Habitat suitability is a poor proxy for landscape connectivity during dispersal and mating movements

Landscape and Urban Planning

Volumn 161, Issue , 2017, Pages 90-102

  Keeley, Annika T H ^a   Beier, Paul ^a   Keeley, Brian W ^a   Fagan, Matthew E ^b  

^a NORTHERN ARIZONA UNIVERSITY   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

Dispersal; Habitat suitability; Landscape connectivity; Landscape resistance; Mating movements; Wildlife corridors

Indexed keywords

EXPONENTIAL FUNCTIONS; FORESTRY; MAMMALS;

DISPERSAL; HABITAT SUITABILITY; LANDSCAPE CONNECTIVITIES; MATING MOVEMENTS; WILDLIFE CORRIDORS;

ECOSYSTEMS;

ARBOREAL SPECIES; CONNECTIVITY; DISPERSAL; HABITAT CORRIDOR; HABITAT FRAGMENTATION; HABITAT QUALITY; HABITAT SELECTION; HOME RANGE; LANDSCAPE ECOLOGY; MAMMAL; MOVEMENT; NEOTROPICAL REGION; PERCEPTION;

ANIMALIA; MAMMALIA; POTOS FLAVUS;

EID: 85011876537     PISSN: 01692046     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.landurbplan.2017.01.007     Document Type: Article

References (61)

