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

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

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

Data from “Environmental correlates of species rank – abundance distributions in global drylands”

Data from Ulrich, W., S. Soliveres, A. Thomas, A. Dougill & F. T. Maestre. Environmental correlates of species rank – abundance distributions in global drylands. Perspectives in Plant Ecology, Evolution and Systematics, doi:10.1016/j.ppees.2016.04.004There are two spreadsheets with data. The spreadsheet "Data" contains the data used in the manuscript. The spreadsheet "Metadata" contains the associated metadata, where a description of all the variables and units can be found. All the methodological details can be found in the article.<br

Table_4_Biodiversity and Ecosystem Functions Across an Afro-Tropical Forest Biodiversity Hotspot.XLSX

Ecosystem functions are important for the resilience of ecosystems and for human livelihood quality. Intact habitats and heterogeneous environments are known to provide a large variety of ecosystem functions. Natural and near natural ecosystems surrounding agroecosystems may positively support crop growing conditions and thus facilitate crop yields. In contrast, monocultures of crops and trees as well as degraded landscapes are known to provide less ecosystem functions. The Taita Hills in southern Kenya are part of the Eastern Afromontane biodiversity hotspot, and represent a habitat mosaic consisting of largely intact cloud forests, agroecosystems and plantations of exotic trees. In this region, subsistence farmers rely on ecosystem functions provided by natural ecosystems. In this study, we analyze three proxies of biodiversity and ecosystem functions, namely pollination activity, predation rates, and arthropod diversity in tree canopies. We set study plots along forest-agroecosystem-gradients, covering cloud forest, forest edge and agricultural fields, as well as plantations of exotic trees. We assessed environmental conditions, to evaluate the extent to which local environmental factors influence ecosystem functions. Based on these data we investigate potential spill over of ecosystem functions from forest into adjoining agroecosystems. For predation rates we found trends of spill over effects from forest interior into the agroecosystem. The expression of ecosystem functions differed among habitat types, with comparatively high predation rates in the forest, high pollinator activity in the open agricultural areas, and highest arthropod diversity along the forest edge. Eucalyptus plantations showed reduced ecosystem functions and lowest arthropod diversity. Local factors such as vegetation cover and flower supply positively influence pollinator activity. Our study show that natural ecosystems may positively contribute ecosystem functions such as predation, while the homogenization of biota through planting of invasive exotic tree species significantly reduce biodiversity and ecosystem functions. Transition habitats such as forest margins, and small-scale ecological enhancement positively influences biodiversity and ecosystem functions.</p

Table_3_Biodiversity and Ecosystem Functions Across an Afro-Tropical Forest Biodiversity Hotspot.XLSX

Ecosystem functions are important for the resilience of ecosystems and for human livelihood quality. Intact habitats and heterogeneous environments are known to provide a large variety of ecosystem functions. Natural and near natural ecosystems surrounding agroecosystems may positively support crop growing conditions and thus facilitate crop yields. In contrast, monocultures of crops and trees as well as degraded landscapes are known to provide less ecosystem functions. The Taita Hills in southern Kenya are part of the Eastern Afromontane biodiversity hotspot, and represent a habitat mosaic consisting of largely intact cloud forests, agroecosystems and plantations of exotic trees. In this region, subsistence farmers rely on ecosystem functions provided by natural ecosystems. In this study, we analyze three proxies of biodiversity and ecosystem functions, namely pollination activity, predation rates, and arthropod diversity in tree canopies. We set study plots along forest-agroecosystem-gradients, covering cloud forest, forest edge and agricultural fields, as well as plantations of exotic trees. We assessed environmental conditions, to evaluate the extent to which local environmental factors influence ecosystem functions. Based on these data we investigate potential spill over of ecosystem functions from forest into adjoining agroecosystems. For predation rates we found trends of spill over effects from forest interior into the agroecosystem. The expression of ecosystem functions differed among habitat types, with comparatively high predation rates in the forest, high pollinator activity in the open agricultural areas, and highest arthropod diversity along the forest edge. Eucalyptus plantations showed reduced ecosystem functions and lowest arthropod diversity. Local factors such as vegetation cover and flower supply positively influence pollinator activity. Our study show that natural ecosystems may positively contribute ecosystem functions such as predation, while the homogenization of biota through planting of invasive exotic tree species significantly reduce biodiversity and ecosystem functions. Transition habitats such as forest margins, and small-scale ecological enhancement positively influences biodiversity and ecosystem functions.</p

Table_2_Biodiversity and Ecosystem Functions Across an Afro-Tropical Forest Biodiversity Hotspot.XLSX

Ecosystem functions are important for the resilience of ecosystems and for human livelihood quality. Intact habitats and heterogeneous environments are known to provide a large variety of ecosystem functions. Natural and near natural ecosystems surrounding agroecosystems may positively support crop growing conditions and thus facilitate crop yields. In contrast, monocultures of crops and trees as well as degraded landscapes are known to provide less ecosystem functions. The Taita Hills in southern Kenya are part of the Eastern Afromontane biodiversity hotspot, and represent a habitat mosaic consisting of largely intact cloud forests, agroecosystems and plantations of exotic trees. In this region, subsistence farmers rely on ecosystem functions provided by natural ecosystems. In this study, we analyze three proxies of biodiversity and ecosystem functions, namely pollination activity, predation rates, and arthropod diversity in tree canopies. We set study plots along forest-agroecosystem-gradients, covering cloud forest, forest edge and agricultural fields, as well as plantations of exotic trees. We assessed environmental conditions, to evaluate the extent to which local environmental factors influence ecosystem functions. Based on these data we investigate potential spill over of ecosystem functions from forest into adjoining agroecosystems. For predation rates we found trends of spill over effects from forest interior into the agroecosystem. The expression of ecosystem functions differed among habitat types, with comparatively high predation rates in the forest, high pollinator activity in the open agricultural areas, and highest arthropod diversity along the forest edge. Eucalyptus plantations showed reduced ecosystem functions and lowest arthropod diversity. Local factors such as vegetation cover and flower supply positively influence pollinator activity. Our study show that natural ecosystems may positively contribute ecosystem functions such as predation, while the homogenization of biota through planting of invasive exotic tree species significantly reduce biodiversity and ecosystem functions. Transition habitats such as forest margins, and small-scale ecological enhancement positively influences biodiversity and ecosystem functions.</p

Table_1_Biodiversity and Ecosystem Functions Across an Afro-Tropical Forest Biodiversity Hotspot.XLSX

Ecosystem functions are important for the resilience of ecosystems and for human livelihood quality. Intact habitats and heterogeneous environments are known to provide a large variety of ecosystem functions. Natural and near natural ecosystems surrounding agroecosystems may positively support crop growing conditions and thus facilitate crop yields. In contrast, monocultures of crops and trees as well as degraded landscapes are known to provide less ecosystem functions. The Taita Hills in southern Kenya are part of the Eastern Afromontane biodiversity hotspot, and represent a habitat mosaic consisting of largely intact cloud forests, agroecosystems and plantations of exotic trees. In this region, subsistence farmers rely on ecosystem functions provided by natural ecosystems. In this study, we analyze three proxies of biodiversity and ecosystem functions, namely pollination activity, predation rates, and arthropod diversity in tree canopies. We set study plots along forest-agroecosystem-gradients, covering cloud forest, forest edge and agricultural fields, as well as plantations of exotic trees. We assessed environmental conditions, to evaluate the extent to which local environmental factors influence ecosystem functions. Based on these data we investigate potential spill over of ecosystem functions from forest into adjoining agroecosystems. For predation rates we found trends of spill over effects from forest interior into the agroecosystem. The expression of ecosystem functions differed among habitat types, with comparatively high predation rates in the forest, high pollinator activity in the open agricultural areas, and highest arthropod diversity along the forest edge. Eucalyptus plantations showed reduced ecosystem functions and lowest arthropod diversity. Local factors such as vegetation cover and flower supply positively influence pollinator activity. Our study show that natural ecosystems may positively contribute ecosystem functions such as predation, while the homogenization of biota through planting of invasive exotic tree species significantly reduce biodiversity and ecosystem functions. Transition habitats such as forest margins, and small-scale ecological enhancement positively influences biodiversity and ecosystem functions.</p