Overview
Background
I'm a quantitative community ecologist with broad experience across terrestrial and marine systems, modern and geological time, local and global scales with both theoretical and practical focus. I'm driven by discovery, interested in myriad topics on how communities form and function, but particularly how we measure and make comparisons between communities.
- Translating anomaly detection to ecology: In a world experiencing climate change, biodiversity loss and other human impacts, detecting anomalous ecological systems accurately and early potentially offers vast benefits to conservation and ecosystem management. Anomaly detection is a fast-moving area of research applied in fields as varied as banking fraud detection, cybersecurity and cancer diagnosis. These fields deal with data as complex and incomplete as ecology, but we haven't plumbed this expertise for benefits to ecology. This is the primary focus of my DECRA.
- Grounding ecological novelty for practical use: Ecologists have been talking about novel systems for twenty years, and related topics (such as "no-analog systems") for even longer. Despite well-cited work on how "novel" can be a useful label for ecological restoration, there's a mismatch between management frameworks, which often use ad-hoc qualitative criteria, and quantitative novelty research, which has been mostly performed at global scales. Understanding how to measure novelty, how analytic choices affect measurements, and how to downscale our inferences to be practicable, has been a focus for me and my colleagues.
- The linguistic evolution of programming languages: The use of scientific programming languages like R, Python and Julia are becoming not only popular, but mandatory skills for researchers. The utility of these languages has been improved by new versions and a plethora of community-created addon packages. This approximates features of natural language evolution, where lexicon changes over time. Understanding the speed and direction of how programming languages evolve can give us a unique insight into how humans learn and alter languages, and how we might ensure they remain understandable into the future. I am currently using GitHub as a vast repository of time-stamped programming “texts”, ripe for linguistic analysis.
- Community ecology through the lens of functional traits: It doesn’t matter who you are, it matters what you do. That applies to organisms too. Despite decades of research into how physiology and life history strategy, often proxied through easy-to-measure “functional traits”, functional ecology is still more niche than it should be. Currently my colleagues and I are exploring how a functional lens alters ecological novelty, but I am always thinking about ecology in the light of how organisms live.
Availability
- Dr Timothy Staples is:
- Available for supervision
Fields of research
Qualifications
- Doctor of Philosophy, The University of Queensland
Works
Search Professor Timothy Staples’s works on UQ eSpace
Featured
2023
Journal Article
Expansion and evolution of the R programming language
Staples, Timothy L. (2023). Expansion and evolution of the R programming language. Royal Society Open Science, 10 (4) 221550, 1-12. doi: 10.1098/rsos.221550
Featured
2022
Journal Article
Emergence patterns of locally novel plant communities driven by past climate change and modern anthropogenic impacts
Staples, Timothy L., Kiessling, Wolfgang and Pandolfi, John M. (2022). Emergence patterns of locally novel plant communities driven by past climate change and modern anthropogenic impacts. Ecology Letters, 25 (6), 1497-1509. doi: 10.1111/ele.14016
Featured
2020
Journal Article
Increased extinction in the emergence of novel ecological communities
Pandolfi, John M., Staples, Timothy L. and Kiessling, Wolfgang (2020). Increased extinction in the emergence of novel ecological communities. Science, 370 (6513), 220-222. doi: 10.1126/science.abb3996
2024
Journal Article
Local compositional change and regional stability across 3000 years of coral reef development
Staples, Timothy L. and Pandolfi, John M. (2024). Local compositional change and regional stability across 3000 years of coral reef development. Global Ecology and Biogeography, 33 (2), 244-258. doi: 10.1111/geb.13787
2023
Journal Article
Mangrove ghost forests provide opportunities for seagrass
Twomey, Alice J., Staples, Timothy L., Remmerswaal, Amelia, Wuppukondur, Ananth and Lovelock, Catherine (2023). Mangrove ghost forests provide opportunities for seagrass. Frontiers in Climate, 5 1284829. doi: 10.3389/fclim.2023.1284829
2023
Journal Article
Sound garden: How snakes respond to airborne and groundborne sounds
Zdenek, Christina N., Staples, Timothy, Hay, Chris, Bourke, Lachlan N. and Candusso, Damian (2023). Sound garden: How snakes respond to airborne and groundborne sounds. PLoS One, 18 (2) e0281285, 1-16. doi: 10.1371/journal.pone.0281285
