Australian advances in vegetation classification and the need for a national, science-based approach
Sarah Luxton
A , Donna Lewis B , Shane Chalwell C , Eda Addicott D and John Hunter E
A School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia. Email: sarahjluxton@outlook.com
B Northern Territory Herbarium, Flora and Fauna Division, Department of Environment, Parks and Water Security (DEPWS), Northern Territory Government, PO Box 496, Palmerston, NT 0831, Australia. Email: donna.lewis@nt.gov.au
C Plantecology Consulting, 50 New Cross Road, Kingsley WA 6026, Australia. Email: shane@plantecology.com.au
D Queensland Herbarium, Mt Coot-tha Road, Toowong, Department of Environment and Science, Queensland Government, Qld 4066, Australia. Email: eda.addicott@des.qld.gov.au
E School of Environmental and Rural Science, Elm Avenue, University of New England, Armidale, NSW 2350, Australia. Email: jhunter8@bigpond.com
Australian Journal of Botany 69(7) 329-338 https://doi.org/10.1071/BT21102
Submitted: 20 August 2021 Accepted: 1 September 2021 Published: 6 October 2021
Journal Compilation © CSIRO 2021 Open Access CC BY-NC
Abstract
This editorial introduces the Australian Journal of Botany special issue ‘Vegetation science for decision-making’. Vegetation science and classification are crucial to understanding Australian landscapes. From the mulga shrublands of the arid interior to the monsoon rain forests of northern Australia, we have culturally and scientifically built upon the delineation of vegetation into recognisable and repeatable patterns. As remote sensing and database capacities increase, this improved capability to measure vegetation and share data also prompts collaboration and synthesis of complex, specialised datasets. Although the task faces significant challenges, the growing body of literature demonstrates a strong discipline. In Australia, purpose-driven products describe vegetation at broad scales (e.g. the National Vegetation Information System, the Terrestrial Ecosystem Research Network). At fine scales however (i.e. that of the vegetation community), no uniform framework or agreed protocols exist. Climate and landform dictate vegetation patterns at broad scales, but microtopography, microclimate and biotic processes act as filters at finer scales. This is the scale where climate-change impacts are most likely to be detected and effected; this is the scale at which a deeper understanding of evolutionary ecology will be achieved, and it is the scale at which species need to be protected. A common language and system for understanding Australian communities and impetus for collecting data at this scale is needed. In the face of ongoing climate and development pressures and an increasingly complex set of tools to manage these threats (e.g. offset policies, cumulative impact assessments), a nationally collaborative approach is needed. It is our hope that this special issue will help to achieve this.
Introduction
The aim of this editorial is to introduce the Australian Journal of Botany special issue ‘Vegetation science for decision-making’, which evolved from a symposium of the same name at the Ecological Society of Australia’s 2019 annual conference in Launceston, Tasmania. We provide broad, global and national contexts for vegetation classification, discuss the importance of the plant community and highlight the main findings of each contribution to the special issue. The main focus – vegetation classification – is a globally important issue in plant science and has been a major feature of Australian vegetation science for well over half a century. It is our hope that this special issue will contribute to a greater understanding of the language, data, methods and applications of vegetation classification, and, importantly, how cross-jurisdictional collaboration can be enhanced.
A global snapshot of vegetation classification
Classification is a fundamental scientific pursuit. From the spectral classification of stars in astronomy, to the morphological and genetic classification of living things into species, the observation of differences and repeating patterns is critical to understanding the processes underlying nature. Vegetation classification helps us to summarise and describe complex patterns of species co-occurrence and its typologies are useful for multiple purposes (Dengler et al. 2008; Austin 2013; De Cáceres et al. 2015). These include: (1) communication about complex vegetation patterns; (2) formulation of hypotheses about the ecological and evolutionary processes shaping these patterns; (3) creation of maps to display the spatial variation of vegetation and related ecosystem properties and services; (4) surveying, monitoring and reporting plant and animal populations, communities and their habitats; and (5) development of coherent management and conservation strategies (De Cáceres et al. 2015).
