Register      Login
Australian Journal of Botany Australian Journal of Botany Society
Southern hemisphere botanical ecosystems
RESEARCH ARTICLE

Comparing data subsets and transformations for reproducing an expert-based vegetation classification of an Australian tropical savanna

Donna Lewis https://orcid.org/0000-0002-3891-3142 A B C , John Patykowski B and Catherine Nano B
+ Author Affiliations
- Author Affiliations

A School of Earth and Environmental Sciences, The University of Queensland, St Lucia, Qld 4072, Australia.

B Flora and Fauna Division, Department of Environment, Parks and Water Security, Northern Territory Government, PO Box 496, Palmerston, NT 0831, Australia.

C Corresponding author. Email: donna.lewis@nt.gov.au

Australian Journal of Botany 69(7) 423-435 https://doi.org/10.1071/BT20164
Submitted: 14 December 2020  Accepted: 11 July 2021   Published: 23 August 2021

Abstract

Mapping vegetation communities requires considerable investment in field data collection, analysis and interpretation. The methods for data collection and analysis can significantly affect field time and the accuracy of the classifications. We test the ability of field data subsets and data pre-treatments to reproduce an intuitively derived vegetation classification within the Australian tropical savanna biome. The data subsets include all strata, upper strata, ground strata, and tree basal area. A range of multivariate techniques were used to describe patterns in the datasets as they related to the a priori vegetation classification. We tested the degree of floristic correlation among the data subsets and the extent to which several data transformations (square root, fourth root, presence or absence) improved the level of agreement between the numerically and the intuitively derived mapping units. Our results implied high redundancy in sampling both basal area and upper strata species cover, and the ground stratum was poorly correlated with the upper stratum. Across all statistical tests, the groups derived from analysis of square root-transformed upper stratum cover data were closely aligned with the expert classification. We propose that a numerical approach using an optimal dataset will produce a meaningful classification for vegetation mapping in poorly known Australian tropical savanna.

Keywords: analysis of similarity, data subsets, data transformation, multidimensional data, ordination, rare species, vegetation mapping.


References

Abed T, Stephens NC (2003) ‘Tree Measurement Manual for Farm Foresters.’ (National Forest Inventory, Bureau of Rural Sciences: Canberra, ACT, Australia)

Addicott E, Laurance SGW (2019) Supervised versus un-supervised classification: a quantitative comparison of plant communities in savanna vegetation. Applied Vegetation Science 22, 373–382.
Supervised versus un-supervised classification: a quantitative comparison of plant communities in savanna vegetation.Crossref | GoogleScholarGoogle Scholar |

Addicott E, Laurance S, Lyons M, Butler D, Neldner J (2018) When rare species are not important: linking plot-based vegetation classifications and landscape-scale mapping in Australian savanna vegetation. Community Ecology 19, 67–76.
When rare species are not important: linking plot-based vegetation classifications and landscape-scale mapping in Australian savanna vegetation.Crossref | GoogleScholarGoogle Scholar |

Addicott E, Neldner VJ, Ryan T (2021) Aligning quantitative vegetation classification and landscape scale mapping: updating the classification approach of the Regional Ecosystem classification system used in Queensland. Australian Journal of Botany.
Aligning quantitative vegetation classification and landscape scale mapping: updating the classification approach of the Regional Ecosystem classification system used in Queensland.Crossref | GoogleScholarGoogle Scholar |

Anderson MJ, McCune BP, Grace J (2003) Analysis of ecological communities. Journal of Experimental Marine Biology and Ecology 289, 303–305.
Analysis of ecological communities.Crossref | GoogleScholarGoogle Scholar |

Anderson MJ, Gorley RN, Clarke KR (2008) ‘PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods.’ (PRIMER-E: Plymouth, UK)

Bedward M, Keith DA, Pressey RL (1992) Homogeneity analysis: assessing the utility of classifications and maps of natural resources. Australian Journal of Ecology 17, 133–139.
Homogeneity analysis: assessing the utility of classifications and maps of natural resources.Crossref | GoogleScholarGoogle Scholar |

Bray JR, Curtis JT (1957) An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs 27, 325–349.
An ordination of the upland forest communities of southern Wisconsin.Crossref | GoogleScholarGoogle Scholar |

Brocklehurst P, Lewis D, Napier D, Lynch D (2007) ‘Northern Territory guidelines and field methodology for vegetation survey and mapping.’ (Northern Territory Department of Natural Resources, Environment and the Arts: Darwin, NT, Australia)

