Joint Modeling of Climate Niches for Adult and Juvenile Trees

  • Souparno Ghosh
  • Kai Zhu
  • Alan E. Gelfand
  • James S. Clark
Article

Abstract

Typical ecological gradient analysis for plant species considers variation in the response along a gradient of covariate values, for example, temperature or precipitation. Response is customarily modeled through the presence/absence or a suitable measure of abundance or both. Such analysis enables the creation of a climate niche or range limits for the species using this covariate. Interest often extends to two climate covariates, thus seeking a climate niche in two-dimensional space. It also seeks to learn whether the niche changes over life stages of the species. For instance, is the niche for juveniles different from that for adults? Across the climate domain, where are seedlings relatively more or less abundant than adults? Adult abundance is measured through basal area, juvenile abundance through seedling counts. Our contribution is to describe a coherent modeling approach to address the foregoing objectives. We construct a hierarchical stochastic specification that jointly models juveniles and adults with regard to their two-dimensional climate niches. Joint modeling of the abundance response surfaces is proposed because seedlings and adults are living jointly, competitively and is justified through exploratory analysis. Joint modeling can be challenging when one response is counts and the other is area. We model adult abundance and then juvenile abundance driven by adult abundance. Due to excess zeroes over our study plots, we employ zero-inflated models for both adult and seedling abundance. We demonstrate the benefits of the joint modeling through out-of-sample predictive performance. Our abundance data come from the USDA Forest Service’s Forest Inventory and Analysis dataset. Our climate data come from the 800 m resolution Parameter-elevation Regressions on Independent Slopes Model dataset. In order to extract a response to climate, we aggregate FIA plots to ecological subsections. At plot scale, micro-scale covariates explain variation in abundance; at a larger spatial scale, climate covariates can explain variation in abundance.

Keywords

Abundance Basal area Hierarchical model Mean annual precipitation Mean winter temperature Zero-inflated models 