Ideally, the purpose of a classification schema should inform the type of data collected (including sampling strategy and primary vegetation attributes) and the protocol (‘class definition procedures’) used for analysis (De Cáceres et al. 2015). For example, a forestry classification may focus on commercial tree species and attributes such as height (Sun et al. 1997). Alternatively, conservation decision-making requires an accurate assessment of understory and rare species (Tierney et al. 2018; Bell and Driscoll 2021), whereas vegetation mapping focuses on key indicator species in the dominant strata, and the inclusion of rare species may hinder rather than inform mapping (Addicott et al. 2018). Across all forms of classification, scale is an essential consideration for appropriate data collection and applications (Levin 1992; McKenzie et al. 2008; Bell and Driscoll 2021; Hunter and Growns 2021; Patykowski et al. 2021).
Vegetation classification has developed from descriptive into a numerically intensive discipline with an extensive literature and complex protocols and methods (Mucina 1997; De Cáceres et al. 2015). Data collection includes decisions regarding survey type (random, stratified, preferential (De Cáceres et al. 2015), data format (presence-absence, frequency, cover, cover-abundance) and plot size (Neldner and Butler 2008; Dengler et al. 2009; Patykowski et al. 2021). Analysis decisions extend from data transformation (Lewis et al. 2021a) and the type of association metric and clustering algorithm used (e.g. hierarchical v. non-hierarchical clustering; Wards v. UPGMA); to whether environmental data is integral or secondary to the classification (supervised v. unsupervised classification; see Wildi 2010, Borcard et al. 2011, Kent 2011 and Legendre and Legendre 2012 for full treatments of vegetation classification methods). A range of software tools are available to analyse data. The more commonly used include R (R Foundation for Statistical Computing, Vienna, Austria, see https://www.R-project.org/), which has well supported and up-to-date vegetation classification packages (e.g. vegan, ver. 2.5-6, J. Oksanen, F. G. Blanchet, M. Friendly, R. Kindt, P. Legendre, D. McGlinn, P. R. Minchin, R. B. O’Hara, G. L. Simpson, P. Solymos, M. H. H. Stevens, E. Szoecs, and H. Wagner, see https://cran.r-project.org/web/packages/vegan/index.html; labdsv, ver. 2.0-1, D. W. Roberts, see https://CRAN.R-project.org/package=labdsv; vegclust, ver. 1.6.5, M. De Cáceres and S. K. Wiser, see https://cran.r-project.org/web/packages/vegclust/index.html); JUICE, which handles large datasets (>100 000 plots) (Tichý 2002; Chytrý and Tichý 2018; Addicott et al. 2021); PRIMER-e (see https://www.primer-e.com/), which does not require use of a command line (Lewis et al. 2021a) and PATN (see https://patn.org/), which can also handle large datasets (>30 000 plots) (Belbin 1993; Luxton et al. 2021). This complexity has likely been a barrier to numerical methods being used to ascribe vegetation types in Australia, although intuitive approaches may have benefits over numerical when the purpose is to create broad map units in wooded systems. In this case, herbaceous species will influence classification results but have a low correlation with remotely sensed patterns (Neldner and Howitt 1991; Addicott et al. 2021). Complexity has also been a barrier to the use of numerical methods in policy and regulatory frameworks and can make the synthesis of historic with current datasets, and across jurisdictional boundaries difficult (Gellie and Hunter 2021; Luxton et al. 2021; Muldavin et al. 2021). These factors, together with the lack of a critical number of practitioners, have likely stymied vegetation classification collaboration efforts within Australia and internationally.
