Habitat use models of spatially auto-correlated data: a case study of the common bottlenose dolphin, Tursiops truncatus truncatus, in southeastern Brazil

References

• Anderwald P, Evans PGH, Dyer R, Dale A, Wright PJ, Hoelzel AR. 2012. Spatial scale and environmental determinants in minke whale habitat use and foraging. Marine Ecology Progress Series 450:259−274. doi: 10.3354/meps09573
   Web of Science ®Google Scholar
• Azzellino A, Gaspari SA, Airoldi S, Lanfredi C. 2008. Biological consequences of global warming: does sea surface temperature affect cetacean distribution in the western Ligurian Sea? Journal of Marine Biological Association of the United Kingdom 88:145–1152. doi:10.1017/S002531540800088X
   Web of Science ®Google Scholar
• Azzelino A, Panigada S, Lanfredi C, Zanardelli M, Airoldi S, Notarbartolo di Sciara G. 2012. Predictive habitat models for managing marine areas: spatial and temporal distribution of marine mammals within the Pelagos Sanctuary (Northwestern Mediterranean sea). Ocean Coastal Management. 67:63–74. doi: 10.1016/j.ocecoaman.2012.05.024
   Web of Science ®Google Scholar
• Bailey H, Corkrey R, Cheney B, Thompson PM. 2013. Analyzing temporally correlated dolphin sightings data using generalized estimating equations. Marine Mammal Science. 29:123–141. doi: 10.1111/j.1748-7692.2011.00552.x
   Web of Science ®Google Scholar
• Barreto AS. 2011. Golfinho nariz de garrafa. In: Rocha-Câmara CC, Câmara IG, Pretto D, editors. Plano Nacional de Ação de Pequenos Cetáceos. Brasilia: Instituto Chico Mendes de Conservação da Biodiversidade; p. 27–29. (In portuguese).
   Google Scholar
• Barton K. 2016. MuMIn: multi-model inference. R package version 1.15.6. https://cran.r-project.org/web/packages/Mu MIn/MuMIn.pdf.
   Google Scholar
• Becker EA, Foley DG, Forney KA, Barlow J, Redfern JV, Gentemann CL. 2012. Forecasting cetacean abundance patterns to enhance management decisions. Endangered Species Research. 16:97–112. doi: 10.3354/esr00390
   Google Scholar
• Bivand R, Altman M, Anselin L, Assunção R, Berke O, Bernat A, Blanchet G, Blankmeyer E, Carvalho M, Christensen B, et al. 2013. spdep: spatial dependence: weighting schemes, statistics and models. R package version 0.5-56. http://CRAN.R-project.org/package=spdep.
   Google Scholar
• Blasi MF, Boitani L. 2012. Modelling fine-scale distribution of the bottlenose dolphin Tursiops truncatus using physiographic features on Filicudi (southern Thyrrenian Sea, Italy). Endangered Species Research. 17:269–228. doi: 10.3354/esr00422
   Google Scholar
• Burnham KP, Anderson DR. 2004. Multimodel inference understanding AIC and BIC in model selection. Sociological Methods and Research. 33:261–304. doi: 10.1177/0049124104268644
   Web of Science ®Google Scholar
• Cafaro V, Angeletti D, Bellisario B, Macali A, Carere C, Alessi J. 2016. Habitat overlap between bottlenose dolphins and seabirds: a pilot study to identify high presence coastal areas in the Tyrrhenian Sea. Journal of Marine Biological Association of the United Kingdom. 96:891–901. doi: 10.1017/S0025315415001447
   Web of Science ®Google Scholar
• Cañadas A, Sagarminaga R, García-Tiscar S. 2002. Cetacean distribution related with depth and slope in the Mediterranean waters off southern Spain. Deep-Sea Research: Oceanographical Research Papers. 49:2053–2073. doi: 10.1016/S0967-0637(02)00123-1
   Web of Science ®Google Scholar
• Carbonel C. 1998. Modelling of upwelling in the coastal area of Cabo Frio (Rio de Janeiro–Brazil). Revista Brasileira de Oceanografia. 46:1–17. doi: 10.1590/S1413-77391998000100001
   Google Scholar
• Carbonel CAAH, Valentin JL. 1999. Numerical modelling of phytoplankton bloom in the upwelling ecosystem of Cabo Frio (Brazil). Ecological Modeling. 116:135–148. doi: 10.1016/S0304-3800(98)00201-4
   Web of Science ®Google Scholar
• Connor RC, Read AJ, Wrangham R. 2000. Male reproductive strategies and social bonds. In: Mann J, Connor RC, Tyack P, Whitehead H, editors. Cetacean societies: field studies of dolphins and dolphins. Chicago: The University of Chicago Press; p. 247–269.
