AusPlotsDesigning a surveillance monitoring network for Australia.Presentation by Ben SparrowWith help from the Ausplots Teamben.sparrow@adelaide.edu.au

Political/Historical context

• Global Financial Crisis• Australian Government response -Stimulus• Favoured Infrastructure – NCRIS (National

Collaborative Research Infrastructure Scheme)• Research infrastructure – Environmental =

TERN• Not tangible infrastructure eg. Roads, but not

classical research either research – need to deliver Data – Different measures of Success

Primarily funded to support / develop ecological research infrastructure

– integrate existing data and make it accessible to the national and global ecosystem sciences community in a

common format; and

– collect new data strategically in areas of high priority to allow subsequent analysis and modeling of the assimilated

data.

In the context of AusPlots the Plots and their associated data are considered to be infrastructure.

TERNthe Terrestrial Ecosystem Research Network

What is TERN?

• A Network of scientists and practitioners collecting and delivering ecological research infrastructure.

• Delivered as a number of facilities:• Auscover: Ecological/ biophysical remote

sensing products• Ausplots: Surveillance monitoring of

Australian ecosystems• ACEAS – A Synthesis facility similar to NCEAS

• Coasts: Info in the interface between terrestrial and marine

• Australian Supersite Network (ASN): Highly instrumented study sites.

• Australian Transect Network (ATN): Data and questions on environmental gradients; Space as a proxy for time

• Eco-informatics – Data delivery warehouse; Fully integrated data

• E-Mast – Ecological and biophysical modelling

• Long Term Ecological Research Network (LTERN): Brings together scientists working on long term sites – Question based targeted monitoring

• Ozflux: a series of flux towers to understand fluxes between land and atmosphere

• Soil and Landscape Grid: Delivering Australian Soil information in line from plot to continent

• Many facilities collaborate together on aspects of their work.

After Eyre et. al. 2011

Population Ecology

Community Ecology

Biogeography/ Landscape Ecology

Types of monitoringAuscover/ E-mast/ ACEAS/ Soil Grid

LTERN/OzFlux/ASN

ATN

Ausplots

Monitoring

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There is ongoing tension between different types of monitoring regarding their relative merits.

Often a monitoring program is judged on what would define a successful monitoring program for a different type of

monitoring.

Each type of monitoring needs to be judged against its aims and objectives.

Which is better?They all have their Place!

All are needed and provide useful contributions to our knowledge of Australian environments.

Each of these endeavours need to cooperate/ collaborate with the others to provide a holistic solution to monitoring.

The most important parts are actually the

arrows!

Surveillance Monitoring• Looks at entire communities ( Is more likely to be concerned with

the trajectory of communities rather than individuals or species)• Versatile and reusable – Useful for many purposes• Drivers unknown (May provide some insight, but that is not the

focus of design)• Broad stakeholder base, given multiple purposes• Detect and quantify change that we don’t know about and weren’t

anticipating • Some hope of method standardisation – If method broad in scope

• Likely to be able to adapt to emerging issues – If method broad in scope

• Has focus areas rather than tightly defined questions – it is likely that this information will inform on many questions.

• Aims to detect and quantify environmental change across large geographical areas.

• Less likely for the same sites to be regularly revisited – Longer re-visit time. (Duration of many years)

• More often assessing long term change rather than shorter term dynamics.

NOT

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Because we want to know if there is a problem, but we don’t have the resources to have the fire

department everywhere all the time!

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Types of environments we work in

Acacia Forests and Woodlands

Chenopod Shrublands, Samphire Shrublands and Forblands

Tussock Grasslands

Mallee Woodlands and Shrublands

Melaleuca Forests and Woodlands

Hummock Grasslands

Eucalypt Woodlands

Eucalypt Open Forests

Tropical Eucalypt Woodlands/Grasslands

AusPlotsAn example of surveillance monitoring

Objectives of AusPlotsNational network of surveillance and ecosystem baseline assessment sites

Developing standardised plot assessment methods to be used for measuring and sampling vegetation and soils, and

Developing and implementing a stratification process to decide the locations of plots, which is applicable at a continental scale, and

Establish permanent plot infrastructure throughout Australia where baseline surveys of vegetation and soils will be conducted

by

Implementing the plot assessment methods developed for measuring and sampling vegetation and soils - in the locations decided, and

- analysing the samples collected, and

Storing the data and making it freely availableTo

enable the detection (and trajectory and magnitude) of environmental change across the continent to be determined.