Despite the challenges however, global advances enable robust solutions and collaborations both within and between countries. For example, VegBank (the vegetation plot database of the Ecological Society of America’s panel on vegetation classification) contains 115 246 plots and includes 10 695 vegetation types, which are recognised in the US National Vegetation Classification (USNVC, see http://vegbank.org/vegbank/index.jsp) (Peet et al. 2012). New vegetation types for the USNVC can be proposed and are reviewed by an expert panel (in a similar vein to the academic peer-review process) before being accepted as an official vegetation type (Peet et al. 2012). In Europe, the European Vegetation Archive (EVA), a centralised database of European plots, has over 1 million plot records (see http://euroveg.org/eva-database) (Chytrý et al. 2016) and the Botanical Information and Ecology Network (BIEN) currently holds 364 477 plots. BIEN also contains other bioinformatic data (e.g. plant traits) and has been working since 2008 to bring together managers of botanical survey data, computer scientists and ecologists interested in synthetic research across scales (see https://bien.nceas.ucsb.edu/bien/, accessed 25 July 2021) (Enquist et al. 2016). sPlot, a global vegetation-plot database initiated by an international working group at the German Centre for Integrative Biodiversity Research in 2013, contains almost two million georeferenced plots and provides a basis for global vegetation analyses (Bruelheide et al. 2019).
Ongoing research into analytical methods also underpins this global push towards synthesising vegetation data and types into comprehensive typologies. Work includes the development of semi-supervised classification, which incorporates new plot records while retaining ‘old’ classification units (Tichý et al. 2014) and fuzzy (noise) clustering. Noise clustering enabled plots to be placed in transition vegetation types or left unassigned until enough data are available to robustly define a vegetation type (De Cáceres et al. 2010; Wiser and De Cáceres 2018). Together, these international efforts to collaborate and overcome data and analysis issues provide a path forward for joint continent-wide efforts within and between jurisdictions – States, Territories and the Commonwealth – in Australia.
Australian vegetation science and classification
In the context of land management and ecology, Australian vegetation classification has been reviewed in several places. Most recently, Keith (2017) provides a comprehensive and up-to-date account of Australian vegetation ecology and science, from the evolutionary biogeography of the Australian flora in the Cenozoic era to in-depth chapters on Australia’s 16 major vegetation types. It also includes a new high-level ecological typology of Australian vegetation, with an evaluation of how ecological processes and legacies shape and delineate the major vegetation types (Keith and Tozer 2017). In the forward to Keith (2017), Groves touches on the origins of vegetation description in Australia (see also Short 2003 for a detailed account), the history of structural and floristic typologies (e.g. Wood 1939; Beadle and Costin 1952; Specht 1970, 1981; Carnahan 1990; Specht and Specht 2000), the emergence of the link between vegetation functionality and type, and the importance of fire in determining vegetation distribution. Sun et al. (1997) provide a detailed summary of the major vegetation classification and mapping systems used by the management agencies with primary responsibilities for forested land in Australia. Gellie et al. (2018a) summarise the density and distribution of plot data and review local classifications by each State and Territory. They also make a case for cross jurisdictional co-operation, including the need for agreed nation-wide classification protocols and procedures, improved plot coverage in data-poor areas, higher standards of plot data curation and plant taxa nomenclature, and a scientifically defensible hierarchical classification that integrates with the International Vegetation Classification (IVC) (see also Table 1 for an updated summary of plot data by jurisdiction).
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Australia has several nation-wide classifications of vegetation at broad scales, with each system having different purposes, advantages, and limitations. They include the Interim Biogeographic Regionalisation for Australia (IBRA) (Thackway and Cresswell 1995), the National Vegetation Information System (NVIS) (National Land and Water Resources Audit 2001) and the Terrestrial Ecosystem Research Network’s Advanced Ecological Knowledge and Observation System (TERN AEKOS) (Sparrow et al. 2020) (which is to be superseded by TERN EcoPlots, see https://ecoplots.tern.org.au; Table 1). IBRA classifies Australia’s landscapes into 89 bioregions and 419 subregions and forms the basis of a comprehensive, adequate and representative (‘CAR’) National Reserve System (Kukkala and Moilanen 2013; Margules and Pressey 2000; National Reserve System Task Group 2009) (see https://www.environment.gov.au/land/nrs/science/ibra). However, it is an ecoregional assessment rather than a vegetation classification typology per se. NVIS was formed in the early 2000s as a spatially explicit national repository for vegetation information and has consistent coverage at the Major Vegetation Groups (Fig. 1) and Subgroups levels, but is patchy at lower levels of the classification (Level V and VI, Association and Sub-association) (National Land and Water Resources Audit 2001; Keith and Tozer 2017; Scarth et al. 2019). Additionally, although lower level units incorporate floristic data (three and five species per strata respectively), they are not associations in the sense of European and North American definitions, which tend to be based on full-floristic data (Willner 2006; Peet and Roberts 2013; van der Maarel and Franklin 2013). TERN’s EcoPlots may prove the forerunner for a nationally integrated plot database and classification. Currently it houses ~98 000 vegetation plots from Queensland, South Australia, Northern Territory, Western Australia, and New South Wales (Table 1). It overcome state-based idiosyncrasies to integrate data between different agencies using a semantic web approach (Guru et al. 2019).
