Landscape layer for resistance
Fukuda, Yusuke; Banks, Sam (2021), Landscape layer for resistance, Dryad, Dataset, https://doi.org/10.5061/dryad.q2bvq83gb
This is raster file (base_cats_new3.asc) that was used to generate the environmental resistance surface with the ResistanceGA R package (Peterman, 2018) to evaluate models of environmental resistance to between-population movement of saltwater crocodiles Crocodylus porosus in the Northern Territory of Australia, represented by individual pairwise genetic distances among individuals. ResistanceGA models pairwise genetic distances in response to pairwise ‘ecological distances’ using linear mixed effects models with a maximum-likelihood population effects (MLPE) random effects structure (Clarke, Rothery, & Raybould, 2002), represented by individual ID in our models. We used Smouse and Peakall (1999) pairwise genetic distance as the response variable for this purpose.We estimated resistance surfaces that optimised random-walk commute distances (Etten, 2018) among the locations of sampled individuals as an explanatory variable in models of pairwise genetic distances among individuals. We ran a single surface optimisation in ResistanceGA (Peterman, 2018) to generate resistance values for the six environmental cover categories and stopped each model after 25 consecutive generations of no improvement in log-likelihood.
We created a categorical resistance surface layer using a 3 km x 3 km cell size raster (with 325 x 202 cells) with cells classified as sea, dry land, and the different types of habitats for C. porosus. We classified habitats into ‘core breeding habitat’, ‘marginal breeding habitat’, ‘core non-breeding habitat’ or ‘marginal non-breeding habitat’, following the definitions in the literature (Fukuda & Cuff, 2013; Fukuda et al., 2007; Webb, 1991). Breeding of C. porosus is highly seasonal during the wet season (November-April) and constrained to temporarily flooded, freshwater waterbodies which are not necessarily the most suitable habitat for saltwater crocodiles outside the breeding period (Campbell et al., 2013; Fukuda & Cuff, 2013; Fukuda et al., 2007; Webb, 1991). The core breeding habitats are the most favourable nesting areas represented by particular vegetation types as defined by Fukuda et al. (2007), while the marginal breeding habitats were identified by broader vegetation communities occasionally used for nesting (Fukuda & Cuff, 2013). The core non-breeding habitats are the most favourable waterbodies that tend to persist outside the breeding season (Fukuda & Cuff, 2013) and does not include known nesting areas. We defined the marginal non-breeding habitats by buffering the core non-breeding habitats by 3 km so that these habitats would include temporary waterbodies that may dry up during the dry season (May-October) or coastal areas with salinity levels similar to seawater (typically 35 parts per thousand). Although C. porosus is highly adapted to the saline environment (Cramp, Meyer, Sparks, & Franklin, 2008; Grigg, Taplin, Harlow, & Wright, 1980; Taplin, 1985), the species occurs in much higher density in brackish or fresh water (Fukuda et al., 2011; Webb & Manolis, 1989) and nesting females and embryos require access to freshwater (Webb, Manolis, Buckworth, & Sack, 1983; Webb, Messel, & Magnusson, 1977). Although some individuals access sea, especially when moving between the rivers (Campbell et al., 2010; Fukuda, Webb, Manolis, Lindner, & Banks, 2019), it is considered less favoured than brackish or freshwater habitats, and dry land is almost inaccessible to crocodiles as suggested by the previous tracking by satellites (Fukuda et al., 2019).
Campbell, H. A., Dwyer, R. G., Irwin, T. R., & Franklin, C. E. (2013). Home range utilisation and long-range movement of estuarine crocodiles during the breeding and nesting season. PLoS ONE, 8(5), e62127. doi: 10.1371/journal.pone.0062127
Campbell, H. A., Watts, M. E., Sullivan, S., Read, M. A., Choukroun, S., Irwin, S. R., & Franklin, C. E. (2010). Estuarine crocodiles ride surface currents to facilitate long-distance travel. Journal of Animal Ecology, 79(5), 955–964. doi: 10.1111/j.1365-2656.2010.01709.x
Clarke, R. T., Rothery, P., & Raybould, A. F. (2002). Confidence Limits for Regression Relationships between Distance Matrices: Estimating Gene Flow with Distance. Journal of Agricultural, Biological, and Environmental Statistics, 7(3), 361–372. Retrieved from JSTOR.
