Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

Peer Reviewed https://deepblue.lib.umich.edu/bitstream/2027.42/150529/1/ajb21328-sup-0002-AppendixS2.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/2/ajb21328-sup-0003-AppendixS3.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/3/ajb21328-sup-0004-AppendixS4.pdf https://deepb...

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Published in:American Journal of Botany
Main Authors: Marx, Hannah E., Richards, Melissa, Johnson, Grahm M., Tank, David C.
Format: Article in Journal/Newspaper
Language:unknown
Published: Idaho Museum of Natural History 2019
Subjects:
Online Access:https://hdl.handle.net/2027.42/150529
https://doi.org/10.1002/ajb2.1328
id ftumdeepblue:oai:deepblue.lib.umich.edu:2027.42/150529
record_format openpolar
institution Open Polar
collection University of Michigan: Deep Blue
op_collection_id ftumdeepblue
language unknown
topic Idaho
mean nearest taxon distance
mean pairwise distance
mega‐phylogeny
vascular plants
high‐throughput sequencing
elevation
community phylogenetics
alpine
Biology
Botany
Science
spellingShingle Idaho
mean nearest taxon distance
mean pairwise distance
mega‐phylogeny
vascular plants
high‐throughput sequencing
elevation
community phylogenetics
alpine
Biology
Botany
Science
Marx, Hannah E.
Richards, Melissa
Johnson, Grahm M.
Tank, David C.
Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness
topic_facet Idaho
mean nearest taxon distance
mean pairwise distance
mega‐phylogeny
vascular plants
high‐throughput sequencing
elevation
community phylogenetics
alpine
Biology
Botany
Science
description Peer Reviewed https://deepblue.lib.umich.edu/bitstream/2027.42/150529/1/ajb21328-sup-0002-AppendixS2.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/2/ajb21328-sup-0003-AppendixS3.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/3/ajb21328-sup-0004-AppendixS4.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/4/ajb21328.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/5/ajb21328-sup-0009-AppendixS9.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/6/ajb21328-sup-0005-AppendixS5.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/7/ajb21328-sup-0007-AppendixS7.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/8/ajb21328-sup-0006-AppendixS6.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/9/ajb21328-sup-0008-AppendixS8.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/10/ajb21328_am.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/11/ajb21328-sup-0001-AppendixS1.pdf
format Article in Journal/Newspaper
author Marx, Hannah E.
Richards, Melissa
Johnson, Grahm M.
Tank, David C.
author_facet Marx, Hannah E.
Richards, Melissa
Johnson, Grahm M.
Tank, David C.
author_sort Marx, Hannah E.
title Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness
title_short Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness
title_full Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness
title_fullStr Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness
title_full_unstemmed Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness
title_sort increasing phylogenetic stochasticity at high elevations on summits across a remote north american wilderness
publisher Idaho Museum of Natural History
publishDate 2019
url https://hdl.handle.net/2027.42/150529
https://doi.org/10.1002/ajb2.1328
genre Arctic
genre_facet Arctic
op_relation Marx, Hannah E.; Richards, Melissa; Johnson, Grahm M.; Tank, David C. (2019). "Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness." American Journal of Botany 106(7): 958-970.
0002-9122
1537-2197
https://hdl.handle.net/2027.42/150529
doi:10.1002/ajb2.1328
American Journal of Botany
Pigot, A. L., and R. S. Etienne. 2015. A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153 – 163.
Choler, P., R. Michalet, and R. M. Callaway. 2001. Facilitation and competition on gradients in alpine plant communities. Ecology 82: 3295 – 3308.
Pennell, M. W., J. M. Eastman, G. J. Slater, J. W. Brown, J. C. Uyeda, R. G. FitzJohn, M. E. Alfaro, and L. J. Harmon. 2014. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics 30: 2216 – 2218.
Consortium of Pacific Northwest Herbaria. 2007‐2018 (continuously updated) Website http://www.pnwherbaria.org/ [accessed 05 March 2013].
