1. Shefferson, R.P. 2022. lefko3: a gentle introduction. Published on R Studio Connect through Bookdown.
  2. Shefferson, R.P., R. Salguero-Gómez, and O. Jones (eds.). 2017. The Evolution of Senescence in the Tree of Life. Cambridge University Press.
  3. Reviews, Editorials, and Opinion Pieces

  4. Shefferson, R.P., H. Jacquemyn, T. Kull, and M.J. Hutchings. 2020. The demography of terrestrial orchids: life history, population dynamics, and conservation. Botanical Journal of the Linnean Society 192:315-332.
  5. Shefferson, R.P. 2019. History sets the stage: macroevolutionary influence on biotic interactions. Journal of Ecology 107:1550-1556.
  6. Takada, T. and R.P. Shefferson. 2018. The long and winding road of evolutionary demography: Preface. Population Ecology 60:3-7.
  7. Shefferson, R.P. and R. Salguero-Gómez. 2015. Eco-evolutionary dynamics in plants: interactive processes at overlapping timescales and their implications. Journal of Ecology 103:789-797.
  8. Salguero-Gómez, R., R.P. Shefferson, and M.J. Hutchings. 2013. Plants do not count… or do they? New perspectives on the universality of senescence. Journal of Ecology 101:545-554.
  9. Shefferson, R.P. 2010. Why are life histories so variable? Nature Education Knowledge 1(12):1.
  10. Shefferson, R.P. 2009. The evolutionary ecology of vegetative dormancy in mature herbaceous perennial plants. Journal of Ecology 97:1000-1009.
  11. Research Articles

  12. Chang, J.-T., Y. Zhang, E. Andronova, L.V. Averyanov, E.G. Filippov, Takayuki Kawahara, R.P. Shefferson, J.-H. Kim, R.C.-C. Hsu, Y.-H. Cho, M.-X. Luo, P.-C. Liao, Y.-I. Lee. In press. Middle Pleistocene climate change influenced northward divergence and cold adaptation in an Asian lady’s slipper orchid, Cypripedium macranthos Sw. (Orchidaceae). Botanical Journal of the Linnean Society.
  13. Gargiulo, R., R.S. Waples, A.K. Grow, R.P. Shefferson, J. Viruel, M.F. Fay, and Tiiu Kull. 2023. Effective population size in a partially clonal plant is not predicted by the number of genetic individuals. Evolutionary Applications 16:750-766.
  14. Bashirzadeh, M., M. Abedi, R.P. Shefferson, and M. Farzam. 2023. Post-fire recovery of plant biodiversity changes depending on time intervals since last fire in semiarid shrublands. Fire 6:103.
  15. Bashirzadeh, M., R.P. Shefferson, and M. Farzam. 2022. Plant-plant interactions determine natural restoration of plant biodiversity over time, in a degraded mined land. Ecology and Evolution 12:e8878.
  16. The Global Urban Evolution Project. 2022. Global urbanization drives adaptation in the plant white clover. Science 375:1275-1281.
  17. Coughlin, E.M., R.P. Shefferson, S. Clark, and N. Wurzburger. 2021. Plant-soil feedbacks and the introduction of Castanea (chestnut) hybrids to eastern North American forests. Restoration Ecology 29:e13326.
  18. Shefferson, R.P., S. Kurokawa, and J. Ehrlén. 2021. lefko3: analyzing individual history through size-classified matrix population models. Methods in Ecology and Evolution 12:378-382.
  19. Ikeda, H., M.A. Callaham, R.P. Shefferson, E.S. Wenk, and C. Fragoso. 2020. A comparison of latitudinal species diversity patterns between riverine and terrestrial earthworms from the North American temperate zone. Journal of Biogeography 47:1373-1382.
  20. Pashirzad, M., H. Ejtehadi, J. Vaezi, and R.P. Shefferson. 2019. Multiple processes at different spatial scales determine beta diversity patterns in a mountain semi-arid rangeland of Khorassan-Kopet Dagh floristic province, NE Iran. Plant Ecology 220:829-844.
