Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi

Molecular Ecology

Volumn 24, Issue 23, 2015, Pages 5770-5777

  Ryberg, Martin ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

barcoding; community ecology; fungi; molecular operational taxonomic units; species delimitation

Indexed keywords

FUNGAL DNA; RIBOSOMAL SPACER DNA;

BIOLOGICAL MODEL; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; FUNGUS; GENETICS; MOLECULAR EVOLUTION;

CLUSTER ANALYSIS; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; FUNGI; MODELS, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84948573559     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13444     Document Type: Review

References (61)

1. Aanen DK, Kuyper TW, Boekhout T, Hoekstra RF, (2000) Phylogenetic relationships in the genus Hebeloma based on ITS1 and 2 sequences, with special emphasis on the Hebeloma crustuliniforme complex. Mycologia, 92, 269-281.
2. Aanen DK, Kuyper TW, Hoekstra RF, (2001) A widely distributed ITS polymorphism within a biological species of the ectomycorrhizal fungus Hebeloma velutipes. Mycological Research, 105, 284-290.
3. Abarenkov K, Henrik Nilsson R, Larsson KH, et al,. (2010) The unite database for molecular identification of fungi-recent updates and future perspectives. New Phytologist, 186, 281-285.
4. Barraclough TG, Fontaneto D, Herniou EA, Ricci C, (2009) The evolutionary nature of diversification in sexuals and asexuals. In: Speciation and Patterns of Diversity (eds, Butlin R, Bridle J, Schluter D,), Ecological Reviews, pp. 29-45. Cambridge University Press, Cambridge, UK.
5. Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW, (2015) Genbank. Nucleic Acids Research, 43, D30.
6. Bergsten J, Bilton DT, Fujisawa T, et al,. (2012) The effect of geographical scale of sampling on DNA barcoding. Systematic Biology, 61, 851-869.
7. Clark PU, Dyke AS, Shakun JD, et al,. (2009) The last glacial maximum. Science, 325, 710-714.
8. Connell JH, (1978) Diversity in tropical rain forests and coral reefs. Science, 199, 1302-1310.
9. De Queiroz K, (2007) Species concepts and species delimitation. Systematic Biology, 56, 879-886.
10. Dettman JR, Jacobson DJ, Taylor JW, (2003) A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution, 57, 2703-2720.
11. Dowton M, Meiklejohn K, Cameron SL, Wallman J, (2014) A preliminary framework for DNA barcoding, incorporating the multispecies coalescent. Systematic Biology, 63, 639-644.
12. Edwards SV, (2009) Is a new and general theory of molecular systematics emerging ? Evolution, 63, 1-19.
13. Faith DP, (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
14. Floyd R, Abebe E, Papert A, Blaxter M, (2002) Molecular barcodes for soil nematode identification. Molecular Ecology, 11, 839-850.
15. Fujisawa T, Barraclough TG, (2013) Delimiting species using single-locus data and the generalized mixed yule coalescent approach: a revised method and evaluation on simulated data sets. Systematic Biology, 62, 707-724.
16. Funk DJ, Omland KE, (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics, 34, 397-423.
17. Geml J, Laursen GA, O'neill K, Nusbaum HC, Taylor DL, (2006) Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria). Molecular Ecology, 15, 225-239.
18. Ghobad-Nejhad M, Nilsson R, Hallenberg N, (2010) Phylogeny and taxonomy of the genus Vuilleminia(Basidiomycota) based on molecular and morphological evidence, with new insights into corticiales. Taxon, 59, 1519-1534.
19. Hallenberg N, Nilsson RH, Antonelli A, Wu SH, Maekawa N, Nordén B, (2007) The Peniophorella praetermissa species complex (Basidiomycota). Mycological Research, 111, 1366-1376.
20. Harder CB, Læssøe T, Frøslev TG, Ekelund F, Rosendahl S, Kjøller R, (2013) A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification. Mycosphere: Journal of Fungal Biology, 117, 764-775.
21. Hartl D, Clark A, (2007) Principles of Population Genetics. Sinauer Associates, Sunderland, Massachusetts.
22. Harvey PH, (1991) The Comparative Method in Evolutionary Biology. Oxford Series in Ecology and Evolution. Oxford University Press, Oxford, New York.
23. Hebert PDN, Cywinska A, Ball SL, de Waard JR, (2003) Biological identifications through DNA barcodes Proceedings of the Royal Society of London. Series B: Biological Sciences, 270, 313-321.
24. Hibbett DS, Ohman A, Kirk PM, (2009) Fungal ecology catches fire. New Phytologist, 184, 279-282.
25. Horton TR, Bruns TD, (2001) The molecular revolution in ectomycorrhizal ecology: peeking into the black-box. Molecular Ecology, 10, 1855-1871.
26. Hughes KW, Petersen RH, Lickey EB, (2009) Using heterozygosity to estimate a percentage DNA sequence similarity for environmental species' delimitation across basidiomycete fungi. New Phytologist, 182, 795-798.
27. Izzo A, Agbowo J, Bruns TD, (2005) Detection of plot-level changes in ectomycorrhizal communities across years in an old-growth mixed-conifer forest. New Phytologist, 166, 619-630.
28. Kasuga T, White TTJ, Taylor JWJ, (2002) Estimation of nucleotide substitution rates in eurotiomycete fungi. Molecular Biology and Evolution, 19, 2318-2324.
