A comparison of hull methods for estimating species ranges and richness maps

References

• Alcantara S. 2010. Evolução da morfologia floral e estrutura de comunidade em um clado de lianas tropicais (Bignonieae, Bignoniaceae) [Ph.D. thesis]. São Paulo: Universidade de São Paulo.
   Google Scholar
• Alcantara S, Oliveira FG, Lohmann LG. 2013. Phenotypic integration in flowers of neotropical lianas: diversification of form with stasis of underlying patterns. Journal of Evolutionary Biology 26:2283–2296.
   PubMed Web of Science ®Google Scholar
• Alcantara S, Ree RH, Martins FR, Lohmann LG. 2014. The effect of phylogeny, environment and morphology on communities of a lianescent clade (Bignonieae, Bignoniaceae) in Neotropical biomes. Plos One 9:e90177.
   PubMed Web of Science ®Google Scholar
• Ballesteros-Mejia L, Kitching IJ, Jetz W, Nagel P, Beck J. 2013. Mapping the biodiversity of tropical insects: species richness and inventory completeness of African sphingid moths. Global Ecology and Biogeography 22:586–595.
   Web of Science ®Google Scholar
• Belmaker J, Jetz W. 2011. Cross-scale variation in species richness–environment associations. Global Ecology and Biogeography 20:464–474.
   Web of Science ®Google Scholar
• Bini LM, Diniz-Filho JAF, Rangel TFLVB, Bastos RP, Pinto MP. 2006. Challenging Wallacean and Linnean shortfalls: knowledge gradients and conservation planning in a biodiversity hotspot. Diversity and Distributions 12:475–482.
   Web of Science ®Google Scholar
• Bivand R, Rundel C, Pebesma E, Stuetz R, Hufthmmer O. 2016. Rgeos: interface to geometry engine – open source (GEOS). R package 0.3-21 [Internet]. Available online at: https://CRAN.R-project.org/package=rgeos (accessed 1 June 2016).
   Google Scholar
• Bombi P, Luiselli L, D’Amen M. 2011. When the method for mapping species matters: defining priority areas for conservation of African freshwater turtles. Diversity and Distributions 17:581–592.
   Web of Science ®Google Scholar
• Braga RT, Grande TO, Barreto BS, Diniz-Filho JAF, Terribile LC. 2014. Elucidating the global elapid (Squamata) richness pattern under metabolic theory of ecology. Acta Oecologica 56:41–46.
   Web of Science ®Google Scholar
• Burgman MA, Fox JC. 2003. Bias in species range estimates from minimum convex polygons: implications for conservation and options for improved planning. Animal Conservation 6:19–28.
   Web of Science ®Google Scholar
• Capinha C, Pateiro-López B. 2014. Predicting species distributions in new areas or time periods with alpha-shapes. Ecological Informatics 24:231–237.
   Web of Science ®Google Scholar
• Chapman AD, Wieczorek J. 2006. Guide to best practices for georeferencing. Copenhagen: Global Biodiversity Information Facility.
   Google Scholar
• Cressie NAC. 1993. Statistics for spatial data analysis. New York (NY): John Wiley & Sons.
   Google Scholar
• Diniz-Filho JAF, Bastos RP, Rangel TFLVB, Bini LM, Carvalho P, Silva RJ. 2005. Macroecological correlates and spatial patterns of anuran description dates in the Brazilian Cerrado. Global Ecology and Biogeography 14:469–477.
   Web of Science ®Google Scholar
• Diniz-Filho JAF, Bini LM, Vieira CM, Blamire D, Terribile LC, Bastos RP, Oliveira G, Barreto BS. 2008. Spatial patterns of terrestrial vertebrate species richness in the Brazilian Cerrado. Zoological Studies 47:146–157.
   Web of Science ®Google Scholar
• Diniz-Filho JAF, Tôrres NM. 2002. Phylogenetic comparative methods and the geographic range size – body size relationship in new world terrestrial carnivore. Evolutionary Ecology 16:351–367.