  21. Shefferson, R.P., W. Bunch, C.C. Cowden, Y.-I. Lee, T. Kartzinel, T. Yukawa, J. Downing, and H. Jiang. 2019. Does evolutionary history determine specificity in broad ecological interactions? Journal of Ecology 107:1582-1593.
  22. Pashirzad, M., H. Ejtehadi, J. Vaezi, and R.P. Shefferson. 2019. Plant-plant interactions influence phylogenetic diversity at multiple spatial scales in a semi-arid mountain rangeland. Oecologia 189:745-755.
  23. Hurskainen, S., K. Alahuhta, H. Hens, A. Jäkäläniemi, T. Kull, R.P. Shefferson, and J. Tuomi. 2018. Prolonged dormancy in orchids incurs absolute and relative costs in large, but not in small plants. Botanical Journal of the Linnean Society 188:426-437.
  24. Pashirzad, M., H. Ejtehadi, J. Vaezi, and R.P. Shefferson. 2018. Spatial scale-dependent phylogenetic signal in species distributions along geographic and elevation gradients in a mountainous rangeland. Ecology & Evolution 8:10364-10373.
  25. Unruh, S.A., M.R. McKain, Y.-I. Lee, T. Yukawa, M. McCormick, R.P. Shefferson, P. Linder, A. Smithson, J. Leebens-Mack, and J.C. Pires. 2018. Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae). American Journal of Botany 105:631-640.
  26. Shefferson, R.P., C.M. Mason, K.M. Kellett, E.W. Goolsby, E. Coughlin, and R.W. Flynn. 2018. The evolutionary impacts of conservation actions. Population Ecology 60:49-59.
  27. Kellett, K.M. and R.P. Shefferson. 2018. Temporal variation in reproductive costs and payoffs shapes the flowering strategy of a Neotropical milkweed, Asclepias curassavica. Population Ecology 60:77-87.
  28. Shefferson, R.P., T. Kull, M.J. Hutchings, K.M. Kellett, E.S. Menges, R.B. Primack, K. Alahuhta, S. Hurskainen, H.M. Alexander, D.S. Anderson, R. Brys, E. Brzosko, S. Dostálik, K. Gregg, Z. Ipser, H. Jacquemyn, A. Jäkäläniemi, J. Jersáková, W.D. Kettle, M. McCormick, A. Mendoza, M.T. Miller, A. Moen, D.-I. Øien, Püttsepp, M. Roy, N. Sather, M.-A. Selosse, N. Sletvold, Z. Stipkova, K. Tali, J. Tuomi, R.J. Warren II, and D.F. Whigham. 2018. Drivers and characteristics of vegetative dormancy across herbaceous perennial plant species. Ecology Letters 21:724-733.
  29. Ulyshen, M.D., R.P. Shefferson, S. Horn, M.K. Taylor, B. Bush, C. Brownie, S. Seibold, and M.S. Strickland. 2017. Below- and above-ground effects of deadwood and termites in plantation forests. Ecosphere 8:e01910.
  30. Shefferson, R.P., R. Mizuta, and M.J. Hutchings. 2017. The evolution of sprouting probability in response to climate change in three dormancy-prone orchid species. Royal Society Open Science 4:160647.
  31. Kull, T., U. Selgis, M.V. Peciña, M. Metsare, A. Ilves, K. Tali, K. Sepp, K. Kull, and R.P. Shefferson. 2016. Factors IUCN threat levels to orchids across Europe on the basis of national red lists. Ecology & Evolution 6:6245-6265.
  32. Shefferson, R.P., M. Roy, U. Puttsepp, and M.-A. Selosse. 2016. Demographic shifts related to mycoheterotrophy and their fitness impacts in two Cephalanthera species. Ecology 97:1452-1462.
  33. Goolsby, E.W. 2015. Pyhlogenetic comparative methods for evaluating the evoluationary history of function-valued traits. Systematic Biology 64:568-578.