References

  1. Bansal, S., Germino, M. J. (2010), Variation in ecophysiological properties among conifers at an ecotonal boundary: comparison of establishing seedlings and established adults at timberline. Journal of Vegetation Science, 21, 133–142.CrossRefGoogle Scholar
  2. Bell, David T. (1975), Germination of Quercus alba L. following flood conditions. University of Illinois Department of Forestry, Forestry Research Report 75-2. Urbana-Champaign. 3 p.Google Scholar
  3. Bechtold, W.A. and Patterson, P.L. (2005), The enhanced forest inventory and analysis program: National sampling design and estimation procedures. General Technical Report, SRS-80 edn. USDA Forest Service, Southern Research Station, Asheville, NC.Google Scholar
  4. Bertrand, R., Gegout, J.-C. and Bontemps, J.-D. (2011), Niches of temperate tree species converge towards nutrient-richer conditions over ontogeny. Oikos, 120, 1479-1488.CrossRefGoogle Scholar
  5. Bellard C., Bertelsmeier C., Leadley P., Thuiller W., Courchamp F. (2012), Impacts of climate change on the future of biodiversity. Ecology Letters, 15, 365–377.CrossRefGoogle Scholar
  6. Botkin D.B, Saxe H., Araujo M.B, Betts, R., Bradshaw, R. H. W., Cedhagen, T., Cheeson, P. et al. (2007), Forecasting the effects of global warming on biodiversity. BioScience, 57, 227–236.CrossRefGoogle Scholar
  7. Broennimann O., Treier U. A., Muller-Scharer H., Thuiller W., Peterson A. T., Guisan A. (2007), Evidence of climatic niche shift during biological invasion. Ecology Letters, 10, 701–709.CrossRefGoogle Scholar
  8. Butterfield B. J., Briggs J. M. (2011), Regeneration niche differentiates functional strategies of desert woody plant species. Oecologia, 165, 477–487.CrossRefGoogle Scholar
  9. Bykova O., Chuine I., Morin X., Higgins S. I. (2012), Temperature dependence of the reproduction niche and its relevance for plant species distributions. Journal of Biogeography, 39, 2191–2200.CrossRefGoogle Scholar
  10. Canham C.D. and Thomas R.Q. (2010), Frequency, not relative abundance, of temperate tree species varies along climate gradients in eastern North America. Ecology, 91, 3433–3440.CrossRefGoogle Scholar
  11. Cavender-Bares J., Bazzaz F. A. (2000), Changes in drought response strategies with ontogeny in Quercus rubra: implications for scaling from seedlings to mature trees. Oecologia, 124, 8–18.CrossRefGoogle Scholar
  12. Chase, J. M and Leibold, M. A. (2003), Ecological Niches: Linking Classical and Contemporary Approaches. Chicago, IL: University of Chicago Press.CrossRefGoogle Scholar
  13. Cleland, D. T., Avers, P. E., McNab, W. H., Jensen, M. E., Bailey, R. G., King, T. and Russell, W. E. (1997). National hierarchical framework of ecological units. In M. S. Boyce and A. Haney, (eds). Ecosystem Management: Applications for Sustainable Forest and Wildlife Resources. New Haven, CT: Yale University Press, pp-181–200Google Scholar
  14. Collins, R. J. and Carson, W. P. (2004), The effects of environment and life stage on Quercus abundance in the eastern deciduous forest, USA: are sapling densities most responsive to environmental gradients? Forest Ecology Management, 201, 241–258.CrossRefGoogle Scholar
  15. Daly, C., Halbleib, M., Smith, J. I., Gibson, W. P., Doggett, M. K., Taylor, G. H., Curtis, J. and Pasteris. P. P. (2008). Physiographically sensitive mapping of climatological temperature and precipitation across the conterminous United States. International Journal of Climatology, 28, 2031–2064.CrossRefGoogle Scholar
  16. Della-Bianca, L., and Olson, D. F. Jr. (1961), Soil-site studies in Piedmont hardwood and pine-hardwood upland forests. Forest Science, 7, 320–329.Google Scholar
  17. Donovan, L. A, Ehleringer, J. R. (1991), Ecophysiological differences among juvenile and reproductive plants of several woody species. Oecologia, 86, 594–597.CrossRefGoogle Scholar
  18. Elith, J., Leathwick, J. R. (2009), Species distribution models: ecological explanation and prediction across space and time. Annual Review of Ecology, Evolution, and Systematics, 40, 677–697.CrossRefGoogle Scholar
  19. Eriksson, O. (2002), Ontogenetic niche shifts and their implications for recruitment in three clonal Vaccinium shrubs: Vaccinium myrtillus, Vaccinium vitis-idaea, and Vaccinium oxycoccos. Canadian Journal of Botany, 80, 635–641.CrossRefGoogle Scholar
  20. Gallagher, R. V., Beaumont, L. J., Hughes, L., Leishman, M. R. (2010), Evidence for climatic niche and biome shifts between native and novel ranges in plant species introduced to Australia. Journal of Ecology, 98, 790–799.CrossRefGoogle Scholar
