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Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage

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Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage OPEN @ACCESS Freely available online ·.@"-PLOS.. IONE Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage 1 14 13 2 3 Gregory Bonito *, Matthew E. Smith , Michael Nowak , Rosanne A. Healy , Gonzalo Guevara , 4 1 5 5 6 Efren Cazares , Akihiko Kinoshita \ Eduardo R. Nouhra , Laura S. Dominguez , Leho Tedersoo , 8 9 10 11 Claude Murae, Yun Wang , Baldomero Arroyo Moreno , Donald H. Pfister , Kazuhide Nara , 12 4 1 Alessandra Zambonelli , James M. Trappe , Rytas Vilgalys 1 Deparment of Biology, Duke University, Durham, North Carolina, United States of America, 2 University of Minnesota, Department of Plant Biology, St. Paul, Minnesota, United States of America, 31nstituto Tecnologico de Ciudad Victoria, Tamaulipas, Mexico, 4 Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, United States of America, Slnstituto Multidisciplinario de Biologfa Vegetal, Cordoba, Argentina, 61nstitute of Ecology and Earth Sciences and the Natural History Museum of Tartu University, Tartu, Estonia, 71nstitute National de Ia Recherche Agronomique et Nancy University, Champenoux, France, 8 New Zealand Institute for Plant & Food Research Ltd, Christchurch, New Zealand, 9 Department of Plant Biology, University of Cordoba, Cordoba, Spain, 10 Farlow Herbarium, Harvard University, Cambridge, Massachusetts, United States of America, 11 Department of Natural Environmental Studies, Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan, 12 Dipartimento di Science Agrarie, Universita di Bologna, Bologna, Italy, 131nstitute of Systematic Botany, University of Zurich, Zurich, Switzerland, 14 Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America Citation: Bonito G, Smith ME, Nowak M, Healy RA, Guevara G, et al. (201 3) Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage. PLoS ONE 8(1): e52765. doi:10.1371/journal.pone.0052765 Editor: Jason E. Stajich, University of California Riverside, United States of America Received September 8, 2011; Accepted November 22, 2012; Published January 2, 2013 Copyright: © 2013 Bonito et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This research was supported through NSF award #0641297, REVSYS: Phylogenetic and Revisionary Systematics of North American Truffles (Tuber). Support was also provided by the Friends of the Farlow, which enabled the senior author to conduct research at the Farlow Herbarium. M.E.S. participated via a postdoctoral fellowship from Harvard University Herbaria. D.H.P. received funding from the David Rockefeller Center for Latin American Studies at Harvard University that supported field work in collaboration with M.E.S. Collections and microscopy were enabled by a grant from the Iowa Science Foundation to R.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: Dr. Yun Wang works at the New Zealand Institute for Plant & Food Research Ltd. The authors confirm that there are no relevant declarations relating to the employment, Consultancy, patents, products in development or marketed products. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. The remaining authors have declared no competing interests. • E-mail: [email protected] Introduction and over I 00 times independently within the Ascomycota, Basidiomycota, and Mucoromycotina [2], the majority of transi­ Truffles are fungi that produce fruiting bodies with spores tions to a truffle form occur in ectomycorrhizal (EcM) fungal sequestered in a spherical mass, belowground or at the soil surface lineages [!]. This pattern suggests that the symbiotic association [!]. Many groups of truffles produce volatile aromatics. Although with plants may be an important driver in the evolution of truffle truflles have evolved in nearly every major group of fleshy fungi PLOS ONE 1 www.plosone.org January 201 3 I Volume 8 I Issue 1 I e52765 Multigene Tuberaceae Phylogeny diversity. Truffles belonging to the Tuberaceae, such as the aromatic contrast, epigeous species of Pezizales routinely have cylindrical asci black truffle Tuber melanosporum Vittad. and white truffle T with S spores per ascus (Fig. I). magnatum Pica, have been collected and consumed by humans Previous phylogenetic studies of Tuberaceae have resolved two for centuries [3). Despite this long history of human use, there are monophyletic Northern hemisphere clades, Tuber and Choiromyces, still many unanswered questions concerning the origin, historical and a Southern hemisphere clade that includes