Pleistocene expansion of the bipolar lichen Cetraria aculeata into the Southern hemisphere

Molecular Ecology

Volumn 22, Issue 7, 2013, Pages 1961-1983

  Fernández Mendoza, Fernando ^a,b   Printzen, Christian ^a,b  

^a SENCKENBERG RESEARCH INSTITUTE   (Germany)

^b BIODIVERSITY AND CLIMATE RESEARCH CENTRE BIK F   (Germany)

Author keywords

amphitropical disjunction; Antarctica; lichenized fungi; Patagonia; Pleistocene; stochastic mapping

Indexed keywords

MITOCHONDRIAL DNA;

ALGORITHM; ARTICLE; ASCOMYCETES; CLASSIFICATION; DNA SEQUENCE; GENE LOCUS; GENETIC POLYMORPHISM; GENETICS; LICHEN (ORGANISM); MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION DENSITY; SPAIN;

ALGORITHMS; ASCOMYCOTA; CLONING, MOLECULAR; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC LOCI; LICHENS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PHYLOGEOGRAPHY; POLYMORPHISM, GENETIC; POPULATION DENSITY; SEQUENCE ANALYSIS, DNA; SPAIN;

CETRARIA ACULEATA; FUNGI;

EID: 84875365390     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12210     Document Type: Article

References (119)

