10.5061/DRYAD.Q2BVQ83GB
Fukuda, Yusuke
0000-0002-8675-318X
Australian National University
Banks, Sam
Charles Darwin University
Landscape layer for resistance
Dryad
dataset
2020
landscape resistance modelling
ResistanceGA
Crocodylus porosus
Saltwater crocodiles
dispersal movements
habitat quality
Genetic distance
Australian National University
https://ror.org/019wvm592
Northern Territory Government*
National Geographic Society
https://ror.org/04bqh5m06
51-16
Equity Trustees
https://ror.org/05psqqq26
HWRE2016R2027NEW
IUCN-SSC Crocodile Specialist Group Student Research Assistance Scheme*
15/5
ACT Herpetological Association
https://ror.org/039tpj237
2021-12-16T00:00:00Z
2021-12-16T00:00:00Z
en
https://doi.org/10.1111/2041-210X.12984
https://doi.org/10.1198/108571102320
https://doi.org/10.1038/sj.hdy.6885180
http://www.herpconbio.org/Volume_8/Issue_3/Fukuda_Cuff_2013.pdf
https://doi.org/10.1071/WR06110
https://doi.org/10.1371/journal.pone.0062127
https://doi.org/10.1242/jeb.015636
https://doi.org/10.1007/BF00346830
https://doi.org/10.1007/BF00684681
https://doi.org/10.1111/j.1365-2656.2010.01709.x
https://doi.org/10.1071/wr9830571
https://doi.org/10.1002/jwmg.191
https://doi.org/10.1371/journal.pone.0205862
Etten, J. van. (2018). gdistance: Distances and Routes on Geographical
Grids (Version 1.2-2). Retrieved from
https://CRAN.R-project.org/package=gdistance
8369 bytes
4
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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). References
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.