Doctor of Philosophy

It is a pleasure to write that I am now, nearly, degreed.

My PhD was recently accepted into the Library at The University of Melbourne. I thought I would mark the occasion with short summary of the beast.

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Some Mallee biodiversity

Overall summary:

Plant height and growth are fundamental to the understanding of species’ ecological strategies, to the description and prediction of ecosystem dynamics and to vegetation management. I explored how plant functional traits can be used to predict woody plant growth for many species.  I demonstrated internal and out-of-sample prediction of species growth trajectories from traits, I dissected methods to evaluate the predictive capacity of growth models and I outlined a virtual ecologist approach to designing robust field studies for complex analysis.

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Ominous skies and more mallee biodiversity

Chapter summaries:

Chapter one incorporates plant functional traits into multi-species hierarchical non-linear models of plant growth. This approach increases our understanding of trait-growth relationships but also aids our ability to draw predictive inferences from them.  I built and parameterized models with a case-study of time since fire in semi-arid mallee woodland. I demonstrated inference by predicting species height-growth trajectories from traits to species with few data, to species with no growth data, only trait information, and for hypothetical species with defined trait combinations.

Chapter two contributed to the growth modeling literature by focusing on evaluating the predictive capacity of non-linear growth models using cross-validation.  I demonstrated why cross-validation is important compared to naïve performance metrics and demonstrated the value of using multiple metrics to capture different aspects of model performance.

Gaining greater predictive capacity in trait-based ecology may also require stronger quantitative tests of model transferability, which is a severe test of how general a model actually is.  In chapter three I tested the out-of-sample predictive ability or transferability of my trait-growth models by using traits to predict the growth trajectories between species in three different ecosystems.

The worth of predictions and inference from data analysis is intimately linked to the statistical and ecological assumptions of fitted models and fundamentally to the data underlying the analysis. My final chapter demonstrated a virtual ecologist approach to aid in the design of studies that use complex analysis techniques.  I used a simulation based on realistic fieldwork constraints such as species detection and occupancy rates, as well as travel times and unpredictable field conditions. This assists planning how much data is needed and how long that data will take to collect for hierarchical multi-species nonlinear models.

Phew!

In the unlikely event someone would like to read my thesis, get in touch and I will send you the open access link.

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Red roads and more mallee biodiversity

 

 

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VicBioCon 2018

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After a successful inaugural Victorian Biodiversity Conference earlier this year, a group of motivated students and early career researchers from a wide range of Victorian Universities (RMIT, La Trobe, Monash, Federation, Charles Sturt, Melbourne, Deakin) have begun planning our next conference to be held 6th-7th of February 2018 at La Trobe University, Melbournehttps://www.vicbiocon.com

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Some colourful examples of Victorian Biodiversity

This event aims to be a low cost and accessible conference to promote networking between graduate and postdoctoral researchers, as well as practitioners in government and NGOs working on research related to Victorian biodiversity.

The conference will provide an important and rare opportunity for young researchers to hear from government, industry and non-governmental organisations, as well as foster inter-University interactions through a series of plenaries, invited talks, workshops and networking opportunities.

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Some more Biodiversity for you … all plant themed, of course. 

Abstract submission closes on the 15th of November, submit yours here: abstract submission!

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Growth races in The Mallee

The second paper from my PhD has been accepted for publication:

Thomas, FM and Vesk, PA (2017) Growth races in The Mallee: height growth in woody plants examined with a trait-based model.  Austral Ecology, early view.

In this paper Peter Vesk and I explore growth trajectories of woody plants in the Victorian Mallee, a semi-arid region of south-eastern Australia.

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An early time-since-fire site in Murray Sunset National Park

We examine the influence of plant functional traits on growth trajectories. We test trait-growth relationships by examining the influence of specific leaf area, woody density, seed size and leaf nitrogen content on three aspects of plant growth; maximum relative growth rate, age at maximum growth and asymptotic height.

Woody plant species in the semi-arid mallee exhibit fast growth trajectories. Small seeded species were likely to be the fastest to reach maximum height, while large-seeded species with high leaf nitrogen were likely the slowest. Tall species had low stem densities and tended to have low specific leaf area.

