Ecography ECOG-03079 Kay, G

Ecography ECOG-03079 Kay, G. M., Tulloch, A., Barton, P. S., Cunningham, S. A., Driscoll, D. and Lindenmayer, D. B. 2017. Species co-occurrence networks show reptile community reorganization under agricultural transformation. – Ecography doi: 10.1111/ecog.03079 Supplementary material SUPPLEMENTARY MATERIAL Species co-occurrence networks show reptile community reorganization under agricultural transformation. Ecography 2017 Geoffrey M. Kay1*, Ayesha Tulloch1, Philip S. Barton1, Saul A. Cunningham1, Don Driscoll2, David B. Lindenmayer1 Contents Appendix 1: Details of the study region. ................................................................................................................. 2 Specifics of the land-use data ............................................................................................................................. 2 Specifics of the reptile data ................................................................................................................................. 3 Appendix 2: Species occupancy and trait information ............................................................................................ 8 Appendix 3: Additional species richness and composition results ........................................................................ 12 Appendix 4: Additional detail and results for co-occurrence analysis .................................................................. 15 Details of network analysis methodology and supporting data ........................................................................ 15 Additional co-occurrence results ...................................................................................................................... 16 Appendix 5: Comparison of co-occurrence results with alternative probabilistic analysis. .................................. 21 Appendix 6: Results from the modularity analysis. ............................................................................................... 26 Appendix 7: Threshold sensitivity analysis. ........................................................................................................... 28 Supporting References .......................................................................................................................................... 31 1 Appendix 1: Details of the study region. Our study is set within a broad agricultural landscape of southeastern Australia, spanning approximately >1000 km north-to-south from Warwick in southern Queensland (28o1’32”S, 152o12’22”E) to Albury in southern New South Wales (36o4’47”S, 146o54’59”E) (Figure A1). This area supports some of the most productive landscapes for cereal cropping and livestock grazing in Australia on account of moderate rainfall (400 – 1200 mm per annum) and moderate to highly fertile soils (Commonwealth of Australia 2013). The dominant vegetation of this region is the critically endangered Box Gum Grassy Woodland (BGGW) ecological community (Figure A2), of which <4% remains following 230 years of broad-scale clearing for agriculture (Lindenmayer et al. 2010). This woodland community comprises a diverse vegetation assemblage consisting of an open tree strata that was originally dominated by white box Eucalyptus albens, yellow box E. melliodora and Blakely’s red gum E. blakelyi and an understorey of native tussock grasses, herbs and scattered shrubs (Commonwealth of Australia 2013). Two broad agro-climatic systems have been defined across this study area (Kay et al. 2016), based on previous classifications of landscapes with similar climate, vegetation and common land-use (Hutchinson et al. 2005). These systems include a winter-rainfall mixed grazing and cropping system (termed Tablelands Region in the main text), and a low-rainfall cropping system (termed Western Region in the main text). Within each region, dominant land-uses include wheat and canola cropping, grazing of improved (exotic) pastures, and grazing of native pastures. The predominant livestock on farms were sheep (Ovis aries) and cattle (Bos taurus). Farm sizes ranged from 100 Ha to in some cases > 5000 ha, with the average closer to 1-2,000 Ha. Specifics of the land-use data For this study system, we considered transformed landscapes as those which had experienced any combination of two key threats in the recent (within 50 year) past: cultivation and fertilization. A critical aspect of our ‘natural’ study is that we combine these key transformation threats (cultivation and fertilization) into a single value used to represent transformation. While understanding the nature of both threats would be useful, 2 combining key threats in this way provides a means to explore the impacts of transformation in a broad sense, acknowledging