2022
Journal Article
Drivers of Acacia and Eucalyptus growth rate differ in strength and direction in restoration plantings across Australia
Staples, Timothy L., Mayfield, Margaret M., England, Jacqueline R. and Dwyer, John M. (2022). Drivers of Acacia and Eucalyptus growth rate differ in strength and direction in restoration plantings across Australia. Ecological Applications, 32 (6) e2636, 1-17. doi: 10.1002/eap.2636
2021
Journal Article
Modelling climatic suitability for myrtle rust with a widespread host species
Meiklejohn, Natalie A., Staples, Timothy L. and Fensham, Rod J. (2021). Modelling climatic suitability for myrtle rust with a widespread host species. Biological Invasions, 24 (3), 831-844. doi: 10.1007/s10530-021-02689-z
2021
Journal Article
Variable response of Red Sea coral communities to recent disturbance events along a latitudinal gradient
Hammerman, Nicholas M., Rodriguez-Ramirez, Alberto, Staples, Timothy L., DeCarlo, Thomas M., Saderne, Vincent, Roff, George, Leonard, Nicole, Zhao, Jian-xin, Rossbach, Susann, Havlik, Michelle N., Duarte, Carlos M. and Pandolfi, John M. (2021). Variable response of Red Sea coral communities to recent disturbance events along a latitudinal gradient. Marine Biology, 168 (12) 177. doi: 10.1007/s00227-021-03984-y
2021
Journal Article
Reef accumulation is decoupled from recent degradation in the central and southern Red Sea
Hammerman, Nicholas M., Roff, George, Rodriguez-Ramirez, Alberto, Leonard, Nicole, Staples, Timothy L., Eyal, Gal, Rossbach, Susann, Havlik, Michelle N., Saderne, Vincent, Zhao, Jian-xin, Duarte, Carlos M. and Pandolfi, John M. (2021). Reef accumulation is decoupled from recent degradation in the central and southern Red Sea. Science of the Total Environment, 809 151176, 1. doi: 10.1016/j.scitotenv.2021.151176
2021
Journal Article
AusTraits, a curated plant trait database for the Australian flora
Falster, Daniel, Gallagher, Rachael, Wenk, Elizabeth H., Wright, Ian J., Indiarto, Dony, Andrew, Samuel C., Baxter, Caitlan, Lawson, James, Allen, Stuart, Fuchs, Anne, Monro, Anna, Kar, Fonti, Adams, Mark A., Ahrens, Collin W., Alfonzetti, Matthew, Angevin, Tara, Apgaua, Deborah M. G., Arndt, Stefan, Atkin, Owen K., Atkinson, Joe, Auld, Tony, Baker, Andrew, von Balthazar, Maria, Bean, Anthony, Blackman, Chris J., Bloomfield, Keith, Bowman, David M. J. S., Bragg, Jason, Brodribb, Timothy J. ... Ziemińska, Kasia (2021). AusTraits, a curated plant trait database for the Australian flora. Scientific Data, 8 (1) 254, 254. doi: 10.1038/s41597-021-01006-6
2021
Journal Article
Janzen–Connell effects partially supported in reef‐building corals: adult presence interacts with settler density to limit establishment
Sims, Carrie A., Sampayo, Eugenia M., Mayfield, Margaret M., Staples, Timothy L., Dalton, Steven J., Gutierrez‐Isaza, Nataly and Pandolfi, John M. (2021). Janzen–Connell effects partially supported in reef‐building corals: adult presence interacts with settler density to limit establishment. Oikos, 130 (8) oik.08110, 1310-1325. doi: 10.1111/oik.08110
2021
Journal Article
Limited relationships between mangrove forest structure and hydro-edaphic conditions in subtropical Queensland, Australia
Hill, Jack W., Bourke, Lachlan A., Horton, Ciara M., Staples, Timothy L. and Lovelock, Catherine E. (2021). Limited relationships between mangrove forest structure and hydro-edaphic conditions in subtropical Queensland, Australia. Estuarine, Coastal and Shelf Science, 248 106930, 106930. doi: 10.1016/j.ecss.2020.106930
2020
Journal Article
Mainstreaming microbes across biomes
Clarke, Laurence J., Jones, Penelope J., Ammitzboll, Hans, Barmuta, Leon A., Breed, Martin F., Chariton, Anthony, Charleston, Michael, Dakwa, Vongai, Dewi, Fera, Eri, Rajaraman, Fountain-Jones, Nicholas M., Freeman, Jules, Kendal, Dave, McDougal, Rebecca, Raes, Eric J., San Sow, Swan Li, Staples, Timothy, Sutcliffe, Brodie, Vemuri, Ravichandra, Weyrich, Laura S. and Flies, Emily J. (2020). Mainstreaming microbes across biomes. BioScience, 70 (7), 589-596. doi: 10.1093/biosci/biaa057
2019
Journal Article
Comparing the recovery of richness, structure and biomass in naturally regrowing and planted reforestation
Staples, Timothy L., Mayfield, Margaret. M., England, Jacqueline R. and Dwyer, John. M. (2019). Comparing the recovery of richness, structure and biomass in naturally regrowing and planted reforestation. Restoration Ecology, 28 (2) rec.13077, 347-357. doi: 10.1111/rec.13077
2019
Journal Article
Productivity does not correlate with species and functional diversity in Australian reforestation plantings across a wide climate gradient
Staples, Timothy L., Dwyer, John M., England, Jacqueline R. and Mayfield, Margaret M. (2019). Productivity does not correlate with species and functional diversity in Australian reforestation plantings across a wide climate gradient. Global Ecology and Biogeography, 28 (10) geb.12962, 1417-1429. doi: 10.1111/geb.12962