   Google Scholar
• Corkeron PJ, Minton G, Collins T, Findlay K, Willson A, Baldwin R. 2011. Spatial models of sparse data to inform cetacean conservation planning: an example from Oman. Endangered Species Research. 15:39–52. doi: 10.3354/esr00367
   Google Scholar
• Costa D. 2008. Energetics. In: Perrin WF, Würsig B, Thewissen JGM, editors. Encyclopedia of marine mammals. Academic Press, Chicago: The University of Chicago Press; p. 383–390 , 500p.
   Google Scholar
• Costa APB, Rosel PE, Daura-Jorge FG, Simões-Lopes PC. 2016. Offshore and coastal common bottlenose dolphins of the western South Atlantic face-to-face: what the skull and the spine can tell us. Marine Mammal Science. 32:1433–1457. doi: 10.1111/mms.12342
   Web of Science ®Google Scholar
• Dalla Rosa L, Ford JK, Trites AW. 2012. Distribution and relative abundance of humpback whales in relation to environmental variables in coastal British Columbia and adjacent waters. Continental Shelf Research. 36:89−104. doi: 10.1016/j.csr.2012.01.017
   Web of Science ®Google Scholar
• Daura-Jorge FG, Cantor M, Ingram S, Lusseau D, Simões-Lopes PC. 2012. The structure of a bottlenose dolphin society is coupled to a unique foraging cooperation with artisanal fishermen. Biology Letters. 8:702–705. doi: 10.1098/rsbl.2012.0174
   PubMed Web of Science ®Google Scholar
• Daura-Jorge FG, Ingram S, Simões-Lopes PC. 2013. Seasonal abundance and adult survival of bottlenose dolphins (Tursiops truncatus) in a community that cooperatively forages with fishermen in southern Brazil. Marine Mammal Science. 29:293–311. doi: 10.1111/j.1748-7692.2012.00571.x
   Web of Science ®Google Scholar
• Daura-Jorge FG, Simões-Lopes PC. 2017. Mark-recapture vs. line-transect abundance estimates of a coastal dolphin population: a case study of Tursiops truncatus from Laguna, southern Brazil. Latin American Journal of Aquatic Mammals. 11:133–143. doi: 10.5597/lajam00222
   Google Scholar
• De Carvalho MS, Rossi-Santos MR. 2011. Sightings of the bottlenose dolphins (Tursiops truncatus) in the Trindade Island, Brazil, South Atlantic Ocean. Marine Biodiversity Records. 4:1–4. doi:10.1017/S1755267211000029.
   Google Scholar
• De Leo FC, Pires-Vanin AMS. 2006. Benthic megafauna communities under influence of the SACW (South Atlantic Central Water) intrusion onto the Brazilian Southeastern shelf: a comparison between an upwelling and a non-upwelling ecosystem. Journal of Marine Systems. 60:268–284. doi: 10.1016/j.jmarsys.2006.02.002
   Web of Science ®Google Scholar
• Di Tullio JC, Fruet PF, Secchi ER. 2015. Identifying critical areas to reduce bycatch of coastal common bottlenose dolphins Tursiops truncatus in artisanal fisheries of the subtropical western South Atlantic. Endangered Species Research. 29:35–50. doi: 10.3354/esr00698
   Web of Science ®Google Scholar
• Díaz-López B, Methion S. 2017. The impact of shellfish farming on common bottlenose dolphins’ use of habitat. Marine Biology. 164:83. doi: 10.1007/s00227-017-3125-x
   Web of Science ®Google Scholar
• Di Beneditto APM, Ramos RMA, Siciliano S, dos Santos RA, Bastos G, Fagundes-Neto E. 2001. Stomach contents of delphinids from Rio de Janeiro, southeastern Brazil. Aquatic Mammals. 27:24–28.