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Some colour from Murray Sunset. Westringia rigida (Lamiaceae); Beyeria opaca (Euphorbiaceae); Acacia brachybotrya (Mimosaceae); Phebalium squamulosum (Rutaceae); Eremophila glabra (Scrophulariaceae) and Halgania cyanea (Boraginaceae).

We modeled plant growth using a hierarchical multi-species model that formally incorporates plant functional traits as species-level predictors of growth, which provides a method for predicting species height growth strategies as a function of their traits.

We further extended this approach by using the modeled relationships from our trait-growth model to predict: growth trajectories of species with limited data; real species with only trait data and; hypothetical species based only on trait coordination. We hope this highlights the potential to use trait information for ecological inference and to generate predictions that could be used for management.

Please email if you would like more information.

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Some fine mallee forms.

 

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Are trait-growth models transferable? Predicting multi-species growth trajectories between ecosystems using plant functional traits

I have a new paper out! Read it here: https://doi.org/10.1371/journal.pone.0176959

Plant functional traits are increasingly used to generalize across species, however few examples exist of predictions from trait-based models being evaluated in new species or new places.  In this paper Peter Vesk and I ask, can we use functional traits to predict growth of unknown species in different areas?

We used three independently collected datasets (thank you Daniel Falster and Annette Muir for contributing their data), each containing data on heights of individuals from non-resprouting plant species over a chronosquence of time-since-fire sites from three ecosystems in south-eastern Australia. We examined the influence of specific leaf area, woody density, seed size and leaf nitrogen content on three aspects of plant growth; maximum relative growth rate, age at maximum growth and asymptotic height.

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Growth curves for species occurring in three different ecosystems

We then tested our capacity to perform out-of-sample prediction of growth trajectories between ecosystems using species functional traits.  We believe there is evidence to suggest that growth trajectories themselves may be fundamentally different between ecosystems and that trait-height-growth relationships may change over environmental gradients.

Please get in touch if you are interested in this work!

 

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The Victorian Biodiversity Managers’ Network

I recently attended a Forum on Planning and Monitoring for Biodiversity Management held by the Indigenous Flora and Fauna Association’s Victorian Biodiversity Managers’ Network, in conjunction with Rob Scott from Naturelinks, hosted at The Arthur Rylah Institute.

The Indigenous Flora and Fauna Association (IFFA) is a volunteer based organization created in 1986 whose aim is “to promote the appreciation, study, conservation and management of indigenous flora and fauna through research and discussion, networking and advocacy, and information exchange”. Check out their website here: http://www.iffa.org.au

The Victorian Biodiversity Managers’ Network is in creation! IFFA recognised the need for a network to promote biodiversity management and to bring together people who manage land for biodiversity in Victoria to facilitate knowledge exchange.

IFFA recently hosted a workshop with a people from a wide range of organisations to brainstorm the scope of a biodiversity managers’ network. From this workshop it was decided the scope and direction of the Victorian Biodiversity Managers’ Network would be to:

  • developing best-practice industry standards and industry promotion
  • information and knowledge sharing using a website and workshops
  • building capacity of biodiversity managers through short courses and industry accreditation

The Forum on Planning and Monitoring for Biodiversity Management was held as one of the first official events of the Victorian Biodiversity Managers’ Network.   One of the benefits of this event and of the Network, was that it brought together many people from different organisations; local councils, consultants, non-government and government organisations, landcare groups and friends networks.

The focus of the day was Planning and Monitoring and this was focused around an introduction to the Open Standards for the Practice of Conservation – a systematic method for managing conservation projects: http://cmp-openstandards.org/

Dr Kate Fitzherbert from Bush Heritage spoke first and discussed their use of the Open Standards for the Practice of Conservation and outlined how this logical and transparent process helps to understand projects in their environmental, political and social context and helps to figure out which are the right factors to monitor.

Doug Evans from Nillumbik Landcare Network spoke about their use of the open standards to outline the collective environmental assets of the Landcare network and figure out cost effective and practical methods to manage them.

Phil Pegler from Parks Victoria spoke about the conservation action planning and the continual evolution of approaches to respond to issues of community and stakeholder engagement, organisation culture, defining goals and measuring success and prioritizing resources.

Emma Mann and Scott Nutt from Banyule City Council presentation showed us their use of GIS technology for data collection, which provides a faster, more precise and easier to access method for collecting and storing environmental data.