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Australian plant ecology provides a backbone for understanding the drivers of vegetation patterns. Australia is the ‘flattest, driest, and geologically oldest vegetated continent’ in the world, with the first European explorers marvelling at the strange plants encountered here (Short 2003; Orians and Milewski 2007). Although patterns of plant diversity are intermediate, our vegetation is highly endemic (>80% taxa) and botanical species discovery is ongoing (Keith and Tozer 2017; Gellie et al. 2018a; Taxonomy Decadal Plan Working Group 2018). For First Nations people, the sorting of plants (and animals) into groups is interwoven with religious and cultural beliefs (McHale 2018). In western science, scale is the key concept that organises our understanding of vegetation patterns and the processes driving them (Levin 1992; Chave 2013). Specifically, in Australia, climate and available energy operate broadly, whereas topography, soils and fire (and other disturbances, e.g. cyclones) act at intermediate scales (Havel 1975; Hunter 2021a). The role of nutrient poverty and fire (Milewski 1983; Orians and Milewski 2007); old v. young landscapes and climatic ‘stability’ (Hopper 2009; Mucina and Wardell-Johnson 2011; Hopper et al. 2021) and alternative stable states (Peterson 1984; Sousa and Connell 1985; Pausas and Dantas 2017) are important, as is the role of competition and top down effects (e.g. grazing) (Greenwood and McKenzie 2001; Trinder et al. 2013).
Fine scale effects are increasingly recognised as influencing species patterns within the broad-scale filters of climate and landform and are an important frontier for vegetation science (Keith and Tozer 2017). Factors include biotic interactions (e.g. pathogens, competition, mutualisms with mycorrhiza (Albornoz et al. 2017; Brundrett et al. 2017), microclimatic and microtopographic effects (e.g. cold air pooling, banded ironstones formations; Curtis et al. 2014; Robinson et al. 2019) and life history traits (Leishman and Westoby 1992; Schwarz et al. 2018). Explicitly modelling processes such as physiology, dispersal, demography and biotic interactions is believed to provide more robust predictions in species distribution models, particularly when extrapolating to novel conditions (Wisz et al. 2013; le Roux et al. 2014; Briscoe et al. 2019). Surveying at this scale enables species discovery, the identification of rare species (Patykowski et al. 2021) and mapping of rare and threatened plant communities (Tierney et al. 2018; Bell and Driscoll 2021). Subsequently, the lack of national standards for data collection, analysis and classification development at this scale has serious negative implications for conservation decision making.