Bureau of Meteorology (2020) Climate statistics for Australian locations: monthly climate statistics – Summary statistics TIMBER CREEK. Available at http://www.bom.gov.au/climate/averages/tables/cw_014850.shtml [Verified 21 October 2020]

Burgman MA, Thompson EJ (1982) Cluster analysis, ordination and dominance-structural classification applied to diverse tropical vegetation at Jabiluka, Northern Territory. Australian Journal of Ecology 7, 375–387.
Cluster analysis, ordination and dominance-structural classification applied to diverse tropical vegetation at Jabiluka, Northern Territory.Crossref | GoogleScholarGoogle Scholar |

Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology 18, 117–143.
Non-parametric multivariate analyses of changes in community structure.Crossref | GoogleScholarGoogle Scholar |

Clarke KR, Gorley RN (2015) ‘PRIMER v7: User Manual/Tutorial.’ (PRIMER-e: Auckland, New Zealand)

Clarke KR, Somerfield PJ, Chapman MG (2006) On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray–Curtis coefficient for denuded assemblages. Journal of Experimental Marine Biology and Ecology 330, 55–80.
On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray–Curtis coefficient for denuded assemblages.Crossref | GoogleScholarGoogle Scholar |

Clarke KR, Somerfield PJ, Gorley RN (2008) Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage. Journal of Experimental Marine Biology and Ecology 366, 56–69.
Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage.Crossref | GoogleScholarGoogle Scholar |

Clarke KR, Gorley RN, Somerfield PJ, Warwick RM (2014) ‘Change in Marine Communities: an Approach to Statistical Analysis and Interpretation’, 3rd edn. (PRIMER-e: Auckland, New Zealand)

Cormack RM (1971) A review of classification. Journal of the Royal Statistical Society. Series A (General) 134, 321–353.
A review of classification.Crossref | GoogleScholarGoogle Scholar |

Cowie I, Cuff N, Lewis D, Jobson P (2017) ‘Checklist of the Vascular Plants of the Northern Territory.’ (Northern Territory Herbarium, Department of Environment and Natural Resources: Palmerston, NT, Australia)

De Cáceres M, Chytrý M, Agrillo E, Attorre F, Botta‐Dukát Z, Capelo J, Czúcz B, Dengler J, Ewald J, Faber‐Langendoen D (2015) A comparative framework for broad‐scale plot‐based vegetation classification. Applied Vegetation Science 18, 543–560.
A comparative framework for broad‐scale plot‐based vegetation classification.Crossref | GoogleScholarGoogle Scholar |

De Cáceres M, Franklin SB, Hunter JT, Landucci F, Dengler J, Roberts DW (2018) Global overview of plot-based vegetation classification approaches. Phytocoenologia 48, 101–112.
Global overview of plot-based vegetation classification approaches.Crossref | GoogleScholarGoogle Scholar |

Dexter E, Rollwagen-Bollens G, Bollens SM (2018) The trouble with stress: a flexible method for the evaluation of nonmetric multidimensional scaling. Limnology and Oceanography, Methods 16, 434–443.
The trouble with stress: a flexible method for the evaluation of nonmetric multidimensional scaling.Crossref | GoogleScholarGoogle Scholar |

Dunster JN, Ahmed M (2013) Chapter 26: Victoria Basin. In ‘Special Publications 5: Geology and Mineral Resources of the Northern Territory’. (Eds M Ahmad, T Munson) pp. 26:1–26:7. (Northern Territory Geological Survey: Darwin, NT, Australia)

English S, Wilkinson C, Barker V (1997) ‘Survey Manual for Tropical Marine Resources.’ (Australian Institute of Marine Science: Townsville, Qld, Australia)

Executive Steering Committee for Australian Vegetation Information (2003) ‘Australian Vegetation Attribute Manual: National Vegetation Information System (Version 6.0).’ (Department of the Environment and Heritage: Canberra, ACT, Australia)

Fox ID, Neldner VJ, Wilson GW, Bannink PJ, Wilson BA, Brocklehurst PS, Clark MJ, Dickinson KJM, Beard JS, Bean AR (2001) ‘The Vegetation of the Australian Tropical Savannas (1:2,000,000 scale map in 3 sheets).’ (Queensland Herbarium, Environmental Protection Agency, Brisbane and the Cooperative Research Centre for the Sustainable Development of Tropical Savannas: Darwin, NT, Australia)