   Google Scholar
• Di Giacomo AB, Ott PH. 2017. Long-term site fidelity and residency patterns of bottlenose dolphins (Tursiops truncatus) in the Tramandaí Estuary, southern Brazil. Latin American Journal of Aquatic Mammals. 11:155–161. doi: 10.5597/00224
   Google Scholar
• Diniz-Filho JAF, Nabout JC, Telles MPDC, Soares TN, Rangel TFL. 2009. A review of techniques for spatial modeling in geographical, conservation and landscape genetics. Genetics and molecular Biology. 32:203–211. doi: 10.1590/S1415-47572009000200001
   PubMed Web of Science ®Google Scholar
• Dormann CF. 2007. Effects of incorporating spatial autocorrelation into the analysis of species distribution data. Global Ecology and Biogeography. 16:129–138. doi: 10.1111/j.1466-8238.2006.00279.x
   Web of Science ®Google Scholar
• Dormann CF, McPherson JM, Araujo MB, Bivand R, Bolliger J, Carl G, Davies RG, Hirzel A, Jetz W, Daniel Kissling W, et al. 2007. Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography. 30:609–628. doi: 10.1111/j.2007.0906-7590.05171.x
   Web of Science ®Google Scholar
• Ferreira CEL, Floeter SR, Gasparini JL, Ferreira BP, Joyeux JC. 2004. Trophic structure patterns of Brazilian reef fishes: a latitudinal comparison. Journal of Biogeography. 31:1093–1116. doi: 10.1111/j.1365-2699.2004.01044.x
   Web of Science ®Google Scholar
• Flores PAC, Fontoura NF. 2006. Ecology of marine tucuxi, Sotalia guianensis, and bottlenose dolphin, Tursiops truncatus, in Baía Norte, Santa Catarina state, Southern Brazil. Latin American Journal of Aquatic Mammals. 5:105–115.
   Google Scholar
• Forcada J. 2008. Distribution. In: W.F. Perrin, B. Würsig, J.G.M. Thewissen, editors. Encyclopedia of Marine Mammals. Chicago: Academic Press; p. 316–321.
   Google Scholar
• Fox J, Weisberg S. 2011. An R companion to applied regression. 2nd ed. Thousand Oaks (CA): Sage.
   Google Scholar
• Fruet PF, Kinas PG, Silva KG, Di Tullio JC, Monteiro DS, Dalla Rosa L, Estima SC, Secchi ER. 2012. Temporal trends in mortality and effects of by-catch on common bottlenose dolphins, Tursiops truncatus, in southern Brazil. Journal of the Marine Biological Association of the United Kingdom. 92:1865–1876. doi:10.1017/S0025315410001888.
   Web of Science ®Google Scholar
• Fruet PF, Secchi ER, Di Tullio JC, Kinas PG. 2011. Abundance of bottlenose dolphins, Tursiops truncatus (Cetacea: Delphinidae), inhabiting the Patos Lagoon estuary, southern Brazil: implications for conservation. Zoologia (Curitiba). 28:23–30. doi:10.1590/S1984-46702011000100004.
   Google Scholar
• Fruet PF, Secchi ER, Di Tullio JC, Simões-Lopes PC, Daura-Jorge FG, Costa APB, Vermuellen E, Flores PAC, Genoves RC, Laporta P, et al. 2017. Genetic divergence between two phenotypically distinct bottlenose dolphin ecotypes suggests separate evolutionary trajectories. Ecology and Evolution. 7:9131–9143. doi: 10.1002/ece3.3335
   PubMed Web of Science ®Google Scholar
• Gill PC, Morrice MG, Page B, Pirzl R, Levings AH, Coyne M. 2011. Blue whale habitat selection and within-season distribution in a regional upwelling system off southern Australia. Marine Ecology Progress Series. 421:243–263. doi: 10.3354/meps08914
   Web of Science ®Google Scholar
• Goodall RNP, Marchesi MC, Pimper LE, Dellabianca N, Benegas LG, Torres MA, Riccialdelli L. 2011. Southernmost records of bottlenose dolphins, Tursiops truncatus. Polar Biology. 34:1085–1090. doi: 10.1007/s00300-010-0954-1
   Web of Science ®Google Scholar
• Goldberger AS, Goldberger ASG. 1991. A course in econometrics. Cambridge, MA: Harvard University Press.