Qian, H., R. E. Ricklefs, and P. S. White. 2005. Beta diversity of angiosperms in temperate floras of eastern Asia and eastern North America. Ecology Letters 8: 15 – 22.
Quintero, I., and W. Jetz. 2018. Global elevational diversity and diversification of birds. Nature 555: 246 – 250.
R Core Team. 2015. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Website https://www.R-project.org/.
Reid, R. R. 1963. Reconnaissance geology of the Sawtooth Range. Idaho Bureau of Mines and Geology 129: 958 – 61.
Richardson, A. D., and A. J. Friedland. 2009. A Review of the Theories to Explain Arctic and Alpine Treelines Around the World. Journal of Sustainable Forestry 28: 218 – 242.
Roquet, C., W. Thuiller, and S. Lavergne. 2012. Building megaphylogenies for macroecology: taking up the challenge. Ecography 35: 958 – 14.
Schlatterer, E. F. 1972. A preliminary description of plant communities found on the Sawtooth, White Cloud, Boulder, and Pioneer Mountains. United States Forest Service Report – Intermountain Region.
Smith, J. M. B., and A. M. Cleef. 1988. Composition and Origins of the World’s Tropicalpine Floras. Journal of Biogeography 15: 631 – 645.
Smith, S. A., and C. W. Dunn. 2008. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24: 715 – 716.
Smith, S. A., and B. C. O’Meara. 2012. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28: 2689 – 2690.
Smith, S. A., J. M. Beaulieu, and M. J. Donoghue. 2009. Mega‐phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9: 958 – 12.
Soltis, D. E., S. A. Smith, N. Cellinese, K. J. Wurdack, D. C. Tank, S. F. Brockington, N. F. Refulio‐Rodriguez, et al. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany 98: 704 – 730.
Stamatakis, A. 2006. RAxML‐VI‐HPC: maximum likelihood‐based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688 – 2690.
Steele, R. W. and the Intermountain Forest Range Experiment Station. 1981. Forest habitat types of central Idaho. U.S. Dept. of Agriculture, Forest Service Intermountain Forest and Range Experiment Station.
Stein, A., K. Gerstner, and H. Kreft. 2014. Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales. Ecology Letters 17: 866 – 880.
Tucker, C. M., M. W. Cadotte, S. B. Carvalho, T. J. Davies, S. Ferrier, S. A. Fritz, R. Grenyer, et al. 2016. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biological Reviews 92: 698 – 715.
Uribe‐Convers, S., M. L. Settles, and D. C. Tank. 2016. A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS ONE 11: e0148203.
Valiente‐Banuet, A., and M. Verdú. 2007. Facilitation can increase the phylogenetic diversity of plant communities. Ecology Letters 10: 1029 – 1036.
Vamosi, S. M., S. B. Heard, J. C. Vamosi, and C. O. Webb. 2009. Emerging patterns in the comparative analysis of phylogenetic community structure. Molecular Ecology 18: 572 – 592.
Vellend, M. 2010. Conceptual Synthesis in Community Ecology. The Quarterly Review of Biology 85: 183 – 206.
Webb, C. O. 2000. Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees. American Naturalist 156: 145 – 155.
Webb, C. O., D. D. Ackerly, M. A. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33: 475 – 505.
Winkler, D. E., R. J. Butz, M. J. Germino, K. Reinhardt, and L. M. Kueppers. 2018. Snowmelt Timing Regulates Community Composition, Phenology, and Physiological Performance of Alpine Plants. Frontiers in Plant Science 9: 1140.
Winter, M., V. Devictor, and O. Schweiger. 2013. Phylogenetic diversity and nature conservation: where are we? Trends in Ecology & Evolution 28: 199 – 204.
Wright, D. H., and J. H. Reeves. 1992. On the Meaning and Measurement of Nestedness of Species Assemblages. Oecologia 92: 416 – 428.
