DOI: 10.5061/dryad.q2bvq83gb
title: Landscape layer for resistance

description: 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.
description: 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
 <em>C. porosus</em>. 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 <i>C. porosus</i> 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
 <i>C. porosus </i>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). 
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