Journal Home > Volume 5 , Issue 1
Background

Knowledge of the different kinds of tree communities that currently exist can provide a baseline for assessing the ecological attributes of forests and monitoring future changes. Forest inventory data can facilitate the development of this baseline knowledge across broad extents, but they first must be classified into forest community types. Here, we compared three alternative classifications across the United States using data from over 117, 000 U.S. Department of Agriculture Forest Service Forest Inventory and Analysis (FIA) plots.

Methods

Each plot had three forest community type labels: (1) "FIA" types were assigned by the FIA program using a supervised method; (2) "USNVC" types were assigned via a key based on the U.S. National Vegetation Classification; (3) "empirical" types resulted from unsupervised clustering of tree species information. We assessed the degree to which analog classes occurred among classifications, compared indicator species values, and used random forest models to determine how well the classifications could be predicted using environmental variables.

Results

The classifications generated groups of classes that had broadly similar distributions, but often there was no one-to-one analog across the classifications. The longleaf pine forest community type stood out as the exception: it was the only class with strong analogs across all classifications. Analogs were most lacking for forest community types with species that occurred across a range of geographic and environmental conditions, such as loblolly pine types. Indicator species metrics were generally high for the USNVC, suggesting that USNVC classes are floristically well-defined. The empirical classification was best predicted by environmental variables. The most important predictors differed slightly but were broadly similar across all classifications, and included slope, amount of forest in the surrounding landscape, average minimum temperature, and other climate variables.

Conclusions

The classifications have similarities and differences that reflect their differing approaches and objectives. They are most consistent for forest community types that occur in a relatively narrow range of environmental conditions, and differ most for types with wide-ranging tree species. Environmental variables at a variety of scales were important for predicting all classifications, though strongest for the empirical and FIA, suggesting that each is useful for studying how forest communities respond to of multi-scale environmental processes, including global change drivers.


menu
Abstract
Full text
Outline
About this article

Classifying forest inventory data into species-based forest community types at broad extents: exploring tradeoffs among supervised and unsupervised approaches

Show Author's information Jennifer K. Costanza1( )Don Faber-Langendoen2John W. Coulston3David N. Wear4
Department of Forestry and Environmental Resources, North Carolina State University, 3041 Cornwallis Rd., Research Triangle Park, Raleigh, NC 27709, USA
NatureServe, 4600 N. Fairfax Dr., 7th Floor, Arlington, VA 22203, USA
Southern Research Station, USDA Forest Service, Blacksburg, VA, USA
Southern Research Station, USDA Forest Service, Raleigh, NC, USA

Abstract

Background

Knowledge of the different kinds of tree communities that currently exist can provide a baseline for assessing the ecological attributes of forests and monitoring future changes. Forest inventory data can facilitate the development of this baseline knowledge across broad extents, but they first must be classified into forest community types. Here, we compared three alternative classifications across the United States using data from over 117, 000 U.S. Department of Agriculture Forest Service Forest Inventory and Analysis (FIA) plots.

Methods

Each plot had three forest community type labels: (1) "FIA" types were assigned by the FIA program using a supervised method; (2) "USNVC" types were assigned via a key based on the U.S. National Vegetation Classification; (3) "empirical" types resulted from unsupervised clustering of tree species information. We assessed the degree to which analog classes occurred among classifications, compared indicator species values, and used random forest models to determine how well the classifications could be predicted using environmental variables.

Results

The classifications generated groups of classes that had broadly similar distributions, but often there was no one-to-one analog across the classifications. The longleaf pine forest community type stood out as the exception: it was the only class with strong analogs across all classifications. Analogs were most lacking for forest community types with species that occurred across a range of geographic and environmental conditions, such as loblolly pine types. Indicator species metrics were generally high for the USNVC, suggesting that USNVC classes are floristically well-defined. The empirical classification was best predicted by environmental variables. The most important predictors differed slightly but were broadly similar across all classifications, and included slope, amount of forest in the surrounding landscape, average minimum temperature, and other climate variables.