  21. Gelman, A., and Rubin, D. (1992). Inference from Iterative Simulation using Multiple Sequences. Statistical Science,7, 547–511Google Scholar
  22. Ghosh, S., Gelfand, A. E., Zhu, K. and Clark, J. S. (2012), The \(k-\)ZIG: Flexible Modeling for Zero-inflated Counts. Biometrics, 68, 878–885.CrossRefMathSciNetMATHGoogle Scholar
  23. Grubb, P. J. (1977) Maintenance of species-richness in plant communities: the importance of the regeneration niche. Biological Reviews of the Cambridge Philosophical Society, 52, 107–145.CrossRefGoogle Scholar
  24. Herault, B., Bachelot, B., Poorter, L., Rossi, V., Bongers, F., Chave, J., Paine, C. E. T., Wagner,F. and Baraloto, C. (2011), Functional traits shape ontogenetic growth trajectories of rain forest tree species. Journal of Ecology, 99, 1431–1440.CrossRefGoogle Scholar
  25. Houter, N. C., Pons, T. L. (2012), Ontogenetic changes in leaf traits of tropical rainforest trees differing in juvenile light requirement. Oecologia, 169, 33–45.CrossRefGoogle Scholar
  26. Ibanez, I., Clark, J. S., Dietze, M. C. (2008), Evaluating the sources of potential migrant species: implications under climate change. Ecological Applications, 18, 1664–1678.CrossRefGoogle Scholar
  27. -------- (2009), Estimating colonization potential of migrant tree species. Global Change Biology, 15, 1173–1188.CrossRefGoogle Scholar
  28. Iverson, L. R., Prasad, A. M. (1998) Predicting abundance of 80 tree species following climate change in the eastern United States. Ecological Monographs, 68, 465–485.CrossRefGoogle Scholar
  29. Keys, J. E., Cleland, D. T. and McNab. W. H. (2007). Delineation, Peer Review, and Refinement of Subregions of the Conterminous United States. General Technical Report, WO-76A edition. USDA Forest Service, Washington, DC.Google Scholar
  30. Kulmatiski, A., Beard, K. H. (2013), Root niche partitioning among grasses, saplings, and trees measured using a tracer technique. Oecologia, 171, 25–37.CrossRefGoogle Scholar
  31. Little, E. L. Jr. (1979). Checklist of United States trees (native and naturalized). U.S. Department of Agriculture, Agriculture Handbook 541. Washington, DC. pp–375.Google Scholar
  32. Martin, T. G., Wintle, B. A., Rhodes, J. R., Kuhnert, P. M., Field, S. A., Low-Choy, S. J., Tyre, A. J. and Possingham, H. P. (2005). Zero tolerance ecology: improving ecological inference by modelling the source of zero observations. Ecology Letters, 8, 1235–1246.CrossRefGoogle Scholar
  33. Maiorano, L., Cheddadi, R., Zimmermann, N. E., Pellissier, N., Petitpierre, B., Pottier, J. et al. (2013), Building the niche through time: using 13,000 years of data to predict the effects of climate change on three tree species in Europe. Global Ecology and Biogeography, 22, 302–317.CrossRefGoogle Scholar
  34. McAlpine, R. G. (1961). Yellow-poplar seedlings intolerant to flooding. Journal of Forestry, 59, 566–568.Google Scholar
  35. McCarthy, E. F. (1933). Yellow-poplar characteristics, growth, and management. U.S. Department of Agriculture, Technical Bulletin 356. Washington, DC. pp–58.Google Scholar
  36. McMahon, S. M., Harrison, S. P., Armbruster, W. S., Bartlein, P. J., Beale, C. M., Edwards, M. E., Kattge, J., Midgley, G., Morin, X.,Prentice, I. C. (2011), Improving assessment and modelling of climate change impacts on global terrestrial biodiversity. Trends in Ecology and Evolution, 26, 249–259.CrossRefGoogle Scholar
  37. McNab, W. H., Cleland, D. T., Freeouf, J. A., Keys, J. E., Nowacki, G. J. and Carpenter, C. A. (2007), Description of “Ecological Subregions: Sections of the Conterminous United States”. General Technical Report, WO-76B edition. USDA Forest Service, Washington, DC.Google Scholar
  38. Minckler, L. S. (1965), White oak (Quercus alba L.). In H. A. Fowells (comp.) Silvics of forest trees of the United States. Washington, DC: U.S. Department of Agriculture, Agriculture Handbook 271. pp-632–637.Google Scholar
  39. Miriti, M. N. (2006). Ontogenetic shift from facilitation to competition in a desert shrub. Journal of Ecology, 94, 973–979.CrossRefGoogle Scholar
  40. Palow, D. T, Nolting, K., Kitajima, K. (2012), Functional trait divergence of juveniles and adults of nine Inga species with contrasting soil preference in a tropical rain forest. Functional Ecology, 26, 1144–1152.CrossRefGoogle Scholar
  41. Parrish, J. A. D. and Bazzaz, F. A. (1985). Ontogenetic niche shifts in old-field annuals.Ecology, 66, 1296–1302.CrossRefGoogle Scholar
