Appendix 1 Development of the Ausplots Fauna Survey Protocol

Appendix 1 Development of the AusPlots Fauna Survey Protocol Surveillance monitoring program The Enhancing long-term surveillance monitoring across Australian program was supported by the Department of the Environment as part of a suite of activities to build Australia’s surveillance monitoring capacity around a small set of terrestrial biodiversity indicators. It is envisaged that this improved capacity will potentially have benefit and applicability to national environmental reporting, for example through the headline environmental indicators (Environment Budget Statement 2014) and State of the Environment reporting.

The Department invested in the ‘Enhanced Surveillance Monitoring’ project with TERN to: . Provide clear guidance on what to survey – what and how – to contribute to a reliable, comprehensive national longitudinal dataset on biodiversity . Collaborate on this with scientific and management organisations engaged in vegetation and fauna monitoring across the continent . Allow non-expert citizen scientists to generate data, which is relevant to local decisions and reporting.

Key elements of this work are about building consensus, building on the best of existing approaches, and development something simple, affordable and meaningful.

Fauna survey protocols A discrete component of this project was to develop fauna survey protocols to complement the existing AusPlots Rangelands Protocols (White et al. 2012), with the aim to: . improve our understanding of distributions, abundance and richness of fauna species across Australia’s rangelands . build understanding of the relationship between habitat dynamics and fauna species population dynamics . provide a baseline against which future change can be assessed . fill a key gap in our ability to understand and report trends in Australian biota . develop an improved understanding to the degree to which vegetation and condition attributes can be used as surrogates for fauna in biodiversity monitoring.

Scope of the fauna survey protocols From this starting point, a national working group of expert stakeholders was formed to collaboratively develop the ‘AusPlots Fauna Survey Protocols’. The purpose of the workshop was to come up with a fit for purpose protocol for how you would monitor fauna for the purpose of surveillance monitoring, ensuring Broadscale repeatable methods.

The working group defined surveillance monitoring for fauna purposes, identified and reviewed methods to achieve fauna monitoring, identified the differences to targeted fauna monitoring, identified jurisdictional and ecosystem differences in standard fauna surveys for inventory purposes, reviewed and discussed the types of information for collection.

The following details were agreed to clarify inclusions in the scope of the fauna survey protocols project. . Fauna community based approach. . Core components to be based on:  pitfall trapping, with a minimum of four consecutive trap nights  focus on mammals and reptiles . Optional components to include:  acoustic sampling  camera trapping  bird surveys  invertebrate sampling. . Need to develop a rule set for when to implement the optional components, especially for Elliott trapping, cage trapping, funnel trapping and active searching. The rules need to consider: community, landscape, terrain, the species likely to be uncounted, and funding. . Need to develop rules (or guidelines) for when whole specimen vouchering should be conducted (timing within the fauna survey, and number of individuals to be collected per cluster of plots). Guidelines need to be consistent with jurisdictional requirements and local museum requirements. . Ideally AusPlots fauna sites will be co-located with AusPlots Rangelands vegetation and soils plots. Sites could be paired and immediately adjacent to the vegetation and soils plot, or clustered, i.e. more than one fauna site in proximity to a vegetation and soils plot. . Stratification to selection location of the fauna sites to be considered with the stratification associated with the vegetation and soils plots.

The following details were agreed to clarify exclusions from the scope of the fauna survey protocols. . Targeted monitoring, particularly at the species level, is not the focus. Targeted monitoring includes specialised survey techniques (including trap types) necessary to adequately species of interest. . Inventory data is considered essentially a bi-product of the surveys, and not the primary focus. . Morphological measurements of captured individuals other than measurements to aid identification and categorise age-classes, is not the focus of the protocols, but seen as additional data to be taken advantage of since the animal is in-the-hand.

Process to develop fauna survey protocols Figure 1 shows the process used to develop the fauna survey protocols. It is important to note that this process is ongoing – this manual (v0.1) represents a basis for ongoing engagement, discussion, and refinement towards a fauna surveys protocol that is nationally accepted and consistent. This kind of wide engagement requires the building of relationships and trust with key stakeholders, a process which takes more time than the length of this project.

