Supplement 1. Software applications used to calculate the nestedness metrics of the present paper.

<h2>File List</h2><blockquote> <p><a href="matrix.zip">matrix.zip</a></p> <blockquote> <p>Contains files: </p> <p><a href="MatrixManual.pdf">MatrixManual.pdf</a><br> <a href="Mat.exe">Mat.exe</a><br> <a href="Matrix.exe">Matrix.exe</a><br> <a href="Mat.f90">Mat.f90</a><br> <a href="Matrix.f90">Matrix.f90</a> </p> </blockquote> <p><a href="nestedness.zip">nestedness.zip</a></p> <blockquote> <p>Contains files:</p> <p><a href="NestednessManual.pdf">NestednessManual.pdf</a><br> <a href="Nestedness.exe">Nestedness.exe</a><br> <a href="Nestedness.f90">Nestedness.f90</a></p> </blockquote> </blockquote><h2>Description</h2><blockquote> <p>The files contain software applications and descriptions (pdf files) of the nestedness and the matrix programs. Source code is written in MS Fortran 90. </p> </blockquote

Supplement 1. Data matrices and source codes of the software used in the paper.

<h2>File List</h2><blockquote> <p><a href="Matrices.txt">Matrices.txt</a></p> <p><a href="SourceCodes.txt">SourceCodes.txt</a></p> </blockquote><h2>Description</h2><blockquote> <p>Matrices.txt contains raw data and references to 185 real abundance matrices used in the present paper. SourceCodes.txt consists of source code of Matrix.exe and CoOcurrence.exe. </p> </blockquote

Appendix C. Statistical methods.

Statistical methods

Appendix B. Sampling methods.

Sampling methods

Appendix A. Physical characteristics of the study sites.

Physical characteristics of the study sites

Appendix E. Presence-absence matrices for bog and forest ants.

Presence-absence matrices for bog and forest ants

Appendix A. A summary of data used in the meta-analysis.

A summary of data used in the meta-analysis

Appendix A. Analytic estimators for rarefaction (interpolation) of Hill numbers of order q = 0, q = 1, and q = 2, given a reference sample.

Analytic estimators for rarefaction (interpolation) of Hill numbers of order q = 0, q = 1, and q = 2, given a reference sample

20151211_insect_hsc70-4_tree_alignment

This is a nexus file with an amino acid alignment and maximum likelihood(PhyML) phylogenetic reconstruction of hsc70-4 for 17 insect species

20151211_insect_hsp40_tree_alignment

This is a nexus file with an amino acid alignment and maximum likelihood(PhyML) phylogenetic reconstruction of hsp40 for 17 insect species