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co‐fundedresearchgrants,co‐fundedbarcodinggrants,andpostdoctoralfellowshipgrants
Guidelines and application form
Bush Blitz represents a globally unique, cross-sector partnership, drawing on the knowledge and expertise of government, non-government organisations, industry and science to document the biodiversity of the oldest continent on earth and provide an international benchmark for biodiversity knowledge. Research Grants are awarded for research projects where the primary aim is to undertake taxonomic research on the Australian biota. This may include projects aiming to barcode and undertake molecular research, or to develop products that aid in the dissemination of taxonomic information, in association with material collected as part of Bush Blitz. This document contains the guidelines and application form for researchers who wish to apply for a Research Grant, a Barcoding Grant or a Postdoctoral Fellowship grant under the program.
Important dates
Applications open 15 February 2010
Applications close 2 April 2010
Applicants notified of results 30 May 2010
Successful applicants receive first payment Before 30 June 2010
Closing date for applications in 2 April 2010
Late applications will not be considered.
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Contents Eligibility Criteria and Email Conditions ................................................................................3 Plain English Summary of proposed research project ..........................................................5
Question 1: Grant type and amount requested .......................................................................................6 Question 2: Co-funding partner/s and contribution..................................................................................6
Institution details ...................................................................................................................7 Question 3: Institution to administer grant...............................................................................................8 Question 4: Nominated administration contact........................................................................................8
Principal/Joint Investigator Details ........................................................................................9 Question 5: Principal and Joint Investigators ......................................................................................110 Question 6: Previous and current ABRS grants ....................................................................................13 Question 7: All other grants...................................................................................................................14
Project participants and project duration ..........................................................................163 Question 8: Project Participants ............................................................................................................17 Question 9: Commencement and completion dates ...........................................................................174
Priority areas for Research Grants ...................................................................................185 Question 10: Research Priorities.........................................................................................................196
Project Details...................................................................................................................207 Question11:Projectdetails ..................................................................................................................229
Project budget...................................................................................................................285 Question 12: Project budget (GST exclusive) .....................................................................................307 Question 13: Assessment of Application...............................................................................................28
Important information..........................................................................................................29 Certification for Principal Investigator and all Joint Investigator(s) ...................................421 Certification for Institution .................................................................................................421 Checklist ...........................................................................................................................422 Attachment A: Bush Blitz taxa groups and their collection ...............................................443 Attachment B: Example of co-funding support letter ........................................................444 Attachment C: Priority Areas for Research Grants ...........................................................465
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Read this before you start your application
Eligibility criteria 1. Applicants must have obtained a commitment for the applicable amount of co-funding for their
application to be considered (see Grant type and co-funding partner/s below for more information).
2. Applicants must have submitted all progress/final reports associated with previous Australian Biological Resources Study (ABRS) National Taxonomy Research Grant Program grants for their application to be considered.
3. Applications are accepted from Australian and International researchers.
4. Up to two grant applications may be submitted by a researcher named as Principal Investigator.
5. A maximum of one grant will be awarded to a researcher in their capacity as a Principal Investigator.
6. Postgraduate students should not apply as Principal Investigator. Research Supplements are available to Ph.D. students to provide additional research support for a project requiring taxonomy or systematics that can be linked to Bush Blitz. Please see the Bush Blitz website for further information.
7. Postdoctoral fellows can apply for a research grant as Principal Investigator or for a postdoctoral fellowship grant as Principal Investigator. Applications may include their own postdoctoral salary. Also, postdoctoral fellows may be included as part of a team applying for a research grant.
8. Postdoctoral fellowship grant applicants must have no more than ten years full-time postdoctoral work experience when the postdoctoral fellowship grant application is submitted.
9. Postdoctoral fellowship grant applicants must be prepared to attend at least three Bush Blitz surveys per year for the duration of the grant.
10. Researchers are expected to be affiliated with an appropriate institution in order to gain access to facilities and material from collections.
This application must be filled in electronically and submitted via email. Emailed applications that do not adhere to the following conditions will not be considered.
Email conditions 1. Applications must be submitted as a single Word document (PDF).
2. All aspects of the application, including the project details and curriculum vitae, must be completed using Arial font in 12 point.
3. The signature page of this document must be received as a secure PDF.
4. Receipt of the application will be acknowledged by an auto reply from ABRS. If this acknowledgment is not received it is your responsibility to contact ABRS to ensure that your application has been received.
5. ABRS accepts no responsibility for emailed applications that arrive with altered formatting. ABRS staff will check the formatting of emailed applications upon receipt and may contact applicants requesting a resubmission if there are any problems. A resubmission must be made within 48 hours of such a request and may require a hard copy delivery or faxed submission.
Please DO NOT alter this form in any way by deleting instructions, headings or text. These are embedded within the form for administrative purposes.
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Plain English Summary of proposed research project
Name of Principal and Joint Investigator/s Michael Bayly PI Patrick Brownsey JI Leon Perrie JI Lara Shepherd JI
Name of Administering Institution The University of Melbourne
Target group of organisms To select which category of organism the proposal targets, please place an x in the appropriate box in the Core Taxa Group table OR complete the Institutional Taxa Group table. See Attachment A for more information about Bush Blitz taxa groups. Barcoding Grant applicants may select only Vascular Plants or Vertebrates.
Core Taxa Group:
Vascular Plants X
Vertebrates (Birds, Mammals, Reptiles, Amphibians)
Lycosidae (wolf spiders)
Mygalomorphae (trapdoor and primitive spiders)
Papilionoidea (butterflies)
Gastropoda (terrestrial and freshwater snails)
Odonata (dragonflies)
Heteroptera (true bugs)
Institutional Taxa Group:
Name of taxon Ferns: with a focus on the families Aspleniaceae, Blechnaceae Hymenophyllaceae and Pteridaceae
Institution for which the taxon is a priority School of Botany, The University of Melbourne (MELU Herbarium)
Project title Taxonomy, phylogeny, biogeography and conservation of Australia’s largest fern families.
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Summary of project In no more than 100 words, please describe the proposed project in plain English terms, including an estimate of the number of taxa to be described or barcoded (as appropriate), the biodiversity informatics products to be produced, why the project is scientifically significant and how it relates to Bush Blitz (specifically referring to the material described in Attachment A) Molecular data will be generated for taxonomic/phylogenetic/biogeographic investigation of four of Australia’s largest fern families: Aspleniaceae, Blechnaceae, Hymenophyllaceae, and Pteridaceae (core Bush Blitz taxa; 37% of Australia’s fern flora). DNA sequence data for every available species will underpin the study. Special focus will be on the Aspleniaceae, where the distribution of genetic diversity in several widespread species will be sampled in detail. Additionally, three Asplenium species complexes involving rare taxa of uncertain distinctiveness will be resolved with DNA-fingerprinting. The project will result in taxonomic revision at both genus- and species-level, and reveal the biogeographic history of these significant Australian ferns.
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Grant type and co-funding partner/s
Grant requested Research Grant applicants, except Postdoctoral Fellowship grant applicants, are expected to seek and identify an additional commitment of co-funding to support their project. No restrictions will be placed on the source of this contribution, but applicants will need to be aware of the rules of other funding agencies, which may limit how funds contributed by them may be used. Salary may be included as co-funding.
In-kind contributions will be recognised but will not replace the requirement for additional funding input. In-kind contributions are contributions that, as part of a commitment to a research project, would normally involve a monetary fee-for-service contribution, but, instead, are provided in the form of services, facilities or consumables.
Grants are applied for under a scheme of set levels of funding, with successful grant applicants guaranteed of receipt of the full amount of funding requested. Table 1 below outlines the Bush Blitz Research Grants available and the amount of co-funding required to be sourced by applicants.
Table 1: Bush Blitz Research Grants
Type of grant & amount (per annum)
Bush Blitz contribution (per annum)
Minimum grant application co-funding contribution (per annum)
Research grant — $45,000 45,000 5,000
Research grant — $90,000 90,000 10,000
Barcoding grant – $120,000 120,000 15,000
Postdoctoral Fellowship grant — $90,000 90,000 0
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Question 1: Grant type and amount requested Please select the grant you are applying for by placing an x in the Grant Requested box below.
Type of grant & amount (per annum)
Bush Blitz contribution
(per annum)
Minimum required
co-contribution Grant
Requested
Research grant — $45,000 45,000 5,000 X
Research grant — $90,000 90,000 10,000
Barcoding grant - $120,000 120,000 15,000
Postdoctoral fellowship grant — $90,000 90,000 0
Question 2: Co-funding partner/s and contribution Please list all co-funding partners and the amount of funding they will contribute to the project. Do not list Bush Blitz or in-kind contributions as co-funding partners here.
Co-funding partner Co-funding contribution
The University of Melbourne
salary $60,505 cash $12,000 Total: $72,505
Museum of New Zealand Te Papa Tongarewa
salary $41,616 cash $12,000 Total: $53,616
Please note: Applicants must attach a letter from each co-funding partner verifying the funding contribution. This letter must be sent to ABRS as a PDF document. Please see Attachment B for a suggested format for co-funding support letters.
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Institution details
Institution to administer the grant Give the name and address of the institution through which the grant for this project will be administered (normally the institution at which the Principal Investigator is employed).
