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Cjb-2015-0186.Pdf Botany Molecular insights into the lichen genus Alectoria (Parmeliaceae) in North America Journal: Botany Manuscript ID cjb-2015-0186.R1 Manuscript Type: Article Date Submitted by the Author: 23-Nov-2015 Complete List of Authors: McMullin, Richard; University of Guelph , Integrative Biology Lendemer, James; New York Botanical Garden Braid, Heather ; Auckland University of Technology, School of Applied Sciences Draft Newmaster, Steven; University of Guelph Infrageneric taxonomy, Parmeliaceae, lichenized fungi, Mcm7 rDNA, ITS Keyword: rDNA https://mc06.manuscriptcentral.com/botany-pubs Page 1 of 33 Botany Molecular insights into the lichen genus Alectoria (Parmeliaceae) in North America Richard Troy McMullin 1,* , James C. Lendemer 2, Heather E. Braid 3, and Steven G. Newmaster 1 1Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada 2Institute of Systematic Botany, The New York Botanical Garden, Bronx NY 10458-5126, U.S.A 3Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand *Corresponding author: [email protected] Draft 1 https://mc06.manuscriptcentral.com/botany-pubs Botany Page 2 of 33 Abstract Alectoria is a genus of fruticose lichen characterised by the presence of usnic acid and conspicuous raised pseudocyphellae. This genus is particularly diverse and abundant in montane, boreal, and Arctic regions of North America. Because intermediate forms have been reported for several species of Alectoria on the continent it has been suggested that these species were initially delimited based on the extremes of morphological gradients. Here, we use the results of molecular phylogenetic analyses of two nuclear genes, ITS and Mcm7 , with 48 representatives of 9 taxa to examine the delineation of 5 taxa that have been previously shown to be related to, or confused with, A. sarmentosa : A. fallacina, A. imshaugii , A. sarmentosa var. sorediosa , A. sarmentosa ssp. vexillifera , and A. vancouverensis . Alectoria fallacina was found to be well- supported and distantly related to A. sarmentosa . Conversely, the other four taxa were recovered as a single monophyletic group with little internal structure which did not support the presently defined morphological species. A provisional taxonomic treatment is proposed pending more detailed study at the population level. DraftAlectoria sarmentosa var. sorediosa is recognized at the species level, which necessitates the new combination: A. sorediosa . An updated key to the North American species of Alectoria is also provided. Key Words Infrageneric taxonomy, infraspecific taxonomy, lichenized fungi, Parmeliaceae, ITS rDNA, Mcm7 rDNA, Appalachians, arctic-alpine. 2 https://mc06.manuscriptcentral.com/botany-pubs Page 3 of 33 Botany Introduction In North America, the fruticose lichen genus Alectoria Ach. (Parmeliaceae) is common throughout the Arctic, as well as on both northern coasts, with a distribution extending southwards in montane habitats of the Appalachian and western mountains (Hawksworth 1972; Brodo and Hawksworth 1977). Disjunct populations of some species also occur in montane habitats of Mexico, and at least one species, A. mexicana Brodo & D. Hawksw., is endemic to that region (Brodo and Hawksworth 1977). The last taxonomic treatment of the genus in North America was by Brodo and Hawksworth (1977), who included eight species and two subspecies. Recently, one species, A. nigricans (Ach.) Nyl., the only member of Alectoria that did not produce usnic acid, has been placed in a distinct genus, Gowardia Halonen et al., based on a molecular phylogenetic analysis (Halonen et al. 2009). With the exception of A. nigricans , the rest of the species have remained as circumscribed and classified by Brodo and Hawksworth (1977). Draft Brodo and Hawksworth (1977) discussed several cases in which the Alectoria taxa they recognized appeared to be linked by intermediates, nonetheless variously treating these taxa as independent species or subspecies. Specifically, they considered three species ( A. imshaugii , A. sarmentosa , and A. vancouverensis ) to display "morphological and chemical intermediaries between all possible combinations" (p. 71). Similarly, they recognized an ecologically and morphologically distinct entity restricted to Arctic and alpine regions as A. sarmentosa ssp. vexillifera based on its chemical similarity to A. sarmentosa ssp. sarmentosa . An additional species, A. fallacina was “tentatively recognized at the species level” by Brodo and Hawksworth (1977, p. 57) following Motyka (1960). However, Brodo and Hawksworth (1977) considered that A. fallacina may actually be a subspecies of A. sarmentosa because of chemical and morphological intermediates. A final variant of A. sarmentosa