Abstract
Historical biogeography helps us keep track of organisms over time and space. However, microbial ecology and evolutionary studies are fraught with challenges due to their unknown life histories, a poor fossil record, and problematic taxonomy. Mycorrhizal fungi are key players for most terrestrial ecosystems and interact with a vast number of plants, including many woody trees that dominate temperate, tropical, and boreal ecosystems. They are also highly polyphyletic and disproportionally diverse globally and across the fungal tree of life, making them biogeographically intriguing. In this review, we focus on describing phylogenetic approaches that have been or could be applied in mycorrhizal biogeographic studies. We start by summarizing molecular-based studies and methods for species delimitation, pointing out the need for robust phylogenetic hypotheses in a phylogenomic or multi-locus framework. We describe methods for the reconstruction of ancestral states or areas and their use in biogeography, also synthesizing some of the progress with respect to generalized patterns in mycorrhizal biogeography. Next, we go through aspects related to time-calibrating fungal phylogenies and their time-of-origin, as well as downstream analyzes involving the estimation of diversification rates. Diversification rate, trait evolution, and phylo-community analyses are also put in the context of relevant evolutionary ecology hypotheses. Finally, we dedicate a section to methodological biases and caveats, which are often associated with global mycological fieldwork and sampling, and some phylogenetic methods.
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Abarenkov K, Nilsson HR, Larsson K-H, Alexander IJ, Eberhardt U, Erland S et al (2010) The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytol 186:281–285
Ackermann M, Doebeli M (2004) Evolution of niche width and adaptive diversification. Evolution 58:2599–2612
Alexander IJ (2006) Ectomycorrhizas – out of Africa? New Phytol 172:589–591
Altschul SF, Gish W, Miller W, Myers EW (1990) Basic local alignment search tool. J Mol Evol 215:403–410
Arnold AE (2007) Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers. Fungal Biol Rev 21:51–66
Arnold AE, Lutzoni F (2007) Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88:541–549
Askin RA, Spicer RA (1995) The late Cretaceous and Cenozoic history of vegetation and climate in Northern and Southern high latitudes. In: Board on Earth Sciences and Resources (ed) Effects of past global change on life, studies in geophysics. National Academy, Washington, DC, pp 156–173
Avise JC (2000) Phylogeography. Harvard University Press, Cambridge
Avise JC (2009) Phylogeography: retrospect and prospect. J Biogeogr 36:3–15
Avise JC, Wollenberg K (1997) Phylogenetics and the origin of species. PNAS 94:7748–7755
Avise JC, Arnold J, Ball RM, Bermingham E (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst 18:489–522
Baas-Becking LGM (1934) Geobiologie of inleiding tot de milieukunde. W.P. Van Stockum & Zoon, The Hague
Bakker den HC, Zuccarello GC, Kuyper TW, Noordeloos ME (2004) Evolution and host specificity in the ectomycorrhizal genus Leccinum. New Phytol 163:201–215
Baldrian P (2009) Ectomycorrhizal fungi and their enzymes in soils: is there enough evidence for their role as facultative soil saprotrophs? Oecologia 161:657–660
Barraclough TG, Nee S (2001) Phylogenetics and speciation. Trends Ecol Evol 16:391–399
Beaulieu JM, O'Meara BC (2016) Detecting hidden diversification shifts in models of trait-dependent speciation and extinction. Syst Biol 65:583–601
Beaulieu JM, Ree RH, Cavender-Bares J, Weiblen GD, Donoghue MJ (2012) Synthesizing phylogenetic knowledge for ecological research. Ecology 93:S4–S13
Beheregaray LB (2008) Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Mol Ecol 17:3754–3774
Beimforde C, Schäfer N, Dörfelt H, Nascimbene PC, Singh H, Heinrichs J, Reitner J, Rana RS, Schmidt AR (2011) Ectomycorrhizas from a Lower Eocene angiosperm forest. New Phytol 192:988–996
Berbee ML, Taylor JW (2001) Fungal molecular evolution: gene trees and geologic time. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) Systematics and evolution. Springer, Berlin, pp 229–245
Berbee ML, Taylor JW (2010) Dating the molecular clock in fungi - how close are we? Fungal Biol Rev 24:1–16
Berendse F, Scheffer M (2009) The angiosperm radiation revisited, an ecological explanation for Darwin’s “abominable mystery”. Ecol Lett 12:865–872
Bidartondo MI (2005) The evolutionary ecology of myco-heterotrophy. New Phytol 167:335–352
Bidartondo MI, et al (2008) Preserving accuracy in GenBank. Science 319:1616a
Bidartondo MI, Bruns TD (2002) Fine-level mycorrhizal specificity in the Monotropoideae (Ericaceae): specificity for fungal species groups. Mol Ecol 11:557–569
Bidartondo MI, Bruns TD (2005) On the origins of extreme mycorrhizal specificity in the Monotropoideae (Ericaceae): performance trade-offs during seed germination and seedling development. Mol Ecol 14:1549–1560
Bielejec F, Rambaut A, Suchard MA, Lemey P (2011) SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics 27:2910–2912
Birand A, Vose A, Gavrilets S (2012) Patterns of species ranges, speciation, and extinction. Am Nat 179:1–21
Bisby GR (1943) Geographical distribution of fungi. Bot Rev 9:466–482
Blackwell M (2011) The Fungi: 1, 2, 3 ... 5.1 million species? Am J Bot 98:426–438
Blackwell M, Hibbett DS, Taylor JW, Spatafora JW (2006) Research coordination networks: a phylogeny for kingdom Fungi (Deep Hypha). Mycologia 98:829–837
Bloomquist EW, Lemey P, Suchard MA (2010) Three roads diverged? Routes to phylogeographic inference. Trends Ecol Evol 25:626–632
Bonfante P, Genre A (2010) Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis. Nat Commun 1:48
Bonito G, Smith ME, Nowak M, Healy RA, Guevara G, Cázares E et al (2013) Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage. PLoS One 8:e52765
Bouckaert R, Lemey P, Dunn M, Greenhill SJ, Alekseyenko AV, Drummond AJ et al (2012) Mapping the origins and expansion of the Indo-European language family. Science 337:957–960
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D et al (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537–e1003536