   Google Scholar
• Griffith DA, Peres-Neto PR. 2006. Spatial modeling in ecology: the flexibility of eigenfunction spatial analysis. Ecology. 87:2603–2613. doi: 10.1890/0012-9658(2006)87[2603:SMIETF]2.0.CO;2
   PubMed Web of Science ®Google Scholar
• Hastie GD, Wilson BE N, Wilson LJ, Parsons KM, Thompson PM. 2004. Functional mechanisms underlying cetacean distribution patterns: hotspots for bottlenose dolphins are linked to foraging. Marine Biology. 144:397–403. doi: 10.1007/s00227-003-1195-4
   Web of Science ®Google Scholar
• Houlahan JE, McKinney ST, Anderson TM, McGill BJ. 2017. The priority of prediction in ecological understanding. Oikos. 126:1–7. doi: 10.1111/oik.03726
   Web of Science ®Google Scholar
• Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (IBAMA). 2001. Mamíferos Aquáticos do Brasil: Plano de Ação Versão II. Brasília, Diretoria de Fauna e Recursos Pesqueiros/IBAMA. 96 p.
   Google Scholar
• Instituto Chico Mendes de conservação da Biodiversidade (ICMBio). 2018. Livro Vermelho da Fauna Brasileira Ameaçada de Extinção: Brasília: ICMBio/MMA.
   Google Scholar
• Keiper CA, Ainley DG, Allen SG, Harvey JT. 2005. Marine mammal occurrence and ocean climate off central California, 1986 to 1994 and 1997 to 1999. Marine Ecology Progress Series. 289:285–306. doi: 10.3354/meps289285
   Web of Science ®Google Scholar
• Kleiber C, Zeileis A. 2008. Applied econometrics with R. New York, NY: Springer.
   Google Scholar
• Lichstein JW, Simons TR, Shriner SA, Franzreb KE. 2002. Spatial autocorrelation and autoregressive models in ecology. Ecological Monographs. 72:445–463. doi: 10.1890/0012-9615(2002)072[0445:SAAAMI]2.0.CO;2
   Web of Science ®Google Scholar
• Lodi L. 2017. Update on the current occurrence of Tursiops truncatus (Montagu, 1821) in Rio de Janeiro State. Latin American Journal of Aquatic Mammals. 11:220–226. doi: 10.5597/lajam00231
   Google Scholar
• Lodi L, Cantor M, Daura-Jorge FG, Monteiro-Neto CA. 2014. A missing piece from a bigger puzzle: declining occurrence of a transient group of bottlenose dolphins off Southeastern Brazil. Marine Ecology. 35:516–527. doi: 10.1111/maec.12108
   Web of Science ®Google Scholar
• Lodi L, Mayerhofer LC, Monteiro-Neto C. 2009. Evaluation of the video-identification technique applied to bottlenose dolphins (Tursiops truncatus) in Cagarras Archipelago, Rio de Janeiro, Brazil. Journal of the Marine Biological Association of the United Kingdom. 89:1077–1081. doi: 10.1017/S0025315408002993
   Web of Science ®Google Scholar
• Lodi R, Tardin RHO. 2018. Site fidelity and residency of common bottlenose dolphins (Cetartiodactyla: Delphinidae) in a coastal insular habitat off southeastern Brazil. Pan-American Journal of Aquatic Sciences. 13:53–63. doi: 10.1016/j.ocecoaman.2018.03.029
   Google Scholar