1. Amo de Paz G, Divakar PK, Cubas P, Lumbsh T, Crespo A, (2011) Origin and diversification of major clades in parmelioid lichens (Parmeliaceae, Ascomycota). PLoS ONE, 6, e28161.
2. Beerli P, (2010) Tutorial: comparison of gene flow models using Bayes factors. Migrate-n. Available at: http://popgen.sc.fsu.edu/Migrate/Tutorials/ Entries/2010/7/12-Day-of-longboarding.html.
3. Beerli P, (2011) Migrate-n v 3.2.6. Available at: http://popgen.sc.fsu. edu/Migrate/Migrate-n.html
4. Beerli P, Palczewski M, (2010) Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics, 185, 313-326.
5. Bell CD, Donoghue MJ, (2005) Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians. Organisms Diversity & Evolution, 5, 147-159.
6. Bickford D, Lohman DJ, Sodhi NS, et al,. (2007) Cryptic species as a window on diversity and conservation. Trends in Ecology & Evolution, 22, 148-155.
7. Bollback JP, (2006) SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.
8. Bray WL, (1900) The relations of the North American flora to that of South America. Science, 12, 709-716.
9. Briggs JC, (1987) Antitropical distribution and evolution in the Indo-West Pacific Ocean. Systematic Zoology, 36, 237-247.
10. Buschbom J, (2007) Migration between continents: geographical structure and long-distance gene flow in Porpidia flavicunda (lichen-forming Ascomycota). Molecular Ecology, 16, 1835-1846.
11. Casano LM, del Campo EM, Garcia-Breijo FJ, et al,. (2011) Two Trebouxia algae with different physiological performances are ever-present in lichen thalli of Ramalina farinacea. Coexistence versus competition?. Environmental Microbiology, 13, 806-818.
12. Castello M, Nimis PL, (1997) Diversity of lichens in Antarctica. In: Antarctic Communities: Species, Structure and Survival (eds, Battaglia B, Valencia J, Walton DWH,), pp. 15-21. Cambridge University Press, Edinburgh.
13. Clark PU, Dyke AS, Shakun JD, et al,. (2009) The last glacial maximum. Science, 325, 710-714.
14. Clement M, Posada D, Crandall KA, (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1659.
15. Corander J, Marttinen P, (2006) Bayesian identification of admixture events using multilocus molecular markers. Molecular Ecology, 15, 2833-2843.
16. Corander J, Tang J, (2007) Bayesian analysis of population structure based on linked molecular information. Mathematical Biosciences, 205, 19-31.
17. Corander J, Waldmann P, Marttinen P, Sillanpää MJ, (2004) BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics, 20, 2363-2369.
18. Corander J, Marttinen P, Tang J, (2009) BAPS: Bayesian Analysis of Population Structure. Structure, Manual v. 5.3. Available at: http://web.abo.fi/fak/mnf//mate/jc/software/baps.html
19. Crespo A, Lumbsch HT, (2010) Cryptic species in lichen-forming fungi. IMA Fungus, 1, 167-170.
20. Crespo A, Pérez-Ortega S, (2010) Cryptic species and species pairs in lichens: a discussion on the relationship between molecular phylogenies and morphological characters. Anales del Jardín Botánico de Madrid, 66, 71-81.
21. Darwin C, (1872) The Origin of Species by Means of Natural Slection; or the Preservation of Favoured Races in the Struggle for Life, 6th edn. Project Gutenberg ebook, London.
22. De Wever A, Leliaert F, Verleyen E, et al,. (2009) Hidden levels of phylodiversity in Antarctic green algae: further evidence for the existence of glacial refugia. Proceedings of the Royal Society. Biological Sciences, 276, 3591-3599.
23. Degnan JH, Rosenberg NA, (2006) Discordance of species trees with their most likely gene trees. PLoS Genetics, 2, 0762-0768.
24. Domaschke S, Fernández-Mendoza F, García MA, et. al. (2012) Low genetic diversity in Antarctic populations of the lichen Cetraria aculeata and its photobiont. Polar Research, 31, 17353.
25. Donoghue MJ, (2011) Bipolar biogeography. Proceedings of the National Academy of Sciences of the United States of America, 108, 6341-6342.
26. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
27. Drummond AJ, Rambaut A, Shapiro B, Pybus O, (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185-1192.
28. Drummond AJ, Ashton B, Buxton S, et al,. (2010) Geneious v. 5.3. Available at: http://www.geneious.com/
29. Du Rietz GE, (1940) Problems of bipolar plant distribution. Acta Phytogeographica Svecica, 13, 215-282.
30. ESRI (2011) ArcGIS Desktop. Available at: http://www.esri.com/.
31. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620.
32. Excoffier L, Laval G, Schneider S, (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
33. Falush D, Stephens M, Pritchard JK, (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
34. Fernández-Mendoza F, Domaschke S, García MA, et al,. (2011) Population structure of mycobionts and photobionts of the widespread lichen Cetraria aculeata. Molecular Ecology, 20, 1208-1232.
35. Frahm JP, (2008) Diversity, dispersal and biogeography of bryophytes (mosses). Biodiversity and Conservation, 17, 277-284.
36. Galloway D, Aptroot A, (1995) Bipolar lichens: a review. Cryptogamic Botany, 5, 184-189.
37. Geml J, (2011) Coalescent analyses reveal contrasting patterns of intercontinental gene flow in arctic-alpine and boreal-temperate fungi. In: Biogeography of Microscopic Organisms: Is Everything Small Everywhere? (ed, Fontaneto D,), pp. 175-190. Cambridge University Press, London.
38. Geml J, Kauff F, Brochmann C, Taylor DL, (2010) Surviving climate changes: high genetic diversity and transoceanic gene flow in two arctic-alpine lichens, Flavocetraria cucullata and F. nivalis (Parmeliaceae, Ascomycota). Journal of Biogeography, 37, 1529-1542.
39. Geml J, Kauff F, Brochmann C, et al,. (2012) Frequent circumarctic and rare transequatorial dispersals in the lichenised agaric genus Lichenomphalia (Hygrophoraceae, Basidiomycota). Fungal Biology, 116, 388-400.
40. Guindon S, Gascuel O, (2003) A Simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696-704.
41. Gussarova G, Popp M, Vitek E, Brochmann C, (2008) Molecular phylogeny and biogeography of the bipolar Euphrasia (Orobanchaceae): recent radiations in an old genus. Molecular Phylogenetics and Evolution, 48, 444-460.
42. Heled J, Drummond AJ, (2010) Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570-580.
43. Hewitt G, (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
44. Hewitt G, (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 359, 183-195.
45. Hickerson MJ, Carstens BC, Cavender-Bares J, et al,. (2010) Phylogeography's past, present, and future: 10 years after Avise, 2000. Molecular Phylogenetics and Evolution, 54, 291-301.
46. Hooker JD, Taylor T, (1844) Lichenes antarctici. London Journal of Botany, 3, 634-658.
47. Huelsenbeck JP, Andolfatto P, (2007) Inference of population structure under a Dirichlet process model. Genetics, 175, 1787-1802.
48. Huelsenbeck JP, Nielsen R, Bollback JP, (2003) Stochastic mapping of morphological characters. Systematic Biology, 52, 131-158.
49. Huelsenbeck JP, Andolfatto P, Huelsenbeck ET, (2011) Structurama: Bayesian inference of population structure. Evolutionary Bioinformatics Online, 7, 55-59.
50. Jakob SS, Martinez-Meyer E, Blattner FR, (2009) Phylogeographic analyses and paleodistribution modeling indicate pleistocene in situ survival of Hordeum species (Poaceae) in southern Patagonia without genetic or spatial restriction. Molecular Biology and Evolution, 26, 907-923.
51. Jakobsson M, Rosenberg NA, (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23, 1801-1806.
52. James SA, O'Kelly MJT, Carter DM, et al,. (2009) Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Research, 19, 626-635.
53. Jukes T, Cantor C, (1969) Evolution of Protein Molecules. Academic Press, New York.
54. Kärnefelt I, (1979) The brown fruticose species of Cetraria. Opera Botanica, 46, 1-150.
55. Kärnefelt I, (1986) The genera Bryocaulon, Coelocaulon and Cornicularia and formely associated taxa. Opera Botanica, 86, 1-90.
56. Kass RE, Raferty AE, (1995) Bayes factors. Journal of the American Statistical Association, 90, 773-795.
57. Knowles LL, Carstens BC, (2007) Delimiting species without monophyletic gene trees. Systematic Biology, 56, 887-895.
58. Kristinsson H, Zhurbenko M, Steen Hansen E, (2010) Panarctic checklist of lichens and lichenicolous fungi. CAFF Technical Report No. 20, CAFF, International Secretariat, Akureyri, Iceland.
59. Leavitt SD, Fankhauser JD, Leavitt DH, et al,. (2011) Complex patterns of speciation in cosmopolitan "rock posy" lichens-discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota). Molecular Phylogenetics and Evolution, 59, 587-602.
60. Leavitt SD, Esslinger TL, Divakar PK, Lumbsch HT, (2012) Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions. BMC Evolutionary Biology, 12, 176.
61. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
62. Lindblom L, Søchting U, (2008) Taxonomic revision of Xanthomendoza borealis and Xanthoria mawsonii (Lecanoromycetes, Ascomycota). Lichenologist, 40, 399-409.
63. Lindner DL, Banik MT, (2011) Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia, 103, 731-740.
64. Liu L, Pearl DK, (2007) Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology, 56, 504-514.
65. Longton RE, (1997) The role of bryophytes and lichens in polar ecosystems. In: Ecology of Arctic Environments: 13th Special Symposium of the British Ecological Society (eds, Woodin SJ, &, Marquiss M,), pp. 69-96. Cambridge University Press, Cambridge.
66. Lumbsch HT, Leavitt SD, (2011) Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi Fungal Diversity, 50, 59-72.
67. Lynch M, Crease TJ, (1990) The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution, 7, 377-394.
68. Maechler M, (2012) Package 'Rmpfr'. Available at: http://cran.r-project. org/web/packages/Rmpfr/vignettes/Rmpfr-pkg.pdf.
69. Martin DP, Lemey P, Lott M, et al,. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26, 2462-2463.
70. Meyer D, Zeileis A, Hornik K, (2006) The Strucplot framework: visualizing multi-way contingency tables with vcd. Journal of Statistical Software, 17, 1-48.
71. Meyer D, Zeileis A, Hornik K, Friendly M, (2011) vcd: Visualizing Categorical Data. Available at: http://cran.r-project.org/web/packages/vcd/ index.html.
72. Mills LS, Allendorft FW, (1996) The one-migrant-per-generation rule in conservation and management. Conservation Biology, 10, 1509-1518.
73. Nei M, (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
74. Newman L, Convey P, Gibson JAE, Linse K, (2009) Antarctic paleobiology: glacial refugia and constraints on past ice-sheet reconstructions. PAGES News, 17, 22-24.
75. Nielsen R, (2002) Mapping mutations on phylogenies. Systematic Biology, 51, 729-739.
76. Nielsen R, Beaumont MA, (2009) Invited review: statistical inferences in phylogeography. Molecular Ecology, 18, 1034-1047.
77. Nylander JAA, Olsson U, Alström P, et al,. (2008a) Accounting for phylogenetic uncertainty in biogeography: a Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus). Systematic Biology, 57, 257-268.
78. Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL, (2008b) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics, 24, 581-583.
79. Ochyra R, Buck WR, (2003) Arctoa furvella, new to Tierra del Fuego, with notes on trans-American bipolar bryogeography. Bryologist, 106, 532-538.
80. Otto-Bliesner BL, Marshall SJ, Overpeck JT, et al,. (2006) Simulating Arctic climate warmth and icefield retreat in the last interglaciation. Science, 311, 1751-1753.
81. Øvstedal DO, Lewis Smith RI, (2001) Lichens of Antarctica and South Georgia: A Guide to their Identification and Ecology. Cambridge University Press, Cambridge.
82. Page RD, Charleston MA, (1997) From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution, 7, 231-240.
83. Pearce DA, Cockell CS, Lindström ES, Tranvik LJ, (2007) First evidence for a bipolar distribution of dominant freshwater lake bacterioplankton. Antarctic Science, 19, 245-252.
84. Pérez-Ortega S, Fernández-Mendoza F, Raggio J, et al,. (2012) Extreme phenotypic plasticity in Cetraria aculeata (lichenized Ascomycota): adaptation or incidental modification? Annals of Botany, 109, 1133-1148.
85. Piercey-Normore MD, DeDuke C, (2011) Fungal farmers or algal escorts: lichen adaptation from the algal perspective. Molecular Ecology, 20, 3708-3710.
86. Piercey-Normore MD, DePriest P, (2001) Algal switching among lichen symbioses. American Journal of Botany, 88, 1490-1498.
87. Popp M, Mirré V, Brochmann C, (2011) A single Mid-Pleistocene long-distance dispersal by a bird can explain the extreme bipolar disjunction in crowberries (Empetrum). Proceedings of the National Academy of Sciences, 108, 6520-6525.
88. Posada D, (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25, 1253-1256.
89. Printzen C, (2008) Uncharted terrain: the phylogeography of arctic and boreal lichens. Plant Ecology and Diversity, 1, 265-271.
90. Printzen C, Ekman S, Tonsberg T, (2003) Phylogeography of Cavernularia hultenii: evidence of slow genetic drift in a widely disjunct lichen. Molecular Ecology, 12, 1473-1486.
91. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 959.