Brown JH (2014) Why are there so many species in the tropics? J Biogeogr 41:8–22
Brown JKM, Hovmøller MS (2002) Aerial dispersal of pathogens on the global and continental scales and its impact on plant disease. Science 297:537–541
Brown WM, George M, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. PNAS 76:1967–1971
Brundrett MC (2002) Coevolution of roots and mycorrhizas of land plants. New Phytol 154:275–304
Bruns TD, Gardes M (1993) Molecular tools for the identification of ectomycorrhizal fungi—taxon-specific oligonucleotide probes for suilloid fungi. Mol Ecol 2:233–242
Bruns TD, Shefferson RP (2004) Evolutionary studies of ectomycorrhizal fungi: recent advances and future directions. Can J Bot 82:1122–1132
Bruns TD, Szaro TM (1992) Rate and mode differences between nuclear and mitochondrial small-subunit rRNA genes in mushrooms. Mol Biol Evol 9:836–855
Bruns TD, Taylor JW (2016) Comment on “Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism”. Science 351:826–826
Bruns TD, White TJ, Taylor JW (1991) Fungal molecular systematics. Annu Rev Ecol Syst 22:525–564
Bruns TD, Szaro TM, Gardes M, Cullings KW (1998) A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis. Mol Ecol 7:257–272
Bruns TD, Bidartondo MI, Taylor DL (2002) Host specificity in ectomycorrhizal communities: what do the exceptions tell us? Integr Comp Biol 42:352–359
Bryson RW, Prendini L, Savary WE, Pearman PB (2014) Caves as microrefugia: Pleistocene phylogeography of the troglophilic North American scorpion Pseudouroctonus reddelli. BMC Evol Biol 14:9
Burgess ND, Edwards D (1991) Classification of uppermost Ordovician to Lower Devonian tubular and lamentous macerals from the Anglo-Welsh Basin. Bot J Linn Soc 106:41–66
Butler MA, King AA (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am Nat 164:683–695
Butlin R, Bridle J, Schluter D (2009) Speciation and patterns of diversity. Cambridge University Press, New York
Cadotte MW, Davies TJ (2016) Phylogenies in ecology. Princeton University Press, Princeton
Cai Q, Tulloss RE, Tang LP, Tolgor B, Zhang P, Chen ZH, Yang ZL (2014) Multi-locus phylogeny of lethal amanitas: implications for species diversity and historical biogeography. BMC Evol Biol 14:143
Camargo A, Morando M, Avila LJ, Sites JW Jr (2012) Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution 66:2834–2849
Carstens BC, Pelletier TA, Reid NM, Satler JD (2013) How to fail at species delimitation. Mol Ecol 22:4369–4383
Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW (2009) The merging of community ecology and phylogenetic biology. Ecol Lett 12:693–715
Chapela IH, Garbelotto M (2004) Phylogeography and evolution in matsutake and close allies inferred by analyses of ITS sequences and AFLPs. Mycologia 96:730–741
Chaudhary VB, Lau MK, Johnson NC (2008) Macroecology of microbes – biogeography of the Glomeromycota. In: Varma A (ed) Mycorrhiza. Springer, Berlin, pp 529–563
Clegg MT, Gaut BS, Learn GH, Morton BR (1994) Rates and patterns of chloroplast DNA evolution. PNAS 91:6795–6801
Corby-Harris V, Pontaroli AC, Shimkets LJ, Bennetzen JL, Habel KE, Promislow DE L (2007) Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster. Appl Environ Microbiol 73:3470–3479
Crisci JV, Katinas L, Posadas P (2003) Historical biogeography. Harvard University Press, Cambridge
Crisp MD, Cook LG (2009) Explosive radiation or cryptic mass extinction? Interpreting signatures in molecular phylogenies. Evolution 63:2257–2265
Cutter AD (2013) Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory. Mol Phylogenet Evol 69:1172–1185
Dahlberg A (2001) Community ecology of ectomycorrhizal fungi: an advancing interdisciplinary field. New Phytol 150:555–562
Davis MP, Midford PE, Maddison W (2013) Exploring power and parameter estimation of the BiSSE method for analyzing species diversification. BMC Evol Biol 13:38
Davison J, Moora M, Öpik M, Adholeya A (2015) Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism. Science 349:970–973
Dayrat B (2005) Towards integrative taxonomy. Biol J Linn Soc 85:407–415
De Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56:879–886
Dennis RL (1969) Fossil mycelium with clamp connections from the Middle Pennsylvanian. Science 163:670–671
Dennis RL (1970) A Middle Pennsylvanian basidiomycete mycelium with clamp connections. Mycologia 62:578–584
Dickie IA, Moyersoen B (2008) Towards a global view of ectomycorrhizal ecology. New Phytol 180:263–265
Dornburg A, Federman S, Eytan RI, Near TJ (2016) Cryptic species diversity in sub-Antarctic islands: a case study of Lepidonotothen. Mol Phylogenet Evol 104:32–43
Dotzler N, Krings M, Taylor TN, Agerer R (2006) Germination shields in Scutellospora (Glomeromycota: Diversisporales, Gigasporaceae) from the 400 million-year-old Rhynie chert. Mycol Prog 5:178–184
Douhan GW, Vincenot L, Gryta H, Selosse M-A (2011) Population genetics of ectomycorrhizal fungi: from current knowledge to emerging directions. Fungal Biol 115:569–597
Drummond AJ, Bouckaert RR (2015) Bayesian evolutionary analysis with BEAST. Cambridge University Press, Cambridge
Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
Drummond AJ, Suchard MA (2010) Bayesian random local clocks, or one rate to rule them all. BMC Biol 8:114
Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG (2003) Measurably evolving populations. Trends Ecol Evol 18:481–488
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4:e88
Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973
Dunstan WA, Dell B, Malajczuk N (1998) The diversity of ectomycorrhizal fungi associated with introduced Pinus spp. in the Southern Hemisphere, with particular reference to Western Australia. Mycorrhiza 8:71–79
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461
Etienne RS, Rosindell J (2012) Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification. Syst Biol 61:204–213
Etienne RS, Haegeman B, Stadler T, Aze T, Pearson PN, Purvis A, Phillimore AB (2012) Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc R Soc B 279:1300–1309
Felsenstein J (1988) Phylogenies and quantitative characters. Annu Rev Ecol Syst 19:445–471
