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Cited by 9Genetic diversity and population structureWildlife Ecology and ConservationAmphibian and Reptile Biology

Implications of past and present genetic connectivity for management of the saltwater crocodile (Crocodylus porosus)

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Lloyd‐Jones, Luke R., Brien, Matthew L., Feutry, Pierre, Lawrence, Emma, Beri, Paul, Booth, Simon, Coulson, Steven, Baylis, Shane M. +3 more·2023·Evolutionary Applications
DOI 10.1111/eva.13545PMC PMC10130557
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Abstract

Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life‐history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distributed of living crocodilians, extending from Sri Lanka to Southeast Asia and down to northern Australia. Given the long‐distance movement capabilities reported for C. porosus, management units are hypothesised to be highly connected by migration. However, the magnitude, scale, and consistency of connection across managed populations are not fully understood. Here we used an efficient genotyping method that combines DArTseq and sequence capture to survey 3000 high‐quality genome‐wide single nucleotide polymorphisms from 1176 C. porosus sampled across nearly the entire range of the species in Queensland, Australia. We investigated historical and present‐day connectivity patterns using fixation and diversity indices coupled with clustering methods and the spatial distribution of kin pairs. We inferred kinship using forward simulation coupled with a kinship estimation method that is robust to unspecified population structure. The results demonstrated that the C. porosus population has substantial genetic structure with six broad populations correlated with geographical location. The rate of gene flow was highly correlated with spatial distance, with greater differentiation along the east coast compared to the west. Kinship analyses revealed evidence of reproductive philopatry and limited dispersal, with approximately 90% of reported first and second‐degree relatives showing a pairwise distance of <50 km between sampling locations. Given the limited dispersal, lack of suitable habitat, low densities of crocodiles and the high proportion of immature animals in the population, future management and conservation interventions should be considered at regional and state‐wide scales.

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  • Recent studies employing genome-wide SNP data have demonstrated substantial phylogeographic structure within C. porosus in Australia, indicating restricted gene flow and regional adaptation.

    “Recent studies employing genome-wide SNP data [68][69][70] have demonstrated substantial phylogeographic structure within C. porosus in Australia, indicating restricted gene flow and regional adaptation.”

    From Mitogenomic Crocodylia phylogeny and population structure of <i>Crocodylus porosus</i> including the extinct Seychelles crocodile (2026) · cites this paper as [70]

    The Results report genome-wide SNP data from Queensland crocodiles, and the Discussion (‘Limited dispersal and site fidelity’; page unavailable) reports substantial geographic genetic differentiation and historically constrained genetic exchange. The cited paper therefore supports the structure and restricted-gene-flow portions of the claim, but the passages do not establish regional adaptation. (LLM, conf=0.88)

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Research works printed but not linked: 71