Key elements of the development process are discussion in more detail below, along with recommended future steps to refine and finish the fauna survey protocols.

National working group A national working group of expert stakeholders was formed to collaboratively develop the ‘AusPlots Fauna Survey Protocols’. A key activity of this working group was a workshop held in February 2015 (minutes available at: http: www.ausplots.org.au/ecosystem-surveillance). The working group defined surveillance monitoring for fauna purposes, identified and reviewed methods to achieve fauna monitoring, identified the key differences to targeted fauna monitoring and identified jurisdictional and ecosystem differences in standard fauna surveys for inventory purposes, thereby defining the scope of the fauna survey protocols, and reviewed and discussed the types of information for collection.

Review of jurisdictional fauna survey methods A literature review collated standard jurisdictional fauna survey methods typically used for inventory surveys, and where available monitoring surveys. A key focus was on animal ethics and permit requirements so that minimum requirements could be easily identified and be incorporated into the various guidelines of the AusPlots Fauna Survey Protocols manual (this document). The goal is to ensure that all AusPlots fauna surveys meet these minimum requirements regardless of the jurisdiction.

Field trials Building on the outcomes of the working group and review of the jurisdictional survey methods, a draft survey method was developed, distributed to working group members for initial review, and field tested in April/May 2015 at Calperum Station (Riverland, South Australia). Four fauna sites were established, each being paired with existing AusPlots Rangelands vegetation and soils plots. Three of the sites (SASMDD008, SASMDD012, SASMDD017) were high-intensity plots, consisting of: 21 pitfalls (buckets) and 8 funnel traps along 3 parallel lines of 7 pitfalls, 10 m apart, total 100 m drift fence for each line, 30 m between lines, with 20 Elliott traps trapped for 5-6 consecutive nights. One medium-intensity fauna site (SASMDD016) was established, consisting of 4 pitfalls (buckets) and 6 funnels in a T-formation, with 20 Elliott’s, trapped for 5 nights. No bird or bat survey techniques were employed. Captured individuals were identified to species level, measured and photographed, and released at the point of capture. Tissue samples were taken from selected individuals, and elected adult individuals were taken as whole specimen vouchers. Both tissue and whole individual specimens were donated to the South Australia Museum. Data from the field trails has been made publicly available via the TERN Eco-informatics SHaRED database and available at http://www.aekos.org.au/dataset/213230.

Through the field testing and subsequent review, key working group members refined the method to produce the v0.1 protocols that are presented in this manual. The following edits were made the field tested survey design: . Trapping module:  The number of pitfalls per site was reduced from 21 to 12 for high-intensity sites, but increased from 4 pitfalls in a T-formation to 6 pitfalls in a single line for medium-intensity sites. The proposed protocols (as presented in v0.1, this manual) involve 2 lines of 6 pitfalls (high intensity sites) or 1 line of 6 pitfalls (medium intensity sites), along 60 m drift fences, with pitfalls 8-10 m apart, and 4 funnel traps per line, in 2 pairs along the line, with an optional 20 Elliott traps, and 2 cage traps.  The number of consecutive trap nights increased from a recommended four nights, to a minimum of five nights and a recommended seven nights.  The type of pitfalls remains to be determined by the survey coordinator. Ideally for logistical reasons, collapsible pitfalls that measure similar dimensions to 20 L buckets are preferred. In environments where agile jumping species, such as hopping-mice (Notomys sp.) and sandhill dunnarts (Sminthopsis psammophila) deeper pitfalls should be used to maximise captures.  The use of Elliott and cage traps remains to be determined by the survey coordinator. . Whole animal vouchering module:  Whole animal vouchers remain a recommendation, with a minimum of 1-2 individuals per cluster. . Tissue specimen module:  Collection of tissue specimens from all captured individuals remains a preferred activity, with the option of only taking a sample from 2 individuals per cluster.

Review and refinement of the protocols Through the field testing and subsequent review, key working group members refined the method to produce the v0.1 protocols that are presented in this manual. Further work is required to refine the methods and bring them to a level that satisfactorily meets the Department’s and other stakeholders needs.