Feng B, Xu J, Wu G, Zeng N-K, Li Y-C, Tolgor B et al (2012) DNA sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the porcini mushrooms. PLoS One 7:e37567–e37512
Feng B, Zhao Q, Xu J, Qin J, Yang ZL (2016) Drainage isolation and climate change-driven population expansion shape the genetic structures of Tuber indicum complex in the Hengduan Mountains region. Sci Rep 6:21811
Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296:1061–1063
FitzJohn RG (2010) Quantitative traits and diversification. Syst Biol 59:619–633
FitzJohn RG (2012) Diversitree: comparative phylogenetic analyses of diversification in R. Methods Ecol Evol 3:1084–1092
Frøslev TG, Matheny PB, Hibbett DS (2005) Lower level relationships in the mushroom genus Cortinarius (Basidiomycota, Agaricales): a comparison of RPB1, RPB2, and ITS phylogenies. Mol Phylogenet Evol 37:602–618
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. Syst Biol 62:707–724
Gardes M, Bruns TD (1996) Community structure of ectomycorrhizal fungi in a Pinus muricata forest: above-and below-ground views. Can J Bot 74:1572–1583
Gavin DG, Fitzpatrick MC, Gugger PF, Heath KD, Rodríguez-Sánchez F, Dobrowski SZ et al (2014) Climate refugia: joint inference from fossil records, species distribution models and phylogeography. New Phytol 204:37–54
Geml J, Laursen GA, O'Neill K, Nusbaum HC, Taylor DL (2006) Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria). Mol Ecol 15:225–239
Geml J, Tulloss RE, Laursen GA, Sazanova NA, Taylor DL (2008) Evidence for strong inter- and intracontinental phylogeographic structure in Amanita muscaria, a wind-dispersed ectomycorrhizal basidiomycete. Mol Phylogenet Evol 48:694–701
Geml J, Timling I, Robinson CH, Lennon N, Nusbaum HC, Brochmann C et al (2011) An arctic community of symbiotic fungi assembled by long-distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA. J Biogeogr 39:74–88
Gernandt DS, Magallón S, Geada López G, Zerón Flores O, Willyard A, Liston A (2008) Use of simultaneous analyses to guide fossil-based calibrations of Pinaceae phylogeny. Int J Plant Sci 169:1086–1099
Giovannetti M, Sbrana C (1998) Meeting a non-host: the behaviour of AM fungi. Mycorrhiza 8:123–130
Goldberg EE, Lancaster LT, Ree RH (2011) Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Syst Biol 60:451–465
Grummer JA, Bryson RW, Reeder TW (2014) Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae). Syst Biol 63:119–133
Halling RE (2001) Ectomycorrhizae: co-evolution, significance, and biogeography. Ann Mo Bot Gard 88:5–13
Halling RE, Osmundson TW, Neves M-A (2008) Pacific boletes: implications for biogeographic relationships. Mycol Res 112:437–447
Hansen TF (1997) Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341–1351
Hawksworth DL (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105:1422–1432
Heath TA, Zwickl DJ, Kim J, Hillis DM (2008) Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst Biol 57:160–166
Heath TA, Huelsenbeck JP, Stadler T (2014) The fossilized birth-death process for coherent calibration of divergence-time estimates. PNAS 111:E2957–E2966
Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Mol Biol Evol 27:570–580
Helgason T, Fitter AH (2009) Natural selection and the evolutionary ecology of the arbuscular mycorrhizal fungi (Phylum Glomeromycota). J Exp Bot 60:2465–2480
Hess J, Pringle A (2014) The natural histories of species and their genomes: asymbiotic and ectomycorrhizal Amanita fungi. Adv Bot Res 70:235–257
Hess J, Skrede I, Wolfe BE, LaButti K, Ohm RA, Grigoriev IV, Pringle A (2014) Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi. Genome Biol Evol 6:1564–1578
Hibbett D (2016) The invisible dimension of fungal diversity. Science 351:1150–1151
Hibbett DS, Binder M (2002) Evolution of complex fruiting-body morphologies in homobasidiomycetes. Proc R Soc B 269:1963–1969
Hibbett DS, Pine EM, Langer E, Langer G, Donoghue MJ (1997a) Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. PNAS 94:12002–12006
Hibbett D, Grimaldi D, Donoghue M (1997b) Fossil mushrooms from Miocene and Cretaceous ambers and the evolution of Homobasidiomycetes. Am J Bot 84:981
Hibbett DS, Gilbert LB, Donoghue MJ (2000) Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 407:506–508
Hibbett DS, Ohman A, Glotzer D, Nuhn M, Kirk P, Nilsson RH (2011) Progress in molecular and morphological taxon discovery in fungi and options for formal classification of environmental sequences. Fungal Biol Rev 25:38–47
Hickerson MJ, Carstens BC, Cavender-Bares J, Crandall KA, Graham CH, Johnson JB et al (2010) Phylogeography’s past, present, and future: 10 years after Avise, 2000. Mol Phylogenet Evol 54:291–301
Hillebrand H (2004) On the generality of the latitudinal diversity gradient. Am Nat 163:192–211
Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM et al (2015) Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 112:12764–12769
Ho SYW (2014) The changing face of the molecular evolutionary clock. Trends Ecol Evol 29:496–503
Ho SYW, Duchêne S (2014) Molecular-clock methods for estimating evolutionary rates and timescales. Mol Ecol 23:5947–5965
Ho SYW, Phillips MJ (2009) Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol 58:367–380
Horak E (1983) Mycogeography in the South Pacific region: Agaricales, Boletales. Aust J Bot 10:1–41
Horton TR, Bruns TD (2001) The molecular revolution in ectomycorrhizal ecology: peeking into the black-box. Mol Ecol 10:1855–1871
Hosaka K, Castellano MA, Spatafora JW (2008) Biogeography of Hysterangiales (Phallomycetidae, Basidiomycota). Mycol Res 112:448–462
Huang J-P, Knowles LL (2016) The species versus subspecies conundrum: quantitative delimitation from integrating multiple data types within a single Bayesian approach in Hercules beetles. Syst Biol 65:685–699
Hubbell SP (2001) The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton
Hughes KW, Petersen RH, Lickey EB (2009) Using heterozygosity to estimate a percentage DNA sequence similarity for environmental species’ delimitation across basidiomycete fungi. New Phytol 182:795–798
Jablonski D (2008) Extinction and the spatial dynamics of biodiversity. PNAS 105:11528–11535
Jargeat P, Martos F, Carriconde F, Gryta H, Moreau P-A, Gardes M (2010) Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota). Mol Ecol 19:5216–5230