Australia faces challenges due to its size and remoteness, but a national vegetation database and classification system (i.e. the ‘Australian Vegetation Classification System (AVCS)’, Gellie et al. (2018b) will enable best-practice analysis, map products, reporting and decision-making. Applications include as a basis for monitoring programs, plant and animal survey stratification, and development assessments (including offsets and cumulative impacts) (Kent 2011; Neldner et al. 2019). Conservation planning and decision making would be better supported (e.g. assessments of representativeness, investment planning and mapping of threatened communities) (Keith and Pellow 2015; Luxton et al. 2021). It would also bring Australia in line with Northern Hemisphere methodology, for example, Europe, where the plant community is the unit of conservation targets (Bakker 2013). Consistency between jurisdictions would likely flow through to major national and international reporting obligations including the Paris agreement and Montreal Protocol (emissions reduction targets, national forest inventory time-series), the IUCN Red List of Ecosystems (Keith et al. 2015), State of the Environment Reporting (Cresswell and Murphy 2017), the National Reserve System (Commonwealth of Australia 1997; National Reserve System Task Group 2009) and the Collaborative Australian Protected Area Database (Collaborative Australian Protected Area Database (CAPAD, Department of Agriculture, Water and the Environment, see https://www.environment.gov.au/land/nrs/science/capad/2020).
National and international quantitative, plot-based classification systems
The AVCS could be built from existing frameworks (e.g. TERN AEKOS) and draw on other national and international frameworks for guidance. Countries that have overcome problems that Australia faces include the USA, the United Kingdom, Czech Republic and New Zealand. VegBank and the USNVC provide direction on both the database infrastructure required to support complex, inter-jurisdictional vegetation datasets and a framework for managing and reviewing new vegetation types (http://usnvc.org/) (Faber-Langendoen et al. 2018). The United Kingdom’s national vegetation classification (UK NVC) contains over 33,000 georeferenced plots (Rodwell 2018). A clear classification approach has been consistently followed and the framework has become the standard for vegetation description among all statutory agencies, non-government organisations, industry, consultancies and academics in the UK (De Cáceres et al. 2015; Rodwell 2018). In the Czech Republic, the Vegetation of the Czech Republic was developed from 1997 to 2013 and based on the analyses of over 100 000 vegetation plot records from the Czech National Phytosociological Database (Chytrý and Tichý 2018). As plot sizes were variable (Otypková and Chytry 2006; Dengler et al. 2009), records from a broad range of plot sizes were still used to prevent data-loss, but were restricted to certain ranges per vegetation type (e.g. 50–1000 m2 for forests; Chytrý and Tichý 2018). New Zealand has also classified its varied and unique vegetation based on plot data, using 5751 plot records from the New Zealand Land Cover Database and the National Vegetation Survey databank. The classification approach used two hierarchically nested levels to define vegetation types (‘forests and shrublands’, measured using cover abundance and ‘herbaceous’ measured using relative species ranks) (Wiser and De Cáceres 2018).
Even more broadly – systems like the European vegetation checklist (EuroVegChecklist, see https://www.synbiosys.alterra.nl/evc/) (Mucina et al. 2016) and the IVC provide a roadmap for consistent, hierarchical classification of vegetation within and between national jurisdictions (Gellie et al. 2018a). The EuroVegChecklist evaluated ~10 000 sources to create a comprehensive list of syntaxonomic units, that were evaluated by experts for ‘floristic and ecological distinctness, clarity of geographic distribution and compliance with the nomenclature code’ (Mucina et al. 2016). Accepted units were compiled into three systems (classes, orders and alliances) for vascular plants, bryophytes and lichens, and algae (Mucina et al. 2016). Alternatively, the IVC is based on the EcoVeg approach and has eight hierarchical levels (Faber-Langendoen et al. 2014, 2018). The six upper levels are based on physiognomy, climatic region and tree leaf morphology, whereas the two base levels incorporate floristics (L7: alliance and L8: association). Both approaches shine a light on ways forward for Australian vegetation classification. The goal: a unified, collaborative approach that allows for innovation, flexibility and growth and is attractive to new researchers.
