What constitutes a community? A co-occurrence exploration of the Costa Rican avifauna

References

• Ricklefs RE. Disintegration of the ecological community. Am Natur. 2008;172(6):741–750. DOI:10.1086/593002.
   PubMed Web of Science ®Google Scholar
• Stroud JT, Bush MR, Ladd MC, et al. Is a community still a community? Reviewing definitions of key terms in community ecology. Ecol Evol. 2015;5(21):4757–4765. DOI:10.1002/ece3.1651
   PubMed Web of Science ®Google Scholar
• RP McIntosh. H. A. Gleason’s ‘individualistic concept’ and theory of animal communities: a continuing controversy. Biol Rev. 1995;70(2):317–357 DOI:10.1111/j.1469-185X.1995.tb01069.x.
   PubMed Web of Science ®Google Scholar
• Gleason HA. The structure and development of the plant association. Bull Torrey Bot Club. 1917;44(10):463–481. DOI:10.2307/2479596.
   Google Scholar
• Gleason HA. The individualistic concept of the plant association. Bull Torrey Bot Club. 1926;53(1):7–26. DOI:10.2307/2479933.
   Google Scholar
• Gleason HA. The individualistic concept of the plant association. Am Natur. 1939;21(1):92–110. DOI:10.2307/2420377.
   Google Scholar
• Clements FE. Plant succession: an analysis of the development of vegetation. Carnegie Institution of Washington. Publication no. 242. Washington: Carnegie Institution of Washington; 1916.
   Google Scholar
• Ulrich W, Kryszewski W, Sewerniak P, et al. A comprehensive framework for the study of species co-occurrences, nestedness and turnover. Oikos. 2017;126(11):1607–1616. DOI:10.1111/oik.04166
   Web of Science ®Google Scholar
• Peterson AT, Soberón J, Ramsey JM, et al. Co-occurrence networks do not support identification of biotic interactions. Biodivers Inform. 2020;15(1):1–10. DOI:10.17161/bi.v15i1.9798
   Web of Science ®Google Scholar
• Stephens CR, Gimenez Heau J, Gonzalez C, et al. Using biotic interaction networks for prediction in biodiversity and emerging diseases. PLoS ONE. 2009;4(5):e5725. DOI:10.1371/journal.pone.0005725
   PubMed Web of Science ®Google Scholar
• Stephens CR, González-Salazar C, Sánchez-Cordero V, et al. Can you judge a disease host by the company it keeps? Predicting disease hosts and their relative importance: a case study for Leishmaniasis. PLoS Negl Trop Dis. 2016;10(10):e0005004. DOI:10.1371/journal.pntd.0005004
   PubMed Web of Science ®Google Scholar
• Blanchet FG, Cazelles K, Gravel D. Co-occurrence is not evidence of ecological interactions. Ecol Lett. 2020;23(7):1050–1063. DOI:10.1111/ele.13525.
   PubMed Web of Science ®Google Scholar
• Hubbell S. A unified theory of biogeography and relative species abundance and its application to tropical rain forests and coral reefs. Coral Reefs. 1997;16(S):S9–21. DOI:10.1007/s003380050237.
   Google Scholar
• Crouch NMA, Capurucho JMG, Hackett SJ, et al. Evaluating the contribution of dispersal to community structure in Neotropical passerine birds. Ecography. 2019;42(2, SI):390–399. DOI:10.1111/ecog.03927
   Web of Science ®Google Scholar
• Cooper JC, Crouch NMA, Ferguson AW, et al. Climatic refugia and reduced extinction correlate with underdispersion in mammals and birds in Africa. Ecol Evol. 2022;12(3):e8752. DOI:10.1002/ece3.8752.
   PubMed Web of Science ®Google Scholar
• Munn C, Terborgh J. Multi-species territoriality in Neotropical foraging flocks. Condor. 1979;81(4):338–347. DOi:10.2307/1366956.
   Web of Science ®Google Scholar
• Jullien M, Thiollay J. Multi-species territoriality and dynamic of neotropical forest understorey bird flocks. J Anim Ecol. 1998;67(2):227–252. DOI:10.1046/j.1365-2656.1998.00171.x.
