Using collections data to infer biogeographic, environmental, and host structure in communities of endophytic fungi

LITERATURE CITED

• Arnold AE, Maynard Z, Gilbert GS. 2001. Fungal endophytes in dicotyledonous neotropical trees: patterns of abundance and diversity. Mycological Research 105:1502–1507.
   Web of Science ®Google Scholar
• Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, Gugger P, Way A, Hofstetter V, Kauff F, Lutzoni F. 2009. A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Systematic Biology 58:283–297.
   Google Scholar
• Bahram M, Peay KG, Tedersoo L. 2015. Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi. New Phytologist 205:1454–1463.
   PubMed Web of Science ®Google Scholar
• Baas Becking LGM. 1934. Geobiologie of inleiding tot de milieukunde. The Hague, the Netherlands: Van Stockum WP, Zoon. 263 p.
   Google Scholar
• Bebber DP, Carine MA, Wood JRI, Wortley AH, Harris DJ, Prance GT, Davidse G, Paige J, Pennington TD, Robson NKB, Scotland RW. 2010. Herbaria are a major frontier for species discovery. Proceedings of the National Academy of Sciences of the United States of America 107:22169–22171.
   Google Scholar
• Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology 10:189.
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B 57:289–300.
   Web of Science ®Google Scholar
• Bowers JE, McLaughlin SP. 1996. Flora of the Huachuca Mountains, a botanically rich and historically significant sky island in Cochise County, Arizona. Journal of the Arizona-Nevada Academy of Science 29:66–107.
   Google Scholar
• Bowman EA, Arnold AE. 2018. Distributions of ectomycorrhizal and foliar endophytic fungal communities associated with Pinus ponderosa along a spatially constrained elevation gradient. American Journal of Botany (in press).
   Google Scholar
• Brown DE, Brennan TC. 2007. A digitized biotic community map for plotting and comparing North American plant and animal distributions. CANOTIA 3:1–12.
   Google Scholar
• Canhos VP, Souza S, Giovanni R, Canhos DAL. 2004. Global biodiversity informatics: setting the scene for a “new world” of ecological modeling. Biodiversity Informatics 1:1–13.
   Google Scholar
• Carbone I, White JB, Miadlikowska J, Arnold AE, Miller MA, Kauff F, U’Ren JM, May G, Lutzoni F. 2016. T-BAS: tree-based alignment selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life. Bioinformatics 33:1160–1168.
   Web of Science ®Google Scholar
• Chagnon PL, U’Ren JM, Miadlikowska J, Lutzoni F, Arnold AE. 2016. Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale. Oecologia 180:181–191.
   PubMed Web of Science ®Google Scholar
• Chen KH, Miadlikowska J, Monár K, Arnold AE, U’Ren JM, Gaya E, Gueidan C, Lutzoni F. 2015. Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order—Phaeomoniellales. Molecular Phylogenetics and Evolution 85:117–130.
   PubMed Web of Science ®Google Scholar
• Cheng TL, Rovito SM, Wake DB, Vredenburg VT. 2011. Coincident mass extirpation of neotropical amphibians with the emergence of the infectious fungal pathogen Batrachochytrium dendrobatidis. Proceedings of the National Academy of Sciences of the United States of America 108:9502–9507.
   Google Scholar
• Coblentz DD, Riitters KH. 2004. Topographic controls on the regional-scale biodiversity of the south-western USA. Journal of Biogeography 31:1125–1138.
   Web of Science ®Google Scholar
• Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida-Martinez LP, Tringe SG. 2015. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytologist 209:798–811.
   PubMed Web of Science ®Google Scholar
• Davis CC, Willis CG, Connolly B, Kelly C, Ellison AM. 2015. Herbarium records are reliable sources of phenological change driven by climate and provide novel insights into species’ phenological cueing mechanisms. American Journal of Botany 102:1599–1609.
   PubMed Web of Science ®Google Scholar
• Dobson AP, Bradshaw AD, Baker AJM. 1997. Hopes for the future: restoration ecology and conservation biology. Science 277:515–522.
   Web of Science ®Google Scholar
• Droissart V, Hardy OJ, Sonké B, Dahdouh-Guebas F, Stévart T. 2012. Subsampling herbarium collections to assess geographic diversity gradients: a case study with endemic Orchidaceae and Rubiaceae in Cameroon. Biotropica 44:44–52.
   Web of Science ®Google Scholar
• Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200.
