Estimates from binomial General Lin- ear Modeling.

<p>Parameter estimates are given on the scale of the model (logits). Exponentiating these terms will convert these estimates to log- odds.</p>†<p>significant at <i>p</i><.10; * <i>p</i><.05; ** <i>p</i><.01; *** <i>p</i><.001.</p>‡<p>the reference category for the Density treatment is five oysters.</p>§<p>the reference category for the Caging treatment is un-caged.</p

Proportional survival of transplanted oysters as a function of density, species, size and caging.

<p>Replicate numbers are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090621#pone-0090621-t001" target="_blank">Table 1</a>. Error bars represent two S.E around the mean.</p

Storm activity and human tampering reduced the number of replicates in this experiment.

<p>Numbers of plots remaining for each treatment combination are presented below.</p

Analysis of Deviance, testing the contribution of each component to the overall model.

<p>Presented is the optimal model only. Terms found not to contribute are not included.</p

Supplement 1. C++ source code containing the algorithms described in this paper and a short description of the program and its options.

<h2>File List</h2><div> <p> </p> <p><a href="paradox.h">paradox.h</a> - header file with main classes and variables<br> (md5: 8743b417ec45676fa1b881038616e806)<br> <a href="paradox.cpp">paradox.cpp</a> - source code dedicated to input and calling relevant functions in 'details.cpp'<br> (md5: 64ed736f2675a05fe8f124362b772bcb)<br> <a href="details.cpp">details.cpp</a> - main source code<br> (md5: 2dd2dcf4612efb0d574982a224e97dcd)<br> <a href="input_params.csv">input_params.csv</a> - initialization parameters<br> (md5: d305d8686a6494a619525f02fdda6220)<br> <a href="readme.txt">readme.txt</a> - description of source code<br> </p></div><h2>Description</h2><div> <p>Code to generate community dynamics to examine changes in the correlations between native and exotic species over time. Additional information is provided in the readme.txt file. Code was written by B. Leung, to whom correspondence regarding these files should be addressed. </p> </div

Percent cover and richness of algae sampled on vertical surfaces of artificial and natural habitats and horizontal reef.

<p>Non-indigenous algae sampled from (a, e) vertical surfaces of habitats and (b, f) horizontal reef and native algae sampled from (c, g) vertical surfaces of habitats and (d, h) horizontal reef. In-situ sampling was conducted at four sites in 2006 and 2007. Individual bars represent sites ordered BA, FT, GB and CL from left to right. Sampling years (06/07) are indicated above the bars. Percent covers for horizontal reef were sampled in a separate survey at three sites at five sampling times (Jan 07, Apr 07, Sep 07, Mar 08, Jun 08). Individual bars represent sites ordered BA, FT, GB from left to right for each sampling time.</p

The Role of Habitat Complexity in Community Development Is Mediated by Resource Availability

<div><p>Habitat complexity strongly affects the structure and dynamics of ecological communities, with increased complexity often leading to greater species diversity and abundance. However, habitat complexity changes as communities develop, and some species alter their environment to themselves provide habitat for other species. Most experimental studies manipulate basal substrate complexity, and while the importance of complexity likely changes during community development, few studies have examined the temporal dynamics of this variable. We used two experiments to quantify the importance of basal substrate complexity to sessile marine invertebrate community development through space and time. First, we compared effects of substrate complexity at 70 sites across ten estuaries. Sites differed in recruitment and community development rates, and after three months provided spatial variation in community development stage. Second, we tested for effects of substrate complexity at multiple times at a single site. In both experiments, complexity affected marine sessile invertebrate community composition in the early stages of community development when resource availability was high. Effects of complexity diminished through time as the amount of available space (the primary limiting resource) declined. Our work suggests the presence of a bare-space threshold, at which structural complexity of the basal substrate is overwhelmed by secondary biotic complexity. This threshold will be met at different times depending on local recruitment and growth rates and is likely to vary with productivity gradients.</p></div

Sediment and light intensity collected during deployment of experimental “reef”.

<p>(a) Sediment (g/dry weight) was collected from individual plates prior to final collection of plates and (b) light (lux) was sampled above the plates with loggers for 28 days during the experiment. The averages are presented for each measure and bars are separated by (a) orientation (horizontal or vertical) and assemblage (new or established) and (a/b) coded for shading treatment (unshaded, shade control or shaded).</p

PERMANOVA results comparing non-indigenous and native invertebrate species percent cover and richness sampled from artificial and natural habitats.

<p>Non-indigenous invertebrate a) percent cover and b) species richness, native invertebrate c) percent cover and d) species richness compared between vertical surfaces of artificial (pilings and pontoons) and natural (reef) habitats. Habitats were sampled at twice at 4 sites. Significant results (p<0.05) are indicated in bold.</p

Appendix A. Parameter values used in simulation models and methods for their derivation.

Parameter values used in simulation models and methods for their derivation