Host jumps shaped the diversity of extant rust fungi (Pucciniales)

New Phytologist

Volumn 209, Issue 3, 2016, Pages 1149-1158

  Mctaggart, Alistair R ^a   Shivas, Roger G ^b   van der Nest, Magriet A ^a   Roux, Jolanda ^a   Wingfield, Brenda D ^a   Wingfield, Michael J ^a  

^a UNIVERSITY OF PRETORIA   (South Africa)

^b DEPARTMENT OF AGRICULTURE AND FISHERIES   (Australia)

Author keywords

Calibration; Host jumps; Host parasite evolution; Mikronegeriaceae; Molecular dating; Pucciniales; Uredinales

Indexed keywords

COEVOLUTION; COMMON ANCESTRY; CRETACEOUS; DIVERGENCE; FUNGUS; SPECIATION (BIOLOGY); SPECIES DIVERSITY;

ACACIA; FABACEAE; MAGNOLIOPHYTA; PUCCINIA PSIDII; SPHAEROPHRAGMIACEAE; UREDINALES;

BASIDIOMYCETES; CALIBRATION; EVOLUTION; HOST PATHOGEN INTERACTION; PHYLOGENY; PHYSIOLOGY; STATISTICAL MODEL;

BASIDIOMYCOTA; BIOLOGICAL EVOLUTION; CALIBRATION; HOST-PATHOGEN INTERACTIONS; LIKELIHOOD FUNCTIONS; PHYLOGENY;

EID: 84954379680     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.13686     Document Type: Article

References (54)