Principal Investigators are expected to have administrative attachment to an institution. The normal criterion for being ‘attached’ is that the Principal Investigator is on an institution’s payroll or is affiliated with an institution and intends to nominate that institution to administer the grant funds for the project.
Administrative contact for grant Please give details of a nominated administrative contact for the grant.
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Question 3: Institution to administer grant
Legal name of institution The University of Melbourne
Short or Trading Name Melbourne Research Office
Street number/PO Box Level 5, Alan Gilbert Building
Street name 161 Barry Street
Suburb/Town Melbourne
State/Territory Victoria
Country Australia
Postcode 3010
ABN 84 002 705 224
Is the institution GST registered? YES
Question 4: Nominated administration contact
Title Ms
Name Anita Vecchies
Position Research Grants Officer (Primary Industries)
Phone +613 / 8344 2054
Fax +613 / 8344 7639
Email [email protected]
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Principal/Joint Investigator details Please provide details of the nominated Principal/Joint Investigators.
The Principal Investigator is the person who has scientific and administrative responsibility for the project and will be the contact person for all correspondence.
A Joint Investigator is anyone else who is making a major contribution to the project, including a Postdoctoral Fellow who is to be employed partially or fully by the grant.
Other persons to be associated with the project are to be listed in the Project Participants in Question 8.
Please note that Honours and Postgraduate students must not apply as Principal Investigators. Research Supplements are available to Ph.D. students to provide additional research support for a project requiring taxonomy or systematics analysis that can be linked to Bush Blitz. Please see the Bush Blitz website for further information.
Table 2: Example format for answering Question 5
Principal/Joint Investigator Example format
Title · given name/s · surname Dr John Smith Citizen
Institution University of Australia
Department/School Department of Science
Address University Road, University Town, NSW 2020
Phone ………/ ……………………
Fax ………/ ……………………
Email ………………………………………………………
Highest qualification · date · institution Ph.D. 1970 Charles Darwin University
Source of salary (%) University of Australia (80%), ABRS (20%)
Source of salary Each Investigator must outline the planned source of salary for each year and percentage for each source, for example, the University of Australia (80%) and Bush Blitz grant (20%). This question is not applicable if the Investigator is retired.
Curriculum Vitae Each Principal and Joint Investigator applying for a grant must supply a curriculum vitae that is a maximum of four pages, using Arial 12 point type, and include references to authored/co-authored publications and products for the past five years. Please highlight those papers or products that have arisen from ABRS grants.
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Question 5: Principal and Joint Investigators
Principal Investigator
Title · given name/s · surname Dr Michael James Bayly
Institution The University of Melbourne
Department/School School of Botany
Address The University of Melbourne VIC 3010
Phone +613 / 8344 5055
Fax +613 / 9347 5460
Email [email protected]
Highest qualification · date · institution Ph.D., 2002, The University of Melbourne
Source of salary (%) Currently The University of Melbourne (50%) and ABRS (50%); From Jan 2011 University of Melbourne (100%)
Joint Investigator
Title · given name/s · surname Dr Patrick Brownsey
Institution Museum of New Zealand Te Papa Tongarewa
Department/School Botany
Address PO Box 467, Wellington, New Zealand
Phone +64 4 / 381 7135
Fax +64 4 / 381 7070
Email [email protected]
Highest qualification · date · institution Ph.D., 1973, University of Leeds, UK
Source of salary (%) Museum of New Zealand (95%), Foundation for Research, Science & Technology Defining NZ’s Land Biota (5%)
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Joint Investigator
Title · given name/s · surname Dr Leon Perrie
Institution Museum of New Zealand Te Papa Tongarewa
Department/School Botany
Address PO Box 467, Wellington, New Zealand
Phone +64 4 / 381 7261
Fax +64 4 / 381 7070
Email [email protected]
Highest qualification · date · institution Ph.D., 2002, Massey University
Source of salary (%) Museum of New Zealand (80%), Foundation for Research, Science & Technology Defining NZ’s Land Biota (20%)
Joint Investigator
Title · given name/s · surname Dr Lara Shepherd
Institution Massey University
Department/School Allan Wilson Centre
Address Private Bag 11 222, Palmerston North, New Zealand
Phone +64 6 / 356 9099 x4779
Fax +64 6 / 350 5626
Email [email protected]
Highest qualification · date · institution Ph.D., 2006, Massey University
Source of salary (%) Marsden grants (Royal Society of New Zealand) 2010 (presently 100%, but can be partially deferred); 2011-2012 (30%)
Please copy and repeat this table for additional Joint Investigators.
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Question 6: Previous and current ABRS grants Have either the Principal or Joint Investigator/s received funding from ABRS in the past five years? Please place an x in the applicable box.
YES: please complete Question 6 X
NO: Go to Question 7
ABRS grant number
Year commenced
Number of years funded
Total funding
Title of project Australian rainforest plants in the family Rutaceae: phylogeny, classification and biogeography
PD2008-02
2008 3 $165,183
Named Investigators M.J. Bayly, P.Y. Ladiges
Please add additional rows as necessary.
Have you submitted progress reports/a final report for all previous grants listed above? Please place an x in the applicable box below. If you answer no you must submit all outstanding reports with this application or the application will be disqualified.
YES: the progress reports/final report for all above grants have been submitted
X
NO: the necessary reports are included with this application
Using a maximum of 200 words, summarise the outputs and outcomes (other than publications) of previous ABRS grants. This may include conferences held, training and mentoring of students. In the publication list in your curriculum vitae, note which publications result from an ABRS grant.
The current ABRS grant to M. Bayly and P. Ladiges will finish in 2010. This project has generated a large quantity of DNA sequence data for the Australian rainforest Rutaceae and is providing new insight into relationships and biogeography, and will result in a revised classification for several groups. In association with this work, an honours and PhD student have been recruited to work on Australian Rutaceae, and another Postdoctoral Fellow (Gareth Holmes, funded by P. Ladiges) has been contributing to the project, and thus receiving further research experience in plant systematics.
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Question 7: All other grants
Please list all other grants the Principal or Joint Investigator/s have held in the past five years.
Granting Agency
Year commenced
Number of years funded
Total funding % time allocated to project
Title of project Phylogeography of Eucalyptus deglupta
The Australia and Pacific Science Foundation
2009 3 $29,978.00
Named Investigators
F. Udovicic, M. Bayly, G. Dean, S.Ariati, C. Webb
5% (Bayly)
Title of project Defining New Zealand’s Land Biota
Foundation for Research Science and Technology (NZ)
2005 12 Currently NZ$275,000 per year
Named Investigators
P. Brownsey, L. Perrie, H. Meudt C. Lehnebach
5% (Brownsey) 20% (Perrie)
Title of project
Fashioning species biodiversity - A perspective from the hybridisation between the New Zealand trees horoeka and houpara.
Marsden (Royal Society of NZ)
2006 2 NZ$140,000
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Named Investigators
L. Perrie, L. Shepherd
20% (Perrie), 40% (Shepherd)
Title of project
Tracing the domestication history and whakapapa (relationships) of cultivated New Zealand plants using DNA markers
Marsden (Royal Society of NZ)
2008 3 NZ$596,000
Named Investigators
L. Shepherd, P. de Lange, N. Roskruge, P. Lockhart
currently 100% (Shepherd)
Title of project
Untangling complex evolution: When the Tree of Life is not a tree at all
Marsden (Royal Society of NZ)
2010 3 NZ$519,000
Named Investigators
B. Holland, L. Shepherd, V. Moulton, K. Huber
30% (Shepherd)
Please add additional rows as necessary.
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Project participants and project duration
Project participants Provide details on the name, category and planned level of involvement of ALL participants to be involved in the project (e.g. Principal and Joint Investigators, overseas collaborators, technical, research or other staff, postgraduate research or Honours students). Also include the total commitment to all projects for Principal and Joint Investigators. Do not include corporate administrative staff (see example below - Table 3).
If the project participant is an Early Career Researcher (ECR) please indicate with an ‘E’ in the ECR column. An early career researcher is defined as a current Ph.D. student or a researcher with less than five years full-time postdoctoral work experience when the grant application is submitted.
Table 3: Example format for project participants
Name Category Planned level of involvement (number of days/month)
ECR
A.A. Smith Principal Investigator 8d/month (16d/month all projects)
B.B. Jones Joint Investigator 4d/month (12d/month all projects) E
unknown Technical officer — to be appointed 6d/month N/A
C.C. Brown Overseas collaborator (USA) 2d/month
unknown Ph.D. student — to be appointed 10d/month E
unknown Postdoctoral Fellow — to be appointed 10d/month E
Commencement and completion dates Please give an estimate of the project commencement and completion dates. Bush Blitz grants are expected to commence by 30 June 2010 and be completed by June 2013. Please note: the paper or product or other deliverable of the grant is expected to be filed at the completion date.
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Question 8: Project Participants
Name Category Planned level of involvement (number of days/month) ECR
M.J. Bayly Principal Investigator 4d/month (12d/month all projects)
L.R. Perrie Joint Investigator 2d/month (10d/month all projects)
P.J. Brownsey Joint Investigator 1d/month (2d/month all projects)
L.D. Shepherd Joint Investigator
6 months full time equivalent
E
D. Ohlsen Ph.D. student 19.5d/month (19.5d/month all projects)
E
unknown Research Assistant- to be appointed 6 months full time equivalent
unknown Honours student — to be appointed
9 month research project (year 2) E
Question 9: Commencement and completion dates Has the project commenced? YES (PhD student only; other work is conditional
on this funding, to start 1 July 2010)
Commencement date 1 / March / 2010.
