Simulated outbreak patterns for those models in the 95% best model confidence sets for <i>G</i>. <i>g</i>. <i>gorilla</i> nests and nest groups (Fig 3a and 3b, respectively) as well as for <i>P</i>. <i>t</i>. <i>troglodytes</i> nests and nest groups (Fig 3c and 3d, respectively).

<p>Each map shows the development of one simulated outbreak in time and space. The green cell depicts the origin of the outbreak. Cells colored in blue to red depict the progression of the outbreak, with blue denoting cells infected first and red denoting cells infected last. The grey shading of the background reflects habitat suitability for great apes (with darker tones indicating more suitable habitat). Note that, with one exception (row 4, column 3), all simulated outbreaks affected a very similar part of the area where the recces were conducted (yellow rectangle).</p

Summary results of simulations for the four responses.

<p>Summary results of simulations for the four responses.</p

Map of the of the survey design in the Odzala region in Congo.

<p>The grey shading of the background reflects habitat suitability for great apes (with darker tones indicating more suitable habitat). The blue line depicts National Route 2, and cells framed in red are those surveyed as part of the project. The black rectangle in the center indicates area shown enlarged in Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154505#pone.0154505.g003" target="_blank">3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154505#pone.0154505.g004" target="_blank">4</a>.</p

Map of the of great ape carcasses discovered in 2006–2007 in the Odzala region of Congo.

<p>Circles indicate locations of great ape carcasses. Carcass clusters are differentiated by color (see in-figure legend). OKNP is indicated in green. The blue line indicates National Route 2 (NR2). The area shown is enlarged in Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154505#pone.0154505.g003" target="_blank">3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154505#pone.0154505.g004" target="_blank">4</a>.</p

Spatio-temporal patterns of ape nest abundance in the study area separately for <i>G</i>. <i>g</i>. <i>gorilla</i> nests and nest groups (a and b, respectively), and <i>P</i>. <i>t</i>. <i>troglodytes</i> nests and nest groups (c and d, respectively).

<p>Within each cell, the numbers of nests or nest groups (square-root transformed) is plotted against the time when the surveys took place (axes are at the same scale within panels (a, b, c, or d), but not across them). For illustrative purposes, