CSIRO OCEANS AND ATMOSPHERE

12 Monthly progress report:

Sawfish and Glyphis Research Program

Richard Pillans March 2016 Client Name: Western Department of Regional Development and Lands (ABN ) 28 807 221 246 Contact person: Eugene Carew

CSIRO Oceans and Atmosphere Citation Pillans, RD (2016). 12 month progress report: Sawfish and Glyphis Research Program CSIRO, Australia. Copyright and disclaimer © 2016 CSIRO To the extent permitted by law, all rights are reserved and no part of this publication covered by copyright may be reproduced or copied in any form or by any means except with the written permission of CSIRO. Important disclaimer CSIRO advises that the information contained in this publication comprises general statements based on scientific research. The reader is advised and needs to be aware that such information may be incomplete or unable to be used in any specific situation. No reliance or actions must therefore be made on that information without seeking prior expert professional, scientific and technical advice. To the extent permitted by law, CSIRO (including its employees and consultants) excludes all liability to any person for any consequences, including but not limited to all losses, damages, costs, expenses and any other compensation, arising directly or indirectly from using this publication (in part or in whole) and any information or material contained in it.

Contents

Executive summary ...... 5 1 Background ...... 6 2 Sawfish and Glyphis Research Program: Approved research projects for 2015/16 ...... 7 Wenlock Glyphis glyphis and sawfish research – ARC linkage grant ...... 7 Glyphis glyphis movement: threats from fisheries ...... 7 Determining adult G. glyphis habitat in ...... 7 Sawfish movement and population status in the Fitzroy River ...... 8 Kimberley Sawfish monitoring and indigenous engagement ...... 9 Pristis pristis genome sequencing ...... 9 PhD in P. pristis genetics ...... 9 Co-investment with future NESP research ...... 10 Ongoing communication with Department of Environment ...... 10 Project management and business development ...... 10

Executive summary

This is the 12 monthly progress report for the Sawfish and Glyphis Research Program being conducted by CSIRO. This report contains a summary of the activities conducted to date and research priorities for the next 1-3 years that have been approved by the Chairperson of the Sawfish and Glyphis Recovery Team, Department of Environment. Research priorities for the next two years will include research surveys, capture, tagging and monitoring of sawfish and speartooth sharks in the Northern Territory, Queensland and Western Australia to value add to the recently completed NERP project as well co-investing in future NESP research which commenced in late 2015. In addition to field research to tag animals with acoustic tags and collect tissue samples for genetic analyses, offset funds will also be used to obtain species-specific markers for Pristis pristis and G. garricki that will enable close kin genetic techniques to be used to obtain population estimates of these species in NT, QLD and WA. Funds from the offset project have made a significant contribution to the analysis and interpretation of G. glyphis close kin genetics which has been able to identify half sibling pairs that resulted in the worlds first estimates of adult population size in the Northern Territory that were presented to the Department of Environment in December 2014. Offset funds have also made a significant contribution to the understanding of movement patterns and habitat use of juvenile G. glyphis in the Wenlock River, QLD through annual tagging of individuals with acoustic tags and the maintenance and downloading of an array of acoustic receivers in the Wenlock and . The Queensland Department of Agriculture, Fisheries and Forestry is currently reviewing the East Coast Net fishery and these data will be used to evaluate the effectiveness of the current management measures and operation of the Inshore Fin Fish Fishery in minimising interactions with and mortality of speartooth sharks (G. glyphis), to ensure the survival and recovery of important populations of the species. This may include consideration of, for example, habitats fished, specifications of the gear used, the timing of fishing operations (seasonal, monthly, daily, tidal), etc. Offset funds have also resulted in more than 200 tissue samples of G. glyphis in the Wenlock River, QLD. These samples have recently been analysed and will enable estimates of adult population size for the Queensland population. Estimates of adult population size will be completed in 2016 together with estimates of juvenile mortality from the acoustic data. Offset funds were used to fund a successful field trip that resulted in the first records of adult G. glyphis in Australia. In a field trip in October 2015, two adult Speartooth Sharks were captured, measured and tagged with satellite tags. The capture of these two animals provided data on the size at maturity for this species which is vital for estimates of population status. The satellite tags are designed to detach from the animals after 90 and 240 days and will hopefully provide data on where adults occur. The distribution of adult G. glyphis remains a key gap in our understanding of this species. This work attracted significant media attention highlighted below. Research in 2016/17 will build on the outcomes of the NERP project and expand to areas in WA and QLD, build on existing collaborations and develop new ones to enable a retrospective analysis of trends in populations of sawfish and Glyphis. With results now starting to flow from the offset funding, CSIRO will soon be in a position to provide promotional material (ie. media friendly text and images) to WADRDL, if that would be of value. CSIRO has committed funds for 0.3 FTE for the duration of the project (10 years) to enable the offset funds to be managed and research priorities to be met.

