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Evolutionary Histories of Soil Fungi Are Reflected in Their Large Ecology Letters, (2014) doi: 10.1111/ele.12311 LETTER Evolutionary histories of soil fungi are reflected in their large- scale biogeography Abstract Kathleen K. Treseder,1* Mia R. Although fungal communities are known to vary along latitudinal gradients, mechanisms underly- Maltz,1 Bradford A. Hawkins,1 ing this pattern are not well-understood. We used high-throughput sequencing to examine the Noah Fierer,2 Jason E. Stajich3 and large-scale distributions of soil fungi and their relation to evolutionary history. We tested the Trop- Krista L. McGuire4 ical Conservatism Hypothesis, which predicts that ancestral fungal groups should be more restricted to tropical latitudes and conditions than would more recently derived groups. We found support for this hypothesis in that older phyla preferred significantly lower latitudes and warmer, wetter conditions than did younger phyla. Moreover, preferences for higher latitudes and lower pre- cipitation levels were significantly phylogenetically conserved among the six younger phyla, possibly because the older phyla possess a zoospore stage that is vulnerable to drought, whereas the younger phyla retain protective cell walls throughout their life cycle. Our study provides novel evidence that the Tropical Conservatism Hypothesis applies to microbes as well as plants and animals. Keywords Latitude, phylum, precipitation, regular septa, snowball earth events, soil, temperature, traits, zoo- spore. Ecology Letters (2014) Here, we test predictions of TCH as they may apply to a INTRODUCTION group of organisms much older than those normally consid- Numerous studies have reported shifts in fungal community ered. The Earth’s paleoclimate was relatively warm and wet composition by latitude, temperature, and precipitation during the earliest evolution of ancestral fungi, whereas severe (Arnold & Lutzoni 2007; Tedersoo et al. 2010, 2012; Kivlin ice ages (Evans et al. 1997; Kopp et al. 2005; Smith 2009) and et al. 2011; Sun et al. 2012; Opik€ et al. 2013). Such spatial drought (Algeo & Scheckler 1998) occurred later in their evo- shifts are expected to contain phylogenetic patterns if we lutionary history. We hypothesized that younger fungal phyla assume that the evolution of key morphological or physiologi- should be more likely to reside in soils of higher latitudes, cal traits of fungal taxa determines their response to tempera- with older lineages having evolved traits that provide maximal ture and precipitation. These traits include possession of cell fitness under warm and wet conditions. We also explored the walls or the presence of regular septa. In turn, these traits distributions of potential traits that could account for the spa- could constrain the geographic distribution of fungal taxa. tial structure of lineage ages. Nevertheless, the relationships between the evolutionary his- We are focusing on the biogeography of soil fungi at the tory of soil fungi and their biogeographical patterns remain phylum level, because we are examining evolutionary histories largely unknown, especially at very large scales. over very long time periods that correspond to divergence at For many terrestrial plants and animals, younger taxa tend this broad taxonomic level. The divergence of fungal phyla to reside at higher latitudes (Hillebrand 2004; Weir & Schluter coincided with key evolutionary events, some of which could 2007; Buckley et al. 2010; Hawkins et al. 2012; Romdal et al. have conferred greater tolerance to stressful environmental 2013). The Tropical Conservatism Hypothesis (TCH) repre- conditions. For example, the ancestral phyla Cryptomycota, sents one potential explanation for this pattern (e.g., Wiens & Chytridiomycota, and Blastocladiomycota each reproduce via Donoghue 2004), whereby older groups that evolved under zoospores, which do not have cell walls; the zoospore form was warmer, wetter conditions are constrained by phylogenetic lost from younger phyla (Liu et al. 2006; Stajich et al. 2009; niche conservatism, making it difficult for them to evolve the James et al. 2013). This event may have coincided with the necessary physiological traits that allow them to proliferate onset of extreme cold periods during the Neoproterozoic under cooler, drier climates. Thus, older groups (and their (Evans et al. 1997; Smith 2009). It is well-documented that fun- traits) are more likely to be restricted to lower latitudes, gal cell walls protect the interior from damage caused by freez- whereas younger groups can reside at higher latitudes. It is ing, desiccation, and osmotic stresses (reviewed in Latge 2007). unknown, however, whether these patterns apply to fungi. Some zoosporic fungi can produce resting or resistant spores 1Department of Ecology and Evolutionary