Predicting plant conservation priorities on a global scale

Significance The International Union for Conservation of Nature (IUCN) Red List of Threatened Species is a key tool for the conservation of biological diversity. The evaluation and addition of species to this list is a time-consuming and costly task, and as such, a large number of species are not listed. For example, only 5% of plant species housed in the Global Biodiversity Information Facility are currently listed on the IUCN Red List. The simple and integrated protocol presented here enables conservation researchers and managers to identify unassessed species most likely at risk and, thus, assists in the direction of resource allocation for conservation. Our results suggest that efforts have been highly skewed geographically, and identify conservation hotspots in need of further evaluation. The conservation status of most plant species is currently unknown, despite the fundamental role of plants in ecosystem health. To facilitate the costly process of conservation assessment, we developed a predictive protocol using a machine-learning approach to predict conservation status of over 150,000 land plant species. Our study uses open-source geographic, environmental, and morphological trait data, making this the largest assessment of conservation risk to date and the only global assessment for plants. Our results indicate that a large number of unassessed species are likely at risk and identify several geographic regions with the highest need of conservation efforts, many of which are not currently recognized as regions of global concern. By providing conservation-relevant predictions at multiple spatial and taxonomic scales, predictive frameworks such as the one developed here fill a pressing need for biodiversity science.

[1]  Stuart L. Pimm,et al.  Global patterns of terrestrial vertebrate diversity and conservation , 2013, Proceedings of the National Academy of Sciences.

[2]  T. Spencer,et al.  Reduction of Wind and Swell Waves by Mangroves , 2012 .

[3]  Deborah L Paul,et al.  Herbarium data: Global biodiversity and societal botanical needs for novel research , 2018, Applications in plant sciences.

[4]  Bertrand Michel,et al.  Correlation and variable importance in random forests , 2013, Statistics and Computing.

[5]  D. Tilman,et al.  Experimental Tests of the Dependence of Arthropod Diversity on Plant Diversity , 1998, The American Naturalist.

[6]  J. G. Burleigh,et al.  Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach. , 2013, American journal of botany.

[7]  Erwan Scornet,et al.  A random forest guided tour , 2015, TEST.

[8]  K. Mäler,et al.  The ecology and economics of biodiversity loss: the research agenda , 1992 .

[9]  Alexandre Antonelli,et al.  Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases? , 2015, Global ecology and biogeography : a journal of macroecology.

[10]  David C. Tank,et al.  Identifying cryptic diversity with predictive phylogeography , 2016, Proceedings of the Royal Society B: Biological Sciences.

[11]  J. Mallet,et al.  Host races in plant-feeding insects and their importance in sympatric speciation. , 2002, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[12]  Alejandro Ruete,et al.  Displaying bias in sampling effort of data accessed from biodiversity databases using ignorance maps , 2015, Biodiversity data journal.

[13]  C. Graham,et al.  Global priorities for conservation across multiple dimensions of mammalian diversity , 2017, Proceedings of the National Academy of Sciences.

[14]  S. Higgins,et al.  TRY – a global database of plant traits , 2011, Global Change Biology.

[15]  H. D. Cooper,et al.  A mid-term analysis of progress toward international biodiversity targets , 2014, Science.

[16]  E J Milner-Gulland,et al.  Quantification of Extinction Risk: IUCN's System for Classifying Threatened Species , 2008, Conservation biology : the journal of the Society for Conservation Biology.

[17]  Peter Bühlmann,et al.  MissForest - non-parametric missing value imputation for mixed-type data , 2011, Bioinform..

[18]  Andrew Gonzalez,et al.  The functional role of producer diversity in ecosystems. , 2011, American journal of botany.

[19]  R. Lande Risks of Population Extinction from Demographic and Environmental Stochasticity and Random Catastrophes , 1993, The American Naturalist.

[20]  Gérard Biau,et al.  Analysis of a Random Forests Model , 2010, J. Mach. Learn. Res..

[21]  Jane Elith,et al.  Detecting Extinction Risk from Climate Change by IUCN Red List Criteria , 2014, Conservation biology : the journal of the Society for Conservation Biology.

[22]  Andy Liaw,et al.  Classification and Regression by randomForest , 2007 .

[23]  Lin Jiang,et al.  Different Effects of Species Diversity on Temporal Stability in Single‐Trophic and Multitrophic Communities , 2009, The American Naturalist.