1. Abrahms, B., Sawyer, S.C., Jordan, N.R., McNutt, J.W., Wilson, A.M., Brashares, J.S., Does wildlife resource selection accurately inform corridor conservation?. Journal of Applied Ecology, 2016, 10.1111/1365-2664.12714.
2. Agnarsson, I., Zambrana-Torrelio, C.M., Flores-Saldana, N.P., May-Collado, L.J., A time-calibrated species-level phylogeny of bats Chiroptera, Mammalia. PLoS Currents, 2011, 3.
3. Agresti, A., Categorical data analysis. 2nd ed., 2002, Wiley, Hoboken (p. 419).
4. Aronesty, E., ea-utils: Command-line tools for processing biological sequencing data. 2011 http://code.google.com/p/ea-utils.
5. Bates, D., Maechler, M., Bolker, B., Walker, S., lme4: Linear mixed-effects models using Eigen and S4. R package version 1. 2014, 1–7 http://CRAN.R-project.org/package=lme4.
6. Beier, P., Majka, D.R., Spencer, W.D., Forks in the road: Choices in procedures for designing wildland linkages. Conservation Biology 22:4 (2008), 836–851, 10.1111/j.1523-1739.2008.00942.x.
7. Blazquez-Cabrera, S., Gastón, A., Beier, P., Garrote, G., Simón, M.Á., Saura, S., Influence of separating home range and dispersal movements on characterizing corridors and effective distances. Landscape Ecology 31 (2016), 2355–2366, 10.1007/s10980-016-0407-5.
8. Bowman, J., Jaeger, J.A.G., Fahrig, L., Dispersal distance of mammals is proportional to home range size. Ecology 83:7 (2002), 2049–2055, 10.2307/3071786.
9. Burnham, K.P., Anderson, D.R., Model selection and multimodel inference: A practical information-theoretic approach. 2002, Springer, New York.
10. Calcagno, V., de Mazancourt, C., glmulti: An R package for easy automated model selection with (generalized) linear models. Journal of Statistical Software 34:12 (2010), 1–29.
11. Clobert, J., Wolff, J.O., Nichols, J.D., Danchin, E., Dhondt, A.A., Introduction. Clobert, J., Danchin, E., Dhondt, A.A., Nichols, J.D., (eds.) Dispersal, 2001, Oxford University Press, New York, ix–xi.
12. Compton, B.W., Rhymer, J.M., McCollough, M., Habitat selection by wood turtles (Clemmys insculpta): An application of paired logistic regression. Ecology 83:3 (2002), 833–843, 10.2307/3071885.
13. Connectivity conservation. Crooks, K.R., Sanjayan, M., (eds.), 2006, Cambridge University Press, Cambridge, UK.
14. Cushman, S.A., Effects of habitat loss and fragmentation on amphibians: A review and prospectus. Biological Conservation 128:2 (2006), 231–240, 10.1016/j.biocon.2005.09.031.
15. Doerr, V.A.J., Barrett, T., Doerr, E.D., Connectivity, dispersal behaviour and conservation under climate change: A response to Hodgson et al. Journal of Applied Ecology 48:1 (2011), 143–147, 10.1111/j.1365-2664.2010.01899.x.
16. Edelman, A.J., Multiple socioecological factors influence timing of natal dispersal in kangaroo rats. Behavioral Ecology and Sociobiology 68:7 (2014), 1123–1131, 10.1007/s00265-014-1723-x.
17. Elliot, N.B., Cushman, S.A., Macdonald, D.W., Loveridge, A.J., The devil is in the dispersers: Predictions of landscape connectivity change with demography. Journal of Applied Ecology 51:5 (2014), 1169–1178, 10.1111/1365-2664.12282.
18. Fagan, M.E., DeFries, R.S., Sesnie, S.E., Arroyo, J.P., Walker, W., Soto, C.,.. Sanchun, A., Land cover dynamics following a deforestation ban in northern Costa Rica. Environmental Research Letters, 8(3), 2013, 10.1088/1748-9326/8/3/034017.
19. Ford, L.S., Hoffmann, R.S., Potos flavus. Mammalian Species 321 (1988), 1–9.
20. Gaston, A., Blazquez-Cabrera, S., Garrote, G., Mateo-Sanchez, M.C., Beier, P., Simon, M.A., Saura, S., Response to agriculture by a woodland species depends on cover type and behavioural state: Insights from resident and dispersing Iberian lynx. Journal of Applied Ecology 53:3 (2016), 814–824, 10.1111/1365-2664.12629.
21. Graves, T., Chandler, R.B., Royle, J.A., Beier, P., Kendall, K.C., Estimating landscape resistance to dispersal. Landscape Ecology 29:7 (2014), 1201–1211, 10.1007/s10980-014-0056-5.
22. Hadfield, J.D., Richardson, D.S., Burke, T., Towards unbiased parentage assignment: Combining genetic, behavioural and spatial data in a Bayesian framework. Molecular Ecology 15:12 (2006), 3715–3730, 10.1111/j.1365-294X.2006.03050.x.