Zanne, A. E., D. C. Tank, W. K. Cornwell, J. M. Eastman, S. A. Smith, R. G. FitzJohn, D. J. McGlinn, et al. 2014. Three keys to the radiation of angiosperms into freezing environments. Nature 506: 89 – 92.
Angiosperm Phylogeny Group. 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 181: 958 – 20.
Baselga, A. 2009. Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography 19: 134 – 143.
Billings, W. D., and H. A. Mooney. 1968. The Ecology of Arctic and Alpine Plants. Biological Reviews 43: 481 – 529.
Borgert, J. A., K. A. Lundeen, and G. D. Thackray. 1999. Glacial Geology of the Southeastern Sawtooth Mountains. In Hughes SS and Thackray GD [eds.], Guidebook to the Geology of Eastern Idaho. Idaho Museum of Natural History. Pocatello, USA: Idaho Museum of Natural History, 205 – 217.
Boucher, F. C., S. Lavergne, M. Basile, P. Choler, and S. Aubert. 2016. Evolution and biogeography of the cushion life form in angiosperms. Perspectives in Plant Ecology, Evolution and Systematics 20: 22 – 31.
Bryant, J. A., C. Lamanna, H. Morlon, A. J. Kerkhoff, B. J. Enquist, and J. L. Green. 2008. Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences, USA 105: 11505 – 11511.
Cadotte, M., C. H. Albert, and S. C. Walker. 2013. The ecology of differences: assessing community assembly with trait and evolutionary distances. Ecology Letters 16: 1234 – 1244.
Cavender‐Bares, J., and A. Wilczek. 2003. Integrating micro‐ and macroevolutionary processes in community ecology. Ecology 84: 592 – 597.
Cavender‐Bares, J., A. Keen, and B. Miles. 2006. Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology 87: S109 – S122.
Cavender‐Bares, J., K. H. Kozak, P. V. A. Fine, and S. W. Kembel. 2009. The merging of community ecology and phylogenetic biology. Ecology Letters 12: 693 – 715.
Cronn, R., B. J. Knaus, A. Liston, P. J. Maughan, M. Parks, J. V. Syring, and J. Udall. 2012. Targeted enrichment strategies for next‐generation plant biology. American Journal of Botany 99: 291 – 311.
Doyle, J. J., and J. L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11 – 15.
Dullinger, S., A. Gattringer, W. Thuiller, D. Moser, N. E. Zimmermann, A. Guisan, W. Willner, et al. 2012. Extinction debt of high‐mountain plants under twenty‐first‐century climate change. Nature Climate Change 2: 619 – 622.
Eastman, J. M., C. E. T. Paine, and O. J. Hardy. 2011. spacodiR: structuring of phylogenetic diversity in ecological communities. Bioinformatics 27: 2437 – 2438.
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spelling ftumdeepblue:oai:deepblue.lib.umich.edu:2027.42/150529 2023-08-20T04:03:11+02:00 Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness Marx, Hannah E. Richards, Melissa Johnson, Grahm M. Tank, David C. 2019-07 application/pdf https://hdl.handle.net/2027.42/150529 https://doi.org/10.1002/ajb2.1328 unknown Idaho Museum of Natural History Wiley Periodicals, Inc. Marx, Hannah E.; Richards, Melissa; Johnson, Grahm M.; Tank, David C. (2019). "Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness." American Journal of Botany 106(7): 958-970. 0002-9122 1537-2197 https://hdl.handle.net/2027.42/150529 doi:10.1002/ajb2.1328 American Journal of Botany Pigot, A. L., and R. S. Etienne. 2015. A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153 – 163. Choler, P., R. Michalet, and R. M. Callaway. 2001. Facilitation and competition on gradients in alpine plant communities. Ecology 82: 3295 – 3308. Pennell, M. W., J. M. Eastman, G. J. Slater, J. W. Brown, J. C. Uyeda, R. G. FitzJohn, M. E. Alfaro, and L. J. Harmon. 2014. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics 30: 2216 – 2218. Consortium of Pacific Northwest Herbaria. 2007‐2018 (continuously updated) Website http://www.pnwherbaria.org/ [accessed 05 March 2013]. Qian, H., R. E. Ricklefs, and P. S. White. 