1 Background

The Glyphis and Sawfish research monitoring project will be carried out between 2013 and 2023 by CSIRO in collaboration with relevant state and territory departments, universities and consultants. Research is aimed at improving knowledge on the distribution, movement, mortality and population estimates of Sawfish and Glyphis across northern Australia.

Following consultation and agreement from the chairperson of the sawfish and Glyphis Species Recovery Team, CSIRO will allocate funds to selected research programs that address objectives from the draft recovery plan for sawfish and Glyphis that include:

• develop research programs to assist conservation of sawfish and Glyphis species ; • improve the information base to allow the development of a quantitative framework to assess the recovery of, and inform management options for sawfish and Glyphis species; • improve community understanding and awareness of sawfish and Glyphis species; • reduce and, where possible, eliminate adverse impacts of habitat degradation and modification on sawfish and Glyphis species • refine research plans on the basis of management needs and information obtained

Over the next two years, research surveys, capture, tagging and monitoring of sawfish and Glyphis will focus on and coastal areas in Western Australia (Fitzroy River and Kimberley coastline) and Queensland (Wenlock and Ducie Rivers) and continue to support ongoing work in the Northern Territory under NESP. Research funding for NESP has completed surveys of NT and WA rivers for G. garricki to obtain genetic samples. Offset funds will be used to pay for laboratory work costs for extracting and sequencing tissues samples that will result in identification of half sibling pairs as well as the stock status (the degree of geographic variability in WA and NT rivers) of this species being understood. Analysis of the number half sib pairs will enable population estimates of G. garricki to be obtained. A summary of existing and planned projects including the amount that Offset funds have contributed to these is provided in Table 1.

2 Sawfish and Glyphis Research Program: Approved research projects for 2015/16

Wenlock River Glyphis glyphis and sawfish research – ARC linkage grant

The recently completed NERP project had a collaborative project with the University of Queensland and Australia Zoo in the Wenlock and Ducie River, Qld. This project is utilising an existing array of ~40 acoustic receivers and an additional 20 receivers deployed by the CSIRO to monitor movement and mortality of Glyphis glyphis and P. pristis in the Wenlock and Ducie River and is also collecting genetic samples for close kin genetics analysis of this population. Offset funds have been used to continue field sampling in 2015 (NERP funding ceased in early 2014) which has resulted in an additional 50 G. glyphis tissues samples for close kin genetics as well acoustic tags being implanted into 20 individuals which will continue to provide data on the long term movement and mortality of juveniles in the Wenlock and Ducie River.

An ARC linkage proposal was successful, with the offset funds contributing $20 000 per annum for three years (2015 – 2017). Offset funds will specifically be used to fund sampling to obtain tissue samples from sawfish and Glyphis, purchase acoustic tags for these species as well maintain the network of acoustic receivers in the Wenlock and Ducie River. This will ensure ongoing collection of tissues for close kin genetics and obtain long term data on movement and habitat use of G. glyphis and P. pristis using a combination of stable isotope and acoustic telemetry. A master’s student (supervised by Dr Pillans) is currently working on the movement of G. glyphis in the Wenlock River and some funds will be directed to the Masters student to ensure continuity of the research being undertaken in this river system.

Wenlock River Glyphis glyphis movement: threats from fisheries

Offset funds have also made a significant contribution to the understanding of movement patterns and habitat use of juvenile G. glyphis in the Wenlock River, QLD through annual tagging of individuals with acoustic tags and the maintenance and downloading of an array of acoustic receivers in the Wenlock and Ducie River. The Queensland Department of Agriculture, Fisheries and Forestry is currently reviewing the East Coast Net fishery and Richard Pillans has been invited to participate in this process to enable the research to inform fisheries management. Data on the movement patterns, habitat use and seasonality of G. glyphis movements in the Wenlock River will be used to evaluate the effectiveness of the current management measures and operation of the Gulf of Carpentaria Inshore Fin Fish Fishery in minimising interactions with and mortality of speartooth sharks (G. glyphis), to ensure the survival and recovery of important populations of the species. This may include consideration of overlap with habitats fished, specifications of the gear used, the timing of fishing operations (seasonal, monthly, daily, tidal etc).