Version 0.1 of the Fauna Protocols Manual is aimed at providing a starting point for future widespread consultation with relevant stakeholders. All modules are considered a draft, whilst some modules of the manual are yet to be fully developed, and will be progressed in the future. It is anticipated that these methods will be further refined in the coming months and years. The AusPlots Rangelands Surveys Protocols manual took several years to refine and it is anticipated that this manual will be refined in the same way.

Figure 1. Overview of the process used to develop the protocols developed in this manual. It is recommended that additional steps be taken for wider consultation and review of the methods before they are adopted as a finished product.

Appendix 2 Checklist to identify the fauna survey modules and activities to be conducted for each fauna plot Note: A checklist should be completed for each plot to be surveyed. Green text indicates mandatory option. Orange text indicates the preferred and recommended option.

Module Technique details Options Trapping How many pitfalls will we use?  12  6  0 (select this for non-trapping sites, then move to next module) What type of pitfalls are warranted?  20 L buckets  Short collapsible  Deep collapsible  Short permanent  Deep permanent How many funnels will we use?  8  4  0 How many Elliott’s will we use?  20  0  Other: How many cages will we use?  2  0  Other: Are any other specific types of traps warranted?  Yes: Specify (justify)  No How many consecutive nights will we trap for?  7  5  Other: (justify) Measuring and What animals will we record morphological measurements of?  All captured individuals marking  Representative sample (mandatory if not all individuals measured) Will we temporarily mark all captured individuals?  Yes (mandatory) Will we permanently mark all captured individuals?  Yes  No  Other: (i.e. selected species only) Tissue Will we take a DNA tissue sample of all captured individuals?  Yes specimen  No (module in Will we take a DNA tissue sample of 1-2 captured individuals of each  Yes (mandatory) development) species for the survey location (i.e. clustered plots within 50 km  No: Please discuss further with AusPlots radius)? Whole animal Will we voucher only 1-2 adult individuals of each species for the survey  Yes vouchering location (following the vouchering decision tree)  No Will we voucher only 1-2 individuals of noteworthy species only for the  Yes survey location (i.e. cluster of plots within 50 km radius) (following the  No: Please discuss further with AusPlots vouchering decision tree) Observations Will we record all opportunistic fauna observations within the plot?  Yes (mandatory) Will we record all opportunistic fauna observations for the survey  Yes location (i.e. general area of the cluster of plots ~30 km radius)?  No Will we conduct active searching for a minimum 60 minutes  Yes (mandatory) within/immediately adjacent to the plot? Will we conduct passive nocturnal headtorching/spotlighting for a  Yes minimum 60 minutes within/immediately adjacent to the plot  No Will we conduct any other justifiable (targeted) observation techniques  Yes: Specify (justify) within/adjacent the plot?  No

Camera Will we set-up remote camera(s)?  Yes: 1 observations  Yes: 4 (module in  No development) Birds Will we conduct 20 minute 2 ha search of the plot and adjacent area for  Yes at least 1 morning and 1 afternoon session?  No Will we conduct a 500 m untimed wider area search around the plot for  Yes: if habitat or likely species warrants it more cryptic species?  No Bats Will we set-up an acoustic sampler to record bat calls for at least 1  Yes (module in night?  No – we will use AnaBats instead development) Will we set-up an AnaBat to record bat calls for at least 1 night?  Yes  No Will we set-up a harp trap either within the plot, or adjacent suitable  Yes: if suitable habitat is present area for at least 1 night?  No Will we conduct mist netting for at least 60 minutes within the plot, or  Yes: if suitable habitat is present adjacent suitable area?  No

Appendix 3 AusPlots plot naming convention Naming convention of the Fauna Plot should follow the AusPlots Rangeland Vegetation and Soils Protocols (White et al., 2012). The plot name is a code that follows the alpha-numeric convention of: . state/territory (2 letters) . plot type (1 letter) (Fauna Plots have been allocated the letter ‘Z’ (i.e. relating to zoology) . bioregion code (3 letters) . plot number (4 numbers).