   Web of Science ®Google Scholar
• Edelsbrunner H, Kirkpatrick DG, Seidel R. 1983. On the shape of a set of points in the plane. Transactions on Information Theory 29:551–559.
   Web of Science ®Google Scholar
• Field R, Hawkins BA, Cornell HV, Currie DJ, Diniz-Filho JAF, Guágan JF, Kaufman DM, Kerr JT, Mittelbach GG, Oberdorff T, et al. 2009. Spatial species-richness gradients across scales: a meta-analysis. Journal of Biogeography 36:132–147.
   Web of Science ®Google Scholar
• Fonseca LHM. 2017. Filogenia, sistemática e evolução de Adenocalymma (Bignonieae, Bignoniaceae) [Ph.D. thesis]. São Paulo: Universidade de São Paulo.
   Google Scholar
• Fonseca LHM, Cabral SM, Agra MF, Lohmann LG. 2015. Taxonomic updates in Dolichandra Cham. (Bignonieae, Bignoniaceae). Phytokeys 46:35–43.
   Web of Science ®Google Scholar
• Fonseca LHM, Cabral SM, Agra MF, Lohmann LG. 2017. Taxonomic revision of Dolichandra (Bignonieae, Bignoniaceae). Auckland: Magnolia Press.
   Google Scholar
• Fonseca LHM, Zuntini AR, Lohmann LG. 2016. Two new species of Adenocalymma (Bignonieae, Bignoniaceae) from the Atlantic Forest of Brazil. Phytotaxa 284:263–272.
   Web of Science ®Google Scholar
• Gaston KJ. 2003. The structure and dynamics of geographic ranges. Oxford (UK): Oxford University Press.
   Google Scholar
• Gentry AH. 1991. The distribution and evolution of climbing plants. In: Putz F, Mooney H, editors. The biology of vines. Cambridge (UK): Cambridge University Press. p. 3–52.
   Google Scholar
• Gomes BM. 2006. Revisão de Pleonotoma Miers (Bignonieae, Bignoniaceae) [Master’s dissertation]. Brasília: Universidade de Brasília.
   Google Scholar
• Gotelli NJ, Colwell RK. 2010. Estimating species richness. In: Magurran AE, McGill BJ, editors. Biological diversity: frontiers in measurement and assessment. Oxford (UK): Oxford University Press. p. 39–54.
   Google Scholar
• Graham CH, Hijmans RJ. 2006. A comparison of methods for mapping species ranges and species richness. Global Ecology and Biogeography 15:578–587.
   Web of Science ®Google Scholar
• Hawkins BA, Diniz-Filho JAF, Bini LM, De Marco P, Blackburn TM. 2007b. Red herrings revisited: spatial autocorrelation and parameter estimation in geographical ecology. Ecography 30:375–384.
   Web of Science ®Google Scholar
• Hawkins BA, Diniz-Filho JAF, Jaramillo CA, Soeller SA. 2007a. Climate, niche conservatism, and the global bird diversity gradient. The American Naturalist 170:S16–S27.
   PubMed Web of Science ®Google Scholar
• Hawkins BA, Field R, Cornell HV, Currie DJ, Guégan JF, Kaufman DM, Kerr JT, Mittelbach GG, Oberdorff T, O’Brien EM, et al. 2003. Energy, water, and broad-scale geographic patterns of species richness. Ecology 84:3105–3117.
   Web of Science ®Google Scholar
• Hopkins MJG. 2007. Modelling the known and unknown plant biodiversity of the Amazon basin. Journal of Biogeography 34:1400–1411.
   Web of Science ®Google Scholar
• Hortal J, Belo F, Diniz-Filho JAF, Lewinsohn TM, Lobo JM, Ladle RJ. 2015. Seven shortfalls that beset large-scale knowledge of biodiversity. The Annual Review of Ecology, Evolution, and Systematics 46:523–549.