  1. Al‐Asadi, H., Petkova, D., Stephens, M., & Novembre, J. (2019). Estimating recent migration and population‐size surfaces. PLoS Genetics, 15(1), e1007908. 30640906 PMC6347299
  2. Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model‐based estimation of ancestry in unrelated individuals. Genome Research, 19(9), 1655– 1664. 19648217 PMC2752134
  3. Allen, G.R. (1974) The marine crocodile, Crocodylus porosus, from Ponape, eastern Caroline Islands, with notes on food habits of crocodiles from the Palau Archipelago. Copeia, 1974(2), 553.
  4. Barrow, D., & Halford, A. R. (2019). A modified biopsy needle with pole for repeatable tissue extraction from free‐ranging crocodiles. Wildlife Society Bulletin, 43(2), 308– 312.
  5. Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological), 57(1), 289– 300.
  6. Bougeard, S., & Dray, S. (2018). Supervised multiblock analysis in R with the ade4 package. Journal of Statistical Software, 86, 1– 17.
  7. Bravington, M. V., Grewe, P. M., & Davies, C. R. (2016). Absolute abundance of southern bluefin tuna estimated by close‐kin mark‐recapture. Nature Communications, 7(1), 1– 8. PMC5114523 27841264
  8. Bravington, M. V., Skaug, H. J., & Anderson, E. C. (2016). Close‐kin mark‐recapture. Statistical Science, 31(2), 259– 274.
  9. Brien, M. L., Gienger, C. M., Browne, C. A., Read, M. A., Joyce, M. J., & Sullivan, S. (2017). Patterns of human–crocodile conflict in Queensland: A review of historical estuarine crocodile (Crocodylus porosus) management. Wildlife Research, 44(4), 281– 290.
  10. Brien, M. L., Webb, G. J., McGuinness, K., & Christian, K. A. (2014). The relationship between early growth and survival of hatchling saltwater crocodiles (Crocodylus porosus) in captivity. PLoS One, 9(6), e100276. 24960026 PMC4069027
  11. 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. 23650510 PMC3641080
  12. 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. 20546063
  13. Cao, R., Somaweera, R., Brittain, K., FitzSimmons, N. N., Georges, A., & Gongora, J. (2020). Genetic structure and diversity of Australian freshwater crocodiles (Crocodylus johnstoni) from the Kimberley, Western Australia. Conservation Genetics, 21(3), 421– 429.
  14. Christie, M. R., Tissot, B. N., Albins, M. A., Beets, J. P., Jia, Y., Ortiz, D. M., Thompson, S. E., & Hixon, M. A. (2010). Larval connectivity in an effective network of marine protected areas. PLoS One, 5(12), e15715. 21203576 PMC3006342
  15. Conn, P. B., Bravington, M. V., Baylis, S., & ver Hoef, J. M. (2020). Robustness of close‐kin mark–recapture estimators to dispersal limitation and spatially varying sampling probabilities. Ecology and Evolution, 10(12), 5558– 5569. 32607174 PMC7319163
  16. Conomos, M. P., Reiner, A. P., Weir, B. S., & Thornton, T. A. (2016). Model‐free estimation of recent genetic relatedness. The American Journal of Human Genetics, 98(1), 127– 148. 26748516 PMC4716688
  17. Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14(8), 2611– 2620. 15969739
  18. Feutry, P., Berry, O., Kyne, P. M., Pillans, R. D., Hillary, R. M., Grewe, P. M., Marthick, J. R., Johnson, G., Gunasekera, R. M., Bax, N. J., & Bravington, M. (2017). Inferring contemporary and historical genetic connectivity from juveniles. Molecular Ecology, 26(2), 444– 456. 27864912
  19. Feutry, P., Devloo‐Delva, F., Tran Lu Y, A., Mona, S., Gunasekera, R. M., Johnson, G., Pillans, R. D., Jaccoud, D., Kilian, A., Morgan, D. L., Saunders, T., Bax, N. J., & Kyne, P. M. (2020). One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark. Molecular Ecology Resources, 20(6), 1470– 1485. 32492756
  20. Fischer, J., & Lindenmayer, D. B. (2000). An assessment of the published results of animal relocations. Biological Conservation, 96(1), 1– 11.
  21. Foster, S. D., Feutry, P., Grewe, P. M., Berry, O., Hui, F. K. C., & Davies, C. R. (2018). Reliably discriminating stock structure with genetic markers: Mixture models with robust and fast computation. Molecular Ecology Resources, 18(6), 1310– 1325. 29943898
  22. Francis, R. M. (2017). Pophelper: An R package and web app to analyse and visualize population structure. Molecular Ecology Resources, 17(1), 27– 32. 26850166
  23. Frankham, R. (2015). Genetic rescue of small inbred populations: Meta‐analysis reveals large and consistent benefits of gene flow. Molecular Ecology, 24(11), 2610– 2618. 25740414
  24. Fukuda, Y., Moritz, C., Jang, N., Webb, G., Campbell, H., Christian, K., Lindner, G., & Banks, S. (2022). Environmental resistance and habitat quality influence dispersal of the saltwater crocodile. Molecular Ecology, 31(4), 1076– 1092. 34865283 PMC9299799
  25. Fukuda, Y., Saalfeld, K., Lindner, G., & Nichols, T. (2013). Estimation of total length from head length of saltwater crocodiles (Crocodylus porosus) in the Northern Territory, Australia. Journal of Herpetology, 47(1), 34– 40.