Jeandroz S, Murat C, Wang Y, Bonfante P, Tacon FL (2008) Molecular phylogeny and historical biogeography of the genus Tuber, the “true truffles”. J Biogeogr 35:815–829
Jones GR (2014) STACEY: species delimitation and phylogeny estimation under the multispecies coalescent bioRxiv, 010199. doi:10.1101/010199
Joy JB, Liang RH, McCloskey RM, Nguyen T, Poon AFY (2016) Ancestral reconstruction. PLoS Comp Biol 12:e1004763–e1004720
Katoh K, Standley DM (2013) MAFFT: multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780
Kauserud H, Stensrud Ø, Decock C, Shalchian-Tabrizi K, Schumacher T (2006) Multiple gene genealogies and AFLPs suggest cryptic speciation and long-distance dispersal in the basidiomycete Serpula himantioides (Boletales). Mol Ecol 15:421–431
Kennedy PG, Garibay-Orijel R, Higgins LM, Angeles-Arguiz R (2011) Ectomycorrhizal fungi in Mexican Alnus forests support the host co-migration hypothesis and continental-scale patterns in phylogeography. Mycorrhiza 21(6):559–568
Kennedy PG, Matheny PB, Ryberg KM, Henkel TW, Uehling JK, Smith ME (2012) Scaling up: examining the macroecology of ectomycorrhizal fungi. Mol Ecol 21:4151–4154
Kennedy PG, Walker JKM, Bogar LM (2015) Interspecific mycorrhizal networks and non-networking hosts: exploring the ecology of the host genus Alnus. In: Horton T (ed) Mycorrhizal networks, Ecological studies, vol 224. Springer, Dordrecht, pp 227–254
Kivlin SN, Hawkes CV, Treseder KK (2011) Global diversity and distribution of arbuscular mycorrhizal fungi. Soil Biol Biochem 43:2294–2303
Knowles LL (2009) Statistical phylogeography. Annu Rev Ecol Evol Syst 40:593–612
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F et al (2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet 47:410–415
Kõljalg U, Larsson K-H, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U et al (2005) UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol 166:1063–1068
Kretzer A, Li Y, Szaro T, Bruns TD (1996) Internal transcribed spacer sequences from 38 recognized species of Suillus sensu lato: phylogenetic and taxonomic implications. Mycologia 88:776
Krings M, Dotzler N, Galtier J, Taylor TN (2011) Oldest fossil basidiomycete clamp connections. Mycoscience 52:18–23
Kumar S (2005) Molecular clocks: four decades of evolution. Nat Rev Genet 6:654–662
Landis MJ, Bedford T (2014) Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. Bioinformatics 30:123–124
Landis MJ, Matzke NJ, Moore BR, Huelsenbeck JP (2013) Bayesian analysis of biogeography when the number of areas is large. Syst Biol 62:789–804
Lavin M, Luckow M (1993) Origins and relationships of tropical North America in the context of the boreotropics hypothesis. Am J Bot 80:1–14
Leavitt SD, Fankhauser JD, Leavitt DH, Porter LD, Johnson LA, St Clair LL (2011a) 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). Mol Phylogenet Evol 59:587–602
Leavitt SD, Johnson L, St Clair LL (2011b) Species delimitation and evolution in morphologically and chemically diverse communities of the lichen-forming genus Xanthoparmelia (Parmeliaceae, Ascomycota) in western North America. Am J Bot 98:175–188
Leavitt SD, Divakar PK, Ohmura Y, Wang L-S, Esslinger TL, Lumbsch HT (2015) Who’s getting around? Assessing species diversity and phylogeography in the widely distributed lichen-forming fungal genus Montanelia (Parmeliaceae, Ascomycota). Mol Phylogenet Evol 90:85–96
Lemey P, Rambaut A, Drummond AJ, Suchard MA (2009) Bayesian phylogeography finds its roots. PLoS Comput Biol 5:e1000520
Lemey P, Rambaut A, Welch JJ, Suchard MA (2010) Phylogeography takes a relaxed random walk in continuous space and time. Mol Biol Evol 27:1877–1885
Lemmon A, Lemmon EM (2008) A likelihood framework for estimating phylogeographic history on a continuous landscape. Syst Biol 57:544–561
LePage B, Currah R, Stockey R, Rothwell G (1997) Fossil ectomycorrhizae from the Middle Eocene. Am J Bot 84:410–412
Lichtwardt RW (1995) Biogeography and fungal systematics. Can J Bot 73:731–737
Lidgard S, Crane PR (1988) Quantitative analyses of the early angiosperm radiation. Nature 331:344–346
Lieberman BS (2003) Paleobiogeography: the relevance of fossils to biogeography. Annu Rev Ecol Evol Syst 34:51–69
Linde CC, Phillips RD, Crisp MD, Peakall R (2014) Congruent species delineation of Tulasnella using multiple loci and methods. New Phytol 201:6–12
Linder HP, Hardy CR, Rutschmann F (2005) Taxon sampling effects in molecular clock dating: an example from the African Restionaceae. Mol Phylogenet Evol 35:569–582
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
Liow LH (2010) Speciation and the fossil record. In: Encyclopedia of life ELS. Wiley, Chichester, pp 1–10
Liu L, Yu L, Kubatko L, Pearl DK, Edwards SV (2009) Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol 53:320–328
Looney BP, Ryberg M, Hampe F, Sánchez-García M, Matheny PB (2016) Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi. Mol Ecol 25:630–647
Lucking R, Huhndorf S, Pfister DH, Plata ER, Lumbsch HT (2009) Fungi evolved right on track. Mycologia 101:810–822
Lumbsch HT, Buchanan PK, May TW, Mueller GM (2008) Phylogeography and biogeography of fungi. Mycol Res 112:423–424
Maddison WP, FitzJohn RG (2015) The unsolved challenge to phylogenetic correlation tests for categorical characters. Syst Biol 64:127–136
Maddison DR, Ruvolo M, Swofford DL (1992) Geographic origins of human mitochondrial DNA: phylogenetic evidence from control region sequences. Syst Biol 41:111–124
Maddison W, Midford P, Otto S (2007) Estimating a binary character’s effect on speciation and extinction. Syst Biol 56:701–710
Magallón S, Sanderson MJ (2001) Absolute diversification rates in angiosperm clades. Evolution 55:1762–1780
Mallo D, Posada D (2016) Multilocus inference of species trees and DNA barcoding. Philos Trans R Soc Lond B 371:20150335
Malloch DW, Pirozynski KA, Raven PH (1980) Ecological and evolutionary significance of mycorrhizal symbioses in vascular plants (a review). PNAS 77:2113–2118
Martin F, Díez J, Dell B, Delaruelle C (2002) Phylogeography of the ectomycorrhizal Pisolithus species as inferred from nuclear ribosomal DNA ITS sequences. New Phytol 153:345–357
Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL et al (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102–112