   Web of Science ®Google Scholar
• [IUCN] International Union for Conservation of Nature. 2014.
   Google Scholar
• Kaehler M 2011. Revisão taxonômica, filogenia, evolução e biogeografia de Lundia DC. (Bignonieae, Bignoniaceae) [Ph.D. thesis]. São Paulo: Universidade de São Paulo.
   Google Scholar
• Kaehler M, Michelangeli FA, Lohmann LG. 2012. Phylogeny of Lundia (Bignoniaceae) based on ndhF and PepC sequences. Taxon 61:368–380.
   Web of Science ®Google Scholar
• Legendre P. 1993. Spatial autocorrelation: trouble or new paradigm? Ecology 74:1659–1673.
   Web of Science ®Google Scholar
• Legendre P, Dale MRT, Fortin MJ, Gurevitch J, Hohn M, Myers D. 2002. The consequences of spatial structure for the design and analysis of ecological field surveys. Ecography 25:601–615.
   Web of Science ®Google Scholar
• Lobo JM, Baselga A, Hortal J, Jiménez-Valverde A, Gómez JF. 2007. How does the knowledge about the spatial distribution of Iberian dung beetle species accumulate over time? Diversity and Distributions 13:772–780.
   Web of Science ®Google Scholar
• Lohmann LG. 2006. Untangling the phylogeny of neotropical lianas (Bignonieae, Bignoniaceae). American Journal of Botany 93:304–318.
   PubMed Web of Science ®Google Scholar
• Lohmann LG, Bell CD, Calió MF, Winkworth RC. 2013. Pattern and timing of biogeographical history in the neotropical tribe Bignonieae (Bignoniaceae). Botanical Journal of the Linnean Society 171:154–170.
   Web of Science ®Google Scholar
• Lohmann LG, Taylor CM. 2014. A new generic classification of tribe Bignonieae (Bignoniaceae). Annals of the Missouri Botanical Garden 99:348–489.
   Web of Science ®Google Scholar
• Loiselle BA, Jorgensen P, Consiglio T, Jiménez I, Blake JB, Lohmann LG, Montiel OM. 2008. Predicting species distributions from herbarium collections: does climate bias in collection sampling influence model outcomes? Journal of Biogeography 35:105–116.
   Web of Science ®Google Scholar
• Mata RA, Tidon R, Oliveira G, Vilela B, Diniz-Filho JAF, Rangel TFLVB, Terribile LC. 2017. Stacked species distribution and macroecological models provide incongruent predictions of species richness for Drosophilidae in the Brazilian savanna. Insect Conservation and Diversity 10:415–424.
   Web of Science ®Google Scholar
• Medeiros MCMP, Lohmann LG. 2014. Two new species of Tynanthus Miers (Bignonieae, Bignoniaceae) from Brazil. Phytokeys 42:77–85.
   Web of Science ®Google Scholar
• Medeiros MCMP, Lohmann LG. 2015a. Phylogeny and biogeography of Tynanthus Miers (Bignonieae, Bignoniaceae). Molecular Phylogenetics and Evolution 85:32–40.
   PubMed Web of Science ®Google Scholar
• Medeiros MCMP, Lohmann LG. 2015b. Taxonomic revision of Tynanthus (Bignonieae, Bignoniaceae). Phytotaxa 216:1–60.
   Web of Science ®Google Scholar
• Meyer C, Jetz W, Guralnick RP, Fritz SA, Kreft H. 2016. Range geometry and socio-economics dominate species-level biases in occurrence information. Global Ecology and Biogeography 25:1181–1193.
   Web of Science ®Google Scholar
• Morueta-Holme N, Enquist BJ, McGill BJ, Boyle B, Jørgensen PM, Ott JE, Peet RK, Símová I, Sloat LL, Thiers B, et al. 2013. Habitat area and climate stability determine geographical variation in plant species range sizes. Ecology Letters 16:1446–1454.