This special issue
This special issue brings together a range of articles from vegetation scientists across Australia, highlighting classification systems, nuances in data collection and analysis methods, and the application to, and implications of, this work for land management and decision-making (Fig. 2). The articles presented here provide a snapshot of challenges faced in vegetation classification and science; from sampling methods (e.g. plot size, type of sampling effort) (Patykowski et al. 2021) through data-pre-treatment (Lewis et al. 2021a) to the use of historical remotely sensed imagery and vegetation data to develop map products (Gellie and Hunter 2021). An overview of how State-based plot-based vegetation data (the Northern Territory’s in this case), together with an assessment of how well data can be utilised for attribution to the National Vegetation Classification System, is provided by Lewis et al. (2021b). Addicott et al. (2021) provides a review of the updated classification approach of the Regional Ecosystem (RE) mapping program used in Queensland. The RE’s are placed in the context of classification systems globally, and an explanation given as to how expert v. quantitatively derived vegetation classes are incorporated in mapping (Addicott et al. 2021). The paper also provides an up-to-date review of classification and cluster evaluation methods in Australia and internationally. Hunter and Growns (2021) use generalised dissimilarity modelling (a semi-supervised form of classification), to identify riparian macrogroups at the landscape scale. Six macrogroups (ecoregions) were identified for NSW (802 000 km2), providing a practical map product for conservation decision-making despite data-poor areas. Bell and Driscoll (2021) outline a new method (data-informed sampling and mapping: D-iSM) for vegetation mapping that ensures that plot-based classifications identify rare and restricted vegetation types. Hunter (2021a, 2021b) highlights the importance of the temporal dimension in defining communities sensitive to inter-annual variation, e.g. ephemeral montane marshes (lagoons) or ephemeral vegetation types associated with the aseasonal climates found in the arid and semi-arid zone. Luxton et al. (2021) use a large plot database (30 000 plots) to develop an updated classification in the northern jarrah forests of south-western Australia and explore how heterogeneity and representativeness are captured by the conservation reserve system.
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It is our hope that this special issue will strengthen relationships between the Commonwealth, and the States and Territories, attract new students to vegetation classification and provide a basis and stimulation for further discussion. We also look to the future – for how Australian vegetation science may be improved with further collaboration nationally, and how we may work globally, for example, by incorporating our classifications into the IVC. Gellie and Hunter (2021) and Muldavin et al. (2021) provide case-studies for how this can be done, with their applications to the flora of eastern NSW and the Eucalyptus tetrodonta and Triodia spp. hummock grasslands and savanna systems across northern Australia (Fig. 2). Muldavin et al. (2021) also discusses how we can be informed by international experience and how our unique vegetation and experiences can also inform and improve international programs for the benefit of all. Nationally and internationally co-ordinated, science-based approaches to vegetation classification will aid communication across jurisdictional boundaries and help to provide consistency in national and international reporting requirements. It will also result in a stronger vegetation science community, which is better placed to face the challenges ahead.
Conflicts of interest
Sarah Luxton, Eda Addicott, John Hunter and Shane Chalwell were guest editors for the ESA Conference special issue for Australian Journal of Botany. Despite this relationship, they did not at any stage have editor-level access to this manuscript while in peer review, as is the standard practice when handling manuscripts submitted by an editor to this journal. Australian Journal of Botany encourages its editors to publish in the journal and they are kept totally separate from the decision-making process for their manuscripts. The authors have no further conflicts of interest to declare.
Declaration of funding
This research did not receive any specific funding.
Acknowledgements
This special issue arose from the symposium ‘Vegetation Science for Decision-Making’ at the 2019 Ecological Society of Australia’s annual conference in Launceston, Tasmania. The symposium was convened after discussions by an informal group of ‘vegetation classificationists’ – consisting of several government employees, students and consultants – about the lack of cross jurisdictional collaboration within the field of vegetation classification. The group is now looking to formalise itself as an ‘Australian Vegetation Classification’ Research Chapter of the Ecological Society of Australia. As such, the group would like to say a hearty thank you to the Ecological Society of Australia, the participants of the symposium, and especially to the reviewers, guest editors and authors for all of your hard work in bringing this special issue together. Our thanks also to Grant Wardell-Johnson and Ashley Sparrow for comments on an earlier draft of the manuscript; and to Ron Avery and Philip Gleeson (NSW), David Storey (Tas.), Felicity Grant (ACT), Bev Yen (Vic.), and Ben Sparrow and Siddeswara Guru (TERN Ecosystem Surveillance) for supplying updated plot information for Table 1.
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