  26. Fukuda, Y., Webb, G., Edwards, G., Saalfeld, K., & Whitehead, P. (2020). Harvesting predators: Simulation of population recovery and controlled harvest of saltwater crocodiles Crocodylus porosus. Wildlife Research, 48(3), 252– 263.
  27. Fukuda, Y., 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. 31461452 PMC6713319
  28. Gogarten, S. M., Sofer, T., Chen, H., Yu, C., Brody, J. A., Thornton, T. A., Rice, K. M., & Conomos, M. P. (2019). Genetic association testing using the GENESIS R/Bioconductor package. Bioinformatics, 35(24), 5346– 5348. 31329242 PMC7904076
  29. Grewe, P. M., Feutry, P., Hill, P. L., Gunasekera, R. M., Schaefer, K. M., Itano, D. G., Fuller, D. W., Foster, S. D., & Davies, C. R. (2015). Evidence of discrete yellowfin tuna (Thunnus albacares) populations demands rethink of management for this globally important resource. Scientific Reports, 5(1), 1– 9. PMC4655351 26593698
  30. Haller, B. C., & Messer, P. W. (2019). SLiM 3: Forward genetic simulations beyond the Wright–fisher model. Molecular Biology and Evolution, 36(3), 632– 637. 30517680 PMC6389312
  31. Hendricks, S., Anderson, E. C., Antao, T., Bernatchez, L., Forester, B. R., Garner, B., Hand, B. K., Hohenlohe, P. A., Kardos, M., Koop, B., Sethuraman, A., Waples, R. S., & Luikart, G. (2018). Recent advances in conservation and population genomics data analysis. Evolutionary Applications, 11(8), 1197– 1211.
  32. Hillary, R. M., Bravington, M. V., Patterson, T. A., Grewe, P., Bradford, R., Feutry, P., Gunasekera, R., Peddemors, V., Werry, J., Francis, M. P., Duffy, C. A. J., & Bruce, B. D. (2018). Genetic relatedness reveals total population size of white sharks in eastern Australia and New Zealand. Scientific Reports, 8(1), 1– 9. 29422513 PMC5805677
  33. Hohenlohe, P. A., Funk, W. C., & Rajora, O. P. (2021). Population genomics for wildlife conservation and management. Molecular Ecology, 30(1), 62– 82. 33145846 PMC7894518
  34. Husby, A. (2022). Wild epigenetics: Insights from epigenetic studies on natural populations. Proceedings of the Royal Society of London. Series B, Biological Sciences, 289(1968), 20211633. PMC8826306 35135348
  35. Jangjoo, M., Matter, S. F., Roland, J., & Keyghobadi, N. (2016). Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network. Proceedings of the National Academy of Sciences of the United States of America, 113(39), 10914– 10919. 27621433 PMC5047165
  36. Jombart, T., & Ahmed, I. (2011). Adegenet 1.3‐1: New tools for the analysis of genome‐wide SNP data. Bioinformatics, 27(21), 3070– 3071. 21926124 PMC3198581
  37. Keenan, K., McGinnity, P., Cross, T. F., Crozier, W. W., & Prodöhl, P. A. (2013). diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors. Methods in Ecology and Evolution, 4(8), 782– 788.
  38. Kool, J. T., Moilanen, A., & Treml, E. A. (2013). Population connectivity: Recent advances and new perspectives. Landscape Ecology, 28(2), 165– 185.
  39. Lewis, J. L., FitzSimmons, N. N., Jamerlan, M. L., Buchan, J. C., & Grigg, G. C. (2013). Mating systems and multiple paternity in the estuarine crocodile (Crocodylus porosus). Journal of Herpetology, 47(1), 24– 33.
  40. Lowe, W. H., & Allendorf, F. W. (2010). What can genetics tell us about population connectivity? Molecular Ecology, 19(15), 3038– 3051. 20618697
  41. Manel, S., & Holderegger, R. (2013). Ten years of landscape genetics. Trends in Ecology & Evolution, 28(10), 614– 621. 23769416
  42. Manichaikul, A., Mychaleckyj, J. C., Rich, S. S., Daly, K., Sale, M., & Chen, W. M. (2010). Robust relationship inference in genome‐wide association studies. Bioinformatics, 26(22), 2867– 2873. 20926424 PMC3025716
  43. Manier, M. K., & Arnold, S. J. (2005). Population genetic analysis identifies source–sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis). Molecular Ecology, 14(13), 3965– 3976. 16262852
  44. Martin, A.D., Quinn, K.M. and Park, J.H. (2011) MCMCpack: Markov chain Monte Carlo in R. Journal of Statistical Software, 42(9), 1– 21. 10.18637/jss.v042.i09 · DOI
  45. Mayne, B., Espinoza, T., Roberts, D., Butler, G. L., Brooks, S., Korbie, D., & Jarman, S. (2021). Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod. Molecular Ecology Resources, 21(7), 2324– 2332. 34161658 PMC8518777
  46. Messel, H., Vorlicek, G. C., Wells, A. G., Green, W. J., & Johnson, A. (1981). Surveys of the tidal Rivers Systems in the Northern Territory of Australia and their crocodile populations. Monograph 1. The Blyth‐Cadell River systems study and the status of Crocodylus porosus in tidal waterways of northern Australia. Pergamon Press.
  47. Messel, H., et al. (1984). Surveys of the Tidal Rivers Systems in the Northern Territory of Australia and their Crocodile Populations. Monograph 18. Population Dynamics of Crocodylus porosus and Status, Management and Recovery. Update 1979‐1983. Pergamon Press.
  48. Mills, L. S., & Allendorf, F. W. (1996). The one‐migrant‐per‐generation rule in conservation and management. Conservation Biology, 10(6), 1509– 1518.