29. Kingman J, (1982) The coalescent. Stochastic Processes and Their Applications, 13, 235-248.
30. Kóljalg U, Nilsson RH, Abarenkov K, et al,. (2013) Towards a unified paradigm for sequence-based identification of fungi. Molecular Ecology, 22, 5271-5277.
31. Larsson E, Sundberg H, (2011) Lyophyllum shimeji, a species associated with lichen pine forest in northern fennoscandia. Mycoscience, 52, 289-295.
32. Lekberg Y, Gibbons SM, Rosendahl S, (2014) Will different OTU delineation methods change interpretation of arbuscular mycorrhizal fungal community patterns ? New Phytologist, 202, 1101-1104.
33. Lindner DL, Carlsen T, Henrik Nilsson R, Davey M, Schumacher T, Kauserud H, (2013) Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi. Ecology and Evolution, 3, 1751-1764.
34. Lücking R, Lawrey JD, Gillevet PM, Sikaroodi M, Dal-Forno M, Berger SA, (2013) Multiple ITS haplotypes in the genome of the lichenized basidiomycete Cora inversa (Hygrophoraceae): fact or artifact ? Journal of Molecular Evolution, 78, 148-162.
35. MacArthur RH, (1967) The Theory of Island Biogeography, Vol 1. Princeton University Press, Princeton, New Jersey.
36. Martinson EO, Herre EA, Machado CA, Arnold AE, (2012) Culture-free survey reveals diverse and distinctive fungal communities associated with developing figs (Ficus spp.) in panama. Advances in Microbial Ecology, 64, 1073-1084.
37. Mayden RL, (1997) A hirarchy of species concepts: the denouement in the saga of the species problem. In: Species the Units of Biodiversity (eds, Claridge MF, Dawah H, Wilson M,), vol. 54 of The systematic association Special Volume Series, pp. 381-424. Chapman & Hall, Cornwall.
38. Mayr E, (1940) Speciation phenomena in birds. The American Naturalist, 74, 249-278.
39. Mishler BD, (2010) Species are not uniquely real biological entities. In: Contemporary Debates in Philosophy of Biology, no. 12 in Contemporary Debates in Philosophy, pp. 110-122. Wiley-Blackwell, Singapore.
40. Mooers A, Gascuel O, Stadler T, Li H, Steel M, (2012) Branch lengths on birth-death trees and the expected loss of phylogenetic diversity. Systematic Biology, 61, 195-203.
41. Myers N, Mittermeier RA, Mittermeier CG, Da Fonseca GA, Kent J, (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853-858.
42. Nee S, May RM, Harvey PH, (1994) The reconstructed evolutionary process. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 344, 305-311.
43. Nilsson R, Hallenberg N, (2003) Phylogeny of the Hypochnicium punctulatum complex as inferred from ITS sequence data. Mycologia, 95, 54-60.
44. Nilsson RH, Hallenberg N, Nordén B, Maekawa N, Wu SH, (2003) Phylogeography of Hyphoderma setigerum (Basidiomycota) in the northern hemisphere. Mycological Research, 107, 645-652.
45. Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH, (2008) Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evolutionary Bioinformatics, 4, 193-201.
46. Pons J, Barraclough TG, Gomez-Zurita J, et al,. (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55, 595-609.
47. Rambaut A, Grass NC, (1997) Seq-gen: an application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences: CABIOS, 13, 235-238.
48. Riesenfeld CS, Schloss PD, Handelsman J, (2004) Metagenomics: genomic analysis of microbial communities. Annual Review of Genetics, 38, 525-552.
49. Ryberg M, Matheny PB, (2012) Asynchronous origins of ectomycorrhizal clades of Agaricales. Proceedings of the Royal Society of London. Series B: Biological Sciences, 279, 2003-2011.
50. Ryberg M, Nilsson RH, Kristiansson E, Töpel M, Jacobsson S, Larsson E, (2008) Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota). BMC Evolutionary Biology, 8, 50.
51. Schluter D, (2000) The Ecology of Adaptive Radiation. Oxford University Press, New York.
52. Schluter D, (2009) Evidence for ecological speciation and its alternative. Science, 323, 737-741.
53. Schoch CL, Seifert KA, Huhndorf S, et al,. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proceedings of the National Academy of Sciences, USA, 109, 6241-6246.
54. Stamatakis A, (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312-1313.
55. Stukenbrock EH, Banke S, Javan-Nikkhah M, McDonald BA, (2007) Origin and domestication of the fungal wheat pathogen Mycosphaerella graminicola via sympatric speciation. Molecular Biology and Evolution, 24, 398-411.
56. Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E, (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21, 2045-2050.
57. Takamatsu S, Matsuda S, (2004) Estimation of molecular clocks for ITS and 28s rDNA in Erysiphales. Mycoscience, 45, 340-344.
58. Taylor JW, Jacobson DJ, Kroken S, et al,. (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology, 31, 21-32.
59. Yamamoto N, Bibby K, (2014) Clustering of fungal community internal transcribed spacer sequence data obscures taxonomic diversity. Applied and Environmental Microbiology, 16, 2491-2500.
60. Yang Z, (2006) Computational Molecular Evolution, vol. 284. Oxford University Press, Oxford.
61. Zhang J, Kapli P, Pavlidis P, Stamatakis A, (2013) A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29, 2869-2876.