   Web of Science ®Google Scholar
• Jones HH, Robinson SK. Patch size and vegetation structure drive changes to mixed-species flock diversity and composition across a gradient of fragment sizes in the Western Andes of Colombia. Condor. 2020;122(2):duaa006. DOI:10.1093/condor/duaa006.
   Web of Science ®Google Scholar
• Guimarães DP, Guilherme E. Structure and home range size of mixed-species bird flocks in a bamboo forest in southwestern Amazonia. Acta Ornithologica. 2021;56(1):95–108. DOI:10.3161/00016454AO2021.56.1.009.
   Web of Science ®Google Scholar
• Fauth JE, Bernardo J, Camara M, et al. Simplifying the jargon of community ecology: a conceptual approach. Am Natur. 1996;147(2):282–286. DOI:10.1086/285850
   Web of Science ®Google Scholar
• R Core Team. R: A language and environment for statistical computing; 2021.
   Google Scholar
• QGIS Development Team. QGIS Geographic Information System; 2021.
   Google Scholar
• Dowle M, Srinivasan A. Data.Table: extension of ‘data.Frame’ [R package version 1.14.0]. Comprehensive R Archive Network (CRAN); 2021.
   Google Scholar
• Auguie B. gridExtra: miscellaneous functions for “Grid” graphics. Comprehensive R Archive Network (CRAN); 2017.
   Google Scholar
• Wickham H, Averick M, Bryan J, et al. Welcome to the Tidyverse. J Open Source Software. 2019;4(43):1686. DOI:10.21105/joss.01686
   Google Scholar
• Garnier S. Viridis: default color maps from “matplotlib”. Comprehensive R Archive Network (CRAN); 2018.
   Google Scholar
• Inkscape Project;2021. Available from: https://inkscape.org.
   Google Scholar
• ImageMagick Studio LLC;2019. Available from: https://imagemagick.org.
   Google Scholar
• Velde M, Cooper JC, Garrod H. Testing the accuracy of species distribution models based on community science data. bioRxiv. 2023. DOI:10.1101/2023.01.13.523331.
   Google Scholar
• Sullivan BL, Wood CL, Iliff MJ, et al. eBird: a citizen-based bird observation network in the biological sciences. Biol Conserv. 2009;142(10):2282–2292. DOI:10.1016/j.biocon.2009.05.006
   Web of Science ®Google Scholar
• Sullivan BL, Aycrigg JL, Barry JH, et al. The eBird enterprise: an integrated approach to development and application of citizen science. Biol Conserv. 2014;169:31–40. DOI:10.1016/j.biocon.2013.11.003.
   Web of Science ®Google Scholar
• Boyle WA. Altitudinal bird migration in North America. Auk. 2017;134(2):443–465. DOI:10.1642/AUK-16-228.1.
   Web of Science ®Google Scholar
• Clements JF, Schulenberg TS, Iliff MJ, et al. The eBird/Clements checklist of birds of the world: v2019. 2019. Available from: https://www.birds.cornell.edu/clementschecklist/download/.
   Google Scholar
• Clements JF, Schulenberg TS, Iliff MJ, et al. The eBird/Clements checklist of birds of the world: v2021.; 2021. Available from: https://www.birds.cornell.edu/clementschecklist/download.
   Google Scholar
• Venables WN, Ripley BD. Modern applied statistics with S. 4th ed. New York: Springer; 2002.
   Google Scholar
• Cooper JC, Maddox JD, McKague K, et al. Multiple lines of evidence indicate ongoing allopatric and parapatric diversification in an afromontane sunbird (Cinnyris reichenowi). Ornithology. 2021;138(2):138. DOI:10.1093/ornithology/ukaa081
   Google Scholar
• Aelst SV, Rousseeuw P. Minimum volume ellipsoid. Wiley Interdiscip Rev Comput Stat. 2009;1(1):71–82. DOI:10.1002/wics.19.
   Google Scholar
• Yañez-Arenas C, Martinez-Meyer E, Mandujano S, et al. Modelling geographic patterns of population density of the white-tailed deer in central Mexico by implementing ecological niche theory. Oikos. 2012;121(12):2081–2089. DOI:10.1111/j.1600-0706.2012.20350.x
   Web of Science ®Google Scholar
• Osorio-Olvera L, Yañez-Arenas C, Martinez-Meyer E, et al. Relationships between population densities and niche-centroid distances in North American birds. Ecol Lett. 2020;23(3):555–564. DOI:10.1111/ele.13453
   PubMed Web of Science ®Google Scholar
• Jiménez L, Soberón J. Estimating the fundamental niche: accounting for the uneven availability of existing climates in the calibration area. Ecol Modell. 2022;464:109823. DOI:10.1016/j.ecolmodel.2021.109823.
