Single nucleotide polymorphism-based dispersal estimates using noninvasive sampling

Ecology and Evolution

Volumn 5, Issue 15, 2015, Pages 3056-3065

  Norman, Anita J ^a   Spong, Göran ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Carnivore; Citizen science; Isolation by distance; Natal dispersal; Pedigree reconstruction; SNPs; Ursus arctos

Indexed keywords

URSUS ARCTOS;

EID: 84938750658     PISSN: None     EISSN: 20457758     Source Type: Journal    
DOI: 10.1002/ece3.1588     Document Type: Article

References (56)

1. Anderson, E. C., and J. C. Garza . 2006. The power of single-nucleotide polymorphisms for large-scale parentage inference. Genetics 172:2567-2582.
2. Arnemo, J. M., P. Ahlqvist, R. Andersen, F. Berntsen, G. Ericsson, J. Odden, et al. 2006. Risk of capture-related mortality in large free-ranging mammals: experiences from Scandinavia. Wildl. Biol. 12:109-113.
3. Baguette, M., S. Blanchet, D. Legrand, V. M. Stevens, and C. Turlure . 2012. Individual dispersal, landscape connectivity and ecological networks. Biol. Rev. 88:310-326.
4. Bellemain, E., J. E. Swenson, D. Tallmon, S. Brunberg, and P. Taberlet . 2005. Estimating population size of elusive animals with DNA from hunter-collected feces : four methods for brown bears. Conserv. Biol. 19:150-161.
5. Bidon, T., N. Schreck, F. Hailer, M. Nilsson, and A. Janke . 2015. Genome-wide search identifies 1.9 megabases from the polar bear Y chromosome for evolutionary analyses. Genome Biol. Evol. doi:10.1093/gbe/evv103.
6. Bonney, R., C. B. Cooper, J. Dickinson, S. Kelling, T. Phillips, K. V. Rosenberg, et al. 2009. Citizen science: a developing tool for expanding science knowledge and scientific literacy. Bioscience 59:977-984.
7. Broquet, T., and E. Petit . 2004. Quantifying genotyping errors in noninvasive population genetics. Mol. Ecol. 13:3601-3608.
8. Broquet, T., and E. J. Petit . 2009. Molecular estimation of dispersal for ecology and population genetics. Annu. Rev. Ecol. Evol. Syst. 40:193-216.
9. Bui, R., R. N. Buliung, and T. K. Remmel . 2012. aspace: a collection of functions for estimating centrographic statistics and computational geometries for spatial point patterns. Version 3.2., http://cran.r-project.org/web/package.
10. Centeno-Cuadros, A., J. Roman, M. Delibes, and J. A. Godoy . 2011. Prisoners in their habitat? Generalist dispersal by habitat specialists: a case study in southern water vole (Arvicola sapidus). PLoS ONE 6:e24613.
11. Csilléry, K., T. Johnson, D. Beraldi, T. Clutton-Brock, D. Coltman, B. Hansson, et al. 2006. Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics 173:2091-2101.
12. Devictor, V., R. J. Whittaker, and C. Beltrame . 2010. Beyond scarcity: citizen science programmes as useful tools for conservation biogeography. Divers. Distrib. 16:354-362.
13. Dey, S., B. Goswami, and A. Joshi . 2013. Effects of symmetric and asymmetric dispersal on the dynamics of heterogeneous metapopulations: two-patch systems revisited. J. Theor. Biol. 345:52-60.
14. Dickinson, J. L., B. Zuckerberg, and D. N. Bonter . 2010. Citizen science as an ecological research tool: challenges and benefits. Annu. Rev. Ecol. Evol. Syst. 41:149-172.
15. Dieckmann, U., B. O'Hara, and W. Weisser . 1999. The evolutionary ecology of dispersal. Trends Ecol. Evol. 14:88-90.
16. Driscoll, D. A., S. C. Banks, P. S. Barton, Ikin, K., P. Lentini, D. B. Lindenmayer, et al. 2014. The trajectory of dispersal research in conservation biology. Systematic review. PLoS ONE 9:e95053.
17. Eiserhardt, W. L., J.-C. Svenning, W. J. Baker, T. L. P. Couvreur, and H. Balslev . 2013. Dispersal and niche evolution jointly shape the geographic turnover of phylogenetic clades across continents. Sci. Rep. 3:1-8.
18. Gandon, S., and F. Rousset . 1999. Evolution of stepping-stone dispersal rates. Proc. Biol. Sci. 266:2507-2513.
19. Glover, K. A., M. M. Hansen, S. Lien, T. D. Als, B. Høyheim, and Ø. Skaala . 2010. A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment. BMC Genet. 11:2.
20. Greenwood, P. J. 1980. Mating systems, philopatry and dispersal in birds and mammals. Anim. Behav. 28:1140-1162.
21. Jombart, T., and I. Ahmed . 2011. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics, 27:3070-3071.
22. Kindberg, J., and J. E. Swenson . 2014. Björnstammens storlek i Sverige 2013 - länsvisa skattningar och trender.
23. Kindberg, J., J. E. Swenson, G. Ericsson, E. Bellemain, C. Miquel, and P. Taberlet . 2011. Estimating population size and trends of the Swedish brown bear Ursus arctos population. Wildl. Biol. 17:114-123.
24. Kock, M. D., R. K. Clark, C. E. Franti, D. A. Jessup, and J. D. Wehausen . 1987. Effects of capture on biological parameters in free-ranging bighorn sheep (Ovis canadensis): evaluation of normal, stressed and mortality outcomes and documentation of postcapture survival. J. Wildl. Dis. 23:652-662.
