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

Neutral colonisations drive high beta-diversity in cavernicole springtails (Collembola)

<div><p>The theory of island biogeography predicts the effects of habitat isolation and size on species richness, community assembly, and the persistence of species. Various studies showed that habitat conditions and the ecology of species are also of relevance in explaining community assembly. Geographically isolated habitats like caves with rather constant environmental conditions provide models to test for the relevance of the above described variables. In this study we analysed springtails living in karst caves of the Romanian Carpathians and Dobrogea region. We considered phylogenetic relatedness, habitat and species characteristics to identify the relevant drivers of community assembly. Our data show that species richness of single caves is low. Neither phylogenetic relatedness nor habitat filtering and competitive interactions seem to shape species composition or to affect species richness. We found that glacial-interglacial cycles with subsequent range contractions and expansions might have led to independent and multiple colonisations of caves. Furthermore, single caves might have acted as refugia and thus might have provided the prerequisite for distinct evolution processes, leading to a high level of endemicity of these animal species.</p></div

Additional file 1: of Evolution of contact and alarm calls in the Kenyan endemic Hinde’s babbler (Aves: Passeriformes)

Numbers of classification within each family of a k-means clustering of contact calls. Colors coincide with the colors given in the main text. Raw data (wav-files) of bird calls recorded and analyzed are available at figshare.com, https://figshare.com/s/ab27b9a4c1aca6897825 . (DOCX 144 kb

The net relatedness index (NRI) of local springtail assemblages was weakly positively related to cave species richness (P < 0.01; Table 1) but did not deviate from random expectation (equiprobable null model) that expects NR values < |2.0| at the two-sided 5% error level.

<p>The net relatedness index (NRI) of local springtail assemblages was weakly positively related to cave species richness (P < 0.01; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0189638#pone.0189638.t001" target="_blank">Table 1</a>) but did not deviate from random expectation (equiprobable null model) that expects NR values < |2.0| at the two-sided 5% error level.</p

Local species richness of Romanian cave dwelling springtails increased significantly with cave length (permutation r² = 0.13, P < 0.001), cave depth (r² = 0.06, P < 0.01), but not with cave altitude (P < 0.1).

<p>Data from 189 caves.</p

General linear modelling (given are partial η² values) indicated cave length to be positively (indicated by the + sign) associated with local cave-dwelling springtail species richness (α-diversity).

<p>The dominant eigenvector of the cave Euclidean distance matrix (EV1) served as covariate to account for possible spatial non-independence of richness and phylogenetic relatedness. The net relatedness index increased with richness and decreased with geographical distance of caves. N = 189.</p

An inverse elevational species richness gradient of Caucasian vascular plants and Encyrtidae (Hymenoptera, Chalcidoidea)

<p>The elevational gradient in biodiversity, i.e. the decrease in species richness with increasing altitude, is well established in ecology. Here, we examined the respective gradient of parasitic hymenopterans (Encyrtidae) and plants in the Lagodekhi National Park (Country of Georgia) across an elevational gradient from 665 m to 2559 m a.s.l. by means of a year-round sampling of insects and a seasonal sampling of plants. Contrary to expectation, we found species richness of both taxa to peak at highest elevations. This unusual pattern was related to particular shifts in vegetation types, from relatively species-poor forests over rich grasslands towards poorer highland scrub vegetation. Our results call for a closer look at elevational gradients and highlights the need for including vegetation types in the assessment of altitudinal diversity gradients.</p

species_matrices_SCT-1_1m²_&_25m²_plots

Given are the cover values [in %] of the vascular species and bryophytes recorded on the permanent plots at the SCT-1 part of the Chicken Creek catchment (see fig. 1) in the study period

species_matrices_SCT-2_1m²_&_25m²_plots

Given are the cover values [in %] of the vascular species and bryophytes recorded on the permanent plots at the SCT-2 part of the Chicken Creek catchment (see fig. 1) in the study period