  49. Mussmann, S. M., Douglas, M. R., Chafin, T. K., & Douglas, M. E. (2019). BA3‐SNPs: Contemporary migration reconfigured in BayesAss for next‐generation sequence data. Methods in Ecology and Evolution, 10(10), 1808– 1813.
  50. Palsbøll, P. J., Berube, M., & Allendorf, F. W. (2007). Identification of management units using population genetic data. Trends in Ecology & Evolution, 22(1), 11– 16. 16982114
  51. Patterson, T. A., Hillary, R. M., Kyne, P. M., Pillans, R. D., Gunasekera, R. M., Marthick, J. R., Johnson, G. J., & Feutry, P. (2022). Rapid assessment of adult abundance and demographic connectivity from juvenile kin pairs in a critically endangered species. Science Advances, 8(51), eadd1679. 36542711 PMC9770943
  52. Pembleton, L. W., Cogan, N. O., & Forster, J. W. (2013). StAMPP: An R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations. Molecular Ecology Resources, 13(5), 946– 952. 23738873
  53. Perkins, D. W., Vickery, P. D., & Shriver, W. G. (2003). Spatial dynamics of source‐sink habitats: Effects on rare grassland birds. The Journal of Wildlife Management, 67, 588– 599.
  54. Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945– 959. 10835412 PMC1461096
  55. Read, M. A., Grigg, G. C., Irwin, S. R., Shanahan, D., & Franklin, C. E. (2007). Satellite tracking reveals long distance coastal travel and homing by translocated estuarine crocodiles, Crocodylus porosus. PLoS One, 2(9), e949. 17895990 PMC1978533
  56. Read, M. A., Miller, J. D., Bell, I. P., & Felton, A. (2004). The distribution and abundance of the estuarine crocodile, Crocodylus porosus, in Queensland. Wildlife Research, 31(5), 527– 534.
  57. Rousset, F. (1997). Genetic differentiation and estimation of gene flow from F‐statistics under isolation by distance. Genetics, 145(4), 1219– 1228. 9093870 PMC1207888
  58. Runge, J. P., Runge, M. C., & Nichols, J. D. (2006). The role of local populations within a landscape context: Defining and classifying sources and sinks. The American Naturalist, 167(6), 925– 938. 16615034
  59. Taplin, L. E. (1987). The management of crocodiles in Queensland, Australia. In G. J. W. Webb, S. C. Manolis, & P. J. Whitehead (Eds.), Wildlife management: crocodiles and alligators (pp. 129– 140). Surrey Beatty and Sons.
  60. Taplin, L. E. (1988). The population status and management of estuarine crocodiles in Queensland – present situation and future prospects (pp. 253– 307). PNG.
  61. Tewksbury, J. J., Levey, D. J., Haddad, N. M., Sargent, S., Orrock, J. L., Weldon, A., Danielson, B. J., Brinkerhoff, J., Damschen, E. I., & Townsend, P. (2002). Corridors affect plants, animals, and their interactions in fragmented landscapes. Proceedings of the National Academy of Sciences of the United States of America, 99(20), 12923– 12926. 12239344 PMC130561
  62. Tucker, A. D., Limpus, C. J., McCallum, H. I., & McDonald, K. R. (1997). Movements and home ranges of Crocodylus johnstoni in the Lynd River, Queensland. Wildlife Research, 24(4), 379– 396.
  63. Waples, R. S., & Gaggiotti, O. (2006). What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology, 15(6), 1419– 1439. 16629801
  64. Waples, R. S., Punt, A. E., & Cope, J. M. (2008). Integrating genetic data into management of marine resources: How can we do it better? Fish and Fisheries, 9(4), 423– 449.
  65. Webb, G., Manolis, S., Whitehead, P., & Letts, G. (1984) A proposal for the transfer of the Australian population of Crocodylus porosus Schneider (1801), from Appendix I to Appendix II of CITES [animal protection; ranching]’, Technical Report‐Conservation Commission of the Northern Territory (Australia) [Preprint]. Conservation Commission of the Northern Territory.
  66. Webb, G.J. and Manolis, S.C. (1993) ‘ Conserving Australia's crocodiles through commercial incentives’. (pp. 250– 256). Transactions of Royal Zoological Society of New South Wales.
  67. Weeks, A. R., Sgro, C. M., Young, A. G., Frankham, R., Mitchell, N. J., Miller, K. A., Byrne, M., Coates, D. J., Eldridge, M. D. B., Sunnucks, P., Breed, M. F., James, E. A., & Hoffmann, A. A. (2011). Assessing the benefits and risks of translocations in changing environments: A genetic perspective. Evolutionary Applications, 4(6), 709– 725. 22287981 PMC3265713
  68. Weir, B. S. (2012). Estimating F‐statistics: A historical view. Philosophy of Science, 79(5), 637– 643. 26405363 PMC4578636
  69. Wilson, G. A., & Rannala, B. (2003). Bayesian inference of recent migration rates using multilocus genotypes. Genetics, 163(3), 1177– 1191. 12663554 PMC1462502
  70. Wright, S. (1949). The genetical structure of populations. Annals of Eugenics, 15(1), 323– 354. 24540312
  71. Zheng, X., Levine, D., Shen, J., Gogarten, S. M., Laurie, C., & Weir, B. S. (2012). A high‐performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics, 28(24), 3326– 3328. 23060615 PMC3519454