92. Provan J, Bennett KD, (2008) Phylogeographic insights into cryptic glacial refugia. Trends in Ecology & Evolution, 23, 564-571.
93. de Queiroz K, (2007) Species concepts and species delimitation. Systematic Biology, 56, 879-886.
94. R Development Core Team (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
95. Rambaut A, Drummond AJ, (2007) Tracer v 1.4. Available at: http://beast.bio.ed.ac.uk.
96. Randlane T, Saag A, Thell A, (1997) A second updated world list of cetrarioid lichens. Bryologist, 100, 109-122.
97. Raven PH, (1963) Amphitropical relationships in the Floras of North and South America. The Quarterly Review of Biology, 38, 151-177.
98. Ritz MS, Millar C, Miller GD, et al,. (2008) Phylogeography of the southern skua complex-rapid colonization of the southern hemisphere during a glacial period and reticulate evolution. Molecular Phylogenetics and Evolution, 49, 292-303.
99. Ronquist F, Sanmartín I, (2011) Phylogenetic methods in biogeography. Annual Review of Ecology, Evolution and Systematics, 42, 441-464.
100. Rundgren M, Ingólfsson Ó, (1999) Plant survival in Iceland during periods of glaciation? Journal of Biogeography, 26, 387-396.
101. Samadi S, Barberousse A, (2009) Species: towards new, well-grounded practices. Biological Journal of the Linnean Society, 97, 217-222.
102. Silvestro D, (2011) Diversification in time and space. Methodological advancement and case studies from the Neotropical plant family Bromeliaceae. Doctoral Dissertation, Johann-Wolfgang-Goethe-Universität, Frankfurt am Main, Germany.
103. Smith JA, Seltzer GO, Farber DL, et al,. (2005) Early local last glacial maximum in the tropical Andes. Science, 308, 678-681.
104. Spieth PT, (1974) Gene flow and genetic differentiation. Genetics, 78, 961-965.
105. Spribille T, (2011) Circumboreal lichen diversification: phylogenetic and phylogeographic Studies in the genus Mycoblastus. Doctoral Dissertation, Karl-Franzens-Universität, Graz, Austria.
106. Spribille T, Klug B, Mayrhofer H, (2011) A phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius (Mycoblastaceae, lichenized Ascomycota) reveals cryptic clades correlated with fatty acid profiles. Molecular Phylogenetics and Evolution, 59, 603-614.
107. Stenroos S, (1993) Taxonomy and distribution of the lichen family Cladoniaceae in the Antarctic and peri-Antarctic regions. Cryptogamic Botany, 3, 310-344.
108. Sun HJ, Friedmann EI, (2005) Communities adjust their temperature optima by shifting producer-to-consumer-ratio, shown in lichens as a model. II. Experimental verification. Microbial Ecology, 49, 528-535.
109. Tamura K, Peterson D, Peterson N, et al,. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
110. Van de Vijver B, Gremmen NJM, Beyens L, (2005) The genus Stauroneis (Bacillariophyceae) in the Antarctic region. Journal of Biogeography, 32, 1791-1798.
111. Wallace AR, (1892) Island Life or the Phenomena and Causes of Insular Faunas and Floras. 2nd and Revised Edition. MacMillan and Co., London.
112. Waples RS, Gaggiotti O, (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity Molecular Ecology, 15, 1419-1439.
113. Wen J, Ickert-Bond SM, (2009) Evolution of the Madrean-Tethyan disjunctions and the North and South American amphitropical disjunctions in plants. Journal of Systematics and Evolution, 47, 331-348.
114. Werth S, (2010) Population genetics of lichen-forming fungi-a review. Lichenologist, 42, 499-519.
115. Winkworth RC, Donoghue MJ, (2005) Viburnum phylogeny based on combined molecular data: Implications for taxonomy and biogeography. American Journal of Botany, 92, 653-666.
116. Winkworth RC, Lundberg J, Donoghue MJ, (2008) Toward a resolution of Campanulid phylogeny, with special reference to the placement of Dipsacales. Taxon, 57, 53-65.
117. Wirtz N, Printzen C, Sancho LG, Lumbsch HT, (2006) The phylogeny and classification of Neuropogon and Usnea (Parmeliaceae, Ascomycota) revisited. Taxon, 55, 367-376.
118. Wirtz N, Printzen C, Lumbsch HT, (2008) The delimitation of Antarctic and bipolar species of neuropogonoid Usnea (Ascomycota, Lecanorales): a cohesion approach of species recognition for the Usnea perpusilla complex. Mycological Research, 112, 472-484.
119. Zeileis A, Meyer D, Hornik K, (2007) Residual-based shadings for visualizing (conditional) independence. Journal of Computational and Graphical Statistics, 16, 507-525.