Gellie NJ, Hunter JT, Benson JS, Kirkpatrick JB, Cheal DC, McCreery K, Brocklehurst P (2018) Overview of plot-based vegetation classification approaches within Australia. Phytocoenologia 48, 251–272.
Overview of plot-based vegetation classification approaches within Australia.Crossref | GoogleScholarGoogle Scholar |

Hnatiuk RJ, Thackway R, Walker J (2009) Vegetation. In ‘Australian Soil and Land Survey: Field Handbook’, 3rd edn. (Ed. National Committee on Soil and Terrain) pp. 73–125. (CSIRO Publishing: Melbourne, Vic., Australia)

Itow S (1991) Species turnover and diversity patterns along an evergreen broad-leaved forest coenocline. Journal of Vegetation Science 2, 477–484.
Species turnover and diversity patterns along an evergreen broad-leaved forest coenocline.Crossref | GoogleScholarGoogle Scholar |

Johnson RW (1980) Studies of a vegetation transect through Brigalow (Acacia harpophylla) forest in central Queensland. Australian Journal of Ecology 5, 287–307.
Studies of a vegetation transect through Brigalow (Acacia harpophylla) forest in central Queensland.Crossref | GoogleScholarGoogle Scholar |

Kemp JE, Kutt AS (2020) Vegetation change 10 years after cattle removal in a savanna landscape. The Rangeland Journal 42, 73–84.
Vegetation change 10 years after cattle removal in a savanna landscape.Crossref | GoogleScholarGoogle Scholar |

Latimer AM, Silander JA, Rebelo AG, Midgley GF (2009) Experimental biogeography: the role of environmental gradients in high geographic diversity in Cape Proteaceae. Oecologia 160, 151–162.
Experimental biogeography: the role of environmental gradients in high geographic diversity in Cape Proteaceae.Crossref | GoogleScholarGoogle Scholar | 19194725PubMed |

Legendre P, Legendre L (2012) Cluster analysis. In ‘Numerical Ecology’, 3rd edn. (Elsevier)

Lehmann CER, Archibald SA, Hoffmann WA, Bond WJ (2011) Deciphering the distribution of the savanna biome. New Phytologist 191, 197–209.
Deciphering the distribution of the savanna biome.Crossref | GoogleScholarGoogle Scholar |

Lehmann CER, Anderson MT, Sankaran M, Higgins SI, Archibald S, Hoffmann WA, Hanan NP, Williams RJ, Fensham RJ, Felfili J, Hutley LB, Ratnam J, Jose JS, Montes R, Franklin D, Russell-Smith J, Ryan CM, Durigan G, Hiernaux P, Haidar R, Bowman DMJS, Bond WJ (2014) Savanna vegetation–fire–climate relationships differ among continents. Science 343, 548–552.
Savanna vegetation–fire–climate relationships differ among continents.Crossref | GoogleScholarGoogle Scholar |

Lengyel A, Podani J (2015) Assessing the relative importance of methodological decisions in classifications of vegetation data. Journal of Vegetation Science 26, 804–815.
Assessing the relative importance of methodological decisions in classifications of vegetation data.Crossref | GoogleScholarGoogle Scholar |

Lengyel A, Landucci F, Mucina L, Tsakalos JL (2018) Joint optimization of cluster number and abundance transformation for obtaining effective vegetation classifications. Journal of Vegetation Science 29, 336–347.
Joint optimization of cluster number and abundance transformation for obtaining effective vegetation classifications.Crossref | GoogleScholarGoogle Scholar |

Lewis D, Phinn S (2011) Accuracy assessment of vegetation community maps generated by aerial photography interpretation: perspective from the tropical savanna, Australia. Journal of Applied Remote Sensing 5, 053565
Accuracy assessment of vegetation community maps generated by aerial photography interpretation: perspective from the tropical savanna, Australia.Crossref | GoogleScholarGoogle Scholar |

Lewis D, Hill J, Cowie ID (2010) Bullo River Station flora and vegetation survey, Northern Territory: and reconnaissance soil-landscape investigation. Technical report number 02/2010D, Department of Natural Resources, Environment, the Arts and Sport, Northern Territory Government, Palmerston, NT, Australia.