• Lodi L, Wedekin LL, Rossi-Santos MR, Marcondes MC. 2008. Movements of the bottlenose dolphin (Tursiops truncatus) in the Rio de Janeiro state, southeastern Brazil. Biota Neotropica. 8:205–209. doi: 10.1590/S1676-06032008000400020
   Google Scholar
• Martinho F, Pereira A, Brito C, Gaspar R, Carvalho I. 2015. Structure and abundance of bottlenose dolphins (Tursiops truncatus) in coastal Setúbal Bay. Portugal. Marine Biology Research. 11:144–156. doi: 10.1080/17451000.2014.894244
   Web of Science ®Google Scholar
• Melo CLC, Santos RA, Bassoi M, Araújo AC, Lailson-Brito J, Dorneles PR, Azevedo AF. 2010. Feeding habits of delphinids (Mammalia: Cetacea) from Rio de Janeiro state, Brazil. Journal of the Marine Biological Association of the United Kingdom. 90:1509–1515. doi: 10.1017/S0025315409991639
   Web of Science ®Google Scholar
• Milmann LC, Danilewicz D, Baumgarten J, Ott PH. 2016. Temporal-spatial distribution of an island-based offshore population of common bottlenose dolphins (Tursiops truncatus) in the equatorial Atlantic. Marine Mammal Science. 33:496–519. doi: 10.1111/mms.12380
   Web of Science ®Google Scholar
• Moura J, Tavares DC, Secco HK, Siciliano S. 2017. Bottlenose dolphins (Tursiops truncatus, Montagu 1821) in central-northern coast of Rio de Janeiro State, Brazil: stranding patterns and insights into feeding habits. Latin American Journal of Aquatic Mammals. 11:191–198. doi: 10.5597/00228
   Google Scholar
• Oliveira LR, Ott PH, Moreno IB, Tavares M, Siciliano S, Bonatto SL. 2017. Effective population size of an offshore population of bottlenose dolphins, Tursiops truncatus, from the São Pedro and São Paulo Archipelago, Brazil. Latin American Journal of Aquatic Mammals. 11:162–169. doi: 10.5597/00225
   Google Scholar
• Pavanato HJ, Mayer FP, Wedekin LL, Engel MH, Kinas PG. 2018. Prediction of humpback whale group densities along the Brazilian coast using spatial autoregressive models. Marine Mammal Science. 34:734–754. doi: 10.1111/mms.12492
   Web of Science ®Google Scholar
• Pirotta E, Matthiopoulos JM, MacKenzie L, Scott-Hayward L, Rendell L. 2011. Modelling sperm whale habitat preference: a novel approach combining transect and follow data. Marine Ecology Progress Series. 436:257–272. doi:10.3354/meps09236.
   Web of Science ®Google Scholar
• Pitchford JL, Howard VA, Shelley JK, Serafin BJS, Coleman AT, Solangi M. 2016. Predictive spatial modelling of seasonal bottlenose dolphin (Tursiops truncatus) distributions in the Mississippi Sound. Aquatic Conservation: Marine and Freshwater Ecosystem. 26:289–306. doi: 10.1002/aqc.2547
   Web of Science ®Google Scholar
• Quin GP, Keough MJ. 2002. Experimental design and data analysis for biologists. Melbourne: Cambridge University Press.
   Google Scholar
• Redfern JV, Ferguson MC, Becker EA, Hyrenbach KD, Good C, Barlow J, Kaschner K, Baumgartner MF, Forney KA, Balance LT, et al. 2006. Techniques for cetacean-habitat modeling. Marine Ecology Progress Series. 310:271–295. doi:10.3354/meps310271.