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Authors
Lloyd‐Jones, L. R., Brien, M. L., Feutry, P., Lawrence, E., Beri, P., Booth, S., Coulson, S., Baylis, S. M., Villiers, K., Taplin, L. E., & Westcott, D. A.
Affiliations
  • Commonwealth Scientific and Industrial Research Organisation (AU)
  • Queensland Government (AU)
  • CSIRO Oceans and Atmosphere (AU)
Corresponding author
Lloyd‐Jones, Luke R.
ORCID
Venue
Evolutionary Applications
Publisher
Wiley
Published
2023-03-31
Volume
16
Issue
4
Pages
911-935
ISSN
  • 1752-4563 (ISSN-L)
  • 1752-4571
DOI
10.1111/eva.13545
PMC
PMC10130557
OpenAlex
W4362450766
Cited by
9
References
0
Citations by year
2026: 3 · 2025: 2 · 2024: 1 · 2023: 3
FWCI
1.49
Type
journal article
Language
en
Update notices
correction (2023-06-22)
Open access
Licence
Locations
  • Evolutionary Applications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Physical Sciences › Environmental Science › Ecology › Wildlife Ecology and Conservation
  • Physical Sciences › Environmental Science › Global and Planetary Change › Amphibian and Reptile Biology
Keywords
saltwater crocodile, Crocodylus porosus, genetic connectivity, population structure, gene flow, kinship, dispersal, conservation management units, DArTseq, single nucleotide polymorphisms, spatial genetic structure, Queensland

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