Determining adult G. glyphis habitat in Queensland

There are currently no records of adult G. glyphis within their known range. This remains a key knowledge gap for the species and one that has been historically difficult to obtain. Long term research in the Wenlock River has illustrated that new born pups first appear in the river between September and November. The best available information on euryhaline species is that females drop the pups at the mouths of rivers

during this period. Two adults were captured in October 2015, providing the first records of mature G. glyphis in Australia. Data from the length of these individuals is the first information on size at maturity and will be vital for estimating demographic parameters needed for mortality estimates. Both tagged with satellite tags that were designed to detach from the animals after 90 and 240 days. These MiniPAT is a pop- up archival transmitting tags (PAT tag, also known as a PSAT) combination of archival and Argos satellite technology. PAT tags are designed to track the large-scale movements and behavior of fish and other animals which do not spend enough time at the surface to allow the use of real-time Argos satellite tags. One of these tags was due to detach in February 2016 but we have not heard from it since deployment suggesting that it has not yet detached from the animal. The other tag is due to detach in July 2016. Once the tags detach and transmit their location to the satellite network, they will provide data on where adult G. glyphis go once they have dropped their pups and mated. Despite no detections of these tagged individuals, the information obtained from this research has confirmed the importance of the as a pupping area and nursery ground for G. glyphis. Data on length at maturity is the first for this species in Australia and the presence of both adult males and females at the mouth of the Wenlock River suggests that mating and parturition (birth) occur in the same area. Genetic samples collected from the adults will be compared with juvenile samples to determine how long these individuals have been reproductively active. This research attracted significant media attention with the following statistics:

Blog published 11 November - https://blog.csiro.au/catching-up-with-the-speartooths-new-shark-specimens/ Views – 502, Shares - 186

Social Facebook engagement – Reached 16,727 people. 201 Likes. 13 shares. 675 post clicks (to the blog). Facebook post by the Threatened Species Commissioner – 149 Likes, 17 shares. Twitter engagement – Post - 16 Retweets

Media: Press release – Media report shows 28 articles with a reach of around 588K people. Interviews – Win Qld, The New Daily, Canberra ABC, Online news coverage in: Discovery, Business Insider, ABC, Cairnspost, New Scientist, NT News, Northern beaches news, Tech Times, Red map etc.

Sawfish movement and population status in the Fitzroy River

A research project that will deploy acoustic receivers and tag P. clavata with internal acoustic tags in the lower reaches of the Fitzroy River and King Sound has been developed with Murdoch University. Offset funds ($48043) have been used to fund a trip to the Fitzroy River to deploy receivers and tag animals. Between mid-August and late September 2015, 17 P. clavata were tagged with VEMCO acoustic tags in Snag and Telegraph Pool. An even split of sexes (8 F, 9 M) and a wide size range (1333-1980 mm TL) were tagged. In addition, nine acoustic receivers were installed within the Fitzroy Estuary and King Sound to monitor the movement and habitat use of tagged animals. Data will be downloaded between March – May 2016 once river levels subside enough to enable receivers to be safely accessed. Once data have been

downloaded, a report will be produced and made available to the Department of Environment and WA State Government.

Kimberley Sawfish monitoring and indigenous engagement

The Kimberley has probably the world’s most unchanged populations of sawfish (Green, Dwarf and Largetooth) and utilising indigenous knowledge and emerging technologies, we will provide baseline estimates of the population status and movement of Green and Dwarf Sawfish (P. zijsron and P. clavata).

This project will aim to enhance and develop capacity by linking scientists with Indigenous Rangers in the Kimberley region, and by linking traditional ecological knowledge with scientific knowledge. By capturing and tagging sawfish with acoustic tags and installing an array of acoustic receivers in known sawfish habitat, we will obtain data on the movement, habitat use and dispersal sawfish. Tissue samples collected from captured animals as well tissue samples from free swimming animals (we will also develop non-lethal methods where animals don’t need to be handled to obtain tissue samples) will facilitate the investigation of population connectivity and status using advancing genetic methods developed in NERP (through population genetics and close kin mark recapture). Ultimately the project will inform the recovery plan and guide management of Healthy Country Plans, IPAs and state and commonwealth marine parks present in the region.

Pristis pristis genome sequencing

Approximately $70000 has been allocated to the genome sequencing of Pristis pristis. This task was originally planned for the NERP project; however the shift in focus to Glyphis glyphis following fewer than expected recaptures prevented this from occurring. Genetic technologies are rapidly advancing and while complete genome sequencing was considered essential for obtaining half sibling pairs, this is no long the case, at least for some species. The cost associated with genome sequencing, as well as the benefits that can be obtained from this investment, have changed since we originally planned on this approach. It is now apparent that DART sequencing which is considerably cheaper than earlier methods, can be used to identify half sibling pairs, without sequencing the entire genome. As a result, $20 000 of offset funds was allocated to DART sequencing of existing P. pristis samples from northern Australia.