discussed by Brodo and Hawksworth (1977) was a rare sorediate form, which was neither classified as a species nor a subspecies, although it was previously recognized as a variety by Hawksworth (1972). Since Brodo and Hawksworth's (1977) monograph, Alectoria has not been the direct subject of a major taxonomic revision and thus the taxonomic uncertainties outlined above remain unresolved. Despite the substantial resources that have been devoted to using molecular data to resolve outstanding questions of generic circumscription and species delimitation in the 3 https://mc06.manuscriptcentral.com/botany-pubs Botany Page 4 of 33 Parmeliaceae (Crespo et al. 2010a,b; Buaruang et al. 2015; de Paz et al. 2010a,b; Del-Prado et al. 2010, 2013; Divakar et al. 2010, 2013; Elix et al. 2010; Lendemer and Hodkinson 2010; Leavitt et al. 2014; Lendemer and Ruiz 2015; Mark et al. 2012; Nelson et al. 2012; Nelsen et al. 2013; Saag et al. 2014), and more specifically the related fruticose genus Bryoria (Myllys et al. 2014; Velmala et al. 2014), Alectoria has not been the direct subject of such a study. Nonetheless, recent molecular studies of Bryoria and Parmeliaceae have included samples of Alectoria and recovered results that strongly suggested further study was needed (Myllys et al. 2014; Halonen et al. 2009). The aim of this study was to examine the current taxonomy of North American Alectoria using molecular phylogenetics. Our objectives were specifically to infer the evolutionary relationships of the taxa within Alectoria and then evaluate these inferences in light of characters traditionally used to delineate taxa in this genus. The results of this study, which drew on extensive field studies and herbarium work carried out by two of the authors (RTM and JCL), are presented here. Draft 4 https://mc06.manuscriptcentral.com/botany-pubs Page 5 of 33 Botany Methods Chemical and morphological study A stereoscopic microscope was used to examine thallus morphology and observe chemical reactions with standard spot-test reagents following Brodo et al. (2001). Thallus chemistry was also examined with thin layer chromatography (TLC) using solvents A and C following Culberson and Kristinsson (1970), with the modification of aluminum-backed silica gel plates in smaller jars (Lendemer 2011). Images were captured with a Canon Elph130IS digital camera. Specimens used to generate new DNA sequence data are housed at the Biodiversity Institute of Ontario Herbarium (OAC) at the University of Guelph and at the New York Botanical Garden (NY). Specimens examined that were not included in the molecular analyses are listed in the Appendix. Molecular data generation, dataset assembly,Draft and taxon sampling Forty-four new sequences were generated from 22 specimens for our study (Table 1). These included one specimen of Gowardia nigricans and the following 21 Alectoria specimens: three of A. fallacina , one of A. imshaugii , one of A. ochroleuca , ten of A. sarmentosa ssp. sarmentosa , two of A. sarmentosa var. sorediosa , two of A. sarmentosa ssp . vexillifera , and two of A. vancouverensis (Table 1). Collection data for these specimens are available on the Barcode of Life Data System (BOLD; Ratnasingham and Hebert 2007) in the public project titled ‘Alectoria Adventure’ (project code: ALECT). For DNA extractions, approximately 15–20 mg of dry lichen thallus was subsampled and homogenised with sterile ceramic beads using a TissueLyser (Qiagen) at 30 Hz for 1 min. DNA was extracted using the NucleoSpin Plant II Kit (Macherey-Nagel) with CTAB buffer following manufacturer's instructions for plants. Two nuclear genes—the minichromosome maintenance protein 7 gene ( Mcm7 ), the ribosomal internal transcribed spacer region (ITS)—and one mitochondrial gene—the mitochondrial small subunit ribosomal gene (mtSSU)—were amplified using the primers and reaction profiles listed in Table 2. The gene regions were amplified in 12.5 µl reaction volumes with 6.25 µl 10% trehalose, 2 µl ddH2O, 1.25 µl 10X buffer, 0.625 µl 5 https://mc06.manuscriptcentral.com/botany-pubs Botany Page 6 of 33 MgCl2 (50 mM), 0.1 µl forward primer (10 µm), 0.1 µl reverse primer (10 µm), 0.0625 µl 10 mM dNTPs, 0.06 µl Platinum Taq polymerase (5 U/µl), and 2 µl of DNA (~ 10–20 ng). A secondary amplification was carried out on samples that did not amplify with the same reaction volumes as above except that 1 µl of PCR product and 1 µl of ddH 2O were used in place of DNA. PCR products were visualised on 1% agarose gel (1X TBE buffer) stained with GelRed (Biotium). Samples with a clean single band were sequenced from the remaining PCR product. Sequencing reactions used the same primers used for PCR amplification and were carried out
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