Completion date 30 / June / 2013
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Priority areas for Research Grants Bush Blitz projects must be consistent with research priorities derived from ABRS Priority Areas for Research Grants 1: Biodiversity, Conservation and Vulnerable and Endangered Species (see Attachment C – Priority Areas for Research Grants). Projects should also aim to support Priority Area 3: Building Taxonomic Capacity. Applicants should familiarise themselves with these priority areas before completing the next section of the application form.
When answering Question 11, state clearly which research priorities are supported by the proposed project and how the project supports them. For example: ‘As a group of vascular plants, Tephrosia are one of the core taxa groups targeted for collection in most Bush Blitz surveys. This project will support priority 1.1 Documenting Australia’s Biodiversity through the documentation of this taxonomic group. This project will also supports priority 1.3 through the taxonomic resolution of a group containing species of conservation concern. Moreover, this project will support priorities 2.1 and 2.2, Training of Early Career Researchers and Knowledge Management, through the engagement of a Ph.D. student and the inclusion of Dr AA Citizen, who has agreed to mentor the Ph.D. student prior to her retirement.’
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Question 10: Research Priorities Please nominate which research priorities the proposed project supports by placing an x in the appropriate box/es:
Priority This Application supports priority x
1: Biodiversity, Conservation and Vulnerable and Endangered Species
1.1 Documenting Australia’s Biodiversity X
1.2 Conservation X
1.3 Vulnerable and Endangered Species X
1.4 Identifying Australia’s Biodiversity X
2: Building Taxonomic Capacity
2.1 Training of Early Career Researcher/s X
2.2 Knowledge Management
2.3 Exchange of International Expertise X
Using a maximum of 200 words, please explain how the research priorities nominated above are supported by the proposed project.
Ferns belong to a core taxon (vascular plants) targeted for Bush Blitz surveys. This project supports priority 1.1 Documenting Australia’s Biodiversity by providing substantial, novel molecular and morphological data for improved knowledge of Australian ferns. It supports priorities 1.2 Conservation and 1.3 Vulnerable and Endangered Species by clarifying the taxonomic status of three rare Asplenium taxa of uncertain distinctiveness, and by identifying geographic areas rich in fern genetic diversity for conservation prioritisation. Priority area 1.4 Identifying Australia’s Biodiversity will be supported by production of a revised morphological key for Aspleniaceae and a set of reference DNA sequences for molecular identifications.
This project builds Australia’s taxonomic capacity through priorities 2.1 Training of Early Career Researchers and 2.3 Exchange of International Expertise. At least one Ph.D. and one honours student will be trained in taxonomy of ferns, a group for which all resident taxonomists are at or approaching retirement (see contributors list for Flora of Australia: 48). International exchange will include: mentoring of students and early career team members by NZ expert P. Brownsey before he retires; a visit to NZ by the Ph.D. student; a visit to Melbourne labs by L. Perrie to impart his expertise in AFLP-DNA fingerprinting.
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Project details
Project aim Please clearly state the primary aims of the project.
Background information Give a brief assessment of the size and status of the group. The applicant must give clear evidence that he/she is familiar with the literature and knows what material exists in collections. The applicant must also provide details on the scope of the project.
Project justification Please indicate what the proposed work will accomplish (include the number of taxa to be described, revised or barcoded if applicable) and why the project is necessary. For example, in the case of a taxonomic revision, it would be appropriate to state why it is considered that a revision is desirable (for example, new material, new techniques, areas not previously collected).
Applicants intending to deliver a biodiversity informatics product should note this must not be the primary focus of the grant. The grant must be for taxonomy research, but may deliver an informatics project as part of the grant. Barcoding projects must have taxonomy or systematic research as their primary focus, but will deliver, as one of the products, barcoding for a taxon group that can be delivered to Genbank or an equivalent publicly available database. Applications focused on barcoding specimens only will not be considered. Barcoding projects must be underpinned by voucher specimens held by a collection, and relate project outcomes to sound taxonomy. The term “barcoding” has been used generically to define the use of DNA markers to identify or separate specimens and does not restrict applicants only to the use of CO1 or other gene regions.
Significance/benefits Outline the general benefits of the grant. Please specifically cover expected outputs (for example, publications in international journals, keys or checklists) and outcomes (for example, advancing scientific knowledge of the biodiversity in Australia’s reserve system). You should relate these outputs and outcomes to the priorities listed in Attachment C. You should also indicate how you will provide data for online resources such as the Australian Faunal Directory, OZCAM, Australia’s Virtual Herbarium or Genbank or provide material for ABRS publications or CD identification series.
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Method Please detail the research procedures you intend to use. Postdoctoral Fellowship grant applicants must attend at least three Bush Blitz surveys per year. For other Research Grants, applications must state whether the Principal Investigator and/or Joint Investigators are prepared to assist with collection of their focus taxon group through Bush Blitz field work. Where applicants do not wish to be involved in survey, applications must specify from which regions of Australia specimens or tissue samples are required and from which institutions they would source deposited Bush Blitz specimens or tissue samples. When defining regions, please specify state or territory and/or IBRA (Interim Biogeographic Regionalisation of Australia) region. Pre-existing material from collections may also be used in Bush Blitz taxonomy projects. Please note what is already available in collections and how this will be used. Estimate the number of taxa to be described or barcoded, using the table provided. Also detail the techniques used to determine specimens. If using molecular techniques, please include the number of samples and clearly define how the project will be related to taxonomy and vouchered specimens.
Personnel and facilities Briefly describe the role of each project participant and provide a description of the facilities at which the research will be based.
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Question 11: Project details Please describe the proposed project using a maximum of six pages.
Project aim This project will combine molecular and morphological data to assess the taxonomy, relationships, biogeography and conservation of four of Australia’s largest fern families. The primary focus will be Australia’s largest fern genus, Asplenium (family Aspleniaceae, c. 35 spp.), but samples from Bush Blitz surveys will also be used for concurrent studies of Blechnaceae (c. 29 spp.), Hymenophyllaceae (c. 45 spp.), and Pteridaceae (c. 58 spp.). For Aspleniaceae, a revised species-level classification will be produced, including a new identification key and a reference set of chloroplast DNA (cpDNA) sequences for all species. Morphological and molecular data will be used to: assess the taxonomic status of doubtful species; understand the histories of species with disjunct distributions; examine widespread and variable species for evidence of cryptic diversity. Population genetic markers (AFLPs) will be used to provide information targeted to the conservation-management of rare species, thereby identifying priority sites for conservation-management. A comprehensive molecular phylogeny, including multiple accessions of all Australian species, and integrating available data from foreign species, will facilitate a re-alignment of generic boundaries, provide insight into the diversity of lineages in Australia (phylogenetic diversity) and their biogeographic connections. The project aims to assess variation in a range of taxa, but specific objectives are to use genetic data to resolve: a) whether the following species should be maintained as distinct: Christmas Island
endemic and critically endangered Asplenium listeri from widespread A. polyodon; Atherton Tableland endemic Asplenium bicentenniale from widespread A. paleaceum; the Carnarvon Range endemic Asplenium carnarvonense from northern Queensland A. capitisyork;
b) how genetic diversity is distributed in widespread and morphologically-variable taxa including Asplenium polyodon, A. australasicum, A. gracillimum, A. flabellifolium and A. aethiopicum, whether they show congruent biogeographic patterns, and whether any harbour cryptic, species-level biodiversity.
For Blechnaceae, Hymenophyllaceae, and Pteridaceae, cpDNA sequencing will be used to identify major Australian lineages, and their relationships to overseas species already sequenced. The aim is to include as many Australian species as possible, represented by multiple accessions, thereby also assessing, in conjunction with morphology, levels of variation within and between species.