  34. Shefferson, R.P., R.J. Warren II, and H.R. Pulliam. 2014. Life history costs make perfect sprouting maladaptive in two herbaceous perennials. Journal of Ecology 102:1318-1328. (In the news)
  35. Kartzinel, T.R., R.P. Shefferson, and D.W. Trapnell. 2013. Relative importance of pollen and seed dispersal across a Neotropical mountain landscape for an epiphytic orchid. Molecular Ecology 22:6048-6059.
  36. Kartzinel, T.R., D.W. Trapnell, and R.P. Shefferson. 2013. Highly diverse and variable mycorrhizal symbiosis in a rare epiphyte is unrelated to broad biogeographic or environmental features. Molecular Ecology 22:5949-5961.
  37. Bunch, W.D., C.C. Cowden, N. Wurzburger, and R.P. Shefferson. 2013. Geography and soil nutrients drive the distribution of fungal associations in a lady’s slipper orchid, Cypripedium acaule. Botany (formerly Canadian Journal of Botany) 91:850-856.
  38. Kartzinel, T.R., D.W. Trapnell, and R.P. Shefferson. 2013. Critical importance of large native trees for conservation of a rare Neotropical epiphyte. Journal of Ecology 101:1429-1438.
  39. Cowden, C.C. and R.P. Shefferson. 2013. Diversity of root-associated fungi of mature Habenaria radiata and Epipactis thunbergii colonizing manmade wetlands in Hiroshima Prefecture, Japan. Mycoscience 54:327-334.
  40. Shefferson, R.P. and D.A. Roach. 2013. Longitudinal analysis in Plantago: strength of selection and reverse age analysis reveal age-indeterminate senescence. Journal of Ecology 101:577-584.
  41. Shefferson, R.P., T. Kull, K. Tali, and K.M. Kellett. 2012. Linking vegetative dormancy to fitness in two long-lived herbaceous perennials. Ecosphere 3:13.
  42. Shefferson, R.P. and D.A. Roach. 2012. The triple helix of Plantago lanceolata: genetics and the environment interact to determine population dynamics. Ecology 93:793-802.
  43. Brys, R., R.P. Shefferson, and H. Jacquemyn. 2011. Impact of intrinsic and extrinsic variables on flowering and reproductive allocation patterns in a perennial iteroparous grassland herb: a ten-year experiment. Oecologia 166:293-303.
  44. Shefferson, R.P., M.K. McCormick, D.F. Whigham, and J.P. O’Neill. 2011. Life history strategy in herbaceous perennials: inferring demographic patterns from aboveground dynamics of a primarily subterranean, myco-heterotrophic orchid. Oikos 120:1291-1300.
  45. Shefferson, R.P., C.C. Cowden, M.K. McCormick, T. Yukawa, Y. Ogura-Tsujita, and T. Hashimoto. 2010. Evolution of host breadth in broad interactions: mycorrhizal specificity in East Asian and North American rattlesnake plantains (Goodyera spp.) and their fungal hosts. Molecular Ecology 19:3008-3017.
  46. Shefferson, R.P. and D.A. Roach. 2010. Longitudinal analysis of Plantago: adaptive benefits of iteroparity in a short-lived, herbaceous perennial. Ecology 91:441-447.
  47. Yukawa, T., Y. Ogura-Tsujita, R.P. Shefferson, and J. Yokoyama. 2009. Mycorrhizal diversity in Apostasia (Orchidaceae) indicates the origin and evolution of the orchid mycorrhiza. American Journal of Botany 96: 1997-2009.
  48. Mesipuu, M., R.P. Shefferson, and T. Kull. 2009. Weather and herbivores influence fertility in the endangered fern Botrychium multifidum (S.G. Gmel.) Rupr. Plant Ecology 203:23-31.
  49. Shefferson, R.P., T. Kull, and K. Tali. 2008. Mycorrhizal interactions of orchids colonizing Estonian mine tailings hills. American Journal of Botany 95:156-164.