23. Heller, F., Adjusting the parameter estimation of the parentage analysis software MasterBayes to the presence of siblings. Thesis. 2009, Massey University, Albany, New Zealand.
24. Hilty, J.A., Lidicker, W.Z. Jr., Merenlender, A.M., Corridor ecology: The science and practice of linking landscapes for biodiversity conservation. 2012, Island Press, Washington, D.C.
25. Kalendar, R., Lee, D., Schulman, A.H., Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics 98:2 (2011), 137–144, 10.1016/j.ygeno.2011.04.009.
26. Kays, R.W., Gittleman, J.L., The social organization of the kinkajou Potos flavus (Procyonidae). Journal of Zoology 253 (2001), 491–504, 10.1017/s0952836901000450.
27. Kays, R.W., Gittleman, J.L., Wayne, R.K., Microsatellite analysis of kinkajou social organization. Molecular Ecology 9:6 (2000), 743–751, 10.1046/j.1365-294x.2000.00921.x.
28. Keeley, A.T.H., Beier, P., Gagnon, J.W., Estimating landscape resistance from habitat suitability: Effects of data source and nonlinearities. Landscape Ecology, 2016, 1–12, 10.1007/s10980-016-0387-5.
29. Koprowski, J.L., Handling tree squirrels with a safe and efficient restraint. Wildlife Society Bulletin 30:1 (2002), 101–103.
30. Lees, A.C., Peres, C.A., Gap-crossing movements predict species occupancy in Amazonian forest fragments. Oikos 118:2 (2009), 280–290, 10.1111/j.1600-0706.2008.16842.x.
31. Lewis, J.S., Rachlow, J.L., Garton, E.O., Vierling, L.A., Effects of habitat on GPS collar performance: Using data screening to reduce location error. Journal of Applied Ecology 44:3 (2007), 663–671, 10.1111/j.1365-2664.2007.01286.x.
32. Li, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:14 (2009), 1754–1760, 10.1093/bioinformatics/btp324.
33. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N.,.. Genome Project Data, P., The sequence alignment/map format and SAMtools. Bioinformatics 25:16 (2009), 2078–2079, 10.1093/bioinformatics/btp352.
34. Mateo-Sanchez, M.C., Balkenhol, N., Cushman, S., Perez, T., Dominguez, A., Saura, S., A comparative framework to infer landscape effects on population genetic structure: Are habitat suitability models effective in explaining gene flow?. Landscape Ecology 30:8 (2015), 1405–1420, 10.1007/s10980-015-0194-4.
35. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A.,.. DePristo, M.A., The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20:9 (2010), 1297–1303, 10.1101/gr.107524.110.
36. McRae, B.H., Shah, V.B., Circuitscape user's guide. 2009, The University of California, Santa Barbara Available at: http://www.circuitscape.org.
37. Milne, I., Stephen, G., Bayer, M., Cock, P.J.A., Pritchard, L., Cardle, L.,.. Marshall, D., Using Tablet for visual exploration of second-generation sequencing data. Briefings in Bioinformatics 14:2 (2013), 193–202, 10.1093/bib/bbs012.
38. Murphy, M.A., Kendall, K.C., Robinson, A., Waits, L.P., The impact of time and field conditions on brown bear (Ursus arctos) faecal DNA amplification. Conservation Genetics 8:5 (2007), 1219–1224, 10.1007/s10592-006-9264-0.
39. Nowakowski, A.J., Veiman-Echeverria, M., Kurz, D.J., Donnelly, M.A., Evaluating connectivity for tropical amphibians using empirically derived resistance surfaces. Ecological Applications 25:4 (2015), 928–942, 10.1890/14-0833.1.
40. Peterman, W.E., Connette, G.M., Semlitsch, R.D., Eggert, L.S., Ecological resistance surfaces predict fine-scale genetic differentiation in a terrestrial woodland salamander. Molecular Ecology 23:10 (2014), 2402–2413, 10.1111/mec.12747.
41. Pfeiffer, I., Brenig, B., X- and Y-chromosome specific variants of the amelogenin gene allow sex determination in sheep (Ovis aries) and European red deer (Cervus elaphus). BMC Genetics, 6, 2005, 10.1186/1471-2156-6-16.
42. Pinho, G.M., da Silva, A.G., Hrbek, T., Venticinque, E.M., Farias, I.P., Kinship and social behavior of lowland tapirs (Tapirus terrestris) in a Central Amazon landscape. Public Library Of Science, 9(3), 2014, 10.1371/journal.pone.0092507.