Complete sequencing of the genome may however, still enable us to discriminate between first cousins which would enable estimates of abundance from an even smaller sample size, and potentially provide information on trends over time, which is why we remain keen on pursuing the sequencing approach. We have therefore recently invested $ 14,842 to conduct a genome survey of the P. pristis genome that will provide a framework for the mapping and sequencing of genome size which will reduce the overall cost of genome sequencing and provide us with a better estimate of the total cost of sequencing the entire genome. Once the results of the genome survey have been fully analyzed, a decision on whether it is worth sequencing the genome will be made. Therefore, while we are still planning on sequencing the genome of P. pristis, this work and the $70 000 allocated to it has been deferred until 2016/7 pending outcomes of the genome survey and rapidly evolving genetic methods.

PhD in P. pristis genetics

Stacy Blane is a PhD student working at Murdoch University and is being supervised by Nicole Phillips and Jenny Chaplin. Stacy is planning on using single nucleotide polymorphism (SNP) genotyping to further

investigate the dispersal patterns of P. pristis that Nicole Philips identified during her PhD and will also assay for adaptively significant variation; the latter will assist in identifying markers for close kin genetics methods. We are currently having discussions with Jenny Chaplin and Stacy to ensure the project’s aims are aligned with the recovery plan. Initial indications are that Stacey will utilize CSIRO and NERP expertise in genetics to analyse Murdoch University sawfish samples using DArT genetic profiling to obtain genome sequences. Using the offset funds, CSIRO will support travel and accommodation costs of Stacy to receive the necessary training from within CSIRO.

Co-investment with future NESP research

$50 000 has been allocated to DART sequencing, Mitochondrial DNA analysis and DNA extraction of G. garricki samples collected in the NERP project as well future NESP research. This species was captured incidental to NERP research and the samples would not otherwise have been used. Analyses will enable estimates of population size as well as the population genetics status (barriers to gene flow) of G. garricki in the NT and WA to be determined.

Ongoing communication with Department of Environment

During 2016, Richard Pillans will travel to Canberra to discuss how offset funds are best spent and to prioritise research for 2017 and beyond. Richard will also attend the workshop “Confronting threats to marine ecosystems through the use of biodiversity offsets” at the Society for Conservation Biology 4th Oceania Congress in Brisbane (July 2016).

Project management and business development

CSIRO has funded 0.3 FTE for Richard Pillans and Mark Bravington to manage the project for the next 10 years. Approximately $5000 per annum will be allocated from the offset funds to domestic travel to attend meetings with collaborators and Department of Environment staff to ensure the offset funds continues to address the recovery plan objectives.

Table 1. Summary of funds invested and allocated for investment in 2016/7.

$ invested in $ allocated for Recipient of Funding Description 2014/5 investment in 2016/17 21,838 Murdoch University P. pristis samples and P. clavata movement 5,000 Murdoch University Training and travel for PhD Student (sawfish genetics) 20,000 20,000 University of Queensland, ARC linkage with UQ CSIRO, Australia Zoo 14,556 Diversity Arrays Technology Genome mapping for P. pristis 908 CDU/CSIRO DNA extraction for P. pristis

50,000 Diversity Arrays Technology/ DART sequence, Mt DNA and DNA NESP extraction of G. garricki 10,000 CSIRO Workshop on prioritising offset funds for sawfish and Glyphis

5,000 CSIRO Attendance of meetings and workshops for Richard Pillans 45,000 CSIRO Determine adult distribution and habitat for the Queensland population of G. glyphis 3,602 30,000 CSIRO, Australia Zoo Ongoing juvenile sampling, tagging and tissue collection for juvenile and adult mortality estimates in the Wenlock River 70,000 CSIRO, Kimberley Land Council Establish long term monitoring of sawfish populations in the Kimberley Total Total 60,904.60 235,000 Unspent funds from 2015/16 ($89,095) will be carried over to 2016/17

CONTACT US FOR FURTHER INFORMATION t +61 7 3833 5953 CSIRO Marine and Atmospheric Research/Wealth from e [email protected] Oceans Flagship w www.csiro.au Richard Pillans t +61 7 3833 5953 e [email protected] YOUR CSIRO w www.cmar.csiro.au Australia is founding its future on science and innovation. Its national science agency, CSIRO, is a powerhouse of ideas, technologies and skills for building prosperity, growth, health and sustainability. It serves governments, industries, business and communities across the nation.