Two Programs

• Ausplots Forests – 48 plots in Tall Eucalypt Forrest – Accurately

quantify Growth of Trees – 1 week a site• Ausplots Rangelands– Rangelands a management – using FAO definition

½ forest– 500+ Sites across the country– 1 day per site– Focus of this presentation

81% of AustraliaWide variety of environments

Wide climatic variationGenerally Data poor / gaps

Where we work

AusPlots

Stage 1. Determining Bioregional groupings using hierarchical clustering techniques

Stage 2. Decisions on which bioregions to sample

Stage 3. GIS analysis within each bioregion

Stage 4. Field Location whilst on ground.

Where? - Stratification

Addresses knowledge gaps

Located where there is a NEED for

data

Respond to local and regional information needs where compatible

Hutchinson et. al., 2005

Prentice/Dong u diag

Relates to a series of Temperature variables

Rela

tes t

o a

serie

s of M

oist

ure

varia

bles

Since the creation of the Rangelands protocols, and their widespread acceptance we’ve added:

» A Tall Eucalypt Forest protocol» A Condition assessment protocol» A Woodlands Protocol» A Vertebrate Fauna Survey Protocol,

With ongoing work on:» A Fungi Protocol» A Ground Dwelling Invertebrates» A Core attributes (quicker) method» Identifying and articulating what re-visits

entail.

New Method Development

Use new / innovative techniques where sensible

Consistent and accurate data Standards, Collection and Curation

A Nationally accepted method

Details all aspects of method

Easy to use and well illustrated

Explains reasoning

Regularly updated

Available at:

http://www.ausplots.org/useourinfrastructure/

Designed to be used with our training course

New modules being added – Check back regularly.

Data collection and curation

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Field Data Collection App: AusScribe

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Data Delivery System

Field Collection

Curation

DatabaseStorage

Retrieval

Data Delivery: Soils to Satellites

http://soils2sat.ala.org.au/ala-soils2sat/login/auth

Data Delivery: Aekoshttp://www.aekos.org.au/

Widespread collaborationExtensive Networking / Collaboration / input to the process

The challenges of this kind of project are greater socially than they are scientifically!

Over 50 national and international collaborators working with us on data collection and analysis.

SA SA

National

NationalNational

Collaborator

TAS QLD

NSW

NSWNSWNTWA

WA NSW

National

TERNTERN

TERN TERN

QLD

Field team

• Based in Adelaide• Provides consistency• Best way to use

scarce resources – Would prefer to have state based teams in the future if funding allowed.• Well equipped• Can train others• Work in conjunction

with state agencies where possible.• Work well together in

trying conditions.

Training courses

• At least one per year

• A day of lectures explaining all aspects of the

method• A day learning

each component of our method

(Vegetation, Soils and Technical

Aspects)• Focuses on

theoretical and practical aspects• Pragmatic• Held in the

Rangelands

OutputsStill early days for the project given that re-visits are

only just starting (along with further roll out)Currently used for validation of groundcoverRangeland management programsTaxonomy – New species and range extensionsModelling of climate change scenariosGovernment are supporting surveillance monitoring

as an essential input to future state of environment reporting.

Inform on soil crust ( and hence erosion)

…and many publications2015Christmas M., Breed M., and Lowe A.J. (In review) Constraints and conservation implications for climate change adaptation in plants. Biological ConservationGuerin G.R., Sweeney S.M., Pisanu P., Caddy-Retalic S., and Lowe A.J. (In review) Establishment of an ecosystem transect to address climate change policy

questions for natural resource management. Environmental ManagementGuerin G.R. and Lowe A.J. (In review) Mapping phylogenetic endemism using georeferenced branch extents. Methods in Ecology and EvolutionGuerin G.R., Ruokolainen L. and Lowe A.J. (In press) A georeferenced implementation of weighted endemism. Methods in Ecology and Evolution2014Bowman D.M.J.S., Williamson G.J., Keenan R.J. and Prior L.D. (2014) A warmer world will reduce tree growth in evergreen broadleaf forests: Evidence from