  50. Shefferson, R.P., D.L. Taylor, M. Weiß, S. Garnica, M.K. McCormick, S. Adams, H.M. Gray, J.W. McFarland, T. Kull, K. Tali, T. Yukawa, T. Kawahara, K. Miyoshi, and Y.-I. Lee. 2007. The evolutionary history of mycorrhizal specificity among lady’s slipper orchids. Evolution 61:1380-1390.
  51. Shefferson, R.P. and E. L. Simms. 2007. Costs and benefits of fruiting to future reproduction in two dormancy-prone orchids. Journal of Ecology 95:865-875.
  52. Shefferson, R.P. and K. Tali. 2007. Dormancy is associated with decreased adult survival in the burnt orchid, Neotinea ustulata. Journal of Ecology 95:217-225.
  53. Shefferson, R.P. 2006. Survival costs of adult dormancy and the confounding influence of size in lady’s slipper orchids, genus Cypripedium. Oikos 115:253-262.
  54. Simms, E.L., D.L. Taylor, J. Povich, R.P. Shefferson, M. Urbina, and Y. Tauszick. 2006. An empirical test of partner choice mechanisms in a legume-rhizobium interaction. Proceedings of the Royal Society of London Series B, Biological Sciences 273:77-81.
  55. Shefferson, R.P., T. Kull, and K. Tali. 2006. Demographic response to shading and defoliation in two woodland orchids. Folia Geobotanica 41:95-106.
  56. Shefferson, R.P., M. Weiß, T. Kull, and D.L. Taylor. 2005. High specificity generally characterizes mycorrhizal association in rare lady’s slipper orchids, genus Cypripedium. Molecular Ecology 14:613-626.
  57. Shefferson, R.P., T. Kull, and K. Tali. 2005. Adult whole-plant dormancy induced by stress in long-lived orchids. Ecology 86:3099-3104.
  58. Bruns, T. and R.P. Shefferson. 2004. Evolutionary studies of ectomycorrhizal fungi: milestones and future directions. Canadian Journal of Botany 82:1122-1132.
  59. Shefferson, R.P., J. Proper, S.R. Beissinger, and E.L. Simms. 2003. Life history trade-offs in a rare orchid: the costs of flowering, dormancy, and sprouting. Ecology 84:1199-1206.
  60. Shefferson, R.P., B. K. Sandercock, J. Proper, and S. R. Beissinger. 2001. Estimating dormancy and survival of a rare herbaceous perennial using mark-recapture models. Ecology 82:145-156.
  61. Book Chapters

  62. Cubaynes, S., S. Galas, M. Richaud, A. Sanz, R. Pradel, G. Tavecchia, F. Colchero, S. Roques, R.P. Shefferson, and C.G. Camarda. In press. Survival analyses. Pages XX-YY in R. Salguero-Gómez and M. Gamelon (eds). Demographic Methods Across the Tree of Life. Oxford University Press.
  63. Cowden, C.C., R.P. Shefferson, and J.E. Mohan. 2019. Mycorrhizal mediation of plant and ecosystem responses to soil warming. Pages 157-174 in J.E. Mohan (ed). Ecosystem consequences of soil warming: microbes, vegetation, fauna and soil biogeochemistry. Academic Press.
  64. Shefferson, R.P., O.R. Jones, and R. Salguero-Gómez. 2017. Introduction: Wilting leaves and rotting branches: reconciling evolutionary perspectives on senescence. Pages 1-20 in Shefferson, R.P., R. Salguero-Gomez, and O. Jones (eds). The Evolution of Senescence in the Tree of Life. Cambridge University Press.
  65. Shefferson, R.P. and C.C. Cowden. 2017. Senescence in the wild: plant-fungal symbioses. Pages 381-400 in Shefferson, R.P., R. Salguero-Gomez, and O. Jones (eds). The Evolution of Senescence in the Tree of Life. Cambridge University Press.