Matheny PB, Aime MC, Bougher NL, Buyck B, Desjardin DE, Horak E et al (2009) Out of the Palaeotropics? Historical biogeography and diversification of the cosmopolitan ectomycorrhizal mushroom family Inocybaceae. J Biogeogr 36:577–592
Matute DR (2006) Cryptic speciation and recombination in the fungus paracoccidioides brasiliensis as revealed by gene genealogies. Mol Biol Evol 23:65–73
Matzke N, McEwen JG, Puccia R, Montes BA, San-Blas G, Bagagli E, et al (2013) BioGeoBEARS: BioGeography with Bayesian (and Likelihood) evolutionary analysis in R scripts. University of California, Berkeley. http://phylo.wikidot.com/biogeobears
McPeek MA (2008) The ecological dynamics of clade diversification and community assembly. Am Nat 172:E270–E284
Meseguer AS, Lobo JM, Ree R, Beerling DJ, Sanmartín I (2015) Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (Hypericaceae). Syst Biol 64:215–232
Mittelbach GG, Schemske DW, Cornell HV, Allen AP, Brown JM, Bush MB et al (2007) Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol Lett 10:315–331
Moen D, Morlon H (2014) Why does diversification slow down? Trends Ecol Evol 29:190–197
Molina R, Massicotte H, Trappe JM (1992) Specificity phenomena in mycorrhizal symbioses: community-ecological consequences and practical implications. In: Allen MF (ed) Mycorrhizal functioning: an integrative plant-fungal process. Chapman & Hall, New York, pp 357–423
Moncalvo J-M, Buchanan PK (2008) Molecular evidence for long distance dispersal across the Southern Hemisphere in the Ganoderma applanatum-australe species complex (Basidiomycota). Mycol Res 112:425–436
Moncalvo JM, Drehmel D, Vilgalys R (2000) Variation in modes and rates of evolution in nuclear and mitochondrial ribosomal DNA in the mushroom genus Amanita (Agaricales, Basidiomycota): phylogenetic implications. Mol Phylogenet Evol 16:48–63
Moncalvo JM, Vilgalys R, Redhead SA (2002) One hundred and seventeen clades of euagarics. Mol Phylogenet Evol 23:357–400
Moore BR, Höhna S, May MR, Rannala B, Huelsenbeck JP (2016) Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures. PNAS 113:9569–9574
Morlon H, Potts MD, Plotkin JB (2010) Inferring the dynamics of diversification: a coalescent approach. PLoS Biol 8:e1000493
Moyersoen B (2006) Pakaraimaea dipterocarpacea is ectomycorrhizal, indicating an ancient Gondwanaland origin for the ectomycorrhizal habit in Dipterocarpaceae. New Phytol 172:753–762
Moyersoen B, Beever RE, Martin F (2003) Genetic diversity of Pisolithus in New Zealand indicates multiple long-distance dispersal from Australia. New Phytol 160:569–579
Mueller GM, Wu Q-X, Huang Y-Q, Guo S-Y, Aldana-Gomez R, Vilgalys R (2001) Assessing biogeographic relationships between North American and Chinese macrofungi. J Biogeogr 28:271–281
Mueller GM, Schmit JP, Leacock PR, Buyck B, Cifuentes J, Desjardin DE et al (2007) Global diversity and distribution of macrofungi. Biodivers Conserv 16:37–48
Muir G, Schlötterer C (1999) Limitations to the phylogenetic use of ITS sequences in closely related species and populations – a case study in Quercus petraea (Matt.) Liebl: http://webdoc.sub.gwdg.de/ebook/y/1999/whichmarker/index.htm. Last Accessed 18 Oct 2016
Nagendran S, Hallen-Adams HE, Paper JM, Aslam N, Walton JD (2009) Reduced genomic potential for secreted plant cell-wall-degrading enzymes in the ectomycorrhizal fungus Amanita bisporigera, based on the secretome of Trichoderma reesei. Fungal Genet Biol 46:427–435
Nagy LG, Hazi J, Szappanos B, Kocsube S, Balint B, Rakhely G et al (2012) The evolution of defense mechanisms correlate with the explosive diversification of autodigesting Coprinellus mushrooms (Agaricales, Fungi). Syst Biol 61:595–607
Nee S (2006) Birth-death models in macroevolution. Annu Rev Ecol Evol Syst 37:1–17
Nee S, Mooers AO, Harvey PH (1992) Tempo and mode of evolution revealed from molecular phylogenies. PNAS 89:8322–8326
Nguyen N, Vellinga EC, Bruns TD, Kennedy P (2016) Phylogenetic assessment of global Suillus ITS sequences supports morphologically defined species and reveals synonymous and undescribed taxa. Mycologia 108(6):1216–1228
Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson K-H (2008) Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinform 4:193–201
O’Donnell K, Cigelnik E, Nirenberg HI (1998) Molecular systematics and phylogeography of the Gibberella fujikuroi species complex. Mycologia 90:465–493
O’Meara BC (2012) Evolutionary inferences from phylogenies: a review of methods. Annu Rev Ecol Evol Syst 43:267–285
O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71:5544–5550
Oda T, Tanaka C, Tsuda M (2004) Molecular phylogeny and biogeography of the widely distributed Amanita species, A. muscaria and A. pantherina. Mycol Res 108:885–896
Öpik M, Zobel M, Cantero JJ, Davison J, Facelli JM, Hiiesalu I et al (2013) Global sampling of plant roots expands the described molecular diversity of arbuscular mycorrhizal fungi. Mycorrhiza 23:411–430
Pagano MC, Oehl F, Silva GA, Maia LC, Silva DK, Cabello MN (2016) Advances in arbuscular mycorrhizal taxonomy. In: Pagano MC (ed) Recent advances on mycorrhizal fungi. Springer, Cham, pp 15–21
Pagel M (1994) Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc R Soc B 255:37–45
Pagel M (1999) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst Biol 48:612–622
Pagel M, Meade A, Barker D (2004) Bayesian estimation of ancestral character states on phylogenies. Syst Biol 53:673–684
Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290
Peay KG, Matheny PB (2016) The biogeography of ectomycorrhizal fungi – a history of life in the subterranean. In: Martin F (ed) Molecular mycorrhizal symbiosis. Wiley, Hoboken, pp 341–362
Peay KG, Bruns TD, Kennedy PG, Bergemann SE, Garbelotto M (2007) A strong species-area relationship for eukaryotic soil microbes: island size matters for ectomycorrhizal fungi. Ecol Lett 10:470–480
Peay KG, Kennedy PG, Bruns TD (2008) Fungal community ecology: a hybrid beast with a molecular master. Bioscience 58:799–810
Peay KG, Bidartondo MI, Arnold AE (2010a) Not every fungus is everywhere: scaling to the biogeography of fungal–plant interactions across roots, shoots and ecosystems. New Phytol 185:878–882
