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Supporting Information Article Title: Increasing Phylogenetic Supporting Information Article title: Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness Authors: Hannah E. Marx, Melissa Richards, Grahm M. Johnson, and David C. Tank Article acceptance date: The following Supporting Information is available for this article: Appendix S1: Table with target-specific primer pair sequences and citations. Appendix S2: Voucher numbers and collection information for each accession. Appendix S3: Accession number for the high-throughput (miseq) or GenBank (ncbi) se- quence used for each gene region and community matrix. Appendix S4: Table summarizing high-throughput sequencing read statistics and aligned sequence length for each gene region. Appendix S5: Maximum likelihood phylograms estimated from concatenated gene regions of each dataset (total combined, GenBank, and high-throughput). Appendix S6: Comparison of phylogenetic community structure between microhabitats within each summit. Appendix S7: Table summarizing phylogenetic α-diversity. Appendix S8: Table summarizing phylogenetic β-diversity. Appendix S9: Comparison of the datasets used to infer phylogenetic relationships among alpine plant species. 1 Table Appendix 1: Table with target-specific primer pair sequences and citations for each gene region (and segments). Primer 5' Primer 5' Sequence 5' Reference 3' Primer 3' Sequence 3' Reference Pair Name White et al. (1990); White et al. (1990); ITS ITS-5 ggAAggAgAAgTCgTAACAAgg ITS-4 TCCTCCgCTTATTgATATgC Baldwin (1992) Baldwin (1992) atpB1 S1494R TCAgTACACAAAgATTTAAggTCAT Hoot et al. (1995) S611 AACgTACTCgTgAAggAAATgATCT Hoot et al. (1995) atpB2 S766R TAACATCTCggAAATATTCCgCCAT Hoot et al. (1995) S2 TATgAgAATCAATCCTACTACTTCT Hoot et al. (1995) ndhF Olmstead and Sweere ndhF Olmstead and Sweere ndhF1 ATggAACAgACATATCAATATgSgTgg gAAAAATTCCCgCCgCTACCATAg 5'-PCR (1994) 803R (1994) Olmstead and Sweere ndhF Olmstead and Sweere ndhF2 ndhF 803 CTATggTAgCggCgggAATTTTTC CgAAACATATAAAATgCRgTTAATCC (1994) 1318R (1994) Olmstead and Sweere ndhF Olmstead and Sweere ndhF3 ndhF 1318 ggATTAACYgCATTTTATATgTTTCg CCCYASATATTTgATACCTTCKCC (1994) 3'-PCR (1994) matK1 matK1F ACTgTATCgCACTATgTATCA Sang et al. (1997) matK4R gCATCTTTTACCCARTAgCgAAg Bremer et al. (2002) matK2 matk3F AAgATgCCTCTTCTTTGCAT Sang et al. (1997) matK3R gATCCgCTgTgATAATgAgA Sang et al. (1997) rbcL Olmstead and Palmer rbcL Olmstead and Palmer rbcL ggCCgTCgACATgTCACCACAAACAgARACTAAAgC gATTTCgCCTgTTTCggCTTgTgCTTTATAAA 5'-PCR (1994) Z674R (1994) a b trn ab CATTACAAATgCgATgCTCT Taberlet et al. (1991) TCTACCgATTTCgCCATATC Taberlet et al. (1991) (B48557) (A49291) c trn cf CgAAATCggTAgACgCTACg Taberlet et al. (1991) f (A50272) ATTTgAACTggTgACACgAg Taberlet et al. (1991) (B49317) 2 * References Baldwin B.G. 1992. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae. Molecular Phylogenetics and Evolution 1:3{16. Bremer B., Bremer K.A., Heidari N., and Erixon P. 2002. Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels. Molecular Phylogenetics and Evolution 24:274{301. Hoot S.B., Culham A., and Crane P.R. 1995. The Utility of atpB Gene Sequences in Resolving Phylogenetic Relationships: Comparison with rbcL and 18S Ribosomal DNA Sequences in the Lardizabalaceae. Annals of the Missouri Botanical Garden 82:194{207. Olmstead R.G. and Palmer J.D. 1994. Chloroplast DNA Systematics: A Review of Methods and Data Analysis. American Journal of Botany 81:1205{1224. Olmstead R.G. and Sweere J.A. 1994. Combining Data in Phylogenetic Systematics: An Empirical Approach Using Three Molecular Data Sets in the Solanaceae. Systematic Biology 43:467{481. Sang T., Crawford D., and Stuessy T. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia 3 (Paeoniaceae). American Journal of Botany 84:1120{1136. Taberlet P., Gielly L., Pautou G., and Bouvet J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17:1105{1109. White T., Bruns T., Lee S., and Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications (M. Innis, D. Gelfand, J. Shinsky, and T. White, eds.), pages 315{322, Academic Press. Table Appendix S2: Voucher numbers and collection information for each accession. MiSeq Species Accession Voucher Number Date Collected Locality WGS N WGS W Number Idaho: Sawtooth National Forest: Sawtooth Mountains: Abies lasiocarpa 14029 Clevenger 2012-022 August 1, 2012 Thompson Peak: Meadow just at base of west side of 44.14219 -115.01358 mountain, just south of a snowpack Idaho: Sawtooth National Forest: Sawtooth Mountians: Abies lasiocarpa 14351 Marx 2013-120 July 22, 2013 Snowyside Peak: along west face and south ridge line (trail to 43.93825 -114.97142 summit) Idaho: Sawtooth National Forest: Sawtooth Mountains: Abies lasiocarpa 14232 Zion 2012-034 August 7, 2012 44.1117 -115.00318 Horstmann Peak: Just below summit to the SW Idaho: Sawtooth National Forest: White Cloud Mountains: Achillea millefolium var alpicola 14287 Marx 2013-193 July 25, 2013 44.04019 -114.58878 Castle Peak: summit down southwest slope to treeline Idaho: Sawtooth National Forest: Pioneer Mountians: 4 Achillea millefolium var alpicola 14431 Marx 2013-228 August 7, 2013 43.77446 -114.15942 Salzburger Spitzl: talus down from summit Idaho: Sawtooth National Forest: Pioneer Mountains: Achillea millefolium var alpicola 14619 Marx 2013-318 August 9, 2013 43.74938 -114.1312 Hyndman Peak: south facing talus/boulder field from summit Idaho: Sawtooth National Forest: White Cloud Mountains: Achillea millefolium var alpicola 14665 Marx 2013-366 August 14, 2013 44.10969 -114.63886 D.O. Lee Peak: collected in alpine meadow Idaho: Sawtooth National Forest: Sawtooth Mountains: Achillea millefolium var alpicola 14136 Zion 2012-014 August 7, 2012 44.1117 -115.00318 Horstmann Peak: Just below summit to the SW Idaho: Sawtooth National Forest: Sawtooth Mountains: Aconogonon phytolaccaefolium 14229 Zion 2012-031 August 7, 2012 44.1117 -115.00318 Horstmann Peak: Just below summit to the SW Idaho: Sawtooth National Forest: Pioneer Mountains: Agoseris aurantiaca 14571 Marx 2013-270 August 9, 2013 43.74357 -114.12403 Hyndman Peak: in meadow above treeline Idaho: Sawtooth National Forest: Pioneer Mountians: Agrostis variabilis NA Marx 2013-220 August 7, 2013 43.76619 -114.15839 Salzburger Spitzl: Meadow above treeline Idaho: Sawtooth National Forest: Pioneer Mountians: Androsace septentrionalis 14464 Marx 2013-263 August 7, 2013 43.77446 -114.15942 Salzburger Spitzl: talus down from summit Idaho: Sawtooth National Forest: Pioneer Mountains: Androsace septentrionalis NA Marx 2013-334 August 9, 2013 43.74938 -114.1312 Hyndman Peak: south facing talus/boulder field from summit Idaho: Sawtooth National Forest: White Cloud Mountains: Androsace septentrionalis 14689 Marx 2013-392 August 14, 2013 44.10277 -114.62859 D.O. Lee Peak: in talus, north face then west to treeline Idaho: Sawtooth National Forest: Sawtooth Mountains: Anemone drummondii 14309 Marx 2013-078 July 19, 2013 44.01108 -114.98117 Mount Cramer: east ridge from summit to treeline Idaho: Sawtooth National Forest: White Cloud Mountains: Anemone drummondii 14682 Marx 2013-385 August 14, 2013 44.10277 -114.62859 D.O. Lee Peak: in talus, north face then west to treeline Idaho: Sawtooth National Forest: Sawtooth Mountains: Anemone drummondii var drummondii 13562 Marx 2012-029 August 10, 2012 44.09333 -115.99681 Braxon Peak: Summit down south face to treeline Continued on next page Table Appendix S2 { continued from previous page MiSeq Species Accession Voucher Number Date Collected Locality WGS N WGS W Number Idaho: Sawtooth National Forest: Sawtooth Mountains: Antennaria alpina 14019 Clevenger 2012-012 August 1, 2012 Thompson Peak: Meadow just at base of west side of 44.14219 -115.01358 mountain, just south of a snowpack Idaho: Sawtooth National Forest: Sawtooth Mountains: Antennaria alpina 14311 Marx 2013-080 July 19, 2013 44.01108 -114.98117 Mount Cramer: east ridge from summit to treeline Idaho: Sawtooth National Forest: Sawtooth Mountains: Antennaria alpina 14322 Marx 2013-091 July 19, 2013 44.01108 -114.98117 Mount Cramer: east ridge from summit to treeline Idaho: Sawtooth National Forest: Sawtooth Mountians: Antennaria alpina 14360 Marx 2013-131 July 22, 2013 43.93825 -114.97142 5 Snowyside Peak: collected at second treeline only Idaho: Sawtooth National Forest: White Cloud Mountains: Antennaria alpina 14258 Marx 2013-164 July 25, 2013 44.04019 -114.58878 Castle Peak: summit down southwest slope to treeline Idaho: Sawtooth National Forest: Pioneer Mountains: Antennaria alpina 14591 Marx 2013-290 August 9, 2013 43.74357 -114.12403 Hyndman Peak: in meadow above treeline Idaho: Sawtooth National Forest: White Cloud Mountains: Antennaria alpina 14661 Marx 2013-362 August 14, 2013 44.10969 -114.63886 D.O. Lee Peak: collected in alpine meadow Idaho: Sawtooth National Forest: White Cloud Mountains: Antennaria alpina 14684 Marx 2013-387 August 14, 2013 44.10277 -114.62859 D.O. Lee Peak: in talus, north face then west to treeline Idaho: Sawtooth National Forest: Pioneer Mountians: Antennaria corymbosa 14418 Marx 2013-212 August 7, 2013 43.76619 -114.15839 Salzburger Spitzl: Meadow above treeline Idaho: Sawtooth National Forest: Sawtooth Mountains: Antennaria lanata 14016 Clevenger 2012-007
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