Background information Phylogenetic analyses of cpDNA have revolutionised the understanding of fern evolution, and driven substantial revision of fern taxonomy (Smith et al. 2006). Yet few Australian species have been included in genetic-based work, and the relationships of Australia’s ferns to those overseas remains unclear. Four of the fern families with the most species in Australia are the Pteridaceae (c. 58 (c. 20 endemic) spp.; including Vittariaceae, Parkeriaceae, and Adiantaceae of Fl.Aus. 48), Hymenophyllaceae (c. 45 (c. 13) spp.), Aspleniaceae (c. 35 (c. 10) spp.), and Blechnaceae (c. 29 (c. 16) spp.) (circumscriptions revised from Fl.Aus. 48 to follow Smith et al. 2006). Much phylogenetic work outside Australia has been done on the Pteridaceae, Hymenophyllaceae, and Aspleniaceae (e.g., Schneider et al. 2005; Schuettpelz et al. 2007; Shepherd et al. 2008a; Hennequin et al. 2010). Genera in the first two have been extensively revised (Rothfels et al. 2008; Ebihara et al. 2006); sequence data will establish appropriate generic attributions for Australian
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species. With the largely southern-hemisphere Blechnaceae, the only previous phylogenetic publication about the core Blechnum group centred on New Zealand (Shepherd et al. 2007a), and indicated a need for generic realignment; it is logical to extend this work to Australia, especially with the high proportion of endemic species. Phylogenetic analyses will also clarify the number of distinct lineages within Australia for each of these families (and their genera), and will highlight biogeographic connections (i.e., where overseas do Australian species have most affinity - temperate or tropical, west or east?; how many times has each family/genus reached or left Australia?; to what extent have there been endemic radiations?). The ‘Austral’ clade of Asplenium that we have previously identified is an exemplar (Perrie & Brownsey 2005a; Shepherd et al. 2008a); some Australian species are known to belong to this clade but the exact membership is unclear. Furthermore, virtually nothing is known about biogeographic patterns of genetic diversity within Australian ferns (i.e., do species have elevated genetic diversity in some regions?; are patterns consistent across species?). Although generic limits in Aspleniaceae remain to be clarified, it largely comprises Asplenium, one of the world’s largest fern genera (c. 700 species) (Smith et al. 2006). Asplenium epitomises the morphological variation, wide distributions, and hybridisation that can complicate species-level taxonomy in ferns (e.g., Perrie & Brownsey 2005b; Shepherd et al. 2008b). Brownsey (1998) highlighted a range of taxonomic problems in Australian Asplenium, but three of particular note involve the following species complexes. All include rare taxa of uncertain taxonomic status. All may belong to an A. aethiopicum/polyodon clade, but their exact inter-relationships require determination by phylogenetic analysis. Asplenium listeri is an ABRS priority for 2010/11. This Christmas Island endemic is critically endangered, with only four extant (and two extinct/not-relocated) populations and <300 individuals (Butz 2004); AVH <http://www.cpbr.gov.au/cgi-bin/avh.cgi> lists only two specimens in Australian herbaria. Morphology clearly allies A. listeri with the widespread (tropical Asia to the Pacific) and exceptionally morphologically-variable A. polyodon (Du Puy 1993), which also occurs on Christmas Island. Although the morphological extremes are distinct on Christmas Island, intermediates occur (Du Puy 1993). Concern remains that A. listeri is merely an environmental form (i.e., of limestone cliffs) of A. polyodon, and so not due its present conservation concern. Asplenium bicentenniale is endemic to the Atherton Tableland. Although rare, its extent is unclear. Only eight specimens occur in Australian herbaria (AVH), comprising only three separate collections and, at the most, two populations. As stated by Brownsey (1998), further investigation is “… needed to determine whether the taxon is merely a local variant of A. paleaceum, or a distinct species”. Recognition of A. paleaceum is complicated by the hybrid swarm it produces with A. attenuatum; these two species are both widespread along Australia’s east coast (Brownsey 1998).
Asplenium carnarvonense is known from the Carnarvon Range (central Queensland) (Brownsey 1998). Ten specimens occur in Australian herbaria (AVH), representing six separate collections and perhaps four populations. Two specimens from the Kroombit SF, several hundred kilometres distant, may also belong to this species (Brownsey 1998). Furthermore, the relationship of A. carnarvonense to the Cape York endemic A. capitisyork requires further investigation; although geographically distant, the two are “very similar” (Brownsey 1998). Like A. bicentenniale above, morphology allies both A. carnarvonense and A. capitisyork with A. paleaceum (Brownsey 1998).
Project justification Outstanding taxonomic questions regarding Australian ferns limit understanding of biodiversity and cloud the assessment of conservation priorities. New tools (e.g. molecular
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data), in addition to morphology, will provide deeper insight into patterns of diversity and into the delimitation, relationships, biogeographic history and population differentiation of taxa. Ferns include many widespread species with disjunct distributions across Australasia and beyond. Widespread taxa necessitate an international perspective when attempting to resolve local taxonomies. They can also harbour hidden or cryptic diversity (Yatabe et al. 2001, 2009) and complex evolutionary (Shepherd et al. 2008b) or biogeographic histories (Shepherd et al. 2007b, 2009) that can be brought to light by molecular data. The extent to which the ferns in Australia are diverged from those elsewhere is unknown, and this impacts conservation assessments that prioritise by lineage-distinctiveness (Faith 2008).
Collectively, our team has international taxonomic expertise on ferns, including all four families and with Asplenium in particular, and experience with applying a range of molecular techniques (including DNA sequencing and AFLP DNA-fingerprinting) to successfully resolve taxonomic, biogeographic and conservation-related questions. By producing DNA sequence for c.130 fern species, this study will provide a phylogenetic framework for understanding four of Australia’s major fern families. This will allow taxonomic realignment of generic boundaries, biogeographic analyses, and the delimitation of clades that need more in-depth study. Alongside these higher-level investigations, we will use Asplenium as an exemplar of species-level taxonomy. Within Asplenium we will focus particularly on the circumscriptions of rare taxa (A. bicentenniale, A. carnarvonense, and the Critically Endangered A. listeri), and the genetic diversity within morphologically variable and/or widespread taxa (e.g., A. polyodon; A. attenuatum, A. paleaceum, and their hybrids; A. aethiopicum; A. australasicum; A. flabellifolium; A. gracillimum; both “Pleurosorus” spp.).
Significance/benefits Study of Australia’s biodiversity and discovery of its evolutionary history fits broadly within the National Research Priority of An Environmentally Sustainable Australia, and aligns in particular with the Priority Goal Sustainable use of Australia’s biodiversity, since taxonomy underpins ecological and other disciplines. This project is aligned to six Bush Blitz/ABRS Research Priorities (Documenting Australia’s Biodiversity; Conservation; Vulnerable and Endangered Species; Identifying Australia’s Biodiversity; Training of Early Career Researchers; Exchange of International Expertise). Aspleniaceae, Blechnaceae, Hymenophyllaceae and Pteridaceae are important targets for such research; collectively they represent c. 37% of the Australia’s fern flora. Among the vascular flora, the ferns are an under-studied group, especially in terms of modern molecular methods, and for which there is a need to improve our taxonomic capacity. This study is national in scope and, in addition to updating Australian taxonomies and conservation priorities, will address how the Australian species relate to the diversity of these large world-wide families.
Outputs
Results will be published in international and Australian refereed journals, such as Australian Systematic Botany, Molecular Ecology, Journal of Biogeography, Molecular Phylogenetics & Evolution, Taxon, or Conservation Genetics. Papers will be presented at appropriate international and Australian Conferences. Published outputs will include: • At least four papers on the phylogeny of Australian ferns (e.g., one each on the
Aspleniaceae, Blechnaceae, Hymenophyllaceae, and Pteridaceae). • A paper on the taxonomic status of Asplenium listeri in relation to A. polyodon. • At least one paper on the status of A. bicentenniale and A. carnarvonense in relation
to the A. paleaceum (including A. capitisyork and A. attenuatum) complex. • At least two papers on the geographic distribution of genetic variation within Asplenium
species widespread in Australia. • A revised morphological key (printed) for identification of Australian Aspleniaceae.
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• A reference set of chloroplast DNA sequences for Australian Aspleniaceae as a basis for molecular identifications; sequences (also deposited in GenBank) for all available Australian members of Blechnaceae, Hymenophyllaceae and Pteridaceae.
Outcomes • Phylogenetic information for Australian Aspleniaceae, Blechnaceae,
Hymenophyllaceae, and Pteridaceae, providing insight into relationships, phylogenetic diversity and biogeographic (both intra- and extra-Australian) history;
• A comprehensive and revised phylogeny-based classification of Aspleniaceae at genus- and species-levels (affecting c. 4 and c. 5-7 species respectively), updating the presently available taxonomy for Australian Aspleniaceae (Brownsey 1998; Australian Plant Census) which is already lagging behind progress in New Zealand and elsewhere;
• Updates to the genus-level taxonomy of Australian Blechnaceae, Hymenophyllaceae, and Pteridaceae.
• Clarification of conservation priorities for several rare or endangered taxa of Asplenium;
• An understanding of how genetic variation is distributed geographically in several widespread Australian Asplenium species, and how these patterns compare with those of other biotic groups;
• Training of one Ph.D. student and at least one honours student, including capture of international taxonomic expertise and building of local capacity;
• The development of molecular tools (sequences, AFLP markers) that can be used for identifications or applied to the revision of other fern taxonomic problems in Australia and elsewhere.
Contributions to ABRS
Voucher specimens from field collections will be deposited in Australian herbaria, and be available through Australia’s Virtual herbarium (AVH); annotations/re-determinations of existing specimens will also contribute to refinement of AVH data. Any taxonomic changes will feed into the Australian Plant Names Index and Australian Plant Census. DNA sequence data will be made publicly available through the GenBank database.
Method Please indicate in the appropriate column the number of taxa to be described, revised or barcoded.
Protists Algae Fungi / Lichens
Bryophytes Vascular plants Terrestrial vertebrates
Terrestrial invertebrates
cpDNA sequences & phylogenetic analysis for c. 130 spp. of Australian Aspleniaceae, Blechnaceae, Hymenophyllaceae, and Pteridaceae, contingent on sampling support from the Bush Blitz surveys. Taxonomies will be revised to reflect phylogeny where necessary. 3 Asplenium species complexes revised; detailed population genetics for 3 rare species & c. 6 widespread Aspleniaceae species.