2005. Beta diversity of angiosperms in temperate floras of eastern Asia and eastern North America. Ecology Letters 8: 15 – 22. Quintero, I., and W. Jetz. 2018. Global elevational diversity and diversification of birds. Nature 555: 246 – 250. R Core Team. 2015. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Website https://www.R-project.org/. Reid, R. R. 1963. Reconnaissance geology of the Sawtooth Range. Idaho Bureau of Mines and Geology 129: 958 – 61. Richardson, A. D., and A. J. Friedland. 2009. A Review of the Theories to Explain Arctic and Alpine Treelines Around the World. Journal of Sustainable Forestry 28: 218 – 242. Roquet, C., W. Thuiller, and S. Lavergne. 2012. Building megaphylogenies for macroecology: taking up the challenge. Ecography 35: 958 – 14. Schlatterer, E. F. 1972. A preliminary description of plant communities found on the Sawtooth, White Cloud, Boulder, and Pioneer Mountains. United States Forest Service Report – Intermountain Region. Smith, J. M. B., and A. M. Cleef. 1988. Composition and Origins of the World’s Tropicalpine Floras. Journal of Biogeography 15: 631 – 645. Smith, S. A., and C. W. Dunn. 2008. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24: 715 – 716. Smith, S. A., and B. C. O’Meara. 2012. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28: 2689 – 2690. Smith, S. A., J. M. Beaulieu, and M. J. Donoghue. 2009. Mega‐phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9: 958 – 12. Soltis, D. E., S. A. Smith, N. Cellinese, K. J. Wurdack, D. C. Tank, S. F. Brockington, N. F. Refulio‐Rodriguez, et al. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany 98: 704 – 730. Stamatakis, A. 2006. RAxML‐VI‐HPC: maximum likelihood‐based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688 – 2690. Steele, R. W. and the Intermountain Forest Range Experiment Station. 1981. Forest habitat types of central Idaho. U.S. Dept. of Agriculture, Forest Service Intermountain Forest and Range Experiment Station. Stein, A., K. Gerstner, and H. Kreft. 2014. Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales. Ecology Letters 17: 866 – 880. Tucker, C. M., M. W. Cadotte, S. B. Carvalho, T. J. Davies, S. Ferrier, S. A. Fritz, R. Grenyer, et al. 2016. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biological Reviews 92: 698 – 715. Uribe‐Convers, S., M. L. Settles, and D. C. Tank. 2016. A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS ONE 11: e0148203. Valiente‐Banuet, A., and M. Verdú. 2007. Facilitation can increase the phylogenetic diversity of plant communities. Ecology Letters 10: 1029 – 1036. Vamosi, S. M., S. B. Heard, J. C. Vamosi, and C. O. Webb. 2009. Emerging patterns in the comparative analysis of phylogenetic community structure. Molecular Ecology 18: 572 – 592. Vellend, M. 2010. Conceptual Synthesis in Community Ecology. The Quarterly Review of Biology 85: 183 – 206. Webb, C. O. 2000. Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees. American Naturalist 156: 145 – 155. Webb, C. O., D. D. Ackerly, M. A. McPeek, and M. J. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33: 475 – 505. Winkler, D. E., R. J. Butz, M. J. Germino, K. Reinhardt, and L. M. Kueppers. 2018. Snowmelt Timing Regulates Community Composition, Phenology, and Physiological Performance of Alpine Plants. Frontiers in Plant Science 9: 1140. Winter, M., V. Devictor, and O. Schweiger. 2013. Phylogenetic diversity and nature conservation: where are we? Trends in Ecology & Evolution 28: 199 – 204. Wright, D. H., and J. H. Reeves. 