2019
Journal Article
Applied ecological research is on the rise but connectivity barriers persist between four major subfields
Staples, Timothy L., Dwyer, John M., Wainwright, Claire E. and Mayfield, Margaret M. (2019). Applied ecological research is on the rise but connectivity barriers persist between four major subfields. Journal of Applied Ecology, 56 (6), 1492-1498. doi: 10.1111/1365-2664.13373
2019
Other Outputs
Ancient DNA from Pandora Reef, GBR
Gomez-Cabrera, Maria, Young, J M, Roff, G, Staples, T, Ortiz, J C, Pandolfi, John M and Cooper, A (2019). Ancient DNA from Pandora Reef, GBR. The University of Queensland. (Dataset) doi: 10.14264/uql.2019.2
2017
Journal Article
Links between community ecology theory and ecological restoration are on the rise
Wainwright, Claire E., Staples, Timothy L., Charles, Lachlan S., Flanagan, Thomas C., Lai, Hao Ran, Loy, Xingwen, Reynolds, Victoria A. and Mayfield, Margaret M. (2017). Links between community ecology theory and ecological restoration are on the rise. Journal of Applied Ecology, 55 (2), 570-581. doi: 10.1111/1365-2664.12975
2016
Journal Article
Potential mechanisms of coexistence in closely related forbs
Staples, Timothy L., Dwyer, John M., Loy, Xingwen and Mayfield, Margaret M. (2016). Potential mechanisms of coexistence in closely related forbs. Oikos, 125 (12), 1812-1823. doi: 10.1111/oik.03180
Supervision
Availability
- Dr Timothy Staples is:
- Available for supervision
Before you email them, read our advice on how to contact a supervisor.
Available projects
-
Measuring marine climate anomalies
There are dire predictions for the ecological consequences of ocean warming. However, climate change models predict increases in environmental volatility, temperature extremes and potentially changes to global currents.
Much work has been done on the local change of climatic conditions via “climate velocity”, and the emergence of global “marine novelty”. Both methods attempt to measure “climatic anomalies”, deviations from the past, but with restrictions and assumptions that do not capture the multifaceted nature of climate nor how taxa experience local environmental conditions.
This project attempts to answer a seemingly simple question: “Where (and how) have ocean environments changed from the past, and where might they change in the future?”
To answer this question, the successful applicant will adapt anomaly detection techniques applied in video surveillance and cancer diagnosis to spatiotemporal climate grids, creating consistent and robust measurements of climate anomalies that extend beyond annual means and global comparisons.
This project forms part of an ARC Discovery Early Career Research Award DE240100398: Advancing detection and understanding of anomalous ecological change, commencing 1st September 2024.
Successful applicant will have:
- Competence in handling, processing, and analysing large data products.
- Proficiency in a statistical programming language (e.g., R, Julia, Python).
- Strong ecological, biological, or climatological expertise. Marine-specific knowledge is advantageous but not required.
- Broad curiosity and be motivated by problem-solving.
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Reframing biodiversity and conservation indicators via ecological anomalies
Biological conservation and ecological restoration are hampered by the need to make complex inferences from limited data. Nowhere is this more evident than in comparisons between communities or ecosystems. It is a challenge to distinguish uniquely pristine or degraded systems within and across geographic and political entities.
Comparing multidimensional observations is an old practice, expansively studied under the frame of “anomaly detection”, applied in fields as varied as cybersecurity, banking fraud detection and cancer diagnosis. Ecological monitoring and management have not, as yet, explored whether these techniques have application for wicked environmental problems.
This project will explore the utility of anomaly detection methods as (1) advancing the concept of complementarity in conservation planning, (2) whole-of-system monitoring to measure ecological health and monitor for early warning signs of degradation and (3) potential development of national and international reporting indicators.
This project forms part of an ARC Discovery Early Career Research Award DE240100398: Advancing detection and understanding of anomalous ecological change, commencing 1st September 2024.
Successful applicant will have:
- Strong ecological or environmental expertise.
- Proficiency in a statistical programming language (e.g., R, Julia, Python).
- Broad curiosity and be motivated by problem-solving.
- A strong interest in conservation and biodiversity management.
Media
Enquiries
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