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Training Session 4 
Topics to cover: 
Vegetation vouchering 
Vouchering for genetics 
Vegetation isotope analysis 
Soil me...
MethodVegetation Vouchering
1.Collect sample 
–ensure large enough sample (to cover an A3 sheet of paper) 
–flowering/fruiting, bark where possible –r...
1.Attach barcode (well) to non-diagnostic part of the sample 
2.Scan barcode in Vouchering module 
3.Provide a field name ...
Press 
Change Papers 
Deliver to herbarium
Method: Vegetation DNA Samples& Leaf Isotope Analysis
Why? 
DNA 
•evolutionary relationships 
•phylogenetic diversity and endemism 
•evolutionary adaption 
•refugia 
•colonisat...
Sampling from voucher specimens 
1. Take around 10cm2from each voucher specimen 
2. Place into a synthetic tea bag and sea...
Sampling from dominant perennial species 
For each dominant perennial species in the plot (i.e. FPC >2% or opaque canopy c...
MethodSoil Metagenomics
Scrape loose material from soil surface 
Use a trowel or small shovel to take a sample from the soil surface 
Ensuring tha...
Tie the calico bag and place in a labelled plastic bag that contains 1/3 of a cup of silica that contains some indicator s...
MethodFauna SurveySally O’Neill
•Improve our understanding of fauna: 
–distributions 
–abundance 
–richness 
•Provide a baseline against which future chan...
Rationale for Fauna Protocol 
•No existing standardisednational fauna monitoring method 
•High level of interest in establ...
… lots of details TBA! 
	 
? 
?
Considerations 
•Refine details of the purpose 
•Who will be doing the surveys? 
•Trapping –types, duration, effort, timin...
•Collation and review of methods currently (and previously undertaken) 
•Review of agency requirements (legislative) 
•Con...
1 
Ben Sparrow TERN Ausplots 
Basal Area from Photopoints….. 
Isitpossible?
Ways it is currently obtained 
22 
Basal Wedge 
DBH Measurement 
Terrestrial LiDAR
An Alternative: A New Photopoint methodPhoto Layout 
23 
•24mm Focal Length 
•Aperture = F11 
•ISO 100 
•Raw Format (+/-JP...
A New Photopoint methodThe Tripod 
24 
Tripod and Star Picket setup 
If terrain not flat then attempt to copy the average ...
A New Photopoint methodRaw outputs 
25 
ETC.
The Scene Reconstruction Process 
26 
IdentifesLike features in images pairs 
Uses this to calculate camera location 
Usin...
DBH Calculations 
Trunks then identified Spectrally, but including 3D information 
A Cylinder is fitted to each trunk 
The...
Trunk Identification and Basal area calculation 
28
Other outputs: pointclouds 
29
Other Outputs: Panoramas 
30
Benefits 
31
Benefits 
32 
Method 
Cost Equipment 
Cost Staff 
Time 
Accuracy 
Direct Harvesting 
* 
*** 
*** 
*** 
Basal Wedge 
* 
* 
...
Future work 
33 
Take account of Occlusion 
Trial and accuracy assess in a variety of ecosystems 
Determine method variati...
Link To Video
Ausplots Training - Session 4
Ausplots Training - Session 4
Ausplots Training - Session 4
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Ausplots Training - Session 4

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Ausplots Training - Session 4 powerpoints - The video presented is available on youtube at: http://youtu.be/0s8zv07wNy0

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Ausplots Training - Session 4