Dr Chris Jones from The Arthur Rylah Institute spoke about monitoring methods for environmental management and gave us an overview of commonly used methods to address different monitoring challenges. He outlined some important questions when thinking about monitoring such as why are you monitoring? What are you trying to monitor? How will you use this data?

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Chris Jones speaking to a full room about monitoring techniques

Lincoln Kern from Practical Ecology discussed and provided some examples of planning and monitoring in the commercial ecological management market, and also introduced the National Standards for the practice of ecological restoration in Australia http://www.seraustralasia.com/pages/standards.html developed by the Society for Ecological Restoration Australasia http://www.seraustralasia.com.

The second part of the Forum was a workshop where Stuart Cowell from Conservation Management took us through a case study using some of the tools and processes of the Open Standards. We learnt about ‘results chains’ and their use in testing possible strategies, identifying conservation actions and prioritising monitoring for conservation management projects.

The final part of the day was a panel discussion about improving planning and monitoring practices in Victoria and an exploration of how The Biodiversity Managers’ Network can support this.

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Workshop participants learning about Open Standard Result Chains

It was a great day and an exciting start to a new network of passionate people who want to manage Victoria’s vegetation using best practices.  The Bushland Managers’ Network will soon have a website; and The Wild Melbourne crew http://wildmelbourne.org were at the forum recording all the talks, so these will become available shortly. In the meantime if you would like anymore information about The Biodiversity Managers’ Network email: vicbmn@gmail.com 


 

 

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Reproductive Maturity in Plants

I presented a poster at this years Ecological Society of Australia Conference, held in Adelaide.  My poster presented my initial ideas for writing a review on reproductive maturity in plants, how this term is quantified and how these data are used in management.  ESA has fabulous student prizes each year (https://www.ecolsoc.org.au/events-and-activities/conferences/student-prizes), and I was fortunate enough to take home a prize from the Australian Flora Foundation, Thanks!

 

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Thirty years after Noble and Slatyer’s (1980) use of minimal demographic data to predict species replacement sequences and vegetation response to recurrent disturbances, ecologists are still ignorant of basic knowledge of life history characteristics for many plant species, and managers are still asking for it.  While qualitative data are reasonably widely available, quantitative data on species life history characteristics are often lacking despite being fundamentally useful for quantifying growth rates and ‘age to reproductive maturity’ for use in ecological fire management.

‘Reproductive maturity’ is a central concept for predicting species responses to disturbance, yet is linguistically vague with uncertainties surrounding what to measure, when, why and how to quantify it. Different types of data can be modelled in different ways.  The probability of reproduction to plant size through logistic regression, if fecundity is directly measured, we can characterise reproductive output with a sigmoid curve, or do both using a ‘hurdle’ model which combines probabilities of being reproductively mature with sized-based estimates of expected reproductive output.  The different data types and the different modelling approaches give us more or less flexible inference that can be used for management.

Please get in touch if you are interested in any of these ideas!

And yes, all photos are my own… and that massive flower took a long time to make!

 

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My Veski Fellowship experience

I was fortunate to receive a Veski Fellowship, which allowed me to travel overseas this year for five-months visiting researchers and managers in Mediterranean regions of the world, as well as a few extra countries with specialists who are doing researched aligned to mine.

A sunset in Spain

I am beginning to try to capture this incredible experience by the written word, and will be posting a series of blogs about my trip. To start with, below is a brief overview of places I went, people I met and things I did.

I began my journey in Los Angeles, California, USA.

The first of many friendly and generous ecologists I met with was Phil Rundel, who is a Distinguished Professor within the School of Ecology and Evolutionary Biology at UCLA. I was very fortunate to benefit from Phil’s hospitality and I enjoyed a tour of the magnificent grounds of UCLA, sat in on one of his field lectures that took place in the impressive Mildred E. Mathias Botanic Garden and enjoyed a fieldtrip with Phil, benefitting from his botanical knowledge, into some of California’s Chaparral.