Peay KG, Garbelotto M, Bruns TD (2010b) Evidence of dispersal limitation in soil microorganisms: isolation reduces species richness on mycorrhizal tree islands. Ecology 91:3631–3640
Peay KG, Schubert MG, Nguyen NH, Bruns TD (2012) Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules. Mol Ecol 21:4122–4136
Peay KG, Kennedy PG, Talbot JM (2016) Dimensions of biodiversity in the Earth mycobiome. Nat Rev Microbiol 14:434–447
Philippe H, Delsuc F, Brinkmann H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36:541–562
Phillimore AB, Price TD (2008) Density-dependent cladogenesis in birds. PLoS Biol 6:e71
Pinto-Sánchez NR, Crawford AJ, Wiens JJ (2014) Using historical biogeography to test for community saturation. Ecol Lett 17:1077–1085
Pirozynski KA (1976) Fossil fungi. Annu Rev Phytopathol 14:237–246
Poinar GO Jr (2014) Bird’s nest fungi (Nidulariales: Nidulariaceae) in Baltic and Dominican amber. Fungal Biol 118:325–329
Poinar GO Jr, Buckley R (2007) Evidence of mycoparasitism and hypermycoparasitism in Early Cretaceous amber. Mycol Res 111:503–506
Põlme S, Bahram M, Yamanaka T, Nara K, Dai YC, Grebenc T et al (2013) Biogeography of ectomycorrhizal fungi associated with alders (Alnus spp.) in relation to biotic and abiotic variables at the global scale. New Phytol 198:1239–1249
Põlme S, Bahram M, Kõljalg U, Tedersoo L (2014) Global biogeography of Alnus-associated Frankia actinobacteria. New Phytol 204:979–988
Pons J, Barraclough T, Gomez-Zurita J, Cardoso A, Duran D, Hazell S et al (2006) Sequence-based species delimitation for the dna taxonomy of undescribed insects. Syst Biol 55:595–609
Porter TM, Skillman JE, Moncalvo J-M (2008) Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario. Mol Ecol 17:3037–3050
Potter PE, Szatmari P (2009) Global Miocene tectonics and the modern world. Earth Sci Rev 96:279–295
Pringle A, Baker DM, Platt JL, Wares JP, Latgé JP, Taylor JW (2005) Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus. Evolution 59:1886–1899
Pringle A, Adams RI, Cross HB, Bruns TD (2009) The ectomycorrhizal fungus Amanita phalloides was introduced and is expanding its range on the west coast of North America. Mol Ecol 18:817–833
Prothero DR, Berggren WA (1992) Eocene-Oligocene climatic and biotic evolution. Princeton University Press, Princeton
Puillandre N, Lambert A, Brouillet S, Achaz G (2011) ABGD, automatic barcode gap discovery for primary species delimitation. Mol Ecol 21:1864–1877
Purvis A (2008) Phylogenetic approaches to the study of extinction. Annu Rev Ecol Evol Syst 39:301–319
Pybus OG, Harvey PH (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proc R Soc B 267:2267–2272
Pybus OG, Rambaut A, Holmes EC (2002) New inferences from tree shape: numbers of missing taxa and population growth rates. Syst Biol 51:881–888
Pyron RA, Wiens JJ (2013) Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity. Proc R Soc B 280:20131622
Pyron RA, Hsieh FW, Lemmon AR, Lemmon EM, Hendry CR (2016) Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria). Zool J Linnean Soc 177:937–949
Qian H, Jin Y (2016) An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure. J Plant Ecol 9:233–239
Qian H, Ricklefs RE (2000) Large-scale processes and the Asian bias in species diversity of temperate plants. Nature 407:180–182
Queloz V, Sieber TN, Holdenrieder O, McDonald BA, Grünig CR (2011) No biogeographical pattern for a root-associated fungal species complex. Glob Ecol Biogeogr 20:160–169
R Core Team (2015) R: a language and environment for statistical computing. Vienna. Retrieved from https://www.R-project.org/
Rabosky DL (2014) Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS One 9:e89543–e89515
Rabosky DL, Goldberg EE (2015) Model inadequacy and mistaken inferences of trait-dependent speciation. Syst Biol 64:340–355
Rabosky DL, Lovette IJ (2008) Density-dependent diversification in North American wood warblers. Proc R Soc B 275:2363–2371
Rabosky DL, Slater GJ, Alfaro ME (2012) Clade age and species richness are decoupled across the eukaryotic tree of life. PLoS Biol 10:e1001381
Rannala B, Yang Z (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645–1656
Rannala B, Yang Z (2013) Improved reversible jump algorithms for Bayesian species delimitation. Genetics 194:245–253
Raup DM (1985) Mathematical models of cladogenesis. Paleobiology 11:42–52
Redecker D, Raab P (2006) Phylogeny of the Glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers. Mycologia 98:885–895
Redecker D, Kodner R, Graham LE (2000) Glomalean fungi from the Ordovician. Science 289:1920–1921
Ree RH, Sanmartín I (2009) Prospects and challenges for parametric models in historical biogeographical inference. J Biogeogr 36:1211–1220
Ree RH, Smith SA (2008) Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst Biol 57:4–14
Reid NM, Carstens BC (2012) Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evol Biol 12:196
Ricklefs RE (2004) A comprehensive framework for global patterns in biodiversity. Ecol Lett 7:1–15
Ricklefs RE (2006) Evolutionary diversification and the origin of the diversity-environment relationship. Ecology 87:S3–13
Ricklefs RE (2007) Estimating diversification rates from phylogenetic information. Trends Ecol Evol 22:601–610
Robinson R (2006) Relaxing the clock brings time back into phylogenetics. PLoS Biol 4:e106
Ronquist F (1997) Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Syst Biol 46:195–203
Ronquist F, Sanmartín I (2011) Phylogenetic methods in biogeography. Annu Rev Ecol Evol Syst 42:441–464
Rosendahl S, McGee P, Morton JB (2009) Lack of global population genetic differentiation in the arbuscular mycorrhizal fungus Glomus mosseae suggests a recent range expansion which may have coincided with the spread of agriculture. Mol Ecol 18:4316–4329
Rouse GE (1962) Plant microfossils from the Burrard formation of western British Columbia. Micropaleontology 8:187–218
Ryberg M (2015) Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi. Mol Ecol 24:5770–5777
Ryberg M, Matheny PB (2011) Dealing with incomplete taxon sampling and diversification of a large clade of mushroom-forming fungi. Evolution 65:1862–1878
Ryberg M, Matheny PB (2012) Asynchronous origins of ectomycorrhizal clades of Agaricales. Proc R Soc B 279:2003–2011