43. Reding, D.M., Cushman, S.A., Gosselink, T.E., Clark, W.R., Linking movement behavior and fine-scale genetic structure to model landscape connectivity for bobcats (Lynx rufus). Landscape Ecology 28:3 (2013), 471–486, 10.1007/s10980-012-9844-y.
44. Reinhardt, K., Köhler, G., Maas, S., Detzel, P., Low dispersal ability and habitat specificity promote extinctions in rare but not in widespread species: The Orthoptera of Germany. Ecography 28 (2005), 593–602.
45. Ribatet, M., Generalized pareto distribution and peaks over threshold. R package. 2012 http://cran.r-project.org/web/packages/POT/index.html. Accessed 10 Nov 2014.
46. Ronce, O., How does it feel to be like a rolling stone? Ten questions about dispersal evolution. Annual Review of Ecology Evolution and Systematics 38 (2007), 231–253, 10.1146/annurev.ecolsys.38.091206.095611.
47. Sanford, R.L. Jr., Paaby, P., Luvall, J.C., Phillips, E., Climate, geomorphology, and aquatic systems. McDade, L.A., Bawa, K.S., Hespenheide, H.A., Hartshorn, G.S., (eds.) La selva: Ecology and natural history of a neotropical rainforest, 1994, The University of Chicago Press, Chicago, IL, 19–33.
48. Savage, J.M., The amphibians and reptiles of Costa Rica: A herpetofauna between two continents, two seas. 2002, The University of Chicago Press, Chicago, IL.
49. Sawyer, S.C., Epps, C.W., Brashares, J.S., Placing linkages among fragmented habitats: Do least-cost models reflect how animals use landscapes?. Journal of Applied Ecology 48:3 (2011), 668–678, 10.1111/j.1365-2664.2011.01970.x.
50. Short Bull, R.A.S., Cushman, S.A., Mace, R., Chilton, T., Kendall, K.C., Landguth, E.L.,.. Luikart, G., Why replication is important in landscape genetics: American black bear in the Rocky Mountains. Molecular Ecology 20:6 (2011), 1092–1107, 10.1111/j.1365-294X.2010.04944.x.
51. Spear, S.F., Balkenhol, N., Fortin, M.J., McRae, B.H., Scribner, K., Use of resistance surfaces for landscape genetic studies: Considerations for parameterization and analysis. Molecular Ecology 19:17 (2010), 3576–3591, 10.1111/j.1365-294X.2010.04657.x.
52. Taylor, P.D., Fahrig, L., Henein, K., Merriam, G., Connectivity is a vital element of landscape structure. Oikos 68:3 (1993), 571–573, 10.2307/3544927.
53. Trainor, A.M., Walters, J.R., Morris, W.F., Sexton, J., Moody, A., Empirical estimation of dispersal resistance surfaces: A case study with red-cockaded woodpeckers. Landscape Ecology 28:4 (2013), 755–767, 10.1007/s10980-013-9861-5.
54. Trakhtenbrot, A., Nathan, R., Perry, G., Richardson, D.M., The importance of long-distance dispersal in biodiversity conservation. Diversity and Distributions 11:2 (2005), 173–181, 10.1111/j.1366-9516.2005.00156.x.
55. Van der Auwera, G.A., Carneiro, M.O., Hartl, C., Poplin, R., del Angel, G., Levy-Moonshine, A.,.. DePristo, M.A., From FastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics, 11, 2013, 1110.
56. Waser, P.M., Hadfield, J.D., How much can parentage analyses tell us about precapture dispersal?. Molecular Ecology 20:6 (2011), 1277–1288, 10.1111/j.1365-294X.2011.05002.x.
57. Wasserman, T.N., Cushman, S.A., Schwartz, M.K., Wallin, D.O., Spatial scaling and multi-model inference in landscape genetics: Martes americana in Northern Idaho. Landscape Ecology 25:10 (2010), 1601–1612, 10.1007/s10980-010-9525-7.
58. Wilson, D.E., Cole, F.R., Nichols, J.D., Rudran, R., Foster, M.S., (eds.) Measuring and monitoring biological diversity: Standard methods for mammals, 1996, Smithsonian Institution Press, Washington, D.C.
59. Zeller, K.A., McGarigal, K., Whiteley, A.R., Estimating landscape resistance to movement: A review. Landscape Ecology 27:6 (2012), 777–797, 10.1007/s10980-012-9737-0.
60. Zeller, K.A., McGarigal, K., Beier, P., Cushman, S.A., Vickers, T.W., Boyce, W.M., Sensitivity of landscape resistance estimates based on point selection functions to scale and behavioral state: Pumas as a case study. Landscape Ecology 29:3 (2014), 541–557, 10.1007/s10980-014-9991-4.
61. Zeller, K.A., McGarigal, K., Cushman, S.A., Beier, P., Vickers, T.W., Boyce, W.M., Using step and path selection functions for estimating resistance to movement: Pumas as a case study. Landscape Ecology 31:6 (2016), 1319–1335, 10.1007/s10980-015-0301-6.