For example, a plot that is within the state of South Australia, is a Fauna Plot type, is within the Stony Plains bioregion, is SAZSTP0001. The tables below identify the codes to apply.

Code State / territory States and territories CT Australian Capital Territory NS New South Wales NT Northern Territory QD Queensland SA South Australia TS Tasmania VC Victoria

Code Bio-region name Code Bio-region name IBRA bioregions ARC Arnhem Coast FSD Great Sandy Desert ARP Arnhem Plateau GUC Gulf Coastal BHC Broken Hill Complex GUP Gulf Plains

BRT Burt Plain GVD Great Victoria Desert

CAR Carnavon HAM Hampton

CEA Central Arnhem LSD Little Sandy Desert

CHC Channel Country MAC MacDonnell Ranges CEK Central Kimberley MDD Murray Darling Depression COO Coolgardie MGD Mitchell Grass Downs COP Cobar Peneplain MII Mount Isa Inlier CER Central Ranges MUL Mulga Lands

CYP Cape York Peninsula MUR Murchsion

DAB Daly Basin NOK Northern Kimberley

DAC Darwin Coastal NLL Nullarbor

DEU Desert Uplands OVP Ord Victoria Plain DAL Dampierland PCK Pine Creek DMR Davenport Murchison Ranges PIL Pilbara DRP Darling River Plains RIV Riverina EIU Einsaleigh Uplands SSD Simpson Strzlecki Dunefields

FIN Finke STP Stony Plains

FLB Flinders Lofty Block STU Stuart Plateau

GAS Gascoyne TAN Tanami

GAW Gawler TIW Tiwi Coburg GID Gibson Desert VIB Victoria Bonaparte GFU Gulf Fall and Uplands YAL Yalgoo AAL Australian Alps NSS NSW South Western Slopes AWB Avon Wheatbelt SYB Sydney Basin

BBN Brigalow Belt North SCP South East Coastal Plain

BBS Brigalow Belt South SEC South East Corner Code Bio-region name Code Bio-region name BEL Ben Lomond SEH South Eastern Highlands CMC Central Mackay Coast SEQ South Eastern Queensland IBRA bioregions – ESP Esperance Plains SWA Swan Coastal Plain (continued) EYB Eyre Yorke Block TCH Tasmanian Central Highlands

FLI Flinders TNM Tasmanian Northern Midlands GSP Geraldton Sandplains TNS Tasmanian Northern Slopes JAF Jarrah Forest TSE Tasmanian South East KAN Kanmantoo TSR Tasmanian Southern Ranges KIN King TWE Tasmanian West MAL Mallee VIM Victorian Midlands NAN Nandewar VVP Victorian Volcanic Plain NCP Naracoorte Coastal Plains WAR Warren NET New England Tablelands WET Wet Tropics NNC NSW North Coast

Code Plot type AusPlots plot types A AusPlots Rangelands T Transects L LTERN F AusPlots Forests G General use (includes training plots) S Super sites Z Fauna (zoology)

Weather Datasheet

Date Time Location where recorded Temperature Precipitation Duration of precipitation Wind descriptive term Cloud cover Other Comments Observer initials