Conclusions

The classifications have similarities and differences that reflect their differing approaches and objectives. They are most consistent for forest community types that occur in a relatively narrow range of environmental conditions, and differ most for types with wide-ranging tree species. Environmental variables at a variety of scales were important for predicting all classifications, though strongest for the empirical and FIA, suggesting that each is useful for studying how forest communities respond to of multi-scale environmental processes, including global change drivers.

Keywords: Big data, Correspondence analysis, Dominant species, Forest communities, Global change, Hierarchical classification, Indicator species, Random forests, Species assemblages

References(80)

Abatzoglou JT (2013) Development of gridded surface meteorological data for ecological applications and modelling. Int J Climatol 33(1):121-131. https://doi.org/10.1002/joc.3413

Arner SL, Woudenberg S, Waters S, Vissage J, Maclean C, Thompson M, Hansen M (2003) National Algorithms for Determining Stocking Class, Stand Size Class, and Forest Type for Forest Inventory and Analysis Plots. http://www.fia.fs.fed.us/library/field-guides-methods-proc/docs/National%20algorithms.doc. Accessed 15 Jan 2015

Bechtold WA, Patterson PL (2005) The enhanced Forest inventory and analysis program - National Sampling Design and estimation procedures. USDA Gen Tech Rep SRS 80:85

Belote RT, Dietz MS, Jenkins CN, McKinley PS, Irwin GH, Fullman TJ, Leppi JC, Aplet GH (2017) Wild, connected, and diverse: building a more resilient system of protected areas. Ecol Appl 27(4):1050-1056

Brandt LA, Butler PR, Handler SD, Janowiak MK, Shannon PD, Swanston CW (2017) Integrating science and management to assess Forest ecosystem vulnerability to climate change. J Forest 115(3):212-221. https://doi.org/10.5849/jof.15-147

Breiman L (2001) Random forests. Mach Learn 45(1):5-32. https://doi.org/10.1023/A:1010933404324

Burns RM, Honkala BH (1990) Silvics of North America: volume 1. Conifers. Agriculture Handbook 654, USDA Forest Service, Washington, p 877

Caldwell PV, Miniat CF, Elliott KJ, Swank WT, Brantley ST, Laseter SH (2016) Declining water yield from forested mountain watersheds in response to climate change and forest mesophication. Glob Chang Biol 22(9):2997-3012. https://doi.org/10.1111/gcb.13309

Cohen J (1960) A coefficient of agreement for norminal scales. Educ Psychol Meas XX:37-46

Costanza JK, Coulston JW, Wear DN (2017) An empirical, hierarchical typology of tree species assemblages for assessing forest dynamics under global change scenarios. PLoS One 12(9):e0184062. https://doi.org/10.1371/%20journal.pone.0184062

Cutler A, Cutler DR, Stevens JR (2012) Random forests. In: Zhang C, Ma Y (eds) Ensemble machine learning: methods and applications. Springer, New York, pp 157-175https://doi.org/10.1007/978-1-4419-9326-7_5
DOI

Cutler DR, Edwards TC, Beard KH, Cutler A, Hess KT, Gibson J, Lawler JJ (2007) Random forests for classification in ecology. Ecology 88(1):2783-2792. https://doi.org/10.1890/07-0539.1

Dengler J, Jansen F, Glöckler F, Peet RK, Cáceres MD, Chytrý M, Ewald J, Oldeland J, Lopez-Gonzalez G, Finckh M, Mucina L, Rodwell JS, Schaminée JHJ, Spencer N (2011) The global index of vegetation-plot databases (GIVD): a new resource for vegetation science. J Veg Sci 22(4):582-597. https://doi.org/10.1111/j.1654-1103.2011.01265.x

DeSantis RD, Moser WK, Li RH, Wear DN, Miles PD (2013) Modeling the effects of emerald ash borer on forest composition in the Midwest and Northeast United States. USDA For Serv Gen Tech Rep NRS-112, North Res Station. pp 1-28https://doi.org/10.2737/NRS-GTR-112
DOI

Dufrene M, Legendre P (1997) Species Assamblages and indicator species: the need for a flexible Asymetrical approach. Ecol Monogr 67:345-366

Duveneck MJ, Thompson JR, Wilson BT (2015) An imputed forest composition map for New England screened by species range boundaries. Forest Ecol Manag 347:107-115