25. Koenig, W. D., D. Van Vuren, and P. N. Hooge . 1996. Detectability, philopatry, and the distribution of dispersal distances in vertebrates. Trends Ecol. Evol. 11:514-517.
26. Kopatz, A., H. G. Eiken, J. Aspi, I. Kojola, C. Tobiassen, K. F. Tirronen, et al. 2014. Admixture and gene flow from Russia in the recovering Northern European brown bear (Ursus arctos). PLoS ONE 9:e97558.
27. Lawson Handley, L. J., and N. Perrin . 2007. Advances in our understanding of mammalian sex-biased dispersal. Mol. Ecol. 16:1559-1578.
28. Lynch, M., and K. Ritland . 1999. Estimation of pairwise relatedness with molecular markers. Genetics 152:1753-1766.
29. Matthysen, E. 2012. Multicausality of dispersal: a review. Pp. 3-18 in J. Clobert, M. Baguette, T. G. Benton and J. M. Bullock, eds. Dispersal ecology and evolution. Oxford Univ. Press, Oxford.
30. McLellan, B. N., and F. W. Hovey . 2001. Natal dispersal of grizzly bears. Can. J. Zool. 79:838-844.
31. Nathan, R. 2001. The challenges of studying dispersal. Trends Ecol. Evol. 16:481-483.
32. Nathan, R., G. Perry, J. T. Cronin, A. E. Strand, and M. L. Cain . 2003. Methods for estimating long-distance dispersal. Oikos 2:261-273.
33. Norman, A. J., N. R. Street, and G. Spong . 2013. De novo SNP discovery in the Scandinavian brown bear (Ursus arctos). PLoS ONE 8:e81012.
34. Ordiz, A., O. G. Støen, S. Sæbø, V. Sahlén, B. E. Pedersen, J. Kindberg, et al. 2013. Lasting behavioural responses of brown bears to experimental encounters with humans. J. Appl. Ecol. 50:306-314.
35. Palsbøll, P. J., M. Zachariah Peery, M. T. Olsen, S. R. Beissinger, and M. Bérubé . 2013. Inferring recent historic abundance from current genetic diversity. Mol. Ecol. 22:22-40.
36. Pemberton, J. M. 2008. Wild pedigrees: the way forward. Proc. R. Soc. B 275:613-621.
37. Pew, J., J. Wang, P. Muir, and T. Frasier . 2014. related: an R package for analysing pairwise relatedness data based on codominant molecular markers.
38. Proctor, M. F., B. N. Mclellan, C. Strobeck, and R. M. R. Barclay . 2004. Gender-specific dispersal distances of grizzly bears estimated by genetic analysis. Can. J. Zool. 82:1108-1118.
39. R Development Core. 2013. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
40. Riester, M., P. F. Stadler, and K. Klemm . 2009. FRANz: reconstruction of wild multi-generation pedigrees. Bioinformatics, 25:2134-2139.
41. Rollins, L. A., L. E. Browning, C. E. Holleley, J. L. Savage, A. F. Russell, and S. C. Griffith . 2012. Building genetic networks using relatedness information: a novel approach for the estimation of dispersal and characterization of group structure in social animals. Mol. Ecol. 21:1727-1740.
42. Rousset, F. 2001. Genetic approaches to the estimation of dispersal rates. Pp. 18-28 in J. Clobert, E. Danchin, A. A. Dhondt and J. D. Nichols, eds. Dispersal. Oxford Univ. Press, Oxford.
43. Schregel, J., A. Kopatz, S. B. Hagen, H. Brøseth, M. E. Smith, S. Wikan, et al. 2012. Limited gene flow among brown bear populations in far Northern Europe? Genetic analysis of the east-west border population in the Pasvik Valley. Mol. Ecol. 21:3474-3488.
44. Spong, G., and S. Creel . 2001. Deriving dispersal distances from genetic data. Proc. R. Soc. B 268:2571-2574.
45. Spong, G. F., S. J. Hodge, A. J. Young, and T. H. Clutton-Brock . 2008. Factors affecting the reproductive success of dominant male meerkats. Mol. Ecol. 17:2287-2299.
46. Støen, O.-G., A. Zedrosser, S. Saebø, and J. E. Swenson . 2006. Inversely density-dependent natal dispersal in brown bears Ursus arctos. Oecologia 148:356-364.
47. Sugg, D. W., R. K. Chesser, F. S. Dobson, and J. L. Hoogland . 1996. Population genetics meets behavioral ecology. Trends Ecol. Evol. 11:338-342.
48. Swenson, J. E., F. Sandegren, and A. Soderberg . 1998. Geographic expansion of an increasing brown bear population: evidence for presaturation dispersal. J. Anim. Ecol. 67:819-826.
49. Taberlet, P., and J. Bouvet . 1994. Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe. Proc. Biol. Sci. 255:195-200.
50. Taberlet, P., and G. Luikart . 1999. Non-invasive genetic sampling and individual identification. Biol. J. Linn. Soc. 68:41-55.
51. Taberlet, P., L. P. Waits, and G. Luikart . 1999. Noninvasive genetic sampling: look before you leap. Trends Ecol. Evol. 14:323-327.
52. Thomas, S. C. 2005. The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations. Philos. Trans. R. Soc. B Biol. Sci. 360:1457-1467.
53. Trakhtenbrot, A., R. Nathan, G. Perry, and D. M. Richardson . 2005. The importance of long-distance dispersal in biodiversity conservation. Divers. Distrib. 11:173-181.
54. Waits, L. P., and D. Paetkau . 2005. Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. J. Wildl. Manage. 69:1419-1433.
55. Waser, P. M., and C. Strobeck . 1998. Genetic signatures of interpopulation dispersal. Trends Ecol. Evol. 13:43-44.
56. Wright, S. 1943. Isolation by distance. Genetics 28:114-138.