Australian temperate and subtropical eucalypt forests. Global Ecology and Biogeography, 23(8): 925-934. (DOI: 10.1111/geb.12171)Breed M.F., Christmas M.J. and Lowe A.J. (2014) Higher levels of multiple paternities increase seedling survival in the long-lived tree Eucalyptus gracilis.PLOS

ONE, 9(2) e90478 (DOI:10.1371/journal.pone.0090478)Guerin G.R., Martín-Forés I., Biffin E., Baruch Z., Breed M.F., Christmas M.J., Cross H.B. and Lowe A.J. (2014) Global change community ecology beyond

species sorting: a quantitative framework based on Mediterranean Biome examples. Global Ecology and Biogeography, 23: 1062–1072.http://dx.doi.org/10.1111/geb.12184

Guerin G.R., Biffin E., Jardine D.I., Cross H.B. and Lowe A.J. (2014) A spatially predictive baseline for monitoring multivariate species occurrences and phylogenetic shifts in Mediterranean southern Australia. Journal of Vegetation Science, 25: 338–348. http://dx.doi.org/10.1111/jvs.12111

McCallum K., Guerin G.R., Breed M.F. and Lowe A.J. (2014) Combining population genetics, species distribution modelling and field assessments to understand a species vulnerability to climate change. Austral Ecology, 39: 17 –28. http://dx.doi.org/10.1111/aec.12041

Prior L.D. and Bowman D.M.J.S. (2014) Across a macro-ecological gradient forest competition is strongest at the most productive sites. Frontiers in Plant Science, 5: 260. (DOI: 10.3389/fpls.2014.00260)

Prior L.D. and Bowman D.M.J.S. (2014) Big eucalypts grow more slowly in a warm climate: evidence of an interaction between tree size and temperature. Global Change Biology, 20(9): 2793-2799. (DOI: 10.1111/gcb.12540)

Schut A.G.T., Wardell-Johnson G.W., Yates C.J., Keppel G., Baran I., Franklin S.E., Hopper S.D., Van Neil K., Mucina L. and Byrne M. (2014) Rapid characterisation of vegetation structure to predict refugia and climate change impacts across a global biodiversity hotspot. PLOS ONE, 9: e82778. (DOI: 10.1371/journal.pone.0082778)

Tapper S-L., Byrne M., Yates C.J., Keppel G., Hopper S.D., Van Niel K., Schut A.G.T., Mucina L. and Wardell-Johnson G.W. (2014) Isolated with persistence or dynamically connected? Genetic patterns in a common granite outcrop endemic. Diversity and Distributions, 20(9): 987-1001 (DOI: 10.1111/ddi.12185)

Tapper S-L., Byrne M., Yates C.J., Keppel G., Hopper S.D., Van Niel K., Schut A.G.T., Mucina L. and Wardell-Johnson G.W. (2014) Long-term isolation and persistence of Stypandra glauca R.Br. (Hemerocallidaceae) on granite outcrops in both mesic and arid environments in southwestern Australia. Journal of Biogeography, 41: 2032-2044. (DOI: 10.1111/jbi.12343)

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Getting our message out

• Presentations to community groups.

• Workshops• Targeted

presentations (state agencies, fed Govt.)

• Briefing ministerial advisors

• Well maintained website• Conference presentations• International reference groups /

tours• Regular TERN Newsletter articles

to large mailing list.

About Our Method

• Practicality/pragmatism has had to prevail

• “It’s not about developing the perfect method, but rather understanding how imperfect the method is.”

Modular Methods• The method has been designed in modules

• Ease of use in the field• For your own purposes (not AusPlots funded) there is the

possibility of only including some modules• For AusPlots and training purposes we will cover all modules

S1

NEN5N4N3N2N1NW

W5

W4

W3

W2

W1

SW S2 S3 S4 S5 SE

E1

E2

E3

E4

E5

What do we collect?

Voucher Specimens for official Identification and future use.