Evans JS, Murphy MA, Holden ZA, Cushman SA (2011) Modeling species distribution and change using random Forest. In: Drew CA, Wiersma YF, Huettmann F (eds) Predictive species and habitat modeling in landscape ecology: concepts and applications. Springer Science+Business Media, New York, pp 139-159https://doi.org/10.1007/978-1-4419-7390-0_8
DOI
Eyre FH (1980) Forest cover types of the United States and Canada. Society of American Foresters, Washington

Faber-Langendoen D, Keeler-Wolf T, Meidinger D, Tart D, Hoagland B, Josse C, Navarro G, Ponomarenko S, Saucier JP, Weakley A, Comer P (2014) EcoVeg: a new approach to vegetation description and classification. Ecol Monogr 84:533-561. https://doi.org/10.1890/13-2334.1

Fei SL, Desprez JM, Potter KM, Jo I, Knott JA, Oswalt CM (2017) Divergence of species responses to climate change. Sci Adv 3(5):e1603055. https://doi.org/10.1126/sciadv.1603055

FGDC (2008) National Vegetation Classification Standard, version 2 FGDC-STD-005-2008. Federal Geographic Data Committee. Reston, Virginia, USA, pp 55 (+ Appendices). Available at: https://www.fgdc.gov/standards/projects/FGDC-standards-projects/vegetation/NVCS_V2_FINAL_2008-02.pdf Accessed 19 Dec 2017
Fralish JS (2004) The keystone role of oak and hickory in the central hardwood forest. Asheville, NC: U.S. Department of Agriculture, Forest Service, Southern Research Station. Gen Tech Rep SRS-73: 78-87

Franklin J, Serra-Diaz JM, Syphard AD, Regan HM (2017) Big data for forecasting the impacts of global change on plant communities. Glob Ecol Biogeogr 26:6-17. https://doi.org/10.1111/geb.12501

Franklin S, Comer P, Evens J, Ezcurra E, Faber-Langendoen D, Franklin J, Jennings M, Josse C, Lea C, Loucks O, Muldavin E, Peet R, Ponomarenko S, Roberts D, Solomeshch A, Keeler-Wolf T, Kley JV, Weakley A, McKerrow A, Burke M, Spurrier C (2015) How a national vegetation classification can help ecological research and management. Front Ecol Environ 13(4):185-186. https://doi.org/10.1890/15.WB.006

Frieswyk CB, Johnston CA, Zedler JB (2007) Identifying and characterizing dominant plants as an indicator of community condition. J Great Lakes Res 33(sp3):125-135. https://doi.org/10.3394/0380-1330(2007)33

Frost CC (2006) History and future of the longleaf pine ecosystem. In: Jose S, Jokela E, Miller D (eds) The longleaf pine ecosystems: ecology, management, and restoration. Springer, New York, pp 9-48https://doi.org/10.1007/978-0-387-30687-2_2
DOI
Gamer M, Lemon J, Fellows I, Singh P (2012) Irr: various coefficients of Interrater reliability and agreement. R package version 0.84. https://CRAN.R-project.org/package=irr. Accessed 30 Aug 2017

Gesch D, Oimoen M, Greenlee S, Nelson C, Steuck M, Tyle D (2002) The National Elevation Dataset. Photogramm Eng Rem S 68:5-11

Greenacre M (2013) The contributions of rare objects in correspondence analysis. Ecology 94(1):241-249. https://doi.org/10.1890/11-1730.1

Hak JC, Comer PJ (2017) Modeling landscape condition for biodiversity assessment-application in temperate North America. Ecol Indic 82:206-216. https://doi.org/10.1016/j.ecolind.2017.06.049

Hanberry BB (2013) Changing eastern broadleaf, southern mixed, and northern mixed forest ecosystems of the eastern United States. Forest Ecol Manag 306:171-178. https://doi.org/10.1016/j.foreco.2013.06.040

Healey SP, Raymond CL, Blakey Lockman I, Hernandez AJ, Garrard C, Huang CQ (2016) Root disease can rival fire and harvest in reducing forest carbon storage. Ecosphere 7(11):e01569. https://doi.org/10.1002/ecs2.1569