Sánchez-Ramírez S, Tulloss RE, Amalfi M, Moncalvo J-M (2015a) Palaeotropical origins, boreotropical distribution and increased rates of diversification in a clade of edible ectomycorrhizal mushrooms (Amanita section Caesareae). J Biogeogr 42:351–363
Sánchez-Ramírez S, Tulloss RE, Guzmán-Dávalos L, Cifuentes-Blanco J, Valenzuela R, Estrada-Torres A et al (2015b) In and out of refugia: historical patterns of diversity and demography in the North American Caesar’s mushroom species complex. Mol Ecol 24:5938–5956
Sánchez-Ramírez S, Etienne RS, Moncalvo J-M (2015c) High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi. Evolution 69:2196–2209
Sanmartín I, van der Mark P, Ronquist F (2008) Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands. J Biogeogr 35:428–449
Sato H, Yumoto T, Murakami N (2007) Cryptic species and host specificity in the ectomycorrhizal genus Strobilomyces (Strobilomycetaceae). Am J Bot 94:1630–1641
Sato H, Tsujino R, Kurita K, Yokoyama K, Agata K (2012) Modelling the global distribution of fungal species: new insights into microbial cosmopolitanism. Mol Ecol 21:5599–5612
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. PNAS 109:6241–6246
Scholl JP, Wiens JJ (2016) Diversification rates and species richness across the tree of life. Proc R Soc B 283:20161334
Schüßler A, Schwarzott D, Walker C (2001) A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol Res 105:1413–1421
Sheedy EM, Van de Wouw AP, Howlett BJ, May TW (2013) Multigene sequence data reveal morphologically cryptic phylogenetic species within the genus Laccaria in southern Australia. Mycologia 105:547–563
Shen Q, Geiser DM, Royse DJ (2002) Molecular phylogenetic analysis of Grifola frondosa (maitake) reveals a species partition separating eastern North American and Asian isolates. Mycologia 94:472–482
Simon UK, Weiß M (2008) Intragenomic variation of fungal ribosomal genes is higher than previously thought. Mol Biol Evol 25:2251–2254
Simon L, Bousquet J, Lévesque RC, Lalonde M (1993) Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants. Nature 363:67–69
Sites JW Jr, Marshall JC (2004) Operational criteria for delimiting species. Annu Rev Ecol Evol Syst 35:199–227
Skrede I, Engh IB, Binder M, Carlsen T, Kauserud H, Bendiksby M (2011) Evolutionary history of Serpulaceae (Basidiomycota): molecular phylogeny, historical biogeography and evidence for a single transition of nutritional mode. BMC Evol Biol 11:230
Smith SE, Read DJ (2010) Mycorrhizal Symbiosis. Academic, New York
Smith SY, Currah RS, Stockey RA (2004) Cretaceous and Eocene poroid hymenophores from Vancouver Island, British Columbia. Mycologia 96:180–186
Solís-Lemus C, Knowles LL, Ané C (2015) Bayesian species delimitation combining multiple genes and traits in a unified framework. Evolution 69:492–507
Stadler T (2011) Mammalian phylogeny reveals recent diversification rate shifts. PNAS 108:6187–6192
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313
Stockinger H, Krüger M, Schüßler A (2010) DNA barcoding of arbuscular mycorrhizal fungi. New Phytol 187:461–474
Stolp H (1988) Microbial ecology: organisms, habitat, and activities. Cambridge University Press, Cambridge
Swofford DL, Maddison WP (1987) Reconstructing ancestral character states under Wagner parsimony. Math Biosci 87:199–229
Szarkándi GJ, Dima B, Kocsubé, S, Vágvölgyi C, Papp T, Nagy LG (2013) The ADiv project: analyzing rates of diversification in the Agaricales. Presented at the joint mycological society of America and American phythopathology society meeting, Austin
Taylor TN, Hass H, Kerp H (1999) The oldest fossil ascomycetes. Nature 399:648
Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21–32
Taylor TN, Hass H, Kerp H, Krings M, Hanlin RT (2005) Perithecial ascomycetes from the 400 million year old Rhynie chert: an example of ancestral polymorphism. Mycologia 97:269–285
Taylor JW, Turner E, Pringle A, Dettman J, Johannesson H (2006) Fungal species: thoughts on their recognition, maintenance and selection. In: Gadd GM, Watkinson SC, Dyer PS (eds) Fungi in the environment. Cambridge University Press, Cambridge, pp 313–339
Taylor TN, Krings M, Taylor EL (2014) Fossil fungi. Academic, London
Tedersoo L, Nara K (2010) General latitudinal gradient of biodiversity is reversed in ectomycorrhizal fungi. New Phytol 185:351–354
Tedersoo L, Smith ME (2013) Lineages of ectomycorrhizal fungi revisited: foraging strategies and novel lineages revealed by sequences from belowground. Fungal Biol Rev 27:83–99
Tedersoo L, Suvi T, Larsson E, Kõljalg U (2006) Diversity and community structure of ectomycorrhizal fungi in a wooded meadow. Mycol Res 110:734–748
Tedersoo L, Sadam A, Zambrano M, Valencia R, Bahram M (2009) Low diversity and high host preference of ectomycorrhizal fungi in Western Amazonia, a neotropical biodiversity hotspot. ISME 4:465–471
Tedersoo L, May TW, Smith ME (2010) Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages. Mycorrhiza 20:217–263
Tedersoo L, Abarenkov K, Nilsson RH, Schüßler A, Grelet G-A, Kohout P et al (2011) Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi. PLoS One 6:e24940
Tedersoo L, Bahram M, Toots M, Diédhiou AG, Henkel TW, Kjøller R et al (2012) Towards global patterns in the diversity and community structure of ectomycorrhizal fungi. Mol Ecol 21:4160–4170
Tedersoo L, Bahram M, Polme S, Koljalg U, Yorou NS, Wijesundera R et al (2014a) Global diversity and geography of soil fungi. Science 346:1256688–1256688
Tedersoo L, Bahram M, Ryberg M, Otsing E, Kõljalg U, Abarenkov K (2014b) Global biogeography of the ectomycorrhizal/sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses. Mol Ecol 23:4168–4183
Treseder KK, Maltz MR, Hawkins BA, Fierer N, Stajich JE, McGuire KL (2014) Evolutionary histories of soil fungi are reflected in their large-scale biogeography. Ecol Lett 17:1086–1093
van der Nest MA, Beirn LA, Crouch JA, Demers JE, de Beer ZW, De Vos L et al (2014) IMA Genome-F 3: draft genomes of Amanita jacksonii, Ceratocystis albifundus, Fusarium circinatum, Huntiella omanensis, Leptographium procerum, Rutstroemia sydowiana, and Sclerotinia echinophila. IMA Fungus 5:472–485