Cramp, R. L., Meyer, E. A., Sparks, N., & Franklin, C. E. (2008). Functional and morphological plasticity of crocodile (Crocodylus porosus) salt glands. The Journal of Experimental Biology, 211(Pt 9), 1482–1489. doi: 10.1242/jeb.015636
Etten, J. van. (2018). gdistance: Distances and Routes on Geographical Grids (Version 1.2-2). Retrieved from https://CRAN.R-project.org/package=gdistance
Fukuda, Y., & Cuff, N. (2013). Vegetation communities as nesting habitat for the saltwater crocodiles in the Northern Territory of Australia. Herpetological Conservation and Biology, 8(3), 641–651.
Fukuda, Y., Whitehead, P., & Boggs, G. (2007). Broad-scale environmental influences on the abundance of saltwater crocodiles (Crocodylus porosus) in Australia. Wildlife Research, 34(3), 167–176. https://doi.org/10.1071/WR06110
Fukuda, Yusuke, Webb, G., Manolis, C., Delaney, R., Letnic, M., Lindner, G., & Whitehead, P. (2011). Recovery of saltwater crocodiles following unregulated hunting in tidal rivers of the Northern Territory, Australia. Journal of Wildlife Management, 75(6), 1253–1266. doi: 10.1002/jwmg.191
Fukuda, Yusuke, Webb, G., Manolis, C., Lindner, G., & Banks, S. (2019). Translocation, genetic structure and homing ability confirm geographic barriers disrupt saltwater crocodile movement and dispersal. PLOS ONE, 14(8), e0205862. doi: 10.1371/journal.pone.0205862
Grigg, G. C., Taplin, L. E., Harlow, P., & Wright, J. (1980). Survival and growth of hatchling Crocodylus porosus in saltwater without access to fresh drinking water. Oecologia, 47(2), 264–266. doi: 10.1007/BF00346830
Peterman, W. E. (2018). ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms. Methods in Ecology and Evolution, 9(6), 1638–1647. doi: 10.1111/2041-210X.12984
Taplin, L. E. (1985). Sodium and water budgets of the fasted estuarine crocodile,Crocodylus porosus, in sea water. Journal of Comparative Physiology B, 155(4), 501–513. doi: 10.1007/BF00684681
Webb, G. J. W. (1991). The influence of season on Australian crocodiles. In M. G. Ridpath, C. D. Haynes, & M. J. D. Williams (Eds.), Monsoonal Australia - Landscape, Ecology and Man in the Northern Lowlands (pp. 125–131). Rotterdam, Netherlands: A.A. Balkema.
Webb, G. J. W., Manolis, S. C., Buckworth, R., & Sack, G. C. (1983). An Examination of Crocodylus porosus nests in two northern Australian freshwater swamps, with an analysis of embryo mortality. Wildlife Research, 10(3), 571–605. doi: 10.1071/wr9830571
Webb, G. J. W., Messel, H., & Magnusson, W. E. (1977). The nesting biology of Crocodylus porosus in Arnhem Land, northern Australia. Copeia, 1977, 238–249.
Webb, Grahame, & Manolis, S. C. (1989). Crocodiles of Australia. Sydney, Australia: Reed Books.
Australian National University
Northern Territory Government
National Geographic Society, Award: 51-16
Holsworth Wildlife Research Endowment, Award: HWRE2016R2027NEW
IUCN-SSC Crocodile Specialist Group Student Research Assistance Scheme, Award: 15/5
ACT Herpetological Association