Extending vegetation site data and ensemble models to predict patterns of foliage cover and species richness for plant functional groups

Ensembles of artificial neural network models can be trained to predict the continuous characteristics of vegetation such as the foliage cover and species richness of different plant functional groups. Our first objective was to synthesise existing site-based observations of native plant species to quantify summed percentage foliage cover and species richness within four functional groups and in totality. Secondly, we generated spatially-explicit, continuous, landscape-scale models of these functional groups, accompanied by maps of the model residuals to show uncertainty. Using a case study from New South Wales, Australia, we aggregated floristic observations from 6806 sites into four common plant growth forms (trees, shrubs, grasses and forbs) representing four different functional groups. We coupled these response data with spatially-complete surfaces describing environmental predictors and predictors that reflect landscape-scale disturbance. We predicted the distribution of foliage cover and species richness of these four plant functional groups over 1.5 million hectares. Importantly, we display spatially explicit model residuals so that end-users have a tangible and transparent means of assessing model uncertainty. Models of richness generally performed well (R2 0.43–0.63), whereas models of cover were more variable (R2 0.12–0.69). RMSD ranged from 1.42 (tree richness) to 29.86 (total native cover). MAE ranged from 1.0 (tree richness) to 20.73 (total native foliage cover). Continuous maps of vegetation attributes can add considerable value to existing maps and models of discrete vegetation classes and provide ecologically informative data to support better decisions across multiple spatial scales.

[1]  W. Bond,et al.  Humboldt and the reinvention of nature , 2018, Journal of Ecology.

[2]  Jennifer A. Miller,et al.  Mapping Species Distributions: Spatial Inference and Prediction , 2010 .

[3]  Richard M Cowling,et al.  Conservation planning in a changing world. , 2007, Trends in ecology & evolution.

[4]  J. Watson,et al.  The Spatial Distribution of Threats to Species in Australia , 2011 .

[5]  D. Lindenmayer,et al.  Size or quality: What matters in vegetation restoration for bird biodiversity in endangered temperate woodlands? , 2018 .

[6]  I. Oliver,et al.  A new Vegetation Integrity metric for trading losses and gains in terrestrial biodiversity value , 2021 .

[7]  J. P. Grime,et al.  Evidence for the Existence of Three Primary Strategies in Plants and Its Relevance to Ecological and Evolutionary Theory , 1977, The American Naturalist.

[8]  Phillip B. Gibbons,et al.  Forest and woodland stand structural complexity: Its definition and measurement , 2005 .

[9]  R. O’Brien,et al.  A Caution Regarding Rules of Thumb for Variance Inflation Factors , 2007 .

[10]  Doreen S. Boyd,et al.  Integrating Biodiversity, Remote Sensing, and Auxiliary Information for the Study of Ecosystem Functioning and Conservation at Large Spatial Scales , 2020, Remote Sensing of Plant Biodiversity.

[11]  Mathieu Marmion,et al.  Does the interpolation accuracy of species distribution models come at the expense of transferability , 2012 .

[12]  H. Olff,et al.  Effects of herbivores on grassland plant diversity. , 1998, Trends in ecology & evolution.

[13]  Miquel De Cáceres,et al.  Towards consistency in vegetation classification , 2012 .

[14]  Elgene O. Box,et al.  Predicting physiognomic vegetation types with climate variables , 1981, Vegetatio.

[15]  G. Harden Flora of New South Wales , 1992 .

[16]  J. Pausas,et al.  Patterns of plant species richness in relation to different environments: An appraisal , 2001 .

[17]  J. Oldeland,et al.  The Global Index of Vegetation-Plot Databases (GIVD): a new resource for vegetation science , 2011 .

[18]  William G. Smith Raunkiaer's "Life-Forms" and Statistical Methods , 1913 .

[19]  Simon Ferrier,et al.  Using abiotic data for conservation assessments over extensive regions : quantitative methods applied across New South Wales, Australia , 2000 .

[20]  D. Driscoll,et al.  Fine-scale variables associated with the presence of native forbs in natural temperate grassland , 2020 .

[21]  Lloyd W. Morrison,et al.  Observer error in vegetation surveys: a review , 2016 .

[22]  J. Evans,et al.  Gradient modeling of conifer species using random forests , 2009, Landscape Ecology.

[23]  D. Opitz,et al.  Popular Ensemble Methods: An Empirical Study , 1999, J. Artif. Intell. Res..

[24]  Antoine Guisan,et al.  Predictive habitat distribution models in ecology , 2000 .

[25]  A. Townsend Peterson,et al.  Novel methods improve prediction of species' distributions from occurrence data , 2006 .

[26]  D. King,et al.  A Range of Earth Observation Techniques for Assessing Plant Diversity , 2020 .

