Network data, Dynamic simulation code, and Statistical analysis code

Network data, Dynamic simulation code, and Statistical analysis cod

Interaction data, phylogenies, and analysis code for paco

Data on the Mendoza pollination network analysed with paco. Phylogenies of both plants and pollinators as well as their interaction network are included. There is also an R script for the analyses. Please note that the interaction network was originally published by Arroyo, M. T. K., Primack, R. B. & Armesto, J. J. (Community studies in pollination ecology in the high temperate Andes of central Chile. I. Pollination mechanisms and altitudinal variation, 1982). The version here has been cleaned to remove unidentified species and to confirm species names are correct

R code for carrying capacities from Native turncoats and indirect facilitation of species invasions

R code for algorithm to define a vector of carrying capacities to allow coexistence of native species

Supplemental figures from Native turncoats and indirect facilitation of species invasions

Supplemental figures showing variation in the number of species and resources separately, and their influence on invasion probability and interaction strength

Food web data for seven coastal food webs with metazoan parasites

Food web data for seven coastal food webs with metazoan parasite

Images of three trophic species versions of the food web of Estero de Punta Banda.

<p>(A) Web with free-living species only. (B) Web with parasite species but not concomitant predation links. (C) Web with parasite species and concomitant links. Green indicates basal taxa, red indicates free-living taxa, and blue indicates parasites. The vertical axis corresponds to short-weighted trophic level <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001579#pbio.1001579-Williams7" target="_blank">[94]</a>. The maximum trophic levels for a taxon in each web are 3.77 (A), 5.68 (B), and 7.16 (C). Images produced with Network3D software <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001579#pbio.1001579-Yoon1" target="_blank">[95]</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001579#pbio.1001579-Williams8" target="_blank">[96]</a>, available by request from [email protected].</p

Visualization of trophic niches of species in Estero de Punta Banda food webs.

<p>MLE values for consumer niche position (<i>c</i>) are on the <i>x</i>-axis and for resource niche value (<i>n</i>) are on the <i>y</i>-axis. (A) Results for the web with free-living species only. (B) Results for the web with parasites but not concomitant links. (C) Results for the web with parasites and concomitant links. Red dots show the resource links for free-living consumers, and blue dots show the resource links for parasite consumers.</p

Scale dependence of MaxEnt model results.

<p>Relative width (<i>W</i>₉₅) of the consumer distribution in relation to MaxEnt expectations, as a function of (A) <i>L/S</i> (links per species), and (B) <i>C</i> (directed connectance; <i>L/S</i>²). Solid black circles show results for 28 previously studied free-living species webs (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001579#pbio.1001579.s012" target="_blank">Table S5</a>). Open black circles show results for the seven coastal free-living species webs analyzed in the current study. Red diamonds show results for the seven coastal webs with parasites but not concomitant links. Blue diamonds show results for the seven coastal webs with parasites and concomitant links. The black line shows the linear regression through the 35 free-living species webs.</p

Basic properties of trophic species food webs.

<p>Fals, Carp, Punt, Flens, Otag, Sylt, and Ythan refer to the food webs for Bahia Falsa, Carpinteria Salt Marsh, Estero de Punta Banda, Flensburg Fjord, Otago Harbor, Sylt Tidal Basin, and Ythan Estuary, respectively. “Free” refers to webs with free-living species only; “Par” refers to webs with parasites but not concomitant links; “ParCon” refers to webs with parasites and concomitant links. <i>S</i>, <i>L</i>, <i>L/</i>S, C, and <i>C</i>_adj are defined in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001579#pbio-1001579-t001" target="_blank">Table 1</a> (Metrics 1–5). <i>S</i>_Free, <i>S</i>_Par, and <i>S</i>_Bas refer to the fraction of taxa that are free-living, parasite, and basal, respectively.</p

Linear regressions for scale dependence of model results.

<p>The <i>R</i>², <i>p</i>-values, and slopes for linear regressions of the dependent variables <i>W</i>_{95 Cons} (width of the consumer resource distribution in relation to MaxEnt expectations), |ME| (absolute value of the average niche ME), and <i>f</i>_L (fraction of links correctly predicted by a one-dimensional probabilistic niche model), as a function of the explanatory variables <i>S</i>, <i>L</i>, <i>L/S</i>, and <i>C</i> (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001579#pbio-1001579-t001" target="_blank">Table 1</a>, Metrics 1–4). Each regression includes the seven free-living species webs currently analyzed and 28 (<i>W</i>_{95 Cons}, <i>f</i>_L) or ten (|ME|) additional food webs (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001579#pbio.1001579.s012" target="_blank">Table S5</a>). Regressions that are significant at a Bonferroni-corrected (<i>n</i> = 4) <i>p</i>-value of 0.0125 are shown in bold.</p