Vellinga EC, Wolfe BE, Pringle A (2009) Global patterns of ectomycorrhizal introductions. New Phytol 181:960–973
Větrovský T, Kolařík M, Žifčáková L, Zelenka T, Baldrian P (2016) The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities. Mol Ecol Resour 16:388–401
Vilgalys R (2003) Taxonomic misidentification in public DNA databases. New Phytol 160:4–5
Vilgalys R, Sun BL (1994) Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences. PNAS 91:4599–4603
Waterman RJ, Bidartondo MI, Stofberg J, Combs JK, Gebauer G, Savolainen V et al (2011) The effects of above- and belowground mutualisms on orchid speciation and coexistence. Am Nat 177:E54–E68
Waterman RJ, Klooster MR, Hentrich H, Bidartondo MI (2012) Species interactions of mycoheterotrophic plants: specialization and its potential consequences. In: Merckx VSFT (ed) Mycoheterotrophy. Springer, New York, pp 267–296
Webb CO, Ackerly DD, McPeek MA, Donoghue MJ (2002) Phylogenies and comunity ecology. Annu Rev Ecol Syst 33:475–505
Welch J, Bromham L (2005) Molecular dating when rates vary. Trends Ecol Evol 20:320–327
Wen J (1999) Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants. Annu Rev Ecol Syst 30:421–455
Werren JH, Windsor D, Guo L (1995) Distribution of Wolbachia among neotropical arthropods. Proc R Soc B 262:197–204
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols. Elsevier, New York, pp 315–322
Wiens JJ, Donoghue MJ (2004) Historical biogeography, ecology and species richness. Trends Ecol Evol 19:639–644
Will K, Mishler B, Wheeler Q (2005) The perils of DNA barcoding and the need for integrative taxonomy. Syst Biol 54:844–851
Wilson AW, Hobbie EA, Hibbett DS (2007) The ectomycorrhizal status of Calostoma cinnabarinum determined using isotopic, molecular, and morphological methods. Can J Bot 85:385–393
Wilson AW, Binder M, Hibbett DS (2011) Effects of gasteroid fruiting body morphology on diversification rates in three independent clades of fungi estimated using binary state speciation and extinction analysis. Evolution 65:1305–1322
Wilson AW, Binder M, Hibbett DS (2012) Diversity and evolution of ectomycorrhizal host associations in the Sclerodermatineae (Boletales, Basidiomycota). New Phytol 194:1079–1095
Wilson AW, Hosaka K, Mueller GM (2016a) Evolution of ectomycorrhizae as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus Laccaria. New Phytol. doi:10.1111/nph.14270
Wilson KA, Auerbach NA, Sam K, Magini AG, Moss ASL, Langhans SD et al (2016b) Conservation research is not happening where it is most needed. PLoS Biol 14:e1002413
Wolfe JA (1978) A paleobotanical interpretation of tertiary climates in the northern hemisphere: data from fossil plants make it possible to reconstruct tertiary climatic changes, which may be correlated with changes in the inclination of the earth’s rotational axis. Am Sci 66:694–703
Wolfe BE, Pringle A (2012) Geographically structured host specificity is caused by the range expansions and host shifts of a symbiotic fungus. ISME 6:745–755
Wolfe BE, Kuo M, Pringle A (2012a) Amanita thiersii is a saprotrophic fungus expanding its range in the United States. Mycologia 104:22–33
Wolfe BE, Tulloss RE, Pringle A (2012b) The irreversible loss of a decomposition pathway marks the single origin of an ectomycorrhizal symbiosis. PLoS One 7:e39597
Wu QX, Mueller GM, Lutzoni FM, Huang YQ, Guo SY (2000) Phylogenetic and biogeographic relationships of eastern Asian and eastern North American disjunct Suillus species (fungi) as inferred from nuclear ribosomal RNA ITS sequences. Mol Phylogenet Evol 17:37–47
Xiang QY, Soltis DE, Soltis PS, Manchester SR, Crawford DJ (2000) Timing the eastern Asian-eastern North American floristic disjunction: molecular clock corroborates paleontological estimates. Mol Phylogenet Evol 15:462–472
Yang Z (2015) Program BPP for species tree estimation and species delimitation. Curr Zool 61:854–865
Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. PNAS 107:9264–9269
Yang Z, Rannala B (2014) Unguided species delimitation using dna sequence data from multiple loci. Mol Biol Evol 31:3125–3135
Yu Y, Harris AJ, Blair C, He X (2015) RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. Mol Phylogenet Evol 87:46–49
Yule GU (1925) A mathematical theory of evolution, based on the conclusions of Dr. JC Willis, FRS. Philos Trans R Soc Lond B 213:21–87
Zachos J, Pagani M, Sloan L, Thomas E, Billups K (2001) Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292:686–693
Zhang J, Kapli P, Pavlidis P, Stamatakis A (2013) A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29:2869–2876
Zhang P, Tang L-P, Cai Q, Xu J-P (2015) A review on the diversity, phylogeography and population genetics of Amanita mushrooms. Mycology 6:1–8
Zhang C, Stadler T, Klopfstein S, Heath TA, Ronquist F (2016) Total-evidence dating under the fossilized birth–death process. Syst Biol 65:228–249
Zhao R-L, Zhou J-L, Chen J, Margaritescu S, Sánchez-Ramírez S, Hyde KD et al (2016) Towards standardizing taxonomic ranks using divergence times – a case study for reconstruction of the Agaricus taxonomic system. Fungal Divers 78:239–292
Zink RM, Blackwell-Rago RC, Ronquist F (2000) The shifting roles of dispersal and vicariance in biogeography. Proc R Soc B 267:497–503
Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic, New York, pp 97–166
Acknowledgements
We would like to thank the non-anonymous referee P. B. Matheny and L. Tedersoo for insightful comments and suggestions on a previous version of the manuscript. S.S.R. additionally thanks J.-M. Moncalvo and K. G. Peay for stimulating conversations about mycorrhizal biogeography, and R. W. Murphy and E. H. Stukenbrock for providing a working space. A.W.W. thanks P. G. Kennedy for suggestions about host recognition methodologies.
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Sánchez-Ramírez, S., Wilson, A.W., Ryberg, M. (2017). Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. In: Tedersoo, L. (eds) Biogeography of Mycorrhizal Symbiosis. Ecological Studies, vol 230. Springer, Cham. https://doi.org/10.1007/978-3-319-56363-3_1
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DOI: https://doi.org/10.1007/978-3-319-56363-3_1
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