Biology, University of California 3Department of Plant Pathology and Microbiology, University of California Irvine, Irvine, CA, 92697, USA Riverside, Riverside, CA, 92521, USA 2Department of Ecology and Evolutionary Biology, Cooperative Institute for 4Barnard College, Columbia University, New York, NY, 10027, USA Research in Environmental Sciences, University of Colorado, Boulder, CO, *Correspondence: E-mail: [email protected] 80309, USA © 2014 John Wiley & Sons Ltd/CNRS 2 K. K. Treseder Letter that allow them to become dormant during stressful condi- season. These soil samples were identical to a subset of those tions, but they nevertheless form zoospores upon germination reported in Fierer & Jackson (2006). (Olson 1973). Thus, their active phases may be relatively lim- ited under stressful conditions. DNA sequencing and analysis Differentiated tissues with regular septa are thought to have evolved in the two youngest phyla (Ascomycota and Basidi- DNA was extracted from 5 to 10 g dry weight of each soil omycota, also known as the Dikarya) during the Devonian sample as described in Lauber et al. (2009). We used universal (Stajich et al. 2009; Kumar et al. 2012; Healy et al. 2013). In fungal primers of Borneman & Hartin (2000) modified for this period, much of the Earth’s land mass was located in the barcoded pyrosequencing to amplify a ~ 422 bp region of the naturally arid zone near the Tropic of Capricorn (Algeo & 18S rRNA gene as in McGuire et al. (2012). This region Scheckler 1998), so land-based fungi should have been extends from nucleotide 817 to 1196 of the 18S sequence of exposed to dry conditions. Regular septa of the Dikarya Saccharomyces cerevisiae and includes the V4 (partial) and V5 include central pores that can be plugged by specialized variable regions (Borneman & Hartin 2000). This primer set organelles, and together they form a regulatory structure that has previously been used to successfully amplify Cryptomy- improves water conservation under dry conditions and cota, Blastocladiomycota, Chytridiomycota, Zygomycota, reduces leakage that might occur from freeze-thaw ruptures Mucoromycotina, Glomeromycota, Ascomycota, and Basidi- (Maruyama et al. 2005; Beck et al. 2013). In comparison, reg- omycota (Borneman & Hartin 2000; Nagahama et al. 2011). ular septa like these are rare within older phyla and are Cryptomycota are classified as fungi (Jones et al. 2011a,b; known to occur in only a few groups within the Kickxellomy- Capella-Gutierrez et al. 2012; James et al. 2013). We obtained cotina (Tretter et al. 2013). Altogether, the elimination of the 52 906 fungal sequences, representing 910 to 1699 sequences zoospore stage and the evolution of regular septa might each per sample. The Quantitative Insights Into Microbial Ecology contribute to the latitudinal distributions of fungal phyla. (QIIME) pipeline was then used to process sequences (Capor- To test our hypothesis, we mapped the distributions of aso et al. 2010). Sequences were quality checked, aligned, and fungal taxa in soils collected from local communities across grouped into phylotypes (hereafter, ‘taxa’) at a 97% sequence the Western Hemisphere. For each taxon, we calculated the similarity cut-off. This cut-off corresponds to approximately average latitudinal distance from the equator (i.e., higher ver- the family level for this DNA region (Anderson et al. 2003). sus lower latitudes), mean annual temperature, and mean One representative sequence from each taxon was chosen. annual precipitation for sites in which the taxon was Each representative sequence was identified to phylum by detected. These were considered the environmental conditions BLAST comparison against all non-environmental fungal ‘preferred’ by each taxon, akin to niche space. Finally, sequences in GenBank (https://www.ncbi.nlm.nih.gov/gen- we related these preferred environments to phylum age and bank/). We double-checked our identifications by manually phylum-level traits. performing BLAST comparisons with curated sequences pro- duced by the Assembling the Fungal Tree of Life (AFTOL) project (James et al. 2006). We randomly selected 910 MATERIALS AND METHODS sequences per sample to control for differences in sequence number among samples. Study sites Altogether, 516 fungal taxa were identified to phylum, and We assayed soils from 47 sites in North and South America. collectively they represented nine phyla (Table S2). A repre- This number of sites was smaller than some other large-scale sentative sequence of each taxon has been submitted to Gen- analyses (e.g., Lauber et al. 2009). Nevertheless, the sites rep- Bank under the BioProject Accession PRJNA237127. One resented a wide range in latitude (28 °Sto69°N), mean hundred seventeen of these taxa matched (≥ 97% identity) a annual temperature (À9.3 to 25.0
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