Some Chaparral in The Santa Monica Mountains

It was also a pleasure to meet Sarah Ratay, a Californian botanist and current PhD student of Phil Rundel. Sarah introduced me to Steve Laymon, another Californian Botanist and the three of us went botanizing over a weekend to Wind Wolves Preserve an impressive Conservation Area in an ecologically unique region of California. We were hunting a particular Genus in the Onagraceae, Clarkia, which Steve is currently compiling a field guide for.

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Two species in the genus Clarkia in Onagraceae, which we hunted in Wind Wolves Preserve.

I also had the pleasure of meeting Martha Whitter, a manager for the National Parks Service in Los Angeles. She showed me a patch of her favourite chaparral, which included an interesting herb field and we discussed fire management in LA and the similarities and differences attitudes, approaches and available data in connection with ecological management between Victoria and California.

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Some Californian species and an example of a herb field moving into a patch of Oak woodlands, before becoming Chaparral in The Santa Monica Mountains.

I met with John Keeley, who works with the United States Geological Survey at the Western Ecological Research Centre which is located at the Sequoia and Kings Canyon Field Station in the National Park . I also met with many of the other friendly and interesting folk who work there, including Nate Stevenson and Tony Carsarcio. This was an excellent opportunity for me to chat with fire managers as well as fire ecologists about fire management within the National Park. I was also fortunate to fit in some more chaparral botanizing, as well as a trip with Jon to visit those Giant Sequoias. It was a pleasure to meet Melanie Keeley who runs the indigenous plant nursery within the National Park and see her propagation skills in action.

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Some fabulous plants of Sequoia National Park, including a Giant Redwood.

I took a drive into the central Californian Valley and went to UC Merced to visit Associate Professor Emily Moran to speak about the kinds of demographic data that are used in complex multi-species plant models, the various places these data may be sourced from and the evaluation of hierarchical models.

I then drove through the Mojave Desert, stopping to look at some Joshua Trees, to UC Riverside, where I met with Professor Helen Regan. By this time, I had explained my research to quite a few scientist and managers, but it seems like everyone has a slightly different research focus and therefore slightly different questions of comments on my research. This was undoubtedly one of the most useful aspects of my trip, having to explain my research over and over and respond to a diverse range of constructive criticism. I really valued my chat with Helen and it left me with a couple of points in my notebook to think about and address in future papers.

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Joshua Trees in the Mojave Desert

I happened to be in town for the 25th Graduate Student meeting of the Californian Botanical Society  and I was asked to be a student judge that day. This was a great opportunity to hear the types of botanical research that is happening in California and it was a pleasure to talk botanical talk in the evening at the Conference Dinner.

I then travelled over the East Coast of The USA, to visit Patuxent Wildlife Research Center . This was a fabulous place to visit, not only to pick the brains of the excellent decision scientists who work there, but also because it was the site of much of the research that was written about in Rachel Carson’s Silent Spring. During my stay I learnt a little about Decision Science with Michael Runge, Jim Nicholls and Sarah Converse. I had seriously helpful discussions about evaluating hierarchical models with Bill Link and Andy Royale and chatted about designing useful field optimization functions with Jim Hines.   From here I travelled to Michigan to undertake a course in Structured Decision Making at The Detroit River International Wildlife Refuge. This was not only a fabulous course, taught by Sean Blomquist and Pat Heglund, but also a fascinating opportunity to listen to reserve managers who were keen to implement the SDM framework into their practices.

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Some ecosystems at Patuxent, it was the beginning of Spring and everything was starting to bloom.

I travelled from The USA to Dublin, Ireland to meet with Professor Yvonne Buckley at Trinity College, Dublin. I am interested in the kinds of data that are used when people research, or use the term ‘reproductive maturity’ in relation to plants. At Trinity College I accessed the species matrix models and worked on code to calculate aspects of reproductive maturity for the species contained within this dataset, such as ‘reproductive value’ and ‘net reproductive rate’.

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A gorgeous Irish Violet

Whilst there I also had the pleasure of meeting Anna Csergo, a post doctoral fellow at Trinity College who steers the Plant PopNet project, which is a global demographic study of Plantago lanceolata (Planataginaceae). An incidental, yet very fortunate opportunity also came to meet Antoine Guisan and Olivier Broennimann. There was another Southern visitor too, Ronny Groenteman from Landcare Research in New Zealand. Ronny works on bio control and is interested in integral projection models of Hypericum perforatum (Hypericaceae) also known as Saint Johns Wart.