Field sampling for molecular and morphological studies: Sampling will capitalise on the Bush Blitz surveys. D. Ohlsen could participate in two relevant surveys (especially in IBRA regions CYP, WT or SEQ), and M. Bayly in one. Sampling of Blechnaceae, Hymenophyllaceae, and Pteridaceae will rely heavily on Bush Blitz surveys. Our project will incorporate vouchered, silica-gel preserved material collected in surveys in all states and territories (in all IBRA regions in which they occur). Additional field-work is proposed
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(detailed in the budget; see justification) for areas critical to the Aspleniaceae component of this project, especially given the detailed infra-specific sampling required, and other target families would also be collected on these trips (further samples would also come through our collaborative networks). We aim to sample all species of Aspleniaceae and, with good Bush Blitz support, envisage sampling c. 80+% of species in the other target families. Samples from rarer taxa will depend on availability and permit conditions. For family-wide phylogenetic analyses, we aim to include 2 accessions per species. Sampling intensities will necessarily be different for phylogenetic datasets, analyses of species complexes, and phylogeographic studies (see budget table as a guide).
Molecular methods: DNA will be isolated and sequenced using our standard protocols for ferns. Two to four chloroplast loci (rbcL, trnL-F, rps4, and another to be identified) will be generated for each species for the family-wide phylogenies. In Asplenium, one or two loci will be sequenced for the detailed sampling of the widespread species we target, as well as most samples of the three focal species complexes (A. listeri/A. polyodon, A. bicentenniale/A. paleaceum/A. attenuatum, A. carnarvonense/A. capitisyork). Additionally, the species complexes will be analysed by AFLP DNA-fingerprinting. AFLP is an excellent tool for delimiting gene-pools and discriminating species (Meudt & Bayly 2008; Perrie & Shepherd 2009); it gives more discrimination than standard sequencing markers. The budget table provides a guide to our sampling for each sub-project. Molecular data analyses: Sequence data will be analysed using a combination of parsimony (in PAUP*), Bayesian (MrBayes), and phylogeographic methods as in previous studies (e.g., Shepherd et al. 2007a,b, 2008a). The AFLP data will be analysed by tree-building, ordination, and Bayesian-clustering (Falush et al. 2007; Meudt & Bayly 2008; Perrie & Shepherd 2009), focusing on species boundaries.
Morphological study: Field collections and herbarium specimens (from MEL and requested on loan from other herbaria) will be used to re-assess the boundaries of accepted taxa. We will particularly emphasise the Asplenium taxa targeted for detailed genetic analyses, with a view to identifying correlations between molecular and morphological variation.
Personnel and facilities PI Michael Bayly has substantial experience in the application of molecular and morphological data to the systematics of a range of plant groups. He will coordinate the project, supervise the Ph.D. and Honours students, oversee activities in Melbourne, do some of the fieldwork and DNA sequencing, and be joint leader in producing outputs (papers). Patrick Brownsey is one of Australasia’s leading and most experienced fern taxonomists, with a strong track-record of publication and extensive knowledge of Aspleniaceae in both New Zealand and Australia. He will provide taxonomic expertise to all members of the team, assist with field-work and contribute to the preparation of papers.
Leon Perrie is a young researcher (Ph.D. 2002) specialising largely on fern systematics and biogeography, with an emphasis on the use of molecular data, and a strong publication record. He will provide molecular experience with Asplenium and, in particular, with AFLP-DNA fingerprinting for species delimitation; assist with field-work; assist with student supervision; be joint leader for the production of papers. Lara Shepherd is an early career researcher (Ph.D. 2006) with skills in the development and application of molecular tools for understanding population genetics and evolution of both plants (including Asplenium and other ferns) and animals. In conjunction with L. Perrie, she will analyse two of the species complexes (A. listeri/A. polyodon and A. carnarvonense/A. capitisyork) with AFLP and DNA sequencing, and generate sequences for complementary New Zealand ferns.
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Ph.D. student Daniel Ohlsen (Uni. Melb.) will participate in most field-work, do DNA sequencing (Aspleniaceae phylogeny), AFLP analyses (delimiting species in the A. bicentenniale/A. paleaceum/A. attenuatum complex), and prepare a revised morphological account of Aspleniaceae in Australia. Daniel completed honours (2009, with M Bayly) on morphological and molecular diversity in the fern family Gleicheniaceae in Australasia (grade: high H1). He has outstanding field skills and would be an excellent contributor to Bush Blitz surveys. He is keen to pursue a career as a plant taxonomist, has good molecular skills, one paper “in press” (Muelleria), and brings to the project an APA scholarship (commenced March 2010).
An Honours student (Uni Melb; to be appointed) will do DNA sequencing to assess diversity and biogeography (comparative phylogeography) of three widespread, mostly temperate, species of Aspleniaceae (A. gracillimum, A. aethiopicum, A. flabellifolium).
The Research Assistant (Uni. Melb.; to be appointed) will perform DNA sequencing of Blechnaceae, Hymenophyllaceae and Pteridaceae, as well as some sequencing for phylogeographic study of widespread species of Aspleniaceae. We would endeavour to attract someone who is in the process of studying for a higher degree in systematics, or who was interested in enrolling in one. Facilities
Most of the molecular and morphological work will be done through the School of Botany at The University of Melbourne. This is a vibrant research department, providing an excellent intellectual environment for research students and staff. We also have links and access to the resources of the National Herbarium of Victoria (MEL) and Royal Botanic Gardens Melbourne where loan material from other herbaria will be received. The genetics of two of the species complexes will be analysed at the Allan Wilson Centre, Massey University, New Zealand, with state-of-the-art molecular labs, and a long history (>10 years) of successfully applying AFLP and other molecular markers to a wide range of plant groups.
The Museum of New Zealand holds New Zealand’s foremost collection of ferns, housing both historical material and active research collections of P. Brownsey and L. Perrie. These will provide valuable material for comparison with Australian specimens, and the resources of the Museum will be available to support a visit by the Ph.D. student and any field work to collect New Zealand material. References: Brownsey (1998) Flora of Australia 48:295–327; Butz (2004) National Recovery Plan for the Christmas Island Spleenwort Asplenium listeri, Natural Heritage Trust; DuPuy (1993) Flora of Australia 50:554–558; Ebihara et al. (2006) Blumea 51:221-280; Faith (2008) Cons.Biol. 22:1461-1470; Falush et al. (2007) Mol.Ecol.Notes 7:574-578; Hennequin et al. (2010) Mol.Phylogenet.Evol. 55:47-59; Meudt & Bayly (2008) Mol.Phylogenet.Evol. 47:319-338; Perrie & Brownsey (2005a) Am.FernJ. 95:1-21; Perrie & Brownsey (2005b) Am.J.Bot. 92:1559-1564; Perrie & Shepherd (2009) Mol.Phylogenet.Evol. 52:74-783; Rothfels et al. (2008) Taxon 57:712-724; Schneider et al. (2005) Proc.R.Soc.B 272:455-460; Schuettpelz et al. (2007) Mol.Phylogenet.Evol. 44:1172-1185; Shepherd et al. (2007a) NZ.J.Bot. 45:67-80; Shepherd et al. (2007b) Mol.Ecol. 16:4536-4549; Shepherd et al. (2008a) Mol.Phylogenet.Evol. 48:176-187; Shepherd et al. (2008b) Mol.Phylogenet.Evol. 49:204-248; Shepherd et al. (2009) J.Biogeogr. 36:1972-1977; Smith et al. (2006) Taxon 55:705-731; Yatabe et al. (2001) Am.J.Bot. 88:1517-1522; Yatabe et al. (2009) Bot.J.Linn.Soc. 160:42-63.
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Project budget Please list all items required for the project for the duration of the grant. All grants awarded will be of three years duration. E.g. for a $90,000 p.a. Research Grant, the TOTAL COSTS should equal approximately $270,000. Total costs may be slightly under (up to 0.5%) the grant amount. Please list in-kind contributions but do not include in the total costs. Expenditure must be quoted in Australian dollars and must not include fringe benefit costs. The following amounts are GST exclusive. Please note: Applicants do not need to cost involvement in Bush Blitz field work as this will be covered as part of the Bush Blitz program.
Table 4: Example budget breakdown for a $90,000 p.a. Research Grant
Bush Blitz funding Cash co-funding
Salary co-funding
Host Institution (in-kind and not in total)
Personnel (salaries + on-costs)
L.Johns, Principal Investigator @ 6% *FTE + #18% on-costs
$31,860
To be appointed, Postdoctoral Fellow Level A Step 6 @ 80% FTE + 18% on-costs
$138,800
P.White, Research Assistant @ 50% FTE + 18% on-costs
$123,900
Total Personnel $262,700 $0 $31,860
Travel
Airfare: Sydney-Melbourne return $300
Melbourne: 5 days Accommodation @ $144/day and meals @ $85.40/day
$1,147
Car Hire: 5 days @ $60/day $300
Total Travel $1,747
Equipment and other expenses $5,000
Computer lease for Research Assistant
$3,000
Professional Binocular Microscope $1,495
Sequencing Cost @ $20/sample $840
Total Equipment and other $5,335
TOTAL COSTS $269,782 $0 $31,860 $5,000
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Personnel Each Investigator must provide an indication of the percentage of time to be devoted to the proposed project. This is expressed as a percentage of Full Time Equivalent (FTE) as shown in example Table 4. Salary rates may include on-costs at the institutional level up to a maximum of 28%, however the percentage of on-costs used must be stated in the Personnel Costs section of the project budget table (see example Table 4). Alternatively, on-costs may be added as an institutional contribution.