   PubMed Web of Science ®Google Scholar
• Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research 8:186–194.
   PubMed Web of Science ®Google Scholar
• Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research 8:175–185.
   PubMed Web of Science ®Google Scholar
• Gazis R, Rehner S, Chaverri P. 2011. Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Molecular Ecology 20:3001–3013.
   PubMed Web of Science ®Google Scholar
• Gilbertson RL, Blackwell M. 1984. Two new Basidiomycetes on living live oak in the southeast and Gulf Coast region. Mycotaxon 20:85–93.
   Web of Science ®Google Scholar
• Gilbertson RL, Blackwell M. 1985. Notes on the wood-rotting fungi on Juniperus in the Gulf Coast region. Mycotaxon 24:325–348.
   Web of Science ®Google Scholar
• Gilbertson RL, Blackwell M. 1987. Notes on the wood-rotting fungi on Juniperus in the Gulf Coast region. II. Mycotaxon 28:369–402.
   Web of Science ®Google Scholar
• Gilbertson RL, Blackwell M. 1988. Some new or unusual corticioid fungi from the Gulf Coast region. Mycotaxon 33:375–386.
   Web of Science ®Google Scholar
• Gilbertson RL, Hemmes DE. 1997. Notes on Hawaiian Coniophoraceae. Mycotaxon 65:427–442.
   Web of Science ®Google Scholar
• Gilbertson RL, Nakasone KK. 2003. New taxa of Hawaiian corticioid fungi are described with keys to Crustoderma, Radulomyces and Scopuloides. Mycologia 95:467–473.
   PubMed Web of Science ®Google Scholar
• Glassman SI, Lubetkin KC, Chung JA, Bruns TD. 2017. The theory of island biogeography applies to ectomycorrhizal fungi in subalpine tree “islands” at a fine scale. Ecosphere 8:e01677.
   Web of Science ®Google Scholar
• Goslee S, Urban D. 2017. ECODIST: dissimilarity-based analysis of ecological data. Available online at https://cran.r-project.org/web/packages/ecodist/.
   Google Scholar
• Graham C, Ferrier S, Huettman F, Moritz C, Peterson A. 2004. New developments in museum-based informatics and applications in biodiversity analysis. Trends in Ecology and Evolution 19:497–503.
   PubMed Web of Science ®Google Scholar
• Guralnick R, Hill A. 2009. Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes. Bioinformatics 25:421–428.
   PubMed Web of Science ®Google Scholar
• Higgins KL, Arnold AE, Miadlikowska J, Sarvate SD, Lutzoni F. 2007. Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. Molecular Phylogenetics and Evolution 42: 543–555.
   Google Scholar
• Hijmans RJ. 2016a. geosphere: spherical trigonometry. R package version 2.4-1. Available from: https://CRAN.R-project.org/package=vegan
   Google Scholar
• Hijmans RJ. 2016b. raster: geographic data analysis and modeling. R package version 2.5-8. [cited YYYY MMM DD]. Available from: https://CRAN.R-project.org/package=raster
   Google Scholar
• Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25:1965–1978.
   Web of Science ®Google Scholar
• Hoffman MT, Arnold AE. 2008. Geographic locality and host identity shape fungal endophyte communities in cupressaceous trees. Mycological Research 112:331–344.
   PubMed Web of Science ®Google Scholar
• Huang Y-L, Devan MMN, U’Ren JM, Furr SH, Arnold AE. 2016. Pervasive effects of wildfire on foliar endophyte communities in montane forest trees. Microbial Ecology 71:452–468.
   PubMed Web of Science ®Google Scholar
• Kumar SS, Hyde KD. 2004. Biodiversity and tissue-recurrence of endophytic fungi in Tripterygium wilfordii. Fungal Diversity17:69–90.
   Google Scholar
• Lavoie C. 2013. Biological collections in an ever changing world: herbaria as tools for biogeographical and environmental studies. Perspectives in Plant Ecology, Evolution and Systematics 15:68–76.
   Web of Science ®Google Scholar
• Lobo JM. 2008. More complex distribution models or more representative data? Biodiversity Informatics 5:14–19.
   Google Scholar
• Lumbsch HT, Buchanan PK, May TW, Mueller GM. 2008. Phylogeography and biogeography of fungi. Mycological Research 112:423–424.