[27]  Lee Belbin,et al.  Which environmental variables should I use in my biodiversity model? , 2012, Int. J. Geogr. Inf. Sci..

[28]  The importance of herbivore density and management as determinants of the distribution of rare plant species , 2017 .

[29]  Michael F. Hutchinson,et al.  New developments and applications in the ANUCLIM spatial climatic and bioclimatic modelling package , 2013, Environ. Model. Softw..

[30]  S. Venkatramanan,et al.  An Introduction to Various Spatial Analysis Techniques , 2019, GIS and Geostatistical Techniques for Groundwater Science.

[31]  Anne Bowser,et al.  Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale , 2018, Biological reviews of the Cambridge Philosophical Society.

[32]  Stephen E. Fick,et al.  WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas , 2017 .

[33]  G. C. Stevens,et al.  Spatial Variation in Abundance , 1995 .

[34]  D. Lindenmayer,et al.  Temporal fragmentation of a critically endangered forest ecosystem , 2020, Austral Ecology.

[35]  E. Warming Oecology of plants , 1909 .

[36]  B. Enquist,et al.  A plant growth form dataset for the New World. , 2016, Ecology.

[37]  Davide Chicco,et al.  Ten quick tips for machine learning in computational biology , 2017, BioData Mining.

[38]  Christopher B. Field,et al.  Mapping the land surface for global atmosphere‐biosphere models: Toward continuous distributions of vegetation's functional properties , 1995 .

[39]  J. Barlow,et al.  Prospects for tropical forest biodiversity in a human-modified world. , 2009, Ecology letters.

[40]  Ian Oliver,et al.  Pitfalls and possible solutions for using geo-referenced site data to inform vegetation models , 2015, Ecol. Informatics.

[41]  Pedro J. Leitão,et al.  Improving Models of Species Ecological Niches: A Remote Sensing Overview , 2019, Front. Ecol. Evol..

[42]  Barry R. Noon,et al.  Utility and limitations of species richness metrics for conservation planning , 2006 .

[43]  S. Sarkar,et al.  Systematic conservation planning , 2000, Nature.

[44]  Anne Bowser,et al.  Building essential biodiversity variables(EBVs) of species distribution and abundanceat a global scale , 2017 .

[45]  Jane Elith,et al.  Fauna habitat modelling and mapping: A review and case study in the Lower Hunter Central Coast region of NSW , 2005 .

[46]  Eddy van der MaareF Numerical syntaxonomy , 1989, Advances in vegetation science.

[47]  Martin Westbrooke,et al.  Is what you see what you get? Visual vs. measured assessments of vegetation condition , 2010 .

[48]  Cristopher Brack,et al.  Fauna-habitat relationships: a basis for identifying key stand structural attributes in temperate Australian eucalypt forests and woodlands , 2006 .

[49]  R. Hobbs,et al.  Biological Consequences of Ecosystem Fragmentation: A Review , 1991 .

[50]  R. Noss Indicators for Monitoring Biodiversity: A Hierarchical Approach , 1990 .

[51]  T. Speck,et al.  Plant growth forms: an ecological and evolutionary perspective. , 2005, The New phytologist.

[52]  Johanna D. Turnbull,et al.  Moving beyond presence and absence when examining changes in species distributions , 2017, Global change biology.

[53]  M. Austin Spatial prediction of species distribution: an interface between ecological theory and statistical modelling , 2002 .

[54]  F. Chapin,et al.  EFFECTS OF BIODIVERSITY ON ECOSYSTEM FUNCTIONING: A CONSENSUS OF CURRENT KNOWLEDGE , 2005 .

[55]  J R Healey,et al.  The repeatability of vegetation classification and mapping. , 2011, Journal of environmental management.

[56]  Galit Shmueli,et al.  To Explain or To Predict? , 2010, 1101.0891.

[57]  Michael Drielsma,et al.  Landscape scenario modelling of vegetation condition , 2006 .

[58]  I. Oliver,et al.  Expert allocation of primary growth form to the New South Wales flora underpins the biodiversity assessment method , 2019, Australasian Journal of Environmental Management.

[59]  Thomas P. Quinn,et al.  Test Set Verification Is An Essential Step in Model Building , 2020 .

[60]  Susan K. Wiser,et al.  New Zealand's forest and shrubland communities: a quantitative classification based on a nationally representative plot network. , 2011 .

[61]  A. Sajid Systematic Evaluation of Kriging and Inverse Distance Weighting Methods for Spatial Analysis of Soil Bulk Density. , 2013 .

[62]  Christopher M. Bishop,et al.  Neural networks for pattern recognition , 1995 .

[63]  M. Austin,et al.  An Ecological Perspective on Biodiversity Investigations: Examples from Australian Eucalypt Forests , 1998 .

