Relationship between passerine species richness and primary productivity (NDVI) in South Africa.

<p>(A) Separately in each biome from the westernmost biome to the easternmost one. Grey symbols represent cell-specific estimates and black lines represent the linear regressions after correcting for spatial auto-correlation and the effect of topographic heterogeneity and water availability. Axes labels as in Fig 2B. (B) Across the study region. The colour scheme refers to the species debt legend. (C) Species debt (see <i>Species debt</i> in the Material and Methods section for definition and computation details). Negative values (dark blue tones) indicate cells with less species than expected (species debt); positive values (orange tones) indicate cells with more species than expected (species build-up). Values used to plot Fig 2 are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133992#pone.0133992.s003" target="_blank">S1 Table</a>.</p

Spatially auto-correlated regressions of taxonomic dispersion (NRI1) against species richness SR, latitude, longitude, water availability (ETR increases with water availability), and primary productivity (NDVI increases with primary productivity).

<p>σ and λ respectively estimate the remaining variance and the autocorrelation coefficient. All variables were standardized to a mean of 0 and standard deviation of 1 before analysis.</p

(A) Biome-specific spatially auto-correlated regressions (MRSAR) of passerine species richness against elevational range in the grid cells (Topo HT; left blank if not selected in the final model), water availability (ETR increases with water availability; left blank if not selected in the final model), and primary productivity (NDVI increases with primary productivity).

<p>* For the Forest and Desert Biomes, regressions were computed across all grid cells where the biome occurred. For other biomes, regressions were implemented for the grid cells with >75% coverage by the biomes.</p><p>σ and λ respectively estimate the remaining variance and the autocorrelation coefficient. All variables were standardized to a mean of 0 and standard deviation of 1 before analysis. (B) Average and standard deviation of biodiversity metrics (estimated and observed species richness, taxonomic dispersion under the two null models) for each biome.</p

Different scenarios of heterogeneity in detection probabilities.

<p>a) Symmetric individual detection probabilities, b) right-skewed (most individuals had a lower detection probability), c) left-skewed (most individuals had a higher detection probability), and d) two-group heterogeneity (individuals with low and high detection probabilities).</p

Example of parts of the capture-resighting histories for a subset of the African White-backed Vultures.

<p>The rows correspond to individuals and the column to months. If a particular bird was seen in a given months, its sighting history contains a ‘1′ in the corresponding column, and ‘0′ otherwise. The capture histories suggest strong heterogeneity in resighting probabilities, probably due to individual differences in movement patterns.</p

Estimates of survival probability.

<p>Mean survival estimates along with the 95% credible interval obtained from a model that ignores heterogeneity (solid symbols and lines) and a model that allows for heterogeneity (open symbols and broken lines) for (a) the African White-backed Vultures data, and (b) the African Penguins data.</p

Parameter estimates of the single season occupancy models fitted using MLE, VB and MCMC.

<p>Parameter estimates of the single season occupancy models fitted using MLE, VB and MCMC.</p

Capture_histories_Mark_fromat_2008_2014

Text file containing capture histories, which is the raw data used in all capture-mark-recapture analyses of Capensibufo rosei in this paper, and are in the format used by program Mark (White and Burnham 1999). Each '1'/'0' represents a positive (captured) or negative (not captured) history respectively, for a particular year from 2008 to 2014; the number thereafter represents n individuals with that particular capture history

Data from SABAP2

Data from SABAP

Predictive distribution of the proportions of occupied sites using the VB Laplace method and the MCMC method for the different bird species.

<p>The accuracy statistics (<i>acc</i>(<i>x</i>)) are displayed in brackets. The <i>acc</i>(<i>x</i>) measure lies between 0 and 1 with a value of 1 indicating a perfect approximation and a value close to 0 indicating a poor approximation by the variational distribution to the true posterior distribution.</p