Mabberley DJ (2008) ‘Mabberley’s Plant-Book: a Portable Dictionary of Plants, their Classification and Uses.’ (Cambridge University Press: Cambridge, UK)

Mistri M, Rossi R (2000) Levels of taxonomic resolution and choice of transformation sufficient to detect community gradients: an approach to hard‐substrata benthic studies. The Italian Journal of Zoology 67, 163–167.
Levels of taxonomic resolution and choice of transformation sufficient to detect community gradients: an approach to hard‐substrata benthic studies.Crossref | GoogleScholarGoogle Scholar |

Mucina L (1997) Classification of vegetation: past, present and future. Journal of Vegetation Science 8, 751–760.
Classification of vegetation: past, present and future.Crossref | GoogleScholarGoogle Scholar |

Mucina L, Daniel G (eds) (2013) ‘Vegetation Mapping in the Northern Kimberley, Western Australia.’ (Curtin University: Perth, WA, Australia)

Neldner VJ, Butler D (2008) Is 500 m2 an effective plot size to sample floristic diversity for Queensland’s vegetation? Cunninghamia 10, 513–519.

Neldner VJ, Howitt CJ (1991) Comparison of an intuitive mapping classification and numerical classifications of vegetation in South-East Queensland, Australia. Vegetatio 94, 141–152.
Comparison of an intuitive mapping classification and numerical classifications of vegetation in South-East Queensland, Australia.Crossref | GoogleScholarGoogle Scholar |

Neldner VJ, Kirkwood AB, Collyer BS (2004) Optimum time for sampling floristic diversity in tropical eucalypt woodlands of northern Queensland. The Rangeland Journal 26, 190–203.
Optimum time for sampling floristic diversity in tropical eucalypt woodlands of northern Queensland.Crossref | GoogleScholarGoogle Scholar |

Neldner VJ, Wilson BA, Dillewaard HA, Ryan TS, Butler DW, McDonald WJF, Addicott EP, Appelman CN (2020) ‘Methodology for survey and mapping of regional ecosystems and vegetation communities in Queensland. Version 5.1.’ Updated March 2020. (Queensland Herbarium, Queensland Department of Environment and Science: Brisbane, Qld, Australia)

NVIS Technical Working Group (2017) ‘Australian Vegetation Attribute Manual: National Vegetation Information System, Version 7.0.’ (Eds MP Bolton MP, C deLacey C, KB Bossard) (Department of the Environment and Energy: Canberra, ACT, Australia)

Olsgard F, Somerfield PJ, Carr MR (1997) Relationship between taxonomic resolution and data transformations in analyses of a macrobenthic community along an established pollution gradient. Marine Ecology Progress Series 149, 173–181.
Relationship between taxonomic resolution and data transformations in analyses of a macrobenthic community along an established pollution gradient.Crossref | GoogleScholarGoogle Scholar |

Patykowski J, Cowie I, Cuff N, Chong C, Nano C, Jobson P, Lewis D (2021) Can sampling for vegetation characterisation surrogate for species richness? Case studies from the wet–dry tropics of northern Australia. Australian Journal of Botany.
Can sampling for vegetation characterisation surrogate for species richness? Case studies from the wet–dry tropics of northern Australia.Crossref | GoogleScholarGoogle Scholar |

Podani J (1989) Comparison of ordinations and classifications of vegetation data. Vegetatio 83, 111–128.
Comparison of ordinations and classifications of vegetation data.Crossref | GoogleScholarGoogle Scholar |

Podani J (2006) Braun-Blanquet’s legacy and data analysis in vegetation science. Journal of Vegetation Science 17, 113–117.
Braun-Blanquet’s legacy and data analysis in vegetation science.Crossref | GoogleScholarGoogle Scholar |

Pontifex IR, Sweet IP (1972) ‘1:250,000 geological series – explanatory notes Auvergne Northern Territory.’ (Department of National Development, Bureau of Mineral Resources, Geology and Geophysics, Australian Government Publishing Service: Canberra, ACT, Australia)

Poos MS, Jackson DA (2012) Addressing the removal of rare species in multivariate bioassessments: the impact of methodological choices. Ecological Indicators 18, 82–90.
Addressing the removal of rare species in multivariate bioassessments: the impact of methodological choices.Crossref | GoogleScholarGoogle Scholar |