   PubMed Web of Science ®Google Scholar
• Maddison WP, Maddison DR. 2017. Mesquite: a modular system for evolutionary analysis. Version 3.2. Available from: http://mesquiteproject.org
   Google Scholar
• Mann DG. 1997. The economics of botanical collections. In: Nudds JR, Pettitt CW, eds. The Value and Valuation of Natural Science Collections: proceedings of the international conference, 19 April 1995, Manchester. Bath, UK: The Geological Society. pp. 68–82.
   Google Scholar
• Martin KJ, Rygiewicz PT. 2005. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiology 5:28.
   PubMed Web of Science ®Google Scholar
• Martiny JBH, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Ovreås L, Reysenbach AL, Smith VH, Staley JT. 2006. Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology 4:102–112.
   PubMed Web of Science ®Google Scholar
• Massimo NC, Devan MMN, Arendt KR, Wilch MH, Riddle JM, Furr SH, Steen C, U’Ren JM, Sandberg DC, Arnold AE. 2015. Fungal endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts. Microbial Ecology 70:61–76.
   PubMed Web of Science ®Google Scholar
• Mateo RG, Croat TB, Felicísimo ÁM, Muñoz J. 2010. Profile or group discriminative techniques? Generating reliable species distribution models using pseudo-absences and target-group absences from natural history collections. Diversity and Distributions 16:84–94.
   Web of Science ®Google Scholar
• McLaughlin SP. 1986. Floristic analysis of the southwestern United States. Great Basin Naturalist 46:46–65.
   Google Scholar
• Miller M, Schwartz T, Pickett B, He S, Klem E, Scheuermann R, Passarotti M, Kaufman S, O’Leary M. 2015. A RESTful API for access to phylogenetic tools via the CIPRES Science Gateway. Evolutionary Bioinformatics 11:43–48.
   PubMed Web of Science ®Google Scholar
• Monacell JT, Carbone I. 2014. Mobyle SNAP workbench: a Web-based analysis portal for population genetics and evolutionary genomics. Bioinformatics 30:1488–1490.
   PubMed Web of Science ®Google Scholar
• Namoff S, Husby CE, Francisco-Ortega J, Noblick LR, Lewis CE, Griffith MP. 2010. How well does a botanical garden collection of a rare palm capture the genetic variation in a wild population? Biological Conservation 143:1110–1117.
   Google Scholar
• Nilsson RH, Veldre V, Hartmann M, Unterseher M, Amend A, Bergsten J, Kristiansson E, Ryberg M, Jumpponen A, Abarenkov K. 2010. An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecology 3:284–287.
   Web of Science ®Google Scholar
• Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H. 2017. vegan: community ecology package. R package version 2.4-3. Available from: https://CRAN.R-project.org/package=vegan
   Google Scholar
• Orme CDL, Davies RG, Olson VA, Thomas GH, Ding TS, Rasmussen PC, Ridgely RS, Stattersfield AJ, Bennett PM, Owens IPF, Blackburn TM, Gaston KJ. 2006. Global patterns of geographic range size in birds. PLoS Biology 4:e208.
   Google Scholar
• Peay KG, Baralota C, Fine PVA. 2013. Strong coupling of plant and fungal community structure across western Amazonian rainforests. The ISME Journal 7:1852–1861.
   Google Scholar
• Peay KG, Bruns TD. 2014. Spore dispersal of basidiomycete fungi at the landscape scale is driven by stochastic and deterministic processes and generates variability in plant–fungi interactions. New Phytologist 204:180–191.
   PubMed Web of Science ®Google Scholar
• Peay KG, Kennedy PG, Davies SJ, Tan S, Bruns TD. 2010. Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone. New Phytologist 185:529–542.
   PubMed Web of Science ®Google Scholar
• Petrini O, Carroll G. 1981. Endophytic fungi in foliage of some Cupressaceae in Oregon. Canadian Journal of Botany 59:629–636.
   Google Scholar
• Põlme S, Bahram M, Yamanaka T, Nara K, Dai YC, Grebenc T, Kraigher H, Toivonen M, Wang P-H, Matsuda Y, Naadel T, Kennedy PG, Kõljalg U, Tedersoo L. 2013. Biogeography of ectomycorrhizal fungi associated with alders (Alnus spp.) in relation to biotic and abiotic variables at the global scale. New Phytologist 198:1239–1249.
   Google Scholar
• Ponder WF, Carter GA, Flemons P, Chapman RR. 2001. Evaluation of museum collection data for use in biodiversity assessment. Conservation Biology 15:648–457.