[64]  I. Oliver,et al.  Species abundance distributions should underpin ordinal cover‐abundance transformations , 2019, Applied Vegetation Science.

[65]  Philip A. Townsend,et al.  Remote Sensing of Plant Biodiversity , 2020 .

[66]  Péter Török,et al.  Mechanisms shaping plant biomass and species richness: plant strategies and litter effect in alkali and loess grasslands , 2013 .

[67]  Andrew K. Skidmore,et al.  Advances in remote sensing of vegetation function and traits , 2015, Int. J. Appl. Earth Obs. Geoinformation.

[68]  James E. M. Watson,et al.  Biodiversity: The ravages of guns, nets and bulldozers , 2016, Nature.

[69]  J. Morgan,et al.  A framework to predict the effects of livestock grazing and grazing exclusion on conservation values in natural ecosystems in Australia. , 2007 .

[70]  D. Lindenmayer,et al.  Landscape modification and habitat fragmentation: a synthesis , 2007 .

[71]  T. M. Smith,et al.  A new model for the continuum concept , 1989 .

[72]  M. Austin,et al.  A new model for the continuum concept , 1989, Vegetatio.

[73]  J. Janssen,et al.  Large vegetation databases and information systems: New instruments for ecological research, nature conservation, and policy making , 2011 .

[74]  Victoria J. Burton,et al.  Has land use pushed terrestrial biodiversity beyond the planetary boundary? A global assessment , 2016, Science.

[75]  Jennifer A. Miller Incorporating Spatial Dependence in Predictive Vegetation Models: Residual Interpolation Methods , 2005 .

[76]  Mahta Moghaddam,et al.  Integration of radar and Landsat-derived foliage projected cover for woody regrowth mapping, Queensland, Australia , 2006 .

[77]  Scarth Peter Tracking Grazing Pressure and Climate Interaction - The Role of Landsat Fractional Cover in Time Series Analysis , 2012 .

[78]  Rob Lesslie,et al.  Land use information for integrated natural resources management—a coordinated national mapping program for Australia , 2006 .

[79]  S. Levin The problem of pattern and scale in ecology , 1992 .

[80]  Mark New,et al.  Ensemble forecasting of species distributions. , 2007, Trends in ecology & evolution.

[81]  Helen M. Regan,et al.  Big data for forecasting the impacts of global change on plant communities , 2017 .

[82]  Josep Peñuelas,et al.  sPlot – A new tool for global vegetation analyses , 2019, Journal of Vegetation Science.

[83]  Michael Drielsma,et al.  Synthesis of pattern and process in biodiversity conservation assessment: a flexible whole‐landscape modelling framework , 2010 .

[84]  Antoine Guisan,et al.  Spatial modelling of biodiversity at the community level , 2006 .

[85]  F. Gilliam,et al.  The Ecological Significance of the Herbaceous Layer in Temperate Forest Ecosystems , 2007 .

[86]  Marvin N. Wright,et al.  SoilGrids250m: Global gridded soil information based on machine learning , 2017, PloS one.

[87]  Susan L Ustin,et al.  Remote sensing of plant functional types. , 2010, The New phytologist.

[88]  S. A. Cain Life-forms and phytoclimate , 2008, The Botanical Review.

[89]  Ladislav Mucina,et al.  Twenty years of numerical syntaxonomy , 1989, Vegetatio.

[90]  M. Turner Landscape ecology in North America: past, present, and future , 2005 .

[91]  David Keith,et al.  Ocean shores to desert dunes : the native vegetation of New South Wales and the ACT , 2004 .

[92]  Alan H. Fielding,et al.  Machine Learning Methods for Ecological Applications , 2012, Springer US.

[93]  Philip A. Townsend,et al.  Prospects and Pitfalls for Spectroscopic Remote Sensing of Biodiversity at the Global Scale , 2020, Remote Sensing of Plant Biodiversity.

[94]  J. Svenning,et al.  Disequilibrium vegetation dynamics under future climate change. , 2013, American journal of botany.

[95]  R. Ewers,et al.  Countering the effects of habitat loss, fragmentation, and degradation through habitat restoration , 2020 .

[96]  P. S. Lake,et al.  Disturbance, patchiness, and diversity in streams , 2000, Journal of the North American Benthological Society.

[97]  R. G. Davies,et al.  Methods to account for spatial autocorrelation in the analysis of species distributional data : a review , 2007 .

[98]  A. Getis The Analysis of Spatial Association by Use of Distance Statistics , 2010 .

[99]  P. Dixon,et al.  Accounting for Spatial Pattern When Modeling Organism- Environment Interactions , 2022 .

[100]  Joop H.J. Schaminée,et al.  Vegetation survey: A new focus for applied vegetation science , 2011 .