Russell-Smith J, Price OF, Murphy BP (2010) Managing the matrix: decadal responses of eucalypt-dominated savanna to ambient fire regimes. Ecological Applications 20, 1615–1632.
Managing the matrix: decadal responses of eucalypt-dominated savanna to ambient fire regimes.Crossref | GoogleScholarGoogle Scholar | 20945763PubMed |

Somerfield PJ, Clarke KR (1995) Taxonomic levels in marine community studies, revisited. Marine Ecology Progress Series 127, 113–119.
Taxonomic levels in marine community studies, revisited.Crossref | GoogleScholarGoogle Scholar |

Sparrow BD, Foulkes JN, Wardle GM, Leitch EJ, Caddy-Retalic S, van Leeuwen SJ, Tokmakoff A, Thurgate NY, Guerin GR, Lowe AJ (2020) A vegetation and soil survey method for surveillance monitoring of rangeland environments. Frontiers in Ecology and Evolution 8, 157
A vegetation and soil survey method for surveillance monitoring of rangeland environments.Crossref | GoogleScholarGoogle Scholar |

Speight JG (2009) Landform. In ‘Australian Soil and Land Survey: Field Handbook’, 3rd edn. (Eds National Committee on Soil and Terrain) pp. 15–55. (CSIRO Publishing: Melbourne, Vic., Australia)

Staver AC, Archibald S, Levin SA (2011) The global extent and determinants of savanna and forest as alternative biome states. Science 334, 230–232.
The global extent and determinants of savanna and forest as alternative biome states.Crossref | GoogleScholarGoogle Scholar | 21998389PubMed |

Sun D, Hnatiuk RJ, Neldner VJ (1997) Review of vegetation classification and mapping systems undertaken by major forested land management agencies in Australia. Australian Journal of Botany 45, 929–948.
Review of vegetation classification and mapping systems undertaken by major forested land management agencies in Australia.Crossref | GoogleScholarGoogle Scholar |

Thackway R, Neldner VJ, Bolton MP (2008) Vegetation. In ‘Australian Soil and Land Survey Handbook: Guidelines for Surveying Soil and Land Resources’. (Eds NJ McKenzie, MJ Grundy, R Webster, AJ Ringrose-Voase) pp. 115–142. (CSIRO Publishing: Melbourne, Vic., Australia)

Tichý L, Hennekens SM, Novák P, Rodwell JS, Schaminée JHJ, Chytrý M (2020) Optimal transformation of species cover for vegetation classification. Applied Vegetation Science 23, 710–717.
Optimal transformation of species cover for vegetation classification.Crossref | GoogleScholarGoogle Scholar |

Vittoz P, Pellacani F, Romanens R, Mainga A, Verrecchia EP, Fynn RW (2020) Plant community diversity in the Chobe Enclave, Botswana: insights for functional habitat heterogeneity for herbivores. Koedoe 62, 1–17.
Plant community diversity in the Chobe Enclave, Botswana: insights for functional habitat heterogeneity for herbivores.Crossref | GoogleScholarGoogle Scholar |

Ward DP, Kutt AS (2009) Rangeland biodiversity assessment using fine scale on-ground survey, time series of remotely sensed ground cover and climate data: an Australian savanna case study. Landscape Ecology 24, 495–507.
Rangeland biodiversity assessment using fine scale on-ground survey, time series of remotely sensed ground cover and climate data: an Australian savanna case study.Crossref | GoogleScholarGoogle Scholar |

Wearne LJ, Morgan JW (2001) Floristic composition and variability of subalpine grasslands in the Mt Hotham region, north-eastern Victoria. Australian Journal of Botany 49, 721–773.
Floristic composition and variability of subalpine grasslands in the Mt Hotham region, north-eastern Victoria.Crossref | GoogleScholarGoogle Scholar |

Williams RJ, Cook GD, Leidloff AC, Bond WJ (2017) Australia’s tropical savannas: vast, ancient and rich landscapes. In ‘Australian Vegetation’, 3rd edn. (Ed. DA Keith) pp. 368–388 (Cambridge University Press: Cambridge, UK)

Wilson BA, Brocklehurst PS, Clark M, Dickinson KJM (1990) Vegetation survey of the Northern Territory, Australia: report number 49, Conservation Commission of the Northern Territory, Palmerston, NT, Australia.

Woinarski J, Mackey B, Nix H, Traill B (2007) ‘The Nature of Northern Australia. Natural Values, Ecological Processes and Future Prospects.’ (ANU E-Press: Canberra, ACT, Australia)