Dinglqa, Red­ biogeography, and ecology of these fungi. dellomyces, and Labyrinthomyces [4, 7). The sister group of the The Tuberaceae are one of the most diverse lineages of exclusively Tuberaceae remains unresolved [4). The related Helvellaceae, truffle forming fungi [4) and are presumably one of the earlier previously regarded as the sister clade of the Tuberaceae (albeit diverging clades within the Pezizomycotina [5). For instance, the without statistical support), arc comprised of species producing genus Tuber (the most speciose of the five genera in the family) was either aboveground "elfin saddle" or sessile cup-shaped fruitbodies estimated to comprise at least ISO species worldwide [6). The loss (e.g. He/vella - see Fig. 2a), or those with a truffle form (e.g. of active spore discharge in fungi is correlated with the transition Balsamia) [4]. from an epigeous to hypogeous fruiting habit [4,7). Hypogeous Dating the origin and diversification of fungi can be a fruitbodies of Tuber species are densely packed with spores contentious science, but methods for molecular dating are produced in globose to subglobose asci (cells in which meiospores improving [19). Because nucleotide substitution rates often differ are formed) and veins of sterile tissue [S). In contrast, epigeous between fungal lineages, a penalized likelihood method and fossil relatives of truffles produce cup-shaped ascoma with elongated calibrations were used by Padovan et al. to estimate divergence uniseriate asci capable of aerial spore discharge [9]. Given this dates within the Ascomycota based on a Bayesian phylogeny of drastic morphological differentiation, Tuber has been hypothesized ISS SSU rDNA [5). They estimated the split of Tuber from other to represent a "late-stage" in the evolutionary transition from an Pezizales occurred around 529 million years ago (Mya). In a more aboveground cup-fungus to a truffle (Fig. I) [I OJ. The species Tuber recent study focusing on the historical biogeography of Tuber, a gennadii (Chatin) Pat. is distinguished by the presence of locules molecular clock approach (with secondary calibration) was used to lined by a palisade of asci and was hypothesized to be a estimate the divergence times of major Tuber clades based on transitional form between epigeous and hypogeous fruiting habits phylogenies inferred from multiple loci (ISS rRNA, 5.8S-ITS2 [II). There are no true epigeous taxa known in the Tuberaceae. rRNA, and fl-tubulin) [20]. Their results indicate that Tuber began The hypogeous fruiting habit of the truffle offers several to diverge during the Triassic or Jurassic between 271-140 Mya. selective advantages. Truffles are characterized by a low surface However, these studies were limited by regional sampling and area-to-volume ratio, therefore a large number of spores are phylogenetic uncertainty, which may confound divergence time produced in a small packet of tissue. Furthermore, while epigeous estimations. fruiting bodies are directly exposed to weather, truffies are Here, we estimate the phylogeny of a global sample of Tuberaceae buffered against moisture and temperature fluctuations that might employing both Maximum Likelihood (ML) and Bayesian otherwise damage or inhibit development of spores. Truffle inference methods based on DNA sequences of four genetic loci: forming fungi have evolved novel mechanisms for spore dispersal ITS rRNA (ITS), 2SS large subunit rRNA (LSU), elongation via small animals that are correlated with the loss of active spore factor 1-cr (EF!cr), and RNA polymerase subunit II (RPB2). The discharge. Many different animal species are attracted by the main aims of this study were to: I) estimate the phylogeny and odors produced by truffle species [!] and truffle spores have been divergence times for major clades of the Turtfriceae; 2) examine their major biogeographic patterns; 3) map characters to the found in the fecal deposits of rodents, marsupials, reptiles and phylogeny and reconstruct important ancestral morphological and gastropods, suggesting that these animals are important dispersal ecological character states; and 4) determine their relationships to agents of truffle spores [12, 13). Indeed, truffle fruitbodies usually have durable, thick-walled spores that can withstand and possibly Southern hemisphere taxa of hitherto unknown phylogenetic benefit from the passage through the digestive tract of animals affinities. We also used the expanded data set to test monophyly of the genus Tuber. [14). The convergent evolution of these traits across a diversity
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