  1. 1. Training Session 4 Topics to cover: Vegetation vouchering Vouchering for genetics Vegetation isotope analysis Soil metagenomics Fauna protocols Photopoints
  2. 2. MethodVegetation Vouchering
  3. 3. 1.Collect sample –ensure large enough sample (to cover an A3 sheet of paper) –flowering/fruiting, bark where possible –root for grasses + leaves (use an envelope for easily lost bits)
  4. 4. 1.Attach barcode (well) to non-diagnostic part of the sample 2.Scan barcode in Vouchering module 3.Provide a field name •either a good guess at taxonomic name OR •a descriptive name that is only current for that site 4.Place in plastic bag Use a small amount of this material for genetic sample ( as discussed in the genetic section)
  5. 5. Press Change Papers Deliver to herbarium
  6. 6. Method: Vegetation DNA Samples& Leaf Isotope Analysis
  7. 7. Why? DNA •evolutionary relationships •phylogenetic diversity and endemism •evolutionary adaption •refugia •colonisation/contraction dynamics Isotope •the reason that the teabag needs to be synthetic •accurate info on carbon and nitrogen content of the leaves •can inform on plant stress, adaption to climate change, assist with modelling etc.
  8. 8. Sampling from voucher specimens 1. Take around 10cm2from 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
  9. 9. Sampling from dominant perennial species For each dominant perennial species in the plot (i.e. FPC >2% or opaque canopy cover >5%) Additional leaf samples should be taken from four individuals across the plot 1. Take around 5cm2from each of four individuals 2. Place into a synthetic tea bag and seal 4. Place in sealed box as before 5. These samples will be used for DNA analyses only. 3. Label with adhesive voucher label and scan with app (to link to voucher specimen and plot)
  10. 10. MethodSoil Metagenomics
  11. 11. Scrape loose material from soil surface Use a trowel or small shovel to take a sample from the soil surface Ensuring that the trowel is not contaminated with soil from another site. Do include surface crust occurring at the site –max depth 3cm. Place the sample in a calico bag and label with a barcode Scan the barcode using the app.
  12. 12. Tie the calico bag and place in a labelled plastic bag that contains 1/3 of a cup of silica that contains some indicator silica Seal the bag Replace the silica until the indicator no longer changes colour Place the 9 plastic bags from the one site into a large calico bag and label for that site.
  13. 13. MethodFauna SurveySally O’Neill
  14. 14. •Improve our understanding of fauna: –distributions –abundance –richness •Provide a baseline against which future change can be assessed •Build understanding of the relationship between habitat dynamics and faunal species population dynamics •Lead to efficiencies in biodiversity monitoring Fauna Protocol Broad Aims
  15. 15. Rationale for Fauna Protocol •No existing standardisednational fauna monitoring method •High level of interest in establishing ‘biodiversity monitoring’ in rangelands •Complement the existing AusPlotsRangelands Survey Protocols Manual
  16. 16. … lots of details TBA! ? ?
  17. 17. Considerations •Refine details of the purpose •Who will be doing the surveys? •Trapping –types, duration, effort, timing •Logistics •Targeted species/guilds/keystones? •Vouchering? •Genetic samples? •Observation methods •Bats?
  18. 18. •Collation and review of methods currently (and previously undertaken) •Review of agency requirements (legislative) •Consult with experts -state agencies, researchers and universities, museums, NRM groups and (reserve) landholders •Draft the method selection •Field trials •Development of the survey protocols manual •Release on the website •…. then what? Development Process
  19. 19. 1 Ben Sparrow TERN Ausplots Basal Area from Photopoints….. Isitpossible?
  20. 20. Ways it is currently obtained 22 Basal Wedge DBH Measurement Terrestrial LiDAR
  21. 21. An Alternative: A New Photopoint methodPhoto Layout 23 •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
  22. 22. A New Photopoint methodThe Tripod 24 Tripod and Star Picket setup If terrain not flat then attempt to copy the average slope.
  23. 23. A New Photopoint methodRaw outputs 25 ETC.
  24. 24. The Scene Reconstruction Process 26 IdentifesLike features in images pairs Uses this to calculate camera location Using Camera location information projects information into 3d space
  25. 25. 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.
  26. 26. Trunk Identification and Basal area calculation 28
  27. 27. Other outputs: pointclouds 29
  28. 28. Other Outputs: Panoramas 30
  29. 29. Benefits 31
  30. 30. Benefits 32 Method Cost Equipment Cost Staff Time Accuracy Direct Harvesting * *** *** *** Basal Wedge * * * * DBH measures * *** *** *** LIDAR *** *** *** *** Photopoints ** * * **
  31. 31. Future work 33 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+ Sites
  32. 32. Link To Video

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