that such threats rarely interact in isolation. We obtained site-level agricultural transformation data by conducting a survey of landholders to identify the cultivation and fertilization histories of landscapes surrounding each of 224 available sites. We classified all areas within 500m radius of each site as either: (i) native (areas with little fertilizer application, with less than 3 applications in total and not fertilized in the previous 15 years), (ii) improved (areas with some history of fertilization or cultivation in the past 15 years), (iii) cropped (five or more crops in the past 15 years), and (iv) other (e.g. infrastructure, water etc) (Figure A4). We removed any sites from further analysis which contained incomplete data (either from the land-use or ecological surveys) or comprised >5% of surrounding area as “other”. We digitized this data using ArcGIS and calculated the proportional area of native, improved and cropped landscapes within 500m radius of each site. We calculated a “proportion unmodified” measure for each site as: ∝ �� ∝ �� = x 100 ∝ �� where ∝ �� is the proportional surrounding area classified as native and ∝ �� is the total area within 500m radius of each site. As mentioned in the main text, we defined sites with ≥70% proportion unmodified as intact and sites with >30% modified (i.e. fertilized or cultivated within 15 years) as modified following classifications of ecosystem threat by Keith et al. (2013). The mean area of surrounding (<500 m) modified landscape for intact sites was 4.8 ± 8.3% and 9.4 ± 10.1% for the Western and Tablelands agro-climatic regions respectively, and 64.5 ± 22.2% and 58.3 ± 19.7% for modified landscapes for the same regions (Table 1, main text). Specifics of the reptile data Reptile surveys were conducted using a repeated time- and area-constrained (20-min x 0.8 ha) active search of natural habitats and inspections of artificial refuge arrays (Figure A4) within each site. Active searches of 3 natural habitat involved scanning each plot for basking or moving animals, raking through leaf litter and grass tussocks, lifting logs and surface rocks and inspecting exfoliating bark. Each array consisted of four roof tiles (32 cm x 42 cm), two sheets of corrugated iron (1 m x 1 m) stacked on top of each other, and four wooden sleepers (1.2 m long). We conducted surveys on clear days with minimal wind between 0900 and 1600 hours by the same group of experienced field ecologists. We identified species using Wilson & Swan (2012), releasing animals once recorded in accordance with Australian National University ethics guidelines (protocols F.ES.04.10 and A2013/38). 4 Figure A1. Location of the study area spanning New South Wales (NSW) and southern Queensland (QLD) of south-eastern Australia showing the location of monitoring sites (n=224) surveyed across the two agro-climatic systems (grey filled). 5 Figure A2. Example of a site from our study area showing the open woodland structure that is typical of the box-gum grassy woodland ecological community. 6 (a) (b) Figure A3. Depiction of the (a) active search and (b) artificial refuge array used in herpetofaunal surveys Figure A4. Example of a completed landuse survey, with different categories of land-use demarked. (Green polygon = remnant woodland, 2 = Native, 3 = Improved, 4 = Cropped landscape). 7 Appendix 2: Species occupancy and trait information Table A1. Species list including total abundance (Abund) and occurrence (‘Occur.’; number of site-level occurrences / total number of sites) for intact and modified landscapes within the two agro-climatic regions across the whole study. Key; ~ denotes increase, denotes decrease and – denotes absent (and stable) Family Scientific Name Abund Occur. Occurrence Whole Study Western Region Tablelands Region intact modified intact modified Agamidae Amphibolurus burnsi 3 1% 3.8% 4.0% ~ 0.0% - − Amphibolurus muricatus 10 4% 7.7% - 4.4% 3.5% Pogona barbata 22 8% 9.6% - 10.0% 8.8% Elapidae Demansia psammophis 7 3% 11.5% - - 1.8% ~ Furina diadema 4 2% 7.7% - - - − Parasuta dwyeri 37 10% 15.4% 4.0% 8.9% 8.8% Pseudechis porphyriacus 3 1% - - − 1.1% 3.5% ~ Pseudonaja textilis 32 11% 5.8% 8.0% ~ 8.9% 19.3% ~ Gekkonidae Christinus marmoratus 82 21% 7.7% 28.0% ~ 18.9% 35.1% ~ Diplodactylus vittatus 42 8% 11.5% 4.0% 8.9% 3.5% Gehyra variegata 11 4% 11.5% 8.0% - - − Heteronotia binoei 19 5% 17.3% 8.0% - - − Nebulifera robusta 5 1% 1.9% 8.0% ~ - - − Strophurus intermedius 4 1% 3.8% - 1.1% - Pygopodidae Aprasia parapulchella 67 5% 1.9% 16.0% ~ 6.7% - Delma inornata 19 7% 3.8% 16.0% ~ 7.8% 3.5% Delma plebeia 14 4% 13.5% 4.0% - - − Delma tincta 3 1% 3.8% - - - − Scincidae Acritoscincus duperreyi 4 1% - - − 2.2% 1.8% 8 Anomalopus leuckartii 16 5% 15.4% 12.0% -

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