1992. On the Meaning and Measurement of Nestedness of Species Assemblages. Oecologia 92: 416 – 428. Zanne, A. E., D. C. Tank, W. K. Cornwell, J. M. Eastman, S. A. Smith, R. G. FitzJohn, D. J. McGlinn, et al. 2014. Three keys to the radiation of angiosperms into freezing environments. Nature 506: 89 – 92. Angiosperm Phylogeny Group. 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 181: 958 – 20. Baselga, A. 2009. Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography 19: 134 – 143. Billings, W. D., and H. A. Mooney. 1968. The Ecology of Arctic and Alpine Plants. Biological Reviews 43: 481 – 529. Borgert, J. A., K. A. Lundeen, and G. D. Thackray. 1999. Glacial Geology of the Southeastern Sawtooth Mountains. In Hughes SS and Thackray GD [eds.], Guidebook to the Geology of Eastern Idaho. Idaho Museum of Natural History. Pocatello, USA: Idaho Museum of Natural History, 205 – 217. Boucher, F. C., S. Lavergne, M. Basile, P. Choler, and S. Aubert. 2016. Evolution and biogeography of the cushion life form in angiosperms. Perspectives in Plant Ecology, Evolution and Systematics 20: 22 – 31. Bryant, J. A., C. Lamanna, H. Morlon, A. J. Kerkhoff, B. J. Enquist, and J. L. Green. 2008. Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences, USA 105: 11505 – 11511. Cadotte, M., C. H. Albert, and S. C. Walker. 2013. The ecology of differences: assessing community assembly with trait and evolutionary distances. Ecology Letters 16: 1234 – 1244. Cavender‐Bares, J., and A. Wilczek. 2003. Integrating micro‐ and macroevolutionary processes in community ecology. Ecology 84: 592 – 597. Cavender‐Bares, J., A. Keen, and B. Miles. 2006. Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology 87: S109 – S122. Cavender‐Bares, J., K. H. Kozak, P. V. A. Fine, and S. W. Kembel. 2009. The merging of community ecology and phylogenetic biology. Ecology Letters 12: 693 – 715. Cronn, R., B. J. Knaus, A. Liston, P. J. Maughan, M. Parks, J. V. Syring, and J. Udall. 2012. Targeted enrichment strategies for next‐generation plant biology. American Journal of Botany 99: 291 – 311. Doyle, J. J., and J. L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11 – 15. Dullinger, S., A. Gattringer, W. Thuiller, D. Moser, N. E. Zimmermann, A. Guisan, W. Willner, et al. 2012. Extinction debt of high‐mountain plants under twenty‐first‐century climate change. Nature Climate Change 2: 619 – 622. Eastman, J. M., C. E. T. Paine, and O. J. Hardy. 2011. spacodiR: structuring of phylogenetic diversity in ecological communities. Bioinformatics 27: 2437 – 2438. IndexNoFollow Idaho mean nearest taxon distance mean pairwise distance mega‐phylogeny vascular plants high‐throughput sequencing elevation community phylogenetics alpine Biology Botany Science Article 2019 ftumdeepblue https://doi.org/10.1002/ajb2.132810.5061/dryad.d06j48t 2023-07-31T20:48:13Z Peer Reviewed https://deepblue.lib.umich.edu/bitstream/2027.42/150529/1/ajb21328-sup-0002-AppendixS2.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/2/ajb21328-sup-0003-AppendixS3.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/3/ajb21328-sup-0004-AppendixS4.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/4/ajb21328.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/5/ajb21328-sup-0009-AppendixS9.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/6/ajb21328-sup-0005-AppendixS5.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/7/ajb21328-sup-0007-AppendixS7.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/8/ajb21328-sup-0006-AppendixS6.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/9/ajb21328-sup-0008-AppendixS8.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/10/ajb21328_am.pdf https://deepblue.lib.umich.edu/bitstream/2027.42/150529/11/ajb21328-sup-0001-AppendixS1.pdf Article in Journal/Newspaper Arctic University of Michigan: Deep Blue American Journal of Botany 106 7 958 970