Heffernan JB, Soranno PA, Angilletta MJ, Buckley LB, Gruner DS, Keitt TH, Kellner JR, Kominoski JS, Rocha AV, Xiao JF, Harms TK, Goring SJ, Koenig LE, McDowell WH, Powell H, Richardson AD, Stow CA, Vargas R, Weathers KC (2014) Macrosystems ecology: understanding ecological patterns and processes at continental scales. Front Ecol Environ 12(1):5-14. https://doi.org/10.1890/130017

Hiers JK, Walters JR, Mitchell RJ, Varner JM, Conner LM, Blanc LA, Stowe J (2014) Ecological value of retaining pyrophytic oaks in longleaf pine ecosystems. J wildlife. Manage 78(3):383-393

Hijmans RJ (2016) Raster: geographic data analysis and modeling. R package version 2.5-8. https://CRAN.R-project.org/package=raster. Accessed 1 June 2017

Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. Int J Climatol 25(15):1965-1978

Hildebrand H, Bennet DM, Cadotte MW (2008) Consequences of dominance: a review of evenness effects on local and regional ecosystem processes. Ecology 89(6):1510-1520

Hoagland B (2000) The vegetation of Oklahoma : a classification for landscape mapping and conservation planning. Southwest Nat 45:385-420

Homer C, Dewitz J, Yang LM, Jin SM, Danielson P, Xian G, Coulston J, Herold N, Wickham J, Megown K (2015) Completion of the 2011 National Land Cover Database for the conterminous United States-representing a decade of land cover change information. Photogramm Eng Rem S 81(5):345-354

Iverson LR, Prasad AM (2001) Potential changes in tree species richness and Forest Community types following climate change. Ecosystems 4(3):186-199. https://doi.org/10.1007/s10021-001-0003-6

Iverson LR, Prasad AM, Matthews SN, Peters M (2008) Estimating potential habitat for 134 eastern US tree species under six climate scenarios. Forest Ecol Manag 254:390-406. https://doi.org/10.1016/j.foreco.2007.07.023

Kardol P, Campany CE, Souza L, Norby RJ, Weltzin JF, Classen AT (2010) Climate change effects on plant biomass alter dominance patterns and community evenness in an experimental old-field ecosystem. Glob Chang Biol 16(10):2676-2687. https://doi.org/10.1111/j.1365-2486.2010.02162.x

Kassambara A, Mundt F (2017) Factoextra: extract and visualize the results of multivariate data analyses. R package version 1.0.4
Koch FH, Coulston JW (2015) One-year (2013), three-year (2011-2013), and five-year (2009-2013) drought maps for the conterminous United States. In: Potter KM, Conkling BL (eds) Forest health monitoring: National Status, trends, and analysis 2014. Gen. Tech. Rep. SRS-GTR-209. US Department of Agriculture, Forest Service, Southern Research Station, Asheville, pp 57-71

Le Roux PC, Pellissier L, Wisz MS, Luoto M (2014) Incorporating dominant species as proxies for biotic interactions strengthens plant community models. J Ecol 102(3):767-775. https://doi.org/10.1111/1365-2745.12239

Levine JM, Bascompte J, Adler PB, Allesina S (2017) Beyond pairwise mechanisms of species coexistence in complex communities. Nature 546:56-64. https://doi.org/10.1038/nature22898

Liang JJ, Crowther TW, Picard N, Wiser S, Zhou M, Alberti G, Schulze ED, McGuire AD, Bozzato F, Pretzsch H, de-Miguel S, Paquette A, Herault B, Scherer-Lorenzen M, Barrett CB, Glick HB, Hengeveld GM, Nabuurs GJ, Pfautsch S, Viana H, Vibrans AC, Ammer C, Schall P, Verbyla D, Tchebakova N, Fischer M, Watson JV, HYH C, Lei XD, Schelhaas MJ, Lu HC, Gianelle D, Parfenova EI, Salas C, Lee E, Lee B, Kim HS, Bruelheide H, Coomes DA, Piotto D, Sunderland T, Schmid B, Gourlet-Fleury S, Sonke B, Tavani R, Zhu J, Brandl S, Vayreda J, Kitahara F, Searle EB, Neldner VJ, Ngugi MR, Baraloto C, Frizzera L, Balazy R, Oleksyn J, Zawila-Niedzwiecki T, Bouriaud O, Bussotti F, Finer L, Jaroszewicz B, Jucker T, Valladares F, Jagodzinski AM, Peri PL, Gonmadje C, Marthy W, O'Brien T, Martin EH, Marshall AR, Rovero F, Bitariho R, Niklaus PA, Alvarez-Loayza P, Chamuya N, Valencia R, Mortier F, Wortel V, Engone-Obiang NL, Ferreira LV, Odeke DE, Vasquez RM, Lewis SL, Reich PB (2016) Positive biodiversity-productivity relationship predominant in global forests. Science 354: aaf8957-1-aaf8957-12. https://doi.org/10.1126/science.aaf8957