See over for the descriptive terms to use Enter your weather observations several times at day (at least morning, midday, afternoon, night), more often if the weather conditions change. Enter the temperature range or descriptive term (blue text) on the datasheet. Temperature Precipitation Showers Usually begin and end suddenly. Relatively short-lived, but may last half an hour. Fall from cumulus clouds, often separated by blue sky. Oct-Mar Temp o C Apr-Sept Temp o C Term Showers may fall in patches rather than across the whole forecast area. Range in intensity from light to very heavy. Max Min Max Min Rain In contrast to showers, rain is steadier and normally falls from stratiform (layer) cloud. Rain can range in intensity from light to very heavy Very hot > 40 - - - Drizzle Fairly uniform precipitation composed exclusively of very small water droplets very close to one another Hot 35-39 > 22 - - Frost Deposit of soft white ice crystals or frozen dew drops on objects near the ground; formed when surface temperature falls below freezing point Warm 30-34 18-21 > 20 - Fog Suspension of very small water droplets in the air, reducing visibility at ground level to less than a kilometre Mild 25-29 15-17 16-20 > 10 Mist Similar to fog, but visibility remains more than a kilometre Cool 20-24 10-14 13-15 5-9 Thunderstorms Thunderstorms are one or more convective clouds in which electrical discharge can be seen as lightning and heard as thunder by a person on the earth's surface. A severe thunderstorm produces one or more of : 1) hail at the ground with diameter of 2 cm or more; 2) wind gusts at the Cold < 20 <10 10-12 1-4 ground of 90 km/h or more; 3) tornadoes; or 4) very heavy rain likely to cause flash flooding Very cold - - < 10 < 1 Duration of precipitation Wind Descriptive term Short duration. Descriptive term Beaufort scale Description Intermittent Precipitation which ceases at times Calm 0 Smoke rises vertically Occasional Precipitation which while not frequent, is recurrent Light winds 1-3 Wind felt on face; leaves rustle Frequent Showers occurring regularly and often Moderate winds 4 Raises dust and loose paper; small branches are moved Continuous Precipitation which does not cease, or ceases only briefly Fresh winds 5 Small trees begin to sway Periods of rain Rain falling most of the time, but with breaks Strong winds 6 Large branches in motion; umbrellas used with difficulty Brief Short duration Near gale 7 Whole trees in motion; inconvenience felt when walking against wind Intermittent Precipitation which ceases at times Gale 8 Twigs break off trees Occasional Precipitation which while not frequent, is recurrent Strong gale 9 Slight structural damage occurs; larger branches break off Frequent Showers occurring regularly and often Storm 10 Seldom experienced inland; trees uprooted Violent storm 11 Very rarely experienced - widespread damage Cloud cover Sunny Little chance of the sun being obscured by cloud. Cloud covering < ¼ of the sky. Note: High level cirrus clouds are often thin and wispy, allowing a considerable amount of sunlight to penetrate them, sufficient to produce shadows. In this case the day could be termed 'sunny' even though the sky may consist of cirrus cloud. Mostly sunny Predominantly more clear sky than cloud. Cloud covering ¼ of the sky. For example, the sun would be obscured by cloud for short periods of time. Partly cloudy Predominantly more clear sky than cloud. Cloud covering ¼ - ¾ of the sky. For example, the sun would be regularly obscured by cloud for short periods of time. Cloudy Predominantly more cloud than clear sky. Cloud covering ¾ - nearly all of the sky. For example, the sun would be obscured by cloud for substantial periods of time. Overcast Sky completely covered with cloud. Cloud expected to cover all of the sky.

Appendix 4 AusPlots Fauna Survey Protocols Datasheet Templates

. Bird survey datasheet

. Captures datasheet

. Diurnal active search datasheet . Nocturnal passive search datasheet

. Opportunistic observations datasheet

. Trap closure datasheet . Trap effort datasheet

. Weather observations datasheet

. Whole specimen voucher datasheet

Bird survey datasheet

Site No. Date Observer name Start time (24 hour) End time (24 hour) Total time (minutes)

Survey type  Was call play-back used? N / Y

20 minute 2 ha List species called:

500 m area search

Location observed/heard Breeding No. Observation type: Seen activity Species (sub-species) name Activity Outside survey Outside survey individuals (s) or Heard (h) Within survey category area – same area – different area (Y/N) habitat () habitat () (if applicable)

Activity categories FO flying overhead ROT resting on tree ROG resting on ground ROS resting on shrub FC flying over circling FOT foraging on tree FOG foraging on ground FOS foraging on shrub FW flying within survey area at strata level Breeding categories NE Nest with eggs RFY Recently fledged young NY Nest with young DBE Diagnostic behaviour (incl. distraction displays, dive bombing, brood patch evident, carrying food repeatedly to nest or hollow) YON Young out of nest SBE Suggestive behaviour (incl. nest building, courtship or copulation, single observations of carrying food)

Captures datasheet

Todays date DD/MM/YY Trap check time (am / pm) Use this sheet for multiple sites! - But new sheet each trapping check session (AM/PM are different)