  66. Shefferson, R.P. 2002. Dormancy and survival in rare terrestrial orchids. Pages 53-66 in Kindlmann, P., J.H. Willems, and D.F. Whigham (eds.). Trends and Fluctuations and Underlying Mechanisms In Terrestrial Orchid Populations. Backhuys Publishers, Leiden, The Netherlands.
  67. Special Issues

  68. Shefferson, R.P. 2019. Macroevolutionary perspectives on biotic interactons. Journal of Ecology.
  69. Takada, T. and R.P.Shefferson (eds.). 2018. Evolutionary demography. Population Ecology.
  70. Shefferson, R.P. and R. Salguero-Gomez (eds.). 2015. Eco-evolutionary feedbacks in plants. Journal of Ecology.
  71. Salguero-Gomez, R. and R. P. Shefferson (eds.). 2013. New perspectives in whole-plant senescence. Journal of Ecology 101:3.
  72. Other Articles (General Interest, Public, Magazine Articles, etc.)

  73. Shefferson, R.P. 2013. Introduction to virtual issue: In honour of Michael Hutchings. Journal of Ecology.
  74. Shefferson, R.P. 2013. Living the ecological good life in Kyoto. Kyoto University Center for Ecological Research News 122:3.
  75. Dissertations and Theses

  76. Zha, Xingxia. 2021. The differing life history strategies of two Pyrola japonica population with different heterotrophic levels and their environmental adaptiveness. BS thesis, Program on Environmental Sciences, University of Tokyo, Tokyo, Japan.
  77. Yin, Rui. 2021. The effects of fungal extinctions on the structure of an orchid-mycorrhizal fungi network. BS thesis, Program on Environmental Sciences, University of Tokyo, Tokyo, Japan.
  78. Peros, Colin. 2020. Urbanization increases nodulation in the legume-Rhizobium symbiosis. MS thesis, Graduate Program on Environmental Sciences, University of Tokyo, Tokyo, Japan.
  79. Holton, Eric. 2019. Density and senescence in the native orchid, Cypripedium parviflorum. MS thesis, Graduate Program on Environmental Sciences, University of Tokyo, Tokyo, Japan.
  80. Watanuki, Lei Ann. 2019. Variation in the life history of plant species in response to urban environments. BS thesis, Program on Environmental Sciences, University of Tokyo, Tokyo, Japan.
  81. Goolsby, Eric W. 2016. Evolution of heavy metal hyperaccumulation in wild sunflowers Helianthus. PhD dissertation, Interdisciplinary Program in Toxicology, University of Georgia, Athens, Georgia, USA. 155pp.
  82. Kellett, Kimberly. 2015. Well-seasoned demography: the importance of intra-annual variation in demography to populations of a Neotropical milkweed, Asclepias curassavica. PhD dissertation, Odum School of Ecology, University of Georgia, Athens, Georgia, USA. 97pp.
  83. Coughlin, Erin. 2015. Plant-soil feedbacks of Castanea dentata reintroduction. MS thesis, Odum School of Ecology, University of Georgia, Athens, Georgia, USA.
  84. Kartzinel, Tyler. 2012. The influence of landscape heterogeneity and species interactions on the distribution of an epiphytic orchid and its genetic variation. PhD dissertation, Odum School of Ecology, University of Georgia, Athens, Georgia, USA. 127pp.
  85. Bunch, William. 2012. Geographic and soil nutrient links in the mycorrhizal association of a rare orchid, Cypripedium acaule. MS thesis, Odum School of Ecology, University of Georgia, Athens, Georgia, USA. 30pp.
  86. Shefferson, R.P. 2004. Evolutionary ecology of rare geophytes: dormancy and mycorrhizae in Cypripedium species. PhD dissertation, Department of Integrative Biology, University of California at Berkeley, Berkeley, California, USA. 199pp.
  87. Shefferson, R.P. 2000. Demographic applications of mark-recapture models to populations of rare herbaceous perennials. MS thesis, Range Management Graduate Group, University of California at Berkeley, Berkeley, California, USA. 95pp.

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