   Web of Science ®Google Scholar
• Promputtha I, Lumyong S, Dhanasekaran V, McKenzie EHC, Hyde KD, Jeewon R. 2007. A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence. Microbial Ecology 53:579–590.
   PubMed Web of Science ®Google Scholar
• Rissler LJ, Apodaca JJ. 2007. Adding more ecology into species delimitation: ecological nich models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus). Systematic Biology 56:924–942.
   PubMed Web of Science ®Google Scholar
• Robbirt KM, Davy AJ, Hutchings MJ, Roberts DL. 2010. Validation of biological collections as a source of phenological data for use in climate change studies: a case study with the orchid Ophrys sphegodes. Journal of Ecology 99:235–241.
   Web of Science ®Google Scholar
• Sandberg DC, Battista LJ, Arnold AE. 2014. Fungal endophytes of aquatic macrophytes: diverse host-generalists characterized by tissue preferences and geographic structure. Microbial Ecology 67:735–747.
   PubMed Web of Science ®Google Scholar
• Saunders M, Glenn AE, Kohn LM. 2010. Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal mechanisms in community processes. Evolutionary Applications 3:525–537.
   PubMed Web of Science ®Google Scholar
• Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109:6241–6246.
   Google Scholar
• Schloss PD. 2009. A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4:e8230.
   PubMed Web of Science ®Google Scholar
• Schloss PD. 2010. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Computational Biology 6:e1000844.
   PubMed Web of Science ®Google Scholar
• Shokralla S, Spall JL, Gibson JF, Hajibabaei M. 2012. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 21:1794–1805.
   PubMed Web of Science ®Google Scholar
• Sun Y, Cai Y, Liu L, Yu F, Farrell ML, Mckendree W, Farmerie W. 2009. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Research 37:e76.
   PubMed Web of Science ®Google Scholar
• Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, Ruiz LV, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Põldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Pärtel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Majuakim L, Lodge DJ, Lee SS, Larsson KH, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo LD, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, De Kesel A, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K. 2014. Global diversity and geography of soil fungi. Science 28:1256688.
   Google Scholar
• U’Ren JM, Arnold AE. 2016. Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America. Peer J 4:e2768.
   PubMed Web of Science ®Google Scholar
• U’Ren JM, Dalling JW, Gallery RE, Maddison DR, Davis EC, Gibson CM, Arnold AE. 2009. Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analyzing fungal environmental samples. Mycological Research 113:432–449.
   PubMed Web of Science ®Google Scholar
• U’Ren JM, Lutzoni F, Miadlikowska J, Arnold AE. 2010. Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens. Microbial Ecology 60:340–353.
   PubMed Web of Science ®Google Scholar
• U’Ren JM, Lutzoni F, Miadlikowska J, Laetsch AD, Arnold AE. 2012. Host and geographic structure of endophytic and endolichenic fungi at a continental scale. American Journal of Botany 99:898–914.
   PubMed Web of Science ®Google Scholar
• U’Ren JM, Miadlikowska J, Zimmerman NB, Lutzoni F, Stajich JE, Arnold AE. 2016. Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Molecular Phylogenetics and Evolution 98:210–232.
   PubMed Web of Science ®Google Scholar
• U’Ren JM, Riddle JM, Monacell JT, Carbone I, Miadlikowska J, Arnold AE. 2014. Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi. Molecular Ecology Resources 14:1032–1048.
   PubMed Web of Science ®Google Scholar
• Vincent JB, Weiblen GD, May G. 2016. Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees. Molecular Ecology 25:825–841.
   PubMed Web of Science ®Google Scholar
• White JR, Navlakha S, Nagarajan N, Ghodsi M-R, Kingsford C, Pop M. 2010. Alignment and clustering of phylogenetic markers—implications for microbial diversity studies. BMC Bioinformatics 11:152.
   PubMed Web of Science ®Google Scholar
• Williams PH, Margules CR, Hilbert DW. 2002. Data requirements and data sources for biodiversity priority area selection. Journal of Biosciences 27:327–338.
   PubMed Web of Science ®Google Scholar
• Yahr R, Schoch CL, Dentinger TM. 2016. Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. Philosophical Transactions of the Royal Society B 371:20150336.
   PubMed Web of Science ®Google Scholar
• Zimmerman NB, Vitousek PM. 2012. Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. Proceedings of the National Academy of Sciences of the United States of America 109:13022–13027.
   Google Scholar