An example of the method used to calculate proportion sapstain cover.

<p>All cut faces (sections) had their proportion of stain cover digitally calculated. (A) shows the entire face of one <i>Pinus radiata</i> cut log section divided into six segments (a–f), and (B) shows a single segment extracted and digitally converted to a bitmap of relative colour intensity, in order to determine proportion sapstain coverage (in this case 0.944 cover of a 214151.04 pixel segment).</p

Comparison of stain distribution per segment between caged and uncaged logs.

<p>Mean sapstain percentage for <i>Pinus radiata</i> log segments (A–F), separated by section along the length of the log for both caged and uncaged logs. Error bars are ± one standard error of the mean.</p

Beetle colonisation and sapstain development in caged versus uncaged logs.

<p>Comparison of average sapstain intensity for (A) uncaged and (B) caged <i>Pinus radiata</i> experimental logs, as well as the corresponding bark beetle (<i>Hylastes ater</i> and <i>Hylurgus ligniperda</i>) colonisation intensity for the same (C) uncaged and (D) caged logs (n = 20 experimental logs in each case). The radial angle of the segment indicates the spatial orientation of the log, with 180° representing the point of ground contact, as indicated by the dashed line. Bark beetle attack intensity is measured as the frequency of attack across logs.</p

Schematic illustration of sampling areas on the experimental logs.

<p>All logs were assessed for bark beetle, other arthropod and sapstain colonisation. Numbers 1 to 8 indicate log sections (cuts are the dashed lines dividing the sections), and letters A to F indicate log segments within each section of the experimental <i>Pinus radiata</i> logs. The two outer sections, where sapstain penetration was expected to be greatest, were cut 20 mm thick, and the remaining length of log was divided into six equal-sized sections (ideally 77 mm, but varying from 75–79 mm, depending on variability between individual logs and individual section-cuts). The entire outer surface of the log was divided into discrete areas (1_A to 8_F) where arthropod colonisation was recorded.</p

Model input data

Data used on model regression, comprising: exotic tree species; phylogenetic relatedness to European native species, geographic distribution and time since introduction; number of native insects expressed in different terms

Supplement 1. Script for the hierarchical model coded in BUGS language and technical specifications.

<h2>File List</h2><div> <p><a href="hierarchical_model_NZ_birds.r">hierarchical_model_NZ_birds.r</a> (MD5: eeeb5ac11c7e8ceacd5bd6fc67d14473)</p> <p>Script for the hierarchical model coded in BUGS language.</p> </div><h2>Description</h2><div> <p>This supplement provides the code of the hierarchical model used in the main analyses. This code can be directly implemented in any BUGS software, although JAGS has proved the most efficient. The code is intended to be easily transferable to similar data sets.</p> <p>Technical specifications for the main text analyses: three chains of 250 000 iterations were run, plus an adaptation period of 1000 iterations. A burnin period of 125 000 iterations was discarded, the remaining 125 000 were used for inference after thinning by 100. These chains took 15 days to run on a server with the following characteristics:</p> <p>CPU: 2 x Intel Xeon X5670 2.93 GHz<br> RAM: 48 GB<br> Operating system: Microsoft Server 2008 - 64bit<br> Disk-capacity: 3.63 TB ( 2 x 2 TB disks in RAID-0 configuration) </p> <p>The data need to be formatted as follows: </p> <p>obs: a three-dimensional array [sites, replicates, species] for bird counts;</p> <p>FOR, NATFOR, ALT, YR, VH, HOUR, HOUR2, HDET, SUBZON, TYH, OBSERV , ST: vectors for covariates, each with one value per site. HOUR2 corresponds to HOUR*HOUR. All continuous variables should be centered and scaled to improve convergence;</p> <p>S: the number of species;</p> <p>R: the number of sites;</p> <p>K: the number of replicates;</p> <p>nobs: the number of different observers;</p> <p>nsubzone: the number of regions;</p> <p>nyear: the number of survey years;</p> <p>NST: the number of guilds (here two, exotic and natives);</p> <p>NTYH: the number of different local habitats.</p> </div

Appendix L. Optimized trapping densities and numbers for sensitivity analyses.

Optimized trapping densities and numbers for sensitivity analyses

Appendix A. Summary of parameters.

Summary of parameters

Appendix E. Invader population growth.

Invader population growth

Appendix B. Details on the autoregressive component accounting for nonindependent temporal replicates when modeling detection probability.

Details on the autoregressive component accounting for nonindependent temporal replicates when modeling detection probability