  42. Pearman, P. B., Guisan, A., Broennimann, O., Randin, C. F. (2008), Niche dynamics in space and time. Trends in Ecology and Evolution, 23, 149–158.CrossRefGoogle Scholar
  43. Peterson, A. T. (2011), Ecological niche conservatism: a time-structured review of evidence. Journal of Biogeography, 38, 817–827.CrossRefGoogle Scholar
  44. Petitpierre, B., Kueffer, C., Broennimann, O., Randin, C., Daehler, C., Guisan, A. (2012) Climatic niche shifts are rare among terrestrial plant invaders. Science, 335, 1344–1348.CrossRefGoogle Scholar
  45. Poorter, L. (1999), Growth responses of 15 rain-forest tree species to a light gradient: the relative importance of morphological and physiological traits. Functional Ecology, 13, 396–410.CrossRefGoogle Scholar
  46. Pyrke, A. F. and Kirkpatrick, J. B. (1994). Growth rate and basal area response curves of four Eucalyptus species on Mt. Wellington, Tasmania. Journal of Vegetation Science, 5, 13–24.CrossRefGoogle Scholar
  47. Quero, J. L, Gomez-Aparicioa, L., Zamoraa, R. and Maestre, F. T. (2008), Shifts in the regeneration niche of an endangered tree (Acer opalus ssp. granatense) during ontogeny: Using an ecological concept for application. Basic and Applied Ecology, 9, 635–644.CrossRefGoogle Scholar
  48. Smith, W.B., Miles, P.D., Perry, C.H. and Pugh, S.A. (2009), Forest resources of the United States, 2007. General Technical Report, WO-78 edn. USDA Forest Service, Washington Office, Washington, DC.Google Scholar
  49. Stohlgren, T. J., Bachand, R. R., Onami, Y., Binkley, D. (1998), Species-environment relationships and vegetation patterns: effects of spatial scale and tree life-stage. Plant Ecology, 135, 215–228.CrossRefGoogle Scholar
  50. Thomas, S. C., Winner, W. E. (2002), Photosynthetic differences between saplings and adult trees: an integration of field results by meta-analysis. Tree Physiology, 22, 117–127.CrossRefGoogle Scholar
  51. Urbieta, I. R., Garcia, L. V., Zavala, M. A., Maranon, T. (2011), Mediterranean pine and oak distribution in southern Spain: is there a mismatch between regeneration and adult distribution? Journal of Vegetation Science, 22, 18–31.CrossRefGoogle Scholar
  52. Warren, R. J., Bradford, M. A. (2011) The shape of things to come: woodland herb niche contraction begins during recruitment in mesic forest microhabitat. Proceedings of the Royal Society B: Biological Sciences, 278, 1390–1398.CrossRefGoogle Scholar
  53. Werner, E. E. and Gilliam, J. F. (1984), The ontogenetic niche and species interactions in size structured populations. Annual Review Of Ecology And Systematics,15, 393–425.CrossRefGoogle Scholar
  54. Wiens, J. J., Graham, C. H. (2005), Niche conservatism: integrating evolution, ecology, and conservation biology. Annual Review of Ecology, Evolution, and Systematics, 36, 519–539.CrossRefGoogle Scholar
  55. Wiens, J. J., Ackerly, D. D., Allen, A. P., Anacker, B. L., Buckley, L. B., Cornell, H. V., Damschen, E. I., Jonathan Davies, T., Grytnes, J. A., Harrison, S. P., Hawkins, B. A., Holt, R. D., McCain, C. M., and Stephens, P. R. (2010), Niche conservatism as an emerging principle in ecology and conservation biology. Ecology Letters, 13, 1310–1324.CrossRefGoogle Scholar
  56. Yang, L. H., Rudolf, V. H. W. (2010) Phenology, ontogeny and the effects of climate change on the timing of species interactions. Ecology Letters, 13, 1–10.CrossRefMATHGoogle Scholar
  57. Young, T.P., Petersen, D.A. and Clary, J.J. (2005). The ecology of restoration: historical links, emerging issues and unexplored realms. Ecology Letters, 8, 662–673.CrossRefGoogle Scholar
  58. Zhu, K., Woodall, C. W., Ghosh, S., Gelfand, A. E., Clark, J. S. (2014), Dual impacts of climate change: forest migration and turnover through life history. Global Change Biology, 20, 251–264.CrossRefGoogle Scholar

Copyright information

© International Biometric Society 2015

Authors and Affiliations

  • Souparno Ghosh
    • 1
  • Kai Zhu
    • 2
    • 3
    • 4
  • Alan E. Gelfand
    • 5
  • James S. Clark
    • 2
  1. 1. Department of Mathematics & StatisticsTexas Tech UniversityLubbockUSA
  2. 2. Nicholas School of the EnvironmentDuke UniversityDurhamUSA
  3. 3.Department of Global EcologyCarnegie Institution for ScienceStanfordUSA
  4. 4.Department of BiologyStanford UniversityStanfordUSA
  5. 5. Department of Statistical ScienceDuke UniversityDurhamUSA

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