[24]  Matthew E Ritchie,et al.  Using the R Package crlmm for Genotyping and Copy Number Estimation. , 2011, Journal of statistical software.

[25]  S. Stuart,et al.  Wildlife in a changing world : an analysis of the 2008 IUCN red list of threatened species , 2009 .

[26]  Zhenyuan Lu,et al.  The taxonomic name resolution service: an online tool for automated standardization of plant names , 2013, BMC Bioinformatics.

[27]  J. P. Grime,et al.  Biodiversity and Ecosystem Functioning: Current Knowledge and Future Challenges , 2001, Science.

[28]  Chao Chen,et al.  Using Random Forest to Learn Imbalanced Data , 2004 .

[29]  E. Wilson,et al.  The Barometer of Life , 2010, Science.

[30]  Michael Hoffmann,et al.  The value of the IUCN Red List for conservation. , 2006, Trends in ecology & evolution.

[31]  Brian D. Farrell,et al.  Diversification at the Insect-Plant Interface , 1992 .

[32]  Åsa Persson,et al.  Editorial: Environmental Policy Integration: Taking stock of policy practice in different contexts , 2018, Environmental Science & Policy.

[33]  Eduard Szöcs,et al.  taxize: taxonomic search and retrieval in R , 2013, F1000Research.

[34]  Steven J. Cooke,et al.  Taxonomic bias and international biodiversity conservation research , 2017 .

[35]  B. Martín‐López,et al.  The pitfall-trap of species conservation priority setting , 2010, Biodiversity and Conservation.

[36]  Aaron D. Peacock,et al.  PLANT DIVERSITY, SOIL MICROBIAL COMMUNITIES, AND ECOSYSTEM FUNCTION: ARE THERE ANY LINKS? , 2003 .

[37]  J. L. Gittleman,et al.  Targeting global conservation funding to limit immediate biodiversity declines , 2013, Proceedings of the National Academy of Sciences.

[38]  M. Winter,et al.  Phylogenetic diversity and nature conservation: where are we? , 2013, Trends in ecology & evolution.

[39]  Richard Grenyer,et al.  Preserving the evolutionary potential of floras in biodiversity hotspots , 2007, Nature.

[40]  G. Tang,et al.  Indian Hedgehog: A Mechanotransduction Mediator in Condylar Cartilage , 2004, Journal of dental research.

[41]  C. Orme,et al.  Predicting the conservation status of data‐deficient species , 2015, Conservation biology : the journal of the Society for Conservation Biology.

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

[43]  M. Luoto,et al.  Drivers of high-latitude plant diversity hotspots and their congruence , 2017 .

[44]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[45]  K. Williams,et al.  Plant blindness and the implications for plant conservation , 2016, Conservation biology : the journal of the Society for Conservation Biology.

[46]  Matthew W. Pennell,et al.  Speciation gradients and the distribution of biodiversity , 2017, Nature.

[47]  R. Mittermeier,et al.  Biodiversity hotspots for conservation priorities , 2000, Nature.

[48]  G. Daily,et al.  Biodiversity loss and its impact on humanity , 2012, Nature.

[49]  D. R. Cutler,et al.  Utah State University From the SelectedWorks of , 2017 .

[50]  Mark C. Brundrett,et al.  Coevolution of roots and mycorrhizas of land plants. , 2002, The New phytologist.

[51]  F. Altermatt,et al.  Bridging ecology and conservation: from ecological networks to ecosystem function , 2017 .

[52]  P. Grandcolas,et al.  Taxonomic bias in biodiversity data and societal preferences , 2017, Scientific Reports.

[53]  A. Cuarón,et al.  An Evaluation of Threatened Species Categorization Systems Used on the American Continent , 2006, Conservation biology : the journal of the Society for Conservation Biology.

[54]  G. Mace,et al.  Bringing Ecosystem Services into Economic Decision-Making: Land Use in the United Kingdom , 2013, Science.

[55]  D. Tilman,et al.  Productivity and sustainability influenced by biodiversity in grassland ecosystems , 1996, Nature.

[56]  R. Aerts,et al.  Consequences of biodiversity loss for litter decomposition across biomes , 2014, Nature.

[57]  Owen L. Petchey,et al.  Biodiversity and Resilience of Ecosystem Functions. , 2015, Trends in ecology & evolution.

[58]  Hadley Wickham,et al.  The Split-Apply-Combine Strategy for Data Analysis , 2011 .