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The Burren – a diverse area of Ireland

I went to Valencia, Spain to meet with Juli Pausas  at Centro de Investigaciones sobre Desertification, a fire ecologist who has published extensively on fire persistence traits in Mediterranean ecosystems. Whilst there, we began writing a paper together on the proportional change of functional groups over a productivity and disturbance gradient, which is an extension of an earlier paper of his. We are going to be including changes in phylogenetic and functional diversity as well as consider multiple fire related functional types in this new analysis.

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Ivy called Yedra in Spanish, also the name of the lovely Yedra Garcia!

The lab that he works in happens to also be full of other excellent people, and it was a delight to meet Miguel Verdu, Patricio Garcia-Fayos, Jose Navarro Cano, Matra Goberna, Alicia Montesinos and Eduardo Perez. I also had the pleasure of spending some time in the field with Yedra Garcia, helping to collect data for her PhD.

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Some burnt Spanish vegetation

From Spain, I jetted South to Cape Town, South Africa.

I went to The University of Cape Town to meet with Emeritus Professor William Bond and Professor Jeremy Midgley. There, my work focused on discussions around the concept of plant reproductive maturity and what it means in different Mediterranean regions for fire management. I was very fortunate to get some field time with both William and Jeremy, and this provided an excellent opportunity for me to see the South African Fynbos, Renosterveld and Savannah ecosystems and compare plant strategies across these different ecosystems, but also to the other Mediterranean ecosystems I had previously visited.  A particular highlight was to visit Hluhluwe-iMfolozi Park in the North East of South Africa, and help out with some fieldwork with two of William’s students; Josh van der Ploeg and Huyam Altayeb, both of whom are working on plants in savannah ecosystem.

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One of around 900 Erica species, many of which look small and pink.

Whilst at UCT, I also met with Ross Turner, an exceptional botanist and an Erica specialist, Heath Beckett, a PhD student of William Bond studying forest-thicket-savannah dynamics and Tristian Charles-Dominic a Post Doctoral Researcher studying plant architecture and functional types in Savannah plants.

Whilst in Cape Town I also visited SAEON – The South African Environmental Observation Network, and I met with Dr Jasper Slingsby who is both a lovely person and an excellent botanist! It was a pleasure to hike over Table Mountain botanizing and collecting climate data with him.

Of course, all of this was interspersed with many walks in the stunning Kirstenbosch Gardens.

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Oh Fynbos… how I miss you.

The final destination of my trip was to Grenoble, France, to practice my French speaking skills and visit Dr Wilfried Thuiller at Laboratoire d’ecologie alpine (LECA) in Grenoble. Here, I discussed using and calculating phylogenetic and functional diversity with Wilfried and Dr Loic Chalmandrier, a recently finished PhD student.

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Some French and Italian Mountains and plants.

Thanks to Dr Amelie Saillard, I was able to visit Lautaret Alpine Botanic Garden, and meet the organisers, botanists and volunteers who keep the gardens running. I was also fortunate to experience a day in the field measuring the demography of Eryngium alpinum (Apiaceae) with Irene Till-Bottraud, the director of LECA and Ceres Barros and Brad Carlson, PhD students of Wilfried Thuiller.

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Eryngium sp. (Apiaceae)

It was fabulous opportunity to see the French Alps and here about Cere’s work with the FATE model. I also got some alpine botanizing done in Italy, with a visit with Dr Matt Tullato, a post doc in LECA to Gran Paradiso National Park. A lovely coincidence occurred and one of our very own Qaecologists, Dr Laura Pollock is now working as a post doc at LECA. We had a productive time together constructing a phylogeny for some of my study species and finishing off a paper on the influence of functional traits on Mallee eucalypt species distributions.

Needless to say, a trip like this is hard to capture briefly! Please stay tuned for some more in depth posts, particularly about the ecological systems I saw and all those plants I photographed!

A huge thank you to everyone who I met overseas, those already mentioned and many un-mentioned here.  One big lesson I learnt, was that the world is packed full of friendly and generous folk, and from my sampled data there seems to be a strong correlation between being an ecologist and being a most excellent person.

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Mimetes sp. (Proteaceae) South Africa.

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