Requests for personnel assistance must show the official designation of the position (Technician, Laboratory Assistant, Postdoctoral Fellow, etc) and the level requested. Technical Assistant rates are to comply with institutional rates for the grade and level applied for. Where a research student is involved and the supervisor is the applicant, funds for personnel assistance must be sought at the current Australian Postgraduate Award rate. Any part-time or short-term assistance must be sought under this heading.
Funding will not be provided for salaries of curatorial staff of collection institutions that are carrying out their normal collection-related duties. Postdoctoral fellows may include their own salary if the institution is not already paying their salary. Postgraduate students may receive stipends as well as other research support.
Travel Travel associated with Bush Blitz field work will be covered separately as part of the Bush Blitz program. All other travel must be clearly associated with the project and requests for travel funds must include a full itinerary and supporting details for the proposed travel. The rates to be used in applications for accommodation, meal cost and vehicle mileages should be reasonable allowance amounts in accordance with Australian Taxation Office guidelines. For more information on rates, please go to www.ato.gov.au/individuals/content.asp?doc=/content/36017.htm&page=1#P83_2010
Equipment and other expenses List all equipment required for the project, including consumables, software, preparation and storage of data etc. Requests for equipment that cost $1,000 or more per item must indicate the cost of the equipment, installation and the name of the manufacturer. Please note you may request justifiable, project-related items such as microscopes or computers. Costs must exclude GST and the applicant must be able to supply quotes if requested. Please note that funding will not be provided for items normally constituting institutional infrastructure, rental of office and laboratory space and internet/email access.
In-kind contributions You may record any in-kind support given by the host institution, such as:
• value placed on curatorial support for collections
• institutional infrastructure such as computer and internet/email access, and
• access to libraries, etc.
Important Your project will be assessed on the budget provided. Any supporting statements, such as why a research assistant at a particular level is needed, or why a certain field trip is necessary, must be included in the Timeline and Budget Justification section in Question 12.
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Question 12: Project budget (GST exclusive)
Bush Blitz funding
Cash co-funding
Salary co-funding
Host Institution (in-kind and not in
total)
Personnel (salaries + on-costs)
M. Bayly, Principal Investigator @ 20% FTE + 27% on costs
$60,505
L. Perrie, Joint Investigator @ 10% FTE + 28% on costs
$26,112
P. Brownsey, Joint Investigator @ 5% FTE + 28% on costs
$15,504
L. Shepherd, Joint Investigator @ 20% FTE + 18% on costs [= 6 months full-time] $34,235
To be appointed, research assistant Grade 2, Level1 (Melb Uni) @ 16.7% FTE + 18% on costs [= 6 months full-time] $30,600
D. Ohlsen APA stipend
$67,500
To be appointed, honours student (year 2): institutional support (in-kind)
$1,500
Total Personnel $64,835 $102,121 $69,000
Travel
Field-work – Christmas Island
Airfares ex Melbourne: 2 x $2190. Accomm: 6 nights x $160. Vehicle hire: 5 x $90. Meals: 7 days x 2 x $60
$6,630
Fieldwork – ex Cairns (Wet Tropics and surrounds)
Airfares: 1 ex Melb ($660); 2 ex Wellington (total $2592). Car hire: 9 x $65. Accomm: 9 x $130. Fuel: 100L @ $1.20. Meals 9 days x 3 x $50 $6,477
Field work – ex Brisbane
Airfares: 1 ex Melb ($482); 1 ex Wellington ($968). Car hire: 10 x $52. Accomm: 9 x $140. Fuel: 250L @ $1.20. Meals 10 days x 2 x $50 $2,530 $2,000
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Fieldwork – ex Cairns (Cape York)
Airfares: 1 ex Melb ($660); 2 ex Wellington (total $2592). 4wd hire: 10 x $115. Accomm: 10 x $130. Fuel: 250L @ $1.20. Meals 10 days x 3 x $50 $7,442
Ph.D. student travel to Wellington, NZ, to learn lab techniques, examine New Zealand material in field and herbarium: Return airfare ($688), budget accommodation and meals (10 days @ $95) $1638
L. Perrie travel to Melbourne lab and herbarium: return airfare ($688); meals & accommodation x 8 days @ $263 $2,792
Student attendance at least one national or International conference to present work (Uni. Melb.) $2,000
Fieldwork – additional collecting Western Australia, Victoria, Tasmania. New South Wales, New Zealand $5,500
Total Travel $18,240 $11,269 $7,500
Equipment and other expenses
DNA isolations c. 1500 @ $5 $6,250 $1,250
DNA sequencing for phylogeny of Australian Aspleniaceae: 90 samples for 4 chloroplast loci @ $30 $10,800
A. listeri/A. polyodon complex.
AFLP (@ $28.50/sample) for 100 samples (5 samples from each of 15 Australian and 5 New Zealand populations).
Sequencing (single locus, single direction; @ $20/sample) for 250 samples (10 samples from each of 15 Australian and 10 New Zealand populations). $5,135
$2,715
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A. bicentenniale/A. paleaceum/A. attenuatum complex.
AFLP (@ $28.50/sample) for 130 samples (5 samples from each of 8 populations for each of A. paleaceum & A. attenuatum; 5 samples from each of 2 populations of A. bicentenniale; 40 samples of hybrids and related species).
Sequencing (single locus, single direction; @ $20/sample) for 200 samples (10 samples from each of 8 populations for each of A. paleaceum & A. attenuatum; 10 samples of A. bicentenniale; 30 hybrid samples). $7,705
A. carnarvonense/A. capitisyork complex.
AFLP (@ $28.50/sample) and sequencing (single locus, single direction; @ $20/sample) for 40 samples (5 samples from each of 4 populations for each species) $1,940
A. australasicum phylogeography.
Sequencing (single locus, single direction; @ $20/sample) for 150 samples (10 samples from each of 15 populations). $3,000
A. aethiopicum phylogeography.
Sequencing (single locus, single direction; @ $20/sample) for 100 samples (10 samples from each of 10 populations). $2,000
A. flabellifolium phylogeography. Sequencing (single locus, single direction; @ $20/sample) for 140 samples (10 samples from each of 10 Australian populations, plus 40 samples from New Zealand). $2,000 $800
Pleurosorus (both species) phylogeography. Sequencing (single locus, single direction; @ $20/sample) for 120 samples (100 Australian samples, plus 20 samples from New Zealand). $2,000 $400
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Phylogeography A. gracillimum and other trans-Tasman species. Sequencing (single locus, single direction; @ $20/sample) for 90 samples (30 widespread Australian samples of A. gracillimum and 30 Australian samples of other trans-Tasman species, plus 30 samples from New Zealand to complement existing New Zealand data). $1,200 $600
Phylogeny of Australian Blechnaceae, Hymenophyllaceae and Pteridaceae.
Sequencing (two chloroplast loci, bidirectional; @ $30/locus/sample) of 250 samples (allowing for multiple samples for some species). $9,850 $5,150
Complementary sequencing of New Zealand Pteridaceae, Hymenophyllaceae, and Blechnaceae to build on existing data. Sequencing (single chloroplast locus, bidirectional; @ $30/locus/sample) for 60 samples. $1,800
In-kind value of laboratory, herbarium and other facilities ($15,000 per annum based on estimated time of lab. use for this project, University of Melbourne space charges)
$45,000
Total Equipment and other $51,880 $12,715 $45,000
TOTAL COSTS $134,955 $23,984 $102,121 $121,500
Please ensure the total costs specified in this budget table cover the duration of the grant.
Ensure you indicate clearly the nature of contributions from each institution involved and from any other sources. Evidence of cash and other co-funding contributions MUST be included with the application (see the Eligibility Criteria at the beginning of this form).
Timeline and Budget Justification Please outline an intended plan of work, including commencement and completion dates for each aspect of the project. Briefly explain why the personnel, travel, items of equipment, databasing and miscellaneous items, requested in the table above, are necessary for the project.
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Year 1 • Field-work in Queensland (Cairns/Townsville & Brisbane), Christmas Island, Victoria,
New South Wales, and New Zealand. • Aspleniaceae DNA-sequencing initiated, including final selection of sequence loci for
overall phylogeny, each of the species-complexes, and the widespread species; at least one sample done for all four initial candidate loci for most Aspleniaceae species.
• Daniel Ohlsen (Ph.D.) student visit to New Zealand (includes some herbarium, lab and field work).
• Arrange loan of herbarium specimens to MEL. Year 2 • Field-work in Queensland (Cape York). • Leon Perrie visits Melbourne labs. • Honours student undertakes detailed investigation of DNA sequences of widespread
temperate species (A. flabellifolium and A. aethiopicum ). • Lara Shepherd analyses (chloroplast sequencing and AFLP) A. listeri/A. polyodon and
A. carnarvonense/A. capitisyork complexes. • Focal loci for other families selected. Lara Shepherd produces chloroplast sequence
from New Zealand Aspleniaceae, Hymenophyllaceae, Pteridaceae, and Blechnaceae to complement existing New Zealand DNA and present Australian work.
