stream bioassessment metrics? Freshw. Sci. 33, 302-311. (doi:10.1086/674782)
21. Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ. 2011 Environmental barcoding: a nextgeneration sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6, e17497. (doi:10.1371/journal.pone.0017497)
22. Gibson JF, Shokralla S, Curry C, Baird DJ, Monk WA, King I, Hajibabaei M. 2015 Large-scale biomonitoring of remote and threatened ecosystems via high-throughput sequencing. PLoS ONE 10, e0138432.
23. Dafforn KA, Baird DJ, Chariton AA, Sun MY, Brown M, Simpson SL, Kelaher BP, Johnston EA. 2014 Faster, higher and stronger? The pros and cons of molecular data for assessing ecosystem condition. Advances in Ecological Research 50, 1-40. (doi:10.1016/B978-0-08-099970-8.00003-8)
24. Webb JM et al. 2012 A DNA barcode library for North American Ephemeroptera: progress and prospects. PLoS ONE 7, e38063. (doi:10.1371/ journal.pone.0038063)
25. Rimet F et al. 2016 R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database. baw016. (doi:10. 1093/database/baw016)
26. Porter TM, Gibson JF, Shokralla S, Baird DJ, Golding GB, Hajibabaei M. 2014 Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naı¨ve Bayesian classifier. Mol. Ecol. Resour. 14, 929-942. (doi:10.1111/1755-0998.12240)
27. Schoch CL et al. 2012 Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci. USA 109, 6241-6246. (doi:10.1073/pnas.1117018109)
28. Hollingsworth PM et al. 2009 A DNA barcode for land plants. Proc. Natl Acad. Sci. USA 106, 12794-12797. (doi:10.1073/pnas.0905845106)
29. Pawlowski J et al. 2012 CBOL Protist Working Group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 10, e1001419. (doi:10.1371/journal.pbio.1001419)
30. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. 1990 Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63. (doi:10.1038/345060a0)
31. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007 Naı¨ve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267. (doi:10.1128/ AEM.00062-07)
32. Gilbert JA et al. 2010 Meeting report: the Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. Stand. Genomic. Sci. 3, 243-248. (doi:10.4056/sigs.1433550)
33. Huttenhower C et al. 2012 Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214. (doi:10.1038/nature11234)
34. Hajibabaei M, Spall JL, Shokralla S, van Konynenburg S. 2012 Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecol. 12, 28. (doi:10.1186/1472-6785-12-28)
35. Ji Y et al. 2013 Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol. Lett. 16, 1245-1257. (doi:10.1111/ele.12162)
36. Leray M, Knowlton N. 2015 DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc. Natl Acad. Sci. USA 112, 2076-2081. (doi:10.1073/ pnas.1424997112)
37. Yu DW, Ji YQ, Emerson BC, Wang XY, Ye CX, Yang CY, Ding Z. 2012 Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol. Evol. 3, 613-623. (doi:10.1111/j.2041-210X.2012.00198.x)
38. Deagle BE, Jarman SN, Coissac E, Pompanon F, Taberlet P. 2014 DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biol. Lett. 10, 20140562. (doi:10. 1098/rsbl.2014.0562)
39. Bienert F, de Danieli S, Miquel C, Coissac E, Poillot C, Brun J-J, Taberlet P. 2012 Tracking earthworm communities from soil DNA. Mol. Ecol. 21, 2017-2030. (doi:10.1111/j.1365-294X.2011.05407.x)
40. Valentini A et al. 2015 Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol. Ecol. 25, 929-942. (doi:10. 1111/mec.13428)
41. Taberlet P et al. 2006 Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res. 35, e14. (doi:10.1093/ nar/gkl938)
42. Kartzinel TR, Chen PA, Coverdale TC, Erickson DL, Kress WJ, Kuzmina ML, Rubestein DI, Wang W, Pringle RM. 2015 DNA metabarcoding illuminates dietary niche partitioning by African large herbivores. Proc. Natl Acad. Sci. USA 112, 8019-8024. (doi:10.1073/pnas.1503283112)
43. Gibson J, Shokralla S, Porter TM, King I, van Konynenburg S, Janzen DH, Hallwachs W, Hajibabaei M. 2014 Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proc. Natl Acad. Sci. USA 111, 8007-8012. (doi:10. 1073/pnas.1406468111)
44. Zhou X et al. 2013 Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience 2, 4. (doi:10.1186/2047-217X-2-4)
45. Liu S et al. 2016 Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis. Mol. Ecol. Resour. 16, 470-479. (doi:10.1111/1755-0998. 12472)