   Web of Science ®Google Scholar
• Soberón J, Peterson AT. Interpretation of models of fundamental ecological niches and species’ distributional areas. Biodivers Inform. 2005;2():1–10. DOI:10.17161/bi.v2i0.4.
   Google Scholar
• Barve N, Barve V, Jimenez-Valverde A, et al. The crucial role of the accessible area in ecological niche modeling and species distribution modeling. Ecol Modell. 2011;222(11):1810–1819. DOI:10.1016/j.ecolmodel.2011.02.011
   Web of Science ®Google Scholar
• Cooper JC, Soberón J . Creating individual accessible area hypotheses improves stacked species distribution model performance. Global Ecol Biogeogr. 2018;27(1):156–165. DOI:10.1111/geb.12678.
   Google Scholar
• RJ H. Raster: geographic data analysis and modeling. Comprehensive R Archive Network (CRAN); 2019.
   Google Scholar
• Bivand R, Keitt T, Pebesma E, et al. Rgdal: bindings for the ‘Geospatial’ data abstraction library [R package rgdal version 1.5-23]. Comprehensive R Archive Network (CRAN); 2021.
   Google Scholar
• Bivand R, Rundel C. Rgeos: interface to geometry engine - Open Source (‘GEOS’). Comprehensive R Archive Network (CRAN); 2020.
   Google Scholar
• Pebesma E. Simple features for R: standardized support for spatial vector data. The R Journal. 2018;10(1):439–446. DOI:10.32614/RJ-2018-009.
   Google Scholar
• Hijmans RJ, Phillips S, Leathwick J, et al. Dismo: species distribution modeling. Comprehensive R Archive Network (CRAN); 2020.
   Google Scholar
• La Sorte FA, Somveille M. Survey completeness of a global citizen-science database of bird occurrence. Ecography. 2020;43(1):34–43. DOI:10.1111/ecog.04632.
   Web of Science ®Google Scholar
• Hunziker P. Velox: fast raster manipulation and extraction. Comprehensive R Archive Network (CRAN); 2017.
   Google Scholar
• White AE, Dey KK, Mohan D, et al. Regional influences on community structure across the tropical-temperate divide. Nat Commun. 2019;10(1):10. DOI:10.1038/s41467-019-10253-6
   PubMedGoogle Scholar
• Novembre J. Variations on a common STRUCTURE: new Algorithms for a valuable model. Genetics. 2014;197(3):809–811. DOI:10.1534/genetics.114.166264.
   PubMed Web of Science ®Google Scholar
• White AE, Dey KK, Stephens M, et al. Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace’s Line. Global Ecol Biogeogr. 2021;30(3):685–696. DOI:10.1111/geb.13250
   Google Scholar
• South A. Rnaturalearth: world map data from natural earth. Comprehensive R Archive Network (CRAN); 2017.
   Google Scholar
• Cooper JC. Hierarchical analyses of avian community biogeography in the Afromontane highlands. Front Biogeogr. 2021;13(4):e51310. DOI:10.21425/F5FBG51310.
   PubMedGoogle Scholar
• Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics. 2004;20(2):289–290. DOI:10.1093/bioinformatics/btg412.
   PubMed Web of Science ®Google Scholar
• Paradis E, Schliep K, Schwartz R. Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 2019;35(3):526–528. DOI:10.1093/bioinformatics/bty633.
   PubMed Web of Science ®Google Scholar
• Kassambara A, Mundt F. Factoextra: extract and visualize the results of multivariate data analyses [R package version 1.0.7]. Comprehensive R Archive Network (CRAN); 2020.
   Google Scholar
• Sokal R, Michener C. A statistical method for evaluating systematic relationships. University of Kansas Sci Bull. 1958;38:1409–1438.
   Google Scholar
• Warren DL, Glor RE, Turelli M. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution. 2008;62(11):2868–2883. DOI:10.1111/j.1558-5646.2008.00482.x.