Species name or comment New/Re-cap Site No. Capture No. Class Method Weight (-bag) Tail (mm) Sex Tissue specimen No. Photo range No. Other comments Field staff initials (or field name or voucher number) (N, Rc)

Marked Head-body/vent (mm) Hind foot (mm) Repro Whole specimen voucher No. Data entry ID (Y/N, colour)

Marked Head-body (mm) Hind foot (mm) Repro Whole specimen voucher No. Data entry ID (Y/N, colour)

Class Method Repro B Bird P-b Pitfall - bucket E Elliott O Observed S Skelton/bones Sc-f Scat-fresh B-e Birds-eggs PY Pouch young (incl. no.) S Scrotal testes F Frog P-s Pitfall - short C Cage G Hand capture H Heard Sc-u Scat-unknown B-c Birds-chicks L Lactating A Abdominal testes M Mammal P-d Pitfall - deep F Funnel D Digging Br-f Burrow-fresh evidence Tk-f Track-fresh N-a Nest-active D Distended teats P Pregnant R Reptile G Hand capture F Feathers Br-u Burrow-unknown Tk-u Track-unknown N-i Nest-inactive B Button teats

Diurnal active search datasheet

Site No. Date Start time End time No. observers Total time

Class Species name or comment Method No. Ind New/ Marked Comment (#photo#, density, other method) Observer Data entry (or field name or voucher number) Re-cap (Y/N, colour) initial ID

Field Required Explanation Survey start/end Yes Can be printed on the datasheets prior to field work. date Site No. Yes Site number or name. Date Yes dd/mm/yy Start time Yes End time Yes No. of observers Yes Total time Yes Total time in minutes spent searching Class Yes B = bird, M = Mammal, R = Reptile, F = Frog. Species name Yes Or ‘?’ and ensure the comments provide voucher numbers, photo numbers or a description See code table. Note: Method Yes fresh scats should be dark in colour (have not faded), not crumbly dry scats are faded (grey not black), and crumbly ‘New’ are animals not previously marked. ‘Re-cap’ are animals previously marked. Only ‘New’ animals are entered into the database. Can also New Re-cap Yes include the texta colour. NA if the animal was not handled or could not be checked previous markings. Marked Yes List colour if marked. List ‘N’ if not marked, List ‘Y’ if marked but you forgot the colour. Note: sex only if certain teat status only if certain number of pouch young and size of pouch young Comment Optional photo numbers voucher number bag number if animal collected if animal was deceased if surveyor killed (i.e. Mus musculus) Observer initials Yes Initials of the field surveyor completing the data sheet, not the initials of the person doing the data entry. Data Entry ID. No / Yes Not required during field work. Data entry responsible person to enter the sequence number (required for uploading our data into the BDBSA).

Nocturnal passive search datasheet

Plot name Date Observer names Start time End time Total time Captures Datasheet

Methods - include spotlight type, head torches etc.

Observations

No. Data entry Class Species Comment individuals ID

Comments

Remember to fill out the Weather Datasheet Opportunistic observations datasheet

Wypt GPS Distance Date Time Class Species name (or voucher number) Method No. Ind Habitat Comment (photo#, condition) Staff Data entry No. No. initial ID

Trap closure datasheet

Date Site No. Trap type Trap number Reason for closure Action to be taken

Trap effort datasheet

Date Time Plot name Trap type (insert new row Number of Date Time Comments installed installed for each trap type) traps installed removed removed

Whole specimen voucher datasheet Whole specimen Species name or comment Weight Tail Ear length Processed Site No. Capture number Capture date Sex Liver taken (Y/N) Comments voucher No. (or field name or voucher number) (bag-) (mm) (mm) by

Head-body Hind-foot Data entry Repro Other Other tissue taken (Y/N) (mm) (mm) ID

Whole specimen Species name or comment Weight Tail Ear length Processed Site No. Capture number Capture date Sex Liver taken (Y/N) Comments voucher No. (or field name or voucher number) (bag-) (mm) (mm) by

Head-body Hind-foot Data entry Repro Other Other tissue taken (Y/N) (mm) (mm) ID