46. McClenaghan B, Gibson JF, Shokralla S, Hajibabaei M. 2015 Discrimination of grasshopper (Orthoptera: Acrididae) diet and niche overlap using nextgeneration sequencing of gut contents. Ecol. Evol. 5, 3046-3055. (doi:10.1002/ece3.1585)
47. Deiner K, Walser J-C, Mächler E, Altermatt F. 2015 Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol. Conserv. 183, 53-63. (doi:10.1016/j.biocon.2014.11.018)
48. Ratnasingham S, Hebert PDN. 2007 BOLD: the Barcode of Life Data System (http://www. barcodinglife.org). Mol. Ecol. Notes 7, 355-364. (doi:10.1111/j.1471-8286.2007.01678.x)
49. Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MGI, Beiko RG. 2013 GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS ONE 8, e69885. (doi:10.1371/journal.pone.0069885)
50. Caporaso JG et al. 2010 QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336. (doi:10.1038/nmeth.f.303)
51. Schloss PD et al. 2009 Introducing mothur: opensource, platform-independent, communitysupported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541. (doi:10.1128/AEM.01541-09)
52. Cole JR et al. 2014 Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633-D642. (doi:10.1093/nar/ gkt1244)
53. Ames SK, Hysom DA, Gardner SN, Lloyd GS, Gokhale MB, Allen JE. 2013 Scalable metagenomic taxonomy classification using a reference genome database. Bioinformatics 29, 2253-2260. (doi:10. 1093/bioinformatics/btt389)
54. Wood DE, Salzberg SL. 2014 Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46. (doi:10.1186/ gb-2014-15-3-r46)
55. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990 Basic local alignment search tool. J. Mol. Biol. 215, 403-410. (doi:10.1016/S0022-2836(05)80360-2)
56. Edgar RC. 2010 Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461. (doi:10.1093/bioinformatics/btq461)
57. Ghodsi M, Liu B, Pop M. 2011 DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC Bioinformatics 12, 271.
58. Mahe´ F, Rognes T, Quince C, de Vargas C, Dunthorn M. 2014 Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2, e593. (doi:10. 7717/peerj.593)
59. Mahe´ F, Rognes T, Quince C, de Vargas C, Dunthorn M. 2015 Swarm v2: highly-scalable and highresolution amplicon clustering. PeerJ 3, e1420. (doi:10.7717/peerj.1420)
60. Mallo D, Posada D. 2016 Multilocus inference of species trees and DNA barcoding. Phil. Trans. R. Soc. B 371, 20150335. (doi:10.1098/rstb.2015.0335)
61. Matsen FA, Kodner RB, Armbrust EV. 2010 pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinform. 11, 538. (doi:10. 1186/1471-2105-11-538)
62. Forest F et al. 2007 Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 445, 757-760. (doi:10.1038/nature05587)
63. MacKenzie DI (ed.). 2006 Occupancy estimation and modeling: inferring patterns and dynamics of species, 324. Amsterdam, The Netherlands: Elsevier.
64. Schmidt P-A, Bálint M, Greshake B, Bandow C, Römbke J, Schmitt I. 2013 Illumina metabarcoding of a soil fungal community. Soil Biol. Biochem. 65, 128-132. (doi:10.1016/j.soilbio.2013.05.014)7
65. Roney NE, Kuparinen A, Hutchings JA. 2015 Comparative analysis of abundance-occupancy relationships for species at risk at both broad taxonomic and spatial scales. Can. J. Zool. 93, 515-519. (doi:10.1139/cjz-2014-0318)
66. Zuckerberg B, Porter WF, Corwin K. 2009 The consistency and stability of abundance-occupancy relationships in large-scale population dynamics. J. Anim. Ecol. 78, 172-181. (doi:10.1111/j.1365-2656.2008.01463.x)
67. Baird DJ, Hajibabaei M. 2012 Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Mol. Ecol. 21, 2039-2044. (doi:10.1111/j.1365-294X. 2012.05519.x)
68. Porter TM, Shokralla S, Baird D, Golding GB, Hajibabaei M. 2016 Ribosomal DNA and plastid markers used to sample fungal and plant communities from wetland soils reveals complementary biotas. PLoS ONE 11, e0142759. (doi:10.1371/journal. pone.0142759)
69. Gibson JF, Stein ED, Baird DJ, Finlayson CM, Zhang X, Hajibabaei M. 2015 Wetland ecogenomics-the next generation of wetland biodiversity and functional assessment. Wetl. Sci. Pract. 32, 27-32.
70. Beiko RG. 2015 Microbial malaise: how can we classify the microbiome? Trends Microbiol. 23, 671-679. (doi:10.1016/j.tim.2015.08.009)
71. Hajibabaei M. 2012 The golden age of DNA metasystematics. Trends Genet. 28, 535-537. (doi:10.1016/j.tig.2012.08.001)
72. Taylor HR, Harris WE. 2012 An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol. Ecol. Resour. 12, 377-388. (doi:10.1111/j.1755-0998.2012.03119.x)