   Web of Science ®Google Scholar
• Roberts JJ, Best DB, Dunn DC, Treml EA, Halpin PN. 2010. Marine geospatial ecology tools: An integrated framework for ecological geoprocessing with ArcGIS, Python, R, MATLAB, and C++. Environmental Modeling & Software. 25:1197–1207. doi: 10.1016/j.envsoft.2010.03.029
   Web of Science ®Google Scholar
• Rossi-Santos M, Wedekin LL, Sousa-Lima RS. 2006. Distribution and habitat use of small cetaceans off Abrolhos Bank, eastern Brazil. Latin American Journal of Aquatic Mammals. 5:23–28. doi: 10.5597/lajam00088
   Google Scholar
• Secchi ER, Botta S, Wiegand MM, Lopez LA, Fruet PF, Genoves RC, Di Tullio JC. 2017. Long-term and gender-related variation in the feeding ecology of common bottlenose dolphins inhabiting a subtropical estuary and the adjacent marine coast in the western South Atlantic. Marine Biology Research. 13:121–134. doi: 10.1080/17451000.2016.1213398
   Web of Science ®Google Scholar
• Simões-Lopes PC, Fabián ME. 1999. Residence patterns and site fidelity in bottlenose dolphins, Tursiops truncatus (Montagu) (Cetacea, Delphinidae) of Southern Brazil. Revista Brasileira de Zoolgia. 16:1017–1024. doi: 10.1590/S0101-81751999000400012
   Google Scholar
• Silva MA, Prieto R, Magalhães S, Seabra MI, Machete M, Hammond PS. 2012. Incorporating information on bottlenose dolphin distribution into marine protected area design. Aquatic Conservation: Marine and Freshwater Ecosystems. 22:122–133. doi: 10.1002/aqc.1243
   Web of Science ®Google Scholar
• Tardin RH, Chun Y, Simão SM, Alves MAS. 2017. Modeling habitat use by Bryde’s whale, Balaenoptera edeni, off southeastern Brazil. Marine Ecology Progress Series. 576:89–103. doi: 10.3354/meps12228
   Web of Science ®Google Scholar
• Tardin RH, Maciel IS, Maricato G, Simao SM, Alves MAS. In press. Occurrence, residency patterns and habitat use of the bottlenose dolphin, Tursiops truncatus truncatus, on two Marine Protected Areas in Southeastern Brazil. Anais da Academia Brasileira de Ciências.
   Google Scholar
• Tardin RH, Simão SM, Alves MAS. 2013. Distribution of Tursiops truncatus in Southeastern Brazil: a modeling approach for summer sampling. Natureza & Conservação. 11:65–74. doi: 10.4322/natcon.2013.011
   Google Scholar
• Walsh C, MacNally R. 2013. hier.part: hierarchical partitioning. R package version 1.0-4. https://CRAN.R-project.org/package=hier.part.
   Google Scholar
• Wedekin LL, Daura-Jorge FG, Rossi-Santos MR, Simões-Lopes PC. 2008. Notas sobre a distribuição, tamanho de grupo e comportamento do golfinho Tursiops truncatus (Cetacea: Delphinidae) na Ilha de Santa Catarina, sul do Brasil. Biota. 8:bn01708042008.
   Google Scholar
• Wells RS. 1991. The role of long-term study in understanding the social structure of a bottlenose community. In: Pryor K, Norris KS, editors. Dolphin societies: discoveries and puzzles. Los Angeles: University of California Press; p. 199–225.
   Google Scholar
• Wells RS, Scott M. 2008. Common bottlenose dolphin. In: Perrin WF, Würsig B, Thewissen JGM, editors. Encyclopedia of marine mammals. Chicago: Academic Press; p. 255–259.
   Google Scholar
• Wells RS, Scott MD, Irwine AB. 1987. The social structure of free ranging bottlenose dolphins. In: Genoways H, editor. Current mammalogy. New York, NY: Plenum Press; p. 247–305.
   Google Scholar
• Whittingham MJ, Stephens PA, Bradbury RB, Freckleton RP. 2006. Why do we still use stepwise modelling in ecology and behaviour? Journal of Animal Ecology. 75:1182–1189. doi: 10.1111/j.1365-2656.2006.01141.x
   PubMed Web of Science ®Google Scholar
• Wickert JC, Von-Eye SM, Oliveira LR, Moreno IB. 2016. Revalidation of Tursiops gephyreus Lahille, 1908 (Cetartiodactyla: Delphinidae) from the southwestern Atlantic Ocean. Journal of Mammalogy. 97:1728–1737. doi: 10.1093/jmammal/gyw139
   Web of Science ®Google Scholar