1. Aime MC. 2006. Toward resolving family-level relationships in rust fungi (Uredinales). Mycoscience 47: 112-122.
2. Aime MC, Matheny PB, Henk DA, Frieders EM, Nilsson RH, Piepenbring M, McLaughlin DJ, Szabo LJ, Begerow D, Sampaio JP et al. 2006. An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia 98: 896-905.
3. Anikster Y, Wahl I. 1979. Coevolution of the rust fungi on Gramineae and Liliaceae and their hosts. Annual Review of Phytopathology 17: 367-403.
4. Baum BR, Savile DBO. 1985. Rusts (Uredinales) of Triticeae: evolution and extent of coevolution, a cladistic analysis. Botanical Journal of the Linnean Society 91: 367-394.
5. Beenken L. 2014. Pucciniales on Annona (Annonaceae) with special focus on the genus Phakopsora. Mycological Progress 13: 791-809.
6. Beenken L, Zoller S, Berndt R. 2012. Rust fungi on Annonaceae II: the genus Dasyspora Berk. & M.A. Curtis. Mycologia 104: 659-681.
7. Berbee ML, Taylor JW. 2010. Dating the molecular clock in fungi - how close are we? Fungal Biology Reviews 24: 1-16.
8. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10: e1003537.
9. Crane PE, Peterson RS. 2007. Mikronegeria fuchsiae sp. nov., a rust fungus on Fuchsia and Phyllocladus in New Zealand. New Zealand Journal of Botany 45: 707-713.
10. nd edn. St. Paul, MN, USA: American Phytopathological Society.
11. rd edn. St Paul, MN, USA: American Phytopathological Society.
12. Cunningham GH. 1931. The rust fungi of New Zealand: together with the biology, cytology and therapeutics of the Uredinales. Dunedin, New Zealand: John McIndoe.
13. Doungsa-ard C, McTaggart AR, Geering ADW, Dalisay TU, Ray J, Shivas RG. 2015. Uromycladium falcatarium sp. nov., the cause of gall rust on Paraserianthes falcataria in south-east Asia. Australasian Plant Pathology 44: 25-30.
14. Drummond AJ, Bouckaert RR. 2015. Bayesian evolutionary analysis with BEAST. Cambridge, UK: Cambridge University Press.
15. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969-1973.
16. Hart JA. 1988. Rust fungi and host plant coevolution: do primitive hosts harbor primitive parasites? Cladistics 4: 339-366.
17. Hedges SB, Marin J, Suleski M, Paymer M, Kumar S. 2015. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution 32: 835-845.
18. Henk DA, Vilgalys R. 2007. Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium. American Journal of Botany 94: 1515-1526.
19. Hennen JF, Buriticá P. 1980. A brief summary of modern rust taxonomic and evolutionary theory. Reports of the Tottori Mycological Institute 18: 243-256.
20. Ho SYM. 2007. Calibrating molecular estimates of substitution rates and divergence times in birds. Journal of Avian Biology 38: 409-414.
21. Katoh K, Asimenos G, Toh H. 2009. Multiple alignment of DNA sequences with MAFFT. In: Posada D, ed. Bioinformatics for DNA sequence analysis. New York, NY, USA: Humana Press, 39-64.
22. Kinloch BB. 2003. White pine blister rust in north america: past and prognosis. Phytopathology 93: 1044-1047.
23. Leppik EE. 1953. Some viewpoints on the phylogeny of rust fungi I. Coniferous rusts. Mycologia 45: 46-74.
24. Leppik EE. 1965. Some viewpoints on the phylogeny of rust fungi. V. Evolution of biological specialization. Mycologia 57: 6-22.
25. Liberato JR, McTaggart AR, Shivas RG. 2014. First report of Masseeëlla capparis in Australia. Australasian Plant Disease Notes 9: 121.
26. Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR. 2012. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology 61: 90-106.
27. Lutz M, Bauer R, Begerow D, Oberwinkler F. 2004. Tuberculina-Thanatophytum/Rhizoctonia crocorum-Helicobasidium: a unique mycoparasitic-phytoparasitic life strategy. Mycological Research 108: 227-238.
28. Magallón S, Hilu KW, Quandt D. 2013. Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates. American Journal of Botany 100: 556-573.
29. Maier W, McTaggart AR, Roux J, Wingfield MJ. 2015. Phakopsora myrtacearum sp. nov., a newly described rust (Pucciniales) on eucalypts in eastern and southern Africa. Plant Pathology. doi: 10.1111/ppa.12406
30. Mao K, Milne RI, Zhang L, Peng Y, Liu J, Thomas P, Mill RR, Renner S. 2012. Distribution of living Cupressaceae reflects the breakup of Pangea. Proceedings of the National Academy of Sciences, USA 109: 7793-7798.
31. McTaggart AR, Doungsa-ard C, Geering ADW, Aime MC, Shivas RG. 2015. A co-evolutionary relationship exists between Endoraecium (Pucciniales) and its Acacia hosts in Australia. Persoonia 35: 50-62.
32. McTaggart AR, Geering ADW, Shivas RG. 2013. Thekopsora minima causes blueberry rust in south-eastern Queensland and northern New South Wales. Australasian Plant Disease Notes 8: 81-83.
33. McTaggart AR, Geering ADW, Shivas RG. 2014. The rusts on Goodeniaceae and Stylidiaceae. Mycological Progress 13: 1017-1025.
34. van der Merwe MM, Walker J, Ericson L, Burdon JJ. 2008. Coevolution with higher taxonomic host groups within the Puccinia/Uromyces rust lineage obscured by host jumps. Mycological Research 112: 1387-1408.
35. Miller JT, Murphy DJ, Ho SYW, Cantrill DJ, Seigler D. 2013. Comparative dating of Acacia: combining fossils and multiple phylogenies to infer ages of clades with poor fossil records. Australian Journal of Botany 61: 436-445.
36. Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24: 581-583.
37. Pegg GS, Giblin FR, McTaggart AR, Guymer GP, Taylor H, Ireland KB, Shivas RG, Perry S. 2014. Puccinia psidii in Queensland, Australia: disease symptoms, distribution and impact. Plant Pathology 63: 1005-1021.
38. Peterson RS. 1974. Rust fungi with Caeoma-like sori on conifers. Mycologia 66: 242-255.
39. Rambaut A, Suchard MA, Xie D, Drummond AJ 2014. Tracer v1.6. [WWW document] URL http://beast.bio.ed.ac.uk/Tracer. [accessed 17 July 2015].
40. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
41. Roy BA. 2001. Patterns of association between Crucifers and their flower-mimic pathogens: host jumps are more common than coevolution or cospeciation. Evolution 55: 41-53.
42. Sauquet H, Ho SYW, Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, Bayly MJ, Bromham L, Brown GK, Carpenter RJ et al. 2012. Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Systematic Biology 61: 289-313.
43. Savile DBO. 1971. Coevolution of the rust fungi and their hosts. The Quarterly Review of Biology 46: 211-218.
44. Savile DBO. 1976. Evolution of the rust fungi (Uredinales) as reflected by their ecological problems. In: Hecht M, Steere W, Wallace B, eds. Evolutionary biology. New York, NY, USA: Springer, 137-207.
45. Savile DBO. 1979. Fungi as aids in higher plant classification. Botanical Review 45: 377-503.
46. Scholler M, Aime MC. 2006. On some rust fungi (Uredinales) collected in an Acacia koa-Metrosideros polymorpha woodland, Mauna Loa Road, Big Island, Hawaii. Mycoscience 47: 159-165.
47. Scholler M, Lutz M, Wood A, Hagedorn G, Mennicken M. 2011. Taxonomy and phylogeny of Puccinia lagenophorae: a study using rDNA sequence data, morphological and host range features. Mycological Progress 10: 175-187.
48. Shivas RG, Beasley DR, McTaggart AR. 2014. Online identification guides for Australian smut fungi (Ustilaginomycotina) and rust fungi (Pucciniales). IMA Fungus 5: 195-202.
49. Sjamsuridzal W, Nishida H, Ogawa H, Kakishima M, Sugiyama J. 1999. Phylogenetic positions of rust fungi parasitic on ferns: evidence from 18S rDNA sequence analysis. Mycoscience 40: 21-27.
50. Stamatakis A. 2014. RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313.
51. Tiffney BH, Barghoorn ES. 1974. The fossil record of the fungi. Occasional Papers of the Farlow Herbarium of Cryptogamic Botany 7: 1-42.
52. Vialle A, Feau N, Allaire M, Didukh M, Martin F, Moncalvo J-M, Hamelin RC. 2009. Evaluation of mitochondrial genes as DNA barcode for Basidiomycota. Molecular Ecology Resources 9: 99-113.
53. de Vienne DM, Refregier G, Lopez-Villavicencio M, Tellier A, Hood ME, Giraud T. 2013. Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. New Phytologist 198: 347-385.
54. Wingfield BD, Ericson L, Szaro T, Burdon JJ. 2004. Phylogenetic patterns in the Uredinales. Australasian Plant Pathology 33: 327-335.