On the methods to assess significance in nestedness analyses

Almeida-Neto M, Ulrich W (2010) A straightforward computational approach for quantifying nestedness using abundance data. Environ Modell Softw 26:173–178. doi: 10.1016/j.envsoft.2010.08.003

Almeida-Neto M, Guimarães P, Guimarães JPR, Loyola RD, Ulrich W (2008) A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos 117:1227–1239. doi: 10.1111/j.2008.0030-1299.16644.x

Atmar W, Patterson BD (1993) The measure of order and disorder in the distribution of species in fragmented habitat. Oecologia 96:373–382. doi: 10.1007/BF00317508

Atmar W, Patterson BD (1995) The nestedness temperature calculator: a visual basic program, including 294 presence–absence matrices. AICS Research, Inc., University Park, NM and The Field Museum, Chicago. http://www.aics-research.com/nestedness/tempcalc.html

Bascompte J, Jordano P, Melián CJ, Olesen JM (2003) The nested assembly of plant–animal mutualistic networks. P Natl Acad Sci USA 100:9383–9387. doi: 10.1073/pnas.1633576100

Baselga A (2010) Multiplicative partition of true diversity yields independent alpha and beta components, additive partition does not. Ecology 91:1974–1981. doi: 10.1890/09-0320.1

Bastolla U, Fortuna MA, Pascual-García A, Ferrera A, Luque B, Bascompte J (2009) The architecture of mutualistic networks minimizes competition and increases biodiversity. Nature 458:1018–1020. doi: 10.1038/nature07950

Carstensen DW, Olesen JM (2009) Wallacea and its nectarivorous birds: nestedness and modules. J Biogeogr 36:1540–1550. doi: 10.1111/j.1365-2699.2009.02098.x

Feng L, Yu G, Zhang XD (2007) Spectral radius of graphs with given matching number. Linear Algebra Appl 422:133–138. doi: 10.1016/j.laa.2006.09.014

Gotelli NJ, Entsminger GL (2001) Swap and fill algorithms in null model analysis: rethinking the knight’s tour. Oecologia 129:281–291. doi: 10.1007/s004420100717

Gotelli NJ, Ulrich W (2012) Statistical challenges in null model analysis. Oikos 121:171–180. doi: 10.1111/j.1600-0706.2011.20301.x

Graham SP, Hassan HK, Burkett-Cadena ND, Guyer C, Unnasch TR (2009) Nestedness of ectoparasite-vertebrate host networks. PLoS One 4:e7873. doi: 10.1371/journal.pone.0007873

Guimarães PR, Guimarães P (2006) Improving the analyses of nestedness for large sets of matrices. Environ Modell Softw 21:1512–1513. doi: 10.1016/j.envsoft.2006.04.002

Jonhson S, Domínguez-García V, Muñoz MA (2013) Factors determining nestedness in complex networks. PLoS One 8:e74025. doi: 10.1371/journal.pone.0074025

Krishna A, Guimarães PR, Jordano P, Bascompte J (2008) A neutral-niche theory of nestedness in mutualistic networks. Oikos 117:1609–1618. doi: 10.1111/j.1600-0706.2008.16540.x

Nielsen A, Bascompte J (2007) Ecological networks, nestedness and sampling effort. J Ecol 95:1134–1141. doi: 10.1111/j.1365-2745.2007.01271.x

Patterson BD, Atmar W (1986) Nested subsets and the structure of insular mammalian faunas and archipelagos. Biol J Linn Soc 28:65–82. doi: 10.1111/j.1095-8312.1986.tb01749.x

Podani J, Schmera D (2011) A new conceptual and methodological framework for exploring and explaining pattern in presence-absence data. Oikos 120:1625–1638. doi: 10.1111/j.1600-0706.2011.19451.x

Podani J, Schmera D (2013) A comparative evaluation of pairwise nestedness measures. Ecography 35:889–900. doi: 10.1111/j.1600-0587.2011.07319.x

Rezende EL, Lavabre JE, Guimarães PR, Jordano P, Bascompte J (2007) Non-random coextinctions in phylogenetically structured mutualistic networks. Nature 448:925–928. doi: 10.1038/nature05956

Staniczenko PPA, Kopp JC, Allesina S (2013) The ghost of nestedness in ecological networks. Nat Commun 4:1391. doi: 10.1038/ncomms2422

Strona G, Stefani F, Galli P, Fattorini S (2011) Reapproaching the centre of origin theory: a case study of siganid fishes (Actinistia: Siganidae). Vie Milieu 61:71–76

Strona G, Galli P, Fattorini S (2013a) Fish parasites resolve the paradox of missing coextinctions. Nat Commun 4:1718. doi: 10.1038/ncomms2723

Strona G, Stefani F, Galli P, Fattorini S (2013b) A protocol to compare nestedness among submatrices. Popul Ecol 55:227–239. doi: 10.1007/s10144-012-0343-4

Strona G, Galli P, Seveso D, Montano S, Fattorini S (2014) Nestedness for Dummies (NeD): a user friendly web interface for exploratory nestedness analysis. J Stat Soft (in press)

Ulrich W (2006) Nestedness––a FORTRAN program for calculating ecological matrix temperatures. http://www.uni.torun.pl/~ulrichw

Ulrich W, Almeida-Neto M (2012) On the meanings of nestedness: back to the basics. Ecography 35:865–871. doi: 10.1111/j.1600-0587.2012.07671.x

Ulrich W, Gotelli NJ (2007) Null model analysis of species nestedness patterns. Ecology 88:1824–1831. doi: 10.1890/06-1208.1

Ulrich W, Gotelli NJ (2012) A null model algorithm for presence–absence matrices based on proportional resampling. Ecol Model 244:20–27. doi: 10.1016/j.ecolmodel.2012.06.030

Ulrich W, Gotelli NJ (2013) Pattern detection in null model analysis. Oikos 122:2–18. doi: 10.1111/j.1600-0706.2012.20325.x

Ulrich W, Almeida-Neto M, Gotelli NG (2009) A consumer’s guide to nestedness analysis. Oikos 118:3–17. doi: 10.1111/j.1600-0706.2008.17053.x

Verdú M, Valiente-Banuet A (2008) The nested assembly of plant facilitation networks prevents species extinctions. Am Nat 172:751–760. doi: 10.1086/593003