Liaw A, Wiener M (2002) Classification and regression by randomForest. R News 2:18-22

Matthews ER, Peet RK, Weakley AS (2011) Classification and description of alluvial plant communities of the piedmont region, North Carolina, USA. Appl Veg Sci 14:485-505

McCune B, Grace JB (2002) Analysis of ecological communities. MjM Software Design, Gleneden Beach

McGill BJ (2010) Matters of scale. Science 328:575-576. https://doi.org/10.1126/science.1188528

Menard S, Faber-Langendoen D, Nelson M (2017) Integrating the U.S. National Vegetation Classification in the U.S. Forest Service FIA Program. Report prepared for USFS-FIA program, Arlington, p 104

Nenadic O, Greenacre M (2007) Correspondence analysis in R, with two- and three-dimensional graphics: the ca package. J Stat Softw 20(3):48202. https://doi.org/10.18637/jss.v020.i03

Neuwirth E (2014) RColorBrewer: ColorBrewer palettes. R package version 1:1-2

Nowacki GJ, Abrams MD (2008) The demise of fire and "mesophication" of forests in the eastern United States. Bioscience 58(2):123-138

O'Connell BM, Conkling BL, Wilson AM, Burrill EA, Turner JA, Pugh SA, Christensen G, Ridley T, Menlove J (2016) The Forest inventory and analysis database: database description and user guide for phase 2 (version 6.1). US Department of Agriculture Forest Service, Washington, DC, USA.https://doi.org/10.2737/FS-FIADB-P2-6.1
DOI
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H (2016) Vegan: community ecology package. R package version 2.4-0. https://CRAN.R-project.org/package=vegan. Accessed 1 July 2017

Palmquist KA, Peet RK, Weakley AS (2014) Changes in plant species richness following reduced fire frequency and drought in one of the most species-rich savannas in North America. J Veg Sci 25(6):1426-1437. https://doi.org/10.1111/jvs.12186

Peet R, Lee M, Jennings M, Faber-Langendoen D (2012) VegBank - a permanent, open-access archive for vegetation-plot data. Biodivers Ecol 4:233-241. https://doi.org/10.7809/b-e.00080

Prasad AM, Iverson LR, Liaw A (2006) Newer classification and regression tree techniques: bagging and random forests for ecological prediction. Ecosystems 9:181-199. https://doi.org/10.1007/s10021-005-0054-1

R Core Team (2017) R: A Language and Environment for Statistical Computing. https://www.r-project.org/ Accessed 10 Aug 2017

Riitters KH, Wickham JD (2012) Decline of forest interior conditions in the conterminous United States. Sci Rep 2:653. https://doi.org/10.1038/srep00653

Roberts DW (2016) Labdsv: ordination and multivariate analysis for ecology. R package version 1.8-0. https://CRAN.R-project.org/package=labdsv. Accessed 15 June 2017

Rogers BM, Jantz P, Goetz SJ (2017) Vulnerability of eastern US tree species to climate change. Glob Chang Biol 23(8):3302-3320. https://doi.org/10.1111/gcb.13585

Rose KC, Graves RA, Hansen WD, Harvey BJ, Qiu JX, Wood SA, Ziter C, Turner MG (2016) Historical foundations and future directions in macrosystems ecology. Ecol Lett 20(2):147-157. https://doi.org/10.1111/ele.12717