Vouchers for genetic and isotope analysis

1. Take around 10 cm2 from each voucher specimen

2. Place into a synthetic tea bag and seal

3. Label with adhesive voucher label and scan with app

4. Place bag in box with ⅓ cup silica granules (self indicating and non-indicating granules)

5. Seal box and ensure it is labelled with plot identifier. Preferably 1 box per plot.Change silica every few days until indicator no longer changes colour.

6. Samples can then be used for isotope and DNA analyses

+ Duplicates for Dominant

species

Laying out the measuring tape between the transect end pegs

First point taken at the ‘0’ Meter mark

Point Intercept

Densiometer

Graduated Staff

Laser Pointer

Field Cover Assessment Device (Gandalf’s Staff)

Assesses canopy cover above the device

Indicates height

Assesses Cover below the device

Field Cover Assessment Device (Gandalf’s Staff)

Any vegetation touching the device between the laser pointer and the densitometer is also included

In this example the substrate is litter as that is what the laser is intersecting

Height is read from the staff

Assessing Cover above the device

• Uses a densitometer

• Ensure the device is level using the bubble level

• Use the cross hairs and small circle to identify what is intersected.

No Intersect

In Canopy - Sky

Eucalyptus sp.

Point Intercept Data

Basal Wedge

Three most dominant species nominated in each

strata, in decreasing order of cover

Structural Information

Ground Layer

Cenchrus cilliaris - 1

Mid Layer

Senna artemisioides ssp. Filifolia - 1

Upper LayerAcacia aneura – 1Acacia estrophiolata – 2Hakea divaricata - 3

Emergent Layer

Acacia estrophiolata - 1

During

After

Leaf Area Index

Soil Metagenomic Samples

9 Samples across the siteTop 3cm of soil and crustDried and stored

Soil Pit

9 x 30cm Subsites to sample variability

Store samples in bags and prepare for NSA on return from the field

Bulk density

• 3 depths at pit.• To calibrate

other measures to soil volume

1

Basal Area from Photopoints…..

• Is it possible?

Ways it is currently obtained

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Basal Wedge

DBH Measurement

Terrestrial LiDAR

An Alternative: A New Photopoint method

Photo Layout

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•24mm Focal Length•Aperture = F11•ISO 100•Raw Format (+/- JPG)•1.3m to centre of lens•Calibration target used•2.5m Baseline•DGPS Location recorded

A New Photopoint methodThe Tripod

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Tripod and Star Picket

setup

If terrain not flat then attempt to

copy the average slope.

A New Photopoint methodRaw outputs

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ETC.

The Scene Reconstruction Process

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Identifes Like features in images pairsUses this to calculate camera location

Using Camera location information projects information into 3d space

DBH Calculations

Trunks then identified Spectrally, but including 3D information

A Cylinder is fitted to each trunk

The Cylinder is cut at 1.3m (DBH) and the area of the cross section is calculated (DBH for the

individual tree)

These DBH’s are then summed for the whole site.

Currently hasa max depth of view, but improvements being worked on.

Trunk Identification and Basal area calculation

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Other outputs: pointclouds

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Other Outputs: Panoramas

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Benefits

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Benefits

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Method Cost Equipment Cost Staff Time Accuracy

Direct Harvesting * *** *** ***

Basal Wedge * * * *

DBH measures * *** *** ***

LIDAR *** *** *** ***

Photopoints ** * * **

Future work

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Take account of Occlusion

Trial and accuracy assess in a variety of ecosystems

Determine method variation needed for different environments

Automate processing (Work Commenced) – Submission for the public using a web interface

Manage Huge Datasets

Process our archive of 300+ SitesWith your help: Assess performance in snow

Non – Australian environmentsPerformance in urban environments.

Link To Video

How to get samples

At Present have collected approximately:>10,000 Soil samples~2700 Soil metagenomic Samples

>15000 Voucher specimens~ 15000 Genetic Samples~ 16000 Dominant Genetic replicates

All of which can be access following standard protocols

Information pack available for download at our website

Details how to get access.

What can AusPlots offer you?www.ausplots.org.au

For details including Volunteering, HDR, Data, methods, Samples, Training, App etc.

Ben.sparrow@adelaide.edu.au08 8313 1201