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Dr Timothy Staples
Dr

Timothy Staples

Email: 
Phone: 
+61 7 336 59154

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

Qualifications

  • Doctor of Philosophy, The University of Queensland

Works

Search Professor Timothy Staples’s works on UQ eSpace

20 works between 2016 and 2024

1 - 20 of 20 works

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

Expansion and evolution of the R programming language

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

Emergence patterns of locally novel plant communities driven by past climate change and modern anthropogenic impacts

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

Increased extinction in the emergence of novel ecological communities

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

Local compositional change and regional stability across 3000 years of coral reef development

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

Mangrove ghost forests provide opportunities for seagrass

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

Sound garden: How snakes respond to airborne and groundborne sounds

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

Drivers of Acacia and Eucalyptus growth rate differ in strength and direction in restoration plantings across Australia

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

Modelling climatic suitability for myrtle rust with a widespread host species

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

Variable response of Red Sea coral communities to recent disturbance events along a latitudinal gradient

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

Reef accumulation is decoupled from recent degradation in the central and southern Red Sea

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

AusTraits, a curated plant trait database for the Australian flora

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

Janzen–Connell effects partially supported in reef‐building corals: adult presence interacts with settler density to limit establishment

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

Limited relationships between mangrove forest structure and hydro-edaphic conditions in subtropical Queensland, Australia

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

Mainstreaming microbes across biomes

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

Comparing the recovery of richness, structure and biomass in naturally regrowing and planted reforestation

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

Productivity does not correlate with species and functional diversity in Australian reforestation plantings across a wide climate gradient

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

Applied ecological research is on the rise but connectivity barriers persist between four major subfields

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

Ancient DNA from Pandora Reef, GBR

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

Links between community ecology theory and ecological restoration are on the rise

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

Potential mechanisms of coexistence in closely related forbs

Funding

Current funding

  • 2024 - 2027
    Advancing detection and understanding of anomalous ecological change
    ARC Discovery Early Career Researcher Award
    Open grant

Past funding

  • 2021 - 2023
    Indicator framework for assessing the condition and recovery capacity of coral reef habitats in the Great Barrier Reef (GBRF project administered by AIMS)
    Australian Institute of Marine Science
    Open grant

Supervision

Availability

Dr Timothy Staples is:
Available for supervision

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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.

  • 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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