Ruefenacht B, Finco MV, Nelson MD, Czaplewski R, Helmer EH, Blackard JA, Holden GR, Lister AJ, Salajanu D, Weyermann D, Winterberger K (2008) Conterminous U.S. and Alaska Forest type mapping using Forest inventory and analysis data. Photogramm Eng Rem S 74(11):1379-1388. https://doi.org/10.14358/PERS.74.11.1379

Schaetzl RJ, Krist FJ, Miller BA (2012) A taxonomically based ordinal estimate of soil productivity for landscape-scale analyses. Soil Sci 177(4):288-299. https://doi.org/10.1097/SS.0b013e3182446c88

Schaetzl RJ, Krist FJ, Stanley K, Hupy CM (2009) The natural soil drainage index: an ordinal estimate of long-term soil wetness. Phys Geogr 30(5):383-409. https://doi.org/10.2747/0272-3646.30.5.383

Shmida A, Wilson MV (1985) Biological determinants of species diversity. J Biogeogr 12:1-20. https://doi.org/10.2307/2845026

Smith WB (2002) Forest inventory and analysis: a national inventory and monitoring program. Environ Pollut 116:S233-S242. https://doi.org/10.1016/S0269-7491(01)00255-X

Soil Survey Staff (2017a) The gridded soil survey geographic (gSSURGO) database. United States Department of Agriculture, Natural Resources Conservation Service. https://gdg.sc.egov.usda.gov/. Accessed 15 Mar 2017
Soil Survey Staff (2017b) Soil survey geographic (STATSGO2) database. United States Department of Agriculture, Natural Resources Conservation Service. https://sdmdataaccess.sc.egov.usda.gov. Accessed 15 Mar 2017

Sork VL, Davis FW, Westfall R, Flint A, Ikegami M, Wang HF, Grivet D (2010) Gene movement and genetic association with regional climate gradients in California valley oak (Quercus Lobata nee) in the face of climate change. Mol Ecol 19(17):3806-3823. https://doi.org/10.1111/j.1365-294X.2010.04726.x

Thompson ID, Guariguata MR, Okabe K, Bahamondez C, Nasi R, Heymell V, Sabogal C (2013) An operational framework for defining and monitoring Forest degradation. Ecol Soc 18(2):art20. https://doi.org/10.5751/ES-05443-180220

Tichý L, Chytrý M, Botta-Dukát Z (2014) Semi-supervised classification of vegetation: preserving the good old units and searching for new ones. J Veg Sci 25(6):1504-1512. https://doi.org/10.1111/jvs.12193

Tierney GL, Faber-Langendoen D, Mitchell BR, Shriver WG, Gibbs JP (2009) Monitoring and evaluating the ecological integrity of forest ecosystems. Front Ecol Environ 7(6):308-316. https://doi.org/10.1890/070176.

USNVC (2016) USNVC [United States National Vegetation Classification] Database, v2.0. Federal Geographic Data Committee, Vegetation Subcommittee, Washington DC. http://www.usnvc.org. Accessed 10 Aug 2017
Venables WN, Ripley BD (2002) Modern applied statistics with S, fourth. Springer, New Yorkhttps://doi.org/10.1007/978-0-387-21706-2
DOI
Wickham H (2017) Tidyverse: easily install and load "Tidyverse" packages. R package version 1.1.1. http://tidyverse.tidyverse.org. Accessed 1 Aug 2017

Zhu K, Woodall CW, Ghosh S, Gelfand AE, Clark JS (2014) Dual impacts of climate change: forest migration and turnover through life history. Glob Chang Biol 20(1):251-264. https://doi.org/10.1111/gcb.12382

Publication history
Copyright
Acknowledgements
Rights and permissions

Publication history

Received: 01 September 2017
Accepted: 14 December 2017
Published: 06 February 2018
Issue date: March 2018

Copyright

© The Author(s) 2018.

Acknowledgements

We thank K. Riitters for spatial data extraction and the forest area density and contagion data, J. Hak for landscape condition data, R. Li for assistance with querying the FIA database, and K. Nimerfro for assignment of macrogroups to FIA plots. Two anonymous referees provided helpful comments that strengthened the manuscript.

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Return