   PubMed Web of Science ®Google Scholar
• Montano-Centellas FA. Interaction networks of avian mixed-species flocks along elevation in the tropical Andes. Ecography. 2020;43(6):930–942. DOI:10.1111/ecog.05135.
   Web of Science ®Google Scholar
• Lomolino MV, Riddle BR, Whittaker RJ, et al. Biogeography. Sunderland, MA: Sinauer Associates; 2006.
   Google Scholar
• Sales LP, Hayward MW, Loyola R. What do you mean by “niche”? Modern ecological theories are not coherent on rhetoric about the niche concept. Acta Oecologica. 2021;110:110. DOI:10.1016/j.actao.2020.103701.
   Web of Science ®Google Scholar
• Elton CS. Animal ecology. London, United Kingdom: Sidgwick & Jackson; 1927.
   Google Scholar
• Grinnell J. Geography and evolution. Ecology. 1924;5(3):225–229. https://www.jstor.org/stable/1929447.
   Google Scholar
• Chase JM, Leibold MA. Ecological niches: linking classical and contemporary approaches. Chicago: University of Chicago Press; 2003.
   Google Scholar
• MacArthur R, Levins R. Limiting similarity convergence and divergence of co-occurring species. Am Natur. 1967;101(921):377. https://www.jstor.org/stable/2459090.
   Web of Science ®Google Scholar
• Hutchinson GE. Concluding remarks. Cold Spring Harb Symp Quant Biol. 1957;22(0):415–427. Cold Spring Harbor Laboratory Press. DOI:10.1101/SQB.1957.022.01.039.
   Google Scholar
• Hubbell SP. The unified neutral theory of biodiversity and biogeography. New Jersey: Princeton University Press; 2001.
   Google Scholar
• Rosindell J, Hubbell SP, Etienne RS. The unified neutral theory of biodiversity and biogeography at age ten. Trends Ecol Evol. 2011;26(7):340–348. DOI:10.1016/j.tree.2011.03.024.
   PubMed Web of Science ®Google Scholar
• Gravel D, Canham C, Beaudet M, et al. Reconciling niche and neutrality: the continuum hypothesis. Ecol Lett. 2006;9(4):399–409. DOI:10.1111/j.1461-0248.2006.00884.x
   PubMed Web of Science ®Google Scholar
• Prum RO. Interspecific social dominance mimicry in birds. Zool J Linn Soc. 2014;172(4):910–941. DOI:10.1111/zoj.12192.
   Web of Science ®Google Scholar
• Cooper JC. Niche theory and its relation to morphology and phenotype in geographic space: a case study in woodpeckers (Picidae). J Avian Biol. 2018;49(10):e01771. DOI:10.1111/jav.01771.
   Web of Science ®Google Scholar
• Billerman SM, Keeney BK, Rodewald PG, et al. Birds of the World. Ithaca, NY, USA: Cornell Ornithology; 2020.
   Google Scholar
• Shipley B, Keddy P. The individualistic and community-unit concepts as falsifiable hypotheses. Vegetatio. 1987;69(1–3):47–55. DOI:10.1007/BF00038686.
   Google Scholar
• Olson DM, Dinerstein E, Wikramanayake ED, et al. Terrestrial ecoregions of the world: a new map of life on earth. BioScience. 2001;51(11):933–938. DOI:10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2
   Web of Science ®Google Scholar
• Dubay SG, Witt CC. Differential high-altitude adaptation and limited gene flow across a mid-elevation hybrid zone in birds. Mol Ecol. 2014;23(14):3551–3565. DOI:10.1111/mec.12836.
   PubMed Web of Science ®Google Scholar
• Lovette IJ, Hochachka WM. Simultaneous effects of phylogenetic niche conservatism and competition on avian community structure. Ecology. 2006;87(sp7):S14–28. DOI:10.1890/0012-9658(2006)87[14:seopnc]2.0.co;2.
   PubMedGoogle Scholar
• de Araujo CB, Marcondes-Machado LO, Costa GC. The importance of biotic interactions in species distribution models: a test of the Eltonian noise hypothesis using parrots. J Biogeogr. 2014;41(3):513–523. DOI:10.1111/j.1466-8238.2007.00359.x.
   Web of Science ®Google Scholar