   PubMed Web of Science ®Google Scholar
• Nogueira A, Rey PJ, Alcántara JM, Feitosa RM, Lohmann LG. 2015. Geographic mosaic of plant evolution: extrafloral nectary variation mediated by ant and herbivore assemblages. Plos One 10:e0123806.
   PubMed Web of Science ®Google Scholar
• O’Brien EM. 2006. Biological relativity to water–energy dynamics. Journal of Biogeography 33:1868–1888.
   Web of Science ®Google Scholar
• Oliveira U, Paglia AP, Brescovit AD, Carvalho CJB, Silva DP, Rezende DT, Leite FSF, Batista JAN, Barbosa JPPP, Stehmann JR, et al. 2016. The strong influence of collection bias on biodiversity knowledge shortfalls of Brazilian terrestrial biodiversity. Diversity and Distributions 22:1232–1244.
   Web of Science ®Google Scholar
• Osorio F, Vallejos R. 2014. SpatialPack: package for analysis of spatial data. R package version 0.2-3 [Internet]. Available online at: http://cran.r-project.org/package=SpatialPack (accessed 1 June 2016)..
   Google Scholar
• Pace MR, Alcantara S, Lohmann LG, Angyalossy V. 2015. Secondary phloem diversity and evolution in Bignonieae (Bignoniaceae). Annals of Botany 116:333–358.
   PubMed Web of Science ®Google Scholar
• Pateiro-López B, Rodríguez-Casal A. 2010. Alphahull: generalization of the convex hull of a sample of points in the plane. R package 2.1 [Internet]. Available online at: https://CRAN.R-project.org/package=alphahull (accessed 1 June 2016).
   Google Scholar
• Pateiro-López B, Rodríguez-Casal A. 2016. Alphahull: generalization of the convex hull of a sample of points in the plane. R package 2.1.
   Google Scholar
• Pena JCC, Kamino LHY, Rodrigues M, Mariano-Neto E, Siqueira MF. 2014. Assessing the conservation status of species with limited available data and disjunct distribution. Biological Conservation 170:130–136.
   Web of Science ®Google Scholar
• Pereira MJ, Palmeirim JM. 2013. Latitudinal diversity gradients in new world bats: are they a consequence of niche conservatism? Plos One 8:e69245.
   PubMed Web of Science ®Google Scholar
• Pool A. 2007a. A revision of the genus Pithecoctenium (Bignoniaceae). Annals of the Missouri Botanical Garden 94:622–642.
   Web of Science ®Google Scholar
• Pool A. 2007b. A revision of the genus Distictis (Bignoniaceae). Annals of the Missouri Botanical Garden 94:791–820.
   Google Scholar
• Pool A. 2008. A revision of the genus Pyrostegia (Bignoniaceae). Annals of the Missouri Botanical Garden 95:495–510.
   Web of Science ®Google Scholar
• Pool A. 2009. A revision of the genus Distictella (Bignoniaceae). Annals of the Missouri Botanical Garden 96:286–323.
   Web of Science ®Google Scholar
• Qian H, Wiens JJ, Zhang J, Zhang Y. 2014. Evolutionary and ecological causes of species richness patterns in North American angiosperm trees. Ecography 37:1–10.
   Google Scholar
• Raedig C, Kreft H. 2011. Influence of different species range types on the perception of macroecological patterns. Systematics and Biodiversity 9:159–170.
   Web of Science ®Google Scholar
• Rocchini D, Hortal J, Lengyel S, Lobo JM, Valverde AJ, Ricotta C, Baraco G, Chiarucci A. 2011. Accounting for uncertainty when mapping species distributions: the need for maps of ignorance. Progress in Physical Geography 35:211–226.