• Daniel Ohlsen finishes Aspleniaceae phylogeny, and analyses (chloroplast sequencing and AFLP) A. bicentenniale/A. paleaceum/A. attenuatum complex.
• Research Assistant hired to undertake remainder of Australian sequencing. Year 3 • Analysis of DNA sequences and AFLP data in conjunction with morphological data. • Papers written. • Revised taxonomy prepared. • Daniel Ohlsen prepares Ph.D thesis.
Personnel. No funds are requested for the salaries of M. Bayly, P. Brownsey or L. Perrie. These are recorded as co-contributions by the respective institutions, based on current salaries (the actual co-contributions will probably be higher, allowing for salary increases). The time-fraction allocated for M. Bayly (20% FTE) is an average across the three years. His time commitment in the first 6 months of the project will be minimal (his time being allocated to an existing ABRS grant), but will increase from Jan 2011.
Salary funds are sought for Joint Investigator L. Shepherd at 16.7% FTE plus on-costs, at current salary (translated from New Zealand to Australian dollars). Dr Shepherd is a highly-skilled evolutionary geneticist, working in the cutting-edge labs of the Allan Wilson Centre. She has extensive experience of DNA sequencing, AFLP DNA-fingerprinting, and genetic work with ferns (including three of the four target families). This will enable her to efficiently process two of the Asplenium species complexes. The 16.7% FTE equates to 6 months full-time.
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Funds are also sought for a Research Assistant based in Melbourne. Their responsibility, in conjunction with M Bayly, will be to do the sequencing not attributed to the Ph.D. student (Daniel Ohlsen), the Honours student, or to L. Shepherd. The RA will primarily produce sequences for Pteridaceae, Hymenophyllaceae, Blechnaceae, Asplenium australasicum, Pleurosorus, and additional sequences for Australian A. polyodon. This is estimated to take 6 months of full-time work (which equates to the 16.7% FTE across the three years, specified in the budget table), and this would be done in year 2. We will seek an RA with an interest in systematics who is enrolled, or would potentially enrol, in a research degree in this field – so that we are also enhancing local capacity in this area.
No funds are sought for a Ph.D. scholarship. D. Ohlsen has this year (March 2010) begun a Ph.D. on Australian Asplenium. The value of his Ph.D. scholarship is listed in the budget as an in-kind contribution. Institutional support (in-kind) will also be provided to cover overheads for the honours student. With Bush Blitz funding, D. Ohlsen’s Ph.D. project would expand to encompass the overall phylogeny of Australian Aspleniaceae plus an in-depth molecular and morphological analysis of the A. bicentenniale/A. paleaceum/A. attenuatum complex.
Travel. Fieldwork is essential to this project in order to obtain good quality material for DNA analyses (especially for AFLP studies) and sufficient numbers of samples for the detailed population genetic study of both rare and widespread species. The Bush Blitz surveys will be tremendous source of material for this work, but additional Asplenium-targeted fieldwork will be required. This will be necessary because: a) some rare species could prove difficult to find/collect and might be missed in general surveys; b) population level analyses will need to include adequate sampling of individuals, which may need extended searching that is also not possible in general surveys; c) studies of variation in widespread species will need to ensure an adequate and geographically representative spread of populations; d) timely completion of various components of the project will require collection timelines that are out-of-step with Bush Blitz surveys; e) some collections will be needed from areas outside of the National Reserve System (or in areas not specifically targeted by Bush Blitz surveys). To this end, four field trips are budgeted. The itineraries of these trips, as outlined here, will revolve mainly around collection of key species of Asplenium, but they will also present good opportunities for targeted sampling of Blechnaceae, Hymenophyllaceae and Pteridaceae.
• Christmas Island (7 days = c. 5 full days on the island and one night in Perth on return journey) to collect from the four known populations of A. listeri and to sample local populations of A. polyodon. Six other target fern species also on island. This trip is contingent on Bush Blitz funding.
• North Queensland (ex Cairns, 9 days): Wet Tropics and surrounding areas, between Cape Tribulation in the north and Mission Beach in the south (localities
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including Mt Windsor Tablelands, Daintree, Atherton Tablelands including Lamb Range, and Wooroonooran National Park). The aim is to sample c. 15 key species of Asplenium (including A. bicentenniale and A. paleaceum) as well as representatives of the other target families. This trip will be funded by the Museum of New Zealand.
• North Queensland (ex Cairns, 10 days), Cape York Peninsula (localities including McIlwraith Ra, Sir William Thompson Range, Iron Range). The primary aim of this trip would be to obtain adequate population sampling of A. capitisyork, but it would also provide the opportunity to collect material of c. 18 species across the four families. This trip is contingent on Bush Blitz funding.
• Southeast Queensland (ex Brisbane, 10 days) to sample c. 12 species of Aspleniaceae including A. carnarvonesne (Carnarvon Range), unassigned populations in Kroombit SF, A. harmanii (Lamington National Park, Mt Warning), with other taxa collected en route between these widespread areas (e.g., Cania Gorge, Kalpowar State Forest, Cooloola). This trip will be funded by the Museum of New Zealand, and extended with Bush Blitz funding.
Funding is budgeted for visits both by the Ph.D. student to travel to Wellington (year 1) and for L. Perrie to visit labs in Melbourne (year 2). The former will allow the student to examine important material at WELT, discuss Asplenium taxonomy with P. Brownsey, get some preliminary training at AFLP analysis, and be involved in some field work (the amounts budgeted are minimal; fieldwork will be covered by the Museum of New Zealand, and some accommodation potentially will be available through colleagues in Wellington). The latter will allow for L. Perrie to assist with AFLP trouble-shooting (by Ph.D. student), to liaise with both the honours student and Research Assistant on their molecular work, and to examine morphological vouchers to assist with identifications and morphological interpretation of results.
All airfare estimates are based on current prices (mostly Qantas super-saver type fares). Vehicle hire rates are based on University of Melbourne corporate rates through Avis. Vehicle charges for local field work are based on the university rate of 60c per km. Our meal and accommodation estimates are generally lower than ATO amounts for “reasonable allowances”. Our estimates are based on the assumption of shared accommodation for all fieldwork participants, and for most trips they are averages for a range of accommodation and meal types (city, regional, and camping for remote areas). Fuel costs are based on estimates of the distances to be travelled (assuming c. 10L of fuel per 100 km) and using current average fuel prices.
Laboratory expenses. Molecular lab work is an essential component of the project and, apart from salaries and fieldwork, will be one of the major costs.
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DNA isolations will use a variety of approaches, including bulk isolations by the Australian Genome Research Facility ($4.5 per sample) and DNA isolation kits for smaller numbers of samples (up to $12 per sample including associated consumables), and the estimate of $5 per sample is for the average of overall costs. The sequencing rate of $30 per sample is also an estimated average based on the costs of lab consumables, PCR reactions, PCR product purifications, and double stranded sequencing, and allowing some margin for PCR optimisation and repeated DNA sequencing or use of internal primers for failed reactions. Single stranded sequencing (estimate $20 per sample) will be used to reduce costs for the large phylogeographic datasets. The AFLP cost ($28.50 per sample) also includes all lab consumables, PCR costs, purchase of labelled primers and capillary electrophoresis of multiplexed loci.
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Question 13: Assessment of Application Please give the details of three potential assessors for external assessment of this application, if required.
Title · given name/s · surname Dr Harald Schneider
Address
Botany Department, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.
Phone +44 20 7942 6058
Fax +44 20 7942 5529
Email [email protected]
Relevance to project proposal World expert on Asplenium phylogeny.
Relationship to applicant (if applicable) Co-authored one paper with P. Brownsey and L. Perrie (2006, on Microsorum).
Title · given name/s · surname Mr Peter Bostock
Address
Queensland Herbarium, Department of Environment and Resource Management, Brisbane Botanic Gardens Mt Coot-tha, Mt Coot-tha Rd, Toowong 4066, Queensland.
Phone 07 3896 9508
Fax 07 3896 9624
Email [email protected]
Relevance to project proposal Expert on Australian, and especially Queensland, ferns. Queensland is a centre of diversity for Australian Asplenium.
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Relationship to applicant (if applicable)
Queensland Herbarium, Department of Environment and Resource Management, Brisbane Botanic Gardens Mt Coot-tha, Mt Coot-tha Rd, Toowong 4066, Queensland.
Title · given name/s · surname Dr Elizabeth Brown
Address Royal Botanic Gardens, Mrs Macquaries Road, Sydney, NSW 2000.
Phone 02 9231 8139
Fax 02 9241 2797
Email [email protected]
Relevance to project proposal Is familiar with both ferns (primarily as a collector) and molecular systematics.
Relationship to applicant (if applicable) Co-authored one paper with P. Brownsey & L. Perrie (2003, on Polystichum); Ph.D. examiner of L. Perrie (2002).
Please list the name/s of any persons to whom you would prefer the application were not sent for external assessment. Please include a justification for this preference.
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Important information
You must read this page
Freedom of Information All relevant documents are subject to freedom of information (FOI) and are available by making a valid application to the
FOI Officer
Department of the Environment, Water, Heritage and the Arts
GPO Box 787
Canberra ACT 2601
in accordance with the Freedom of Information Act 1982.