   Web of Science ®Google Scholar
• Roque FO, Zampiva NK, Valente-Neto F, Menezes JFS, Hamada N, Pepinelli M, Siqueira T, Swan C. 2016. Deconstructing richness patterns by commonness and rarity reveals bioclimatic and spatial effects in black fly metacommunities. Freshwater Biology 61:923–932.
   Web of Science ®Google Scholar
• R Core Team. 2017. R: A language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
   Google Scholar
• Scheiner SM. 2003. Six types of species-area curves. Global Ecology and Biogeography 12:441–447.
   Web of Science ®Google Scholar
• Schnitzer SA, Mangan SA, Dalling JW, Baldeck CA, Hubbell SP, Ledo A, Muller-Landau H, Tobin MF, Aguilar S, Brassfield D, et al. 2012. Liana abundance, diversity, and distribution on Barro Colorado Island, Panama. Plos One 7:e52114.
   PubMed Web of Science ®Google Scholar
• Schulman L, Toivonen T, Ruokolainen K. 2007. Analysing botanical collecting effort in Amazonia and correcting for it in species range estimation. Journal of Biogeography 34:1388–1399.
   Web of Science ®Google Scholar
• Sheth SN, Lohmann LG, Consiglio T, Jiménez I. 2008. Effects of detectability on estimates of geographic range size in Bignonieae. Conservation Biology 22:200–211.
   PubMed Web of Science ®Google Scholar
• Silva-Castro MM. 2010. Estudos taxonômicos, filogenéticos e biossistemáticos em Mansoa DC. (Bignonieae - Bignoniaceae) [Ph.D. thesis]. Feira de Santana: Universidade Estadual de Feira de Santana.
   Google Scholar
• Sokal RR, Rohlf FJ. 1995. Biometry: the principles and practice of statistics in biological research. New York (NY): WH Freeman.
   Google Scholar
• Sousa-Baena MS, Sinha NR, Lohmann LG. 2014. Evolution and development of tendrils in Bignonieae (Lamiales, Bignoniaceae). Annals of the Missouri Botanical Garden 99:323–347.
   Web of Science ®Google Scholar
• Terribile LC, Diniz-Filho JAF, Rodríguez MA, Rangel TFLVB. 2009. Richness patterns, species distributions and the principle of extreme deconstruction. Global Ecology and Biogeography 18:123–136.
   Web of Science ®Google Scholar
• Tomašových A, Jablonski D. 2016. Decoupling of latitudinal gradients in species and genus geographic range size: a signature of clade range expansion. Global Ecology and Biogeography 26:288–303.
   Web of Science ®Google Scholar
• Trabucco A, Zomer RJ. 2010. Global soil water balance geospatial database [Internet]. Available online at: http://www.cgiar-csi.org/ (accessed 1 June 2017).
   Google Scholar
• Tsianou MA, Koutsias N, Mazaris AD, Kallimanis AS. 2016. Climate and landscape explain richness patterns depending on the type of species’ distribution data. Acta Oecologica 74:19–27.
   Web of Science ®Google Scholar
• Whittaker RJ, Willis KJ, Field R. 2001. Scale and species richness: towards a general, hierarchical theory of species diversity. Journal of Biogeography 28:453–470.
   Web of Science ®Google Scholar
• Zuntini AR. 2015. Revisão, filogenia e biogeografia de Bignonia L. (Bignoniaceae) [Ph.D. thesis]. São Paulo: Universidade de São Paulo.
   Google Scholar
• Zuntini AR, Lohmann LG, Taylor CM. 2015a. problematic specimens turn out to be two undescribed species of bignonia (bignoniaceae). Phytokeys 56:7–18.
   Web of Science ®Google Scholar
• Zuntini AR, Taylor CM, Lohmann LG. 2015b. Deciphering the neotropical Bignonia binata species complex (Bignoniaceae). Phytotaxa 219:69–77.
   Web of Science ®Google Scholar