Protection of information The ABRS Advisory Committee may evaluate applications for grants with the assistance of peers in the scientific community both within Australia and overseas. Applicants may wish to indicate any person(s) they do not wish to be approached as assessors and these must be listed in the space provided on the application form. Names of assessors are not released to applicants. Assessors of applications are requested to destroy their copy of the application after completing their assessment. This destruction must be by shredding or pulping, or, in the case of electronic records, rendering the copy unreadable. The ABRS Advisory Committee and ABRS officers are bound to observe confidentiality.
Appeals mechanism There is an appeals mechanism for those applicants who believe their proposal has been unfairly treated in terms of the administrative procedures only. Appeals in relation to the content of the proposal, assessor reports or academic judgments made by the Advisory Committee will not be heard. The Advisory Committee will not participate in discussion relating to academic judgments made on grant applications. Applicants wishing to appeal against a decision, based on administrative procedures, may do so by notifying the Director of ABRS in writing. Appeals must be lodged within 28 days from the date on the letter of notification of the outcome of a grant application. An appeals panel of three people will be convened to consider appeals. If the appeals panel finds evidence the original decision was the result of undue administrative process, it will direct the application be reappraised.
Permits All collecting activities carried out as part of Bush Blitz must be undertaken in full compliance with the laws and regulations of the States and Territories of the Commonwealth of Australia. There are substantial fines for illegal collecting in most States, and these are enforced. A range of authorities in each of the States and Territories is responsible for the issue of permits for biological collection. Relevant information may be obtained from the leading wildlife management agency, museum or herbarium in each State or Territory, who should be consulted, in any case, as part of the planning process.
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Genetic resources A permit is required to collect biological samples for genetic/biochemical research in Commonwealth areas. There are similar requirements in Queensland and the Northern Territory, and other States are considering the introduction of such measures. Contact details for each of the State and Territory management authorities can be seen at: http://www.environment.gov.au/biodiversity/science/access/index.html.
Lodging of specimens and digital records All specimens and tissue samples collected and digital records created in relation to Bush Blitz will be lodged with a recognised permanent collection, such as a State/Territory museum or State/Territory herbarium.
Animal ethics Where the Activity involves the use and care of living non-human vertebrate animals or tissue for scientific purposes, the Principal Investigator must obtain review of and approval for such scientific purposes from a recognised animal ethics committee operating under the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes. The Principal Investigator agrees to provide the Department with a certificate of compliance with the appropriate guidelines prior to the commencement of any such scientific activities.
Submission of Progress and Final Reports In submitting this application I/we agree, if successful, to provide ABRS with all progress reports and a final report by the due dates.
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You must read and sign this page Certification for Principal Investigator and all Joint Investigator/s I certify to the best of my knowledge that:
1. I/we have read, understood and agree to all conditions contained in the Important information section of this document
2. all the details on this application are correct and complete, and 3. all persons listed in the application form as Joint Investigators have agreed to take part in the
proposed research. Principal Investigator signature Principal Investigator name Date
Michael Bayly 27 / Mar / 2010
Joint Investigator signature Joint Investigator name Date
Patrick Brownsey 27 / Mar / 2010
Joint Investigator signature Joint Investigator name Date
Leon Perrie 27 / Mar / 2010
Joint Investigator signature Joint Investigator name Date
Lara Shepherd 27 / Mar / 2010
Certification for Institution I certify that:
1. adequate research support and facilities will be made available for the Investigator/s or Fellow to complete the project
2. the institutional equipment and resources will be available for the duration of the project, and
3. the information in Question 12 (for the non-Bush Blitz funding contributions) is correct.
Head of Administering Institution (or nominee) signature Name and designation
Institution Date
……/….../20.....
ABRS must receive a secure PDF of this page, signed. See Checklist for more information.
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Checklist Please read this list and ensure you have completed all items prior to submitting your application. Have you:
• Filled in all questions using Arial font 12 point type?
• Completed the Project Details using the supplied subheadings?
• Completed the Project Details section in no more than six pages?
• Had the application signed by the Principal and all Joint Investigators?
• Had the application signed by the Administering Institution?
• Included letters of support from co-funding partners, that include the amount of funding to be credited to the project?
• Included a four-page maximum length curriculum vitae for Principal and Joint Investigators?
• Included any outstanding progress or final reports relating to previous ABRS grants?
Once you have answered yes to all these questions, you must submit by email your application (PDF word document), a secure PDF of the signature page and supporting co-funding documentation (PDF) by email by the closing date.
Address to send documentation:
By Email [email protected]
Business Address Grants and Business Officer
Australian Biological Resources Study Department of the Environment, Water, Heritage and the Arts GPO Box 787 Canberra ACT 2601
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Attachment A: Bush Blitz taxa groups and their collection Applications must specify what Bush Blitz material, or what material proposed to be collected as part of Bush Blitz, will be studied. There are two options for identifying what material will be used in grants:
1 Core Taxa There are a number of taxa targeted for collection in most Bush Blitz surveys. These are:
• Vascular plants
• Terrestrial Vertebrates (birds, mammals, reptiles, amphibians)
• Lycosidae (wolf spiders)
• Mygalomorphae (trapdoor and primitive spiders)
• Papilionoidea (butterflies)
• Gastropoda (terrestrial and freshwater snails)
• Odonata (dragonflies)
• Heteroptera (true bugs)
Material from these taxa groups will be held at various institutions and available for use by applicants.
2 Institutional Taxa There are a number of taxa flagged by individual collections institutions as collection and research priorities under Bush Blitz. If the application is related to these taxa groups, the application must specify:
• the taxa group
• for which institution the taxa group is a priority
• from what regions of Australia material is required, and
• whether the applicant is prepared to assist with collection of the taxa group through Bush Blitz field work.
It is the responsibility of applicants to liaise with collections institutions about their priorities.
Please note: Applicants do not need to cost involvement in Bush Blitz field work in their applications as this will be covered as part of the Bush Blitz program. Instead, applicants need to indicate in which regions they wish to be involved in survey and from which regions they require specimens.
Pre-existing material from collections may also be used in Bush Blitz taxonomy projects. Applications should specify how this will be undertaken.
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Attachment B: Example co-funding support letter
Principal Investigator [Enter Text Here]
Phone [Enter Text Here]
"[Name of co-funding contact]" [Institution] [Address] [Suburb] "[City State Postcode]"
LETTER OF SUPPORT "[PROJECT TITLE]"
"[Please specify the amount of the funding contribution ]"
"[Optional - please outline any in-kind support being provided]"
"[Optional - enter any terms and conditions imposed]"
Yours sincerely
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Attachment C: Priority Areas for Research Grants
1 Biodiversity, Conservation and Vulnerable and Endangered Species Taxonomic and systematics research provides information that is fundamental to the understanding and management of our biological world. To be considered for funding under this criteria, researchers are required to demonstrate the intended project will encompass one or more of the following areas:
1.1 Documenting Australia’s Biodiversity: Studies that contribute to documentation of Australia’s biodiversity, through identification, revision and documentation of understudied taxonomic groups
- This may include, for example, studies of taxonomic groups in largely unexplored habitats or a molecular project providing taxonomic insight into a taxa group where morphological taxonomy has failed to make an impact.
1.2 Conservation: Taxonomic research or barcoding research (with a systematics and/or phylogentic component) that provides critical data underpinning national responses to human-induced change, for conservation planning (particularly as regards the long-term biodiversity conservation objectives of the National Reserve System), or for the rehabilitation of degraded environments
- This may include, for example, taxonomic or systematics research on a group likely to be effective as an indicator of climate change, or a molecular project enabling reserve prioritisation.
1.3 Vulnerable and Endangered Species: Taxonomic research or barcoding research (with a systematics and/or phylogentic component) that contributes to a greater knowledge of Australia’s vulnerable and endangered biological heritage, especially that listed under the Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act)
- This may include, for example, a revision of a genus to clearly establish the taxonomic position and conservation status of undescribed species, including species currently listed under the EPBC Act.
1.4 Identifying Australia’s Biodiversity: Tools and products that contribute to the identification of Australia’s biodiversity
- This may include, for example, an identification key for a taxonomic group at a national scale, or molecular projects that make genetic information publicly available.
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2 Building Taxonomic Capacity This criterion focuses on support for training and/or recruitment of taxonomists, especially for research on critical taxonomic groups. To be considered for funding under this criterion, the researcher is required to demonstrate that the proposed project will encompass one or more of the following areas:
2.1 Training of early career researcher/s: Taxonomic studies that include clearly specified opportunities for capture and passage of skills and information from professionals to junior colleagues
- This may include a project where there is a component that includes a clearly documented opportunity for passing knowledge from a more senior taxonomist to an early career researcher.
2.2 Knowledge Management: Taxonomic studies that include clearly specified opportunities for capture and passage of skills and information from retired professionals to younger colleagues
- This may include a project where there is a component that includes a clearly documented opportunity for passing knowledge from a retired taxonomist.
2.2 Exchange of International Expertise: Projects that facilitate international exchange of research expertise and training in areas that will boost Australia's taxonomic capacity
- The lasting benefits to Australian taxonomy must be clearly specified and must include capacity building
- For example, support may be sought for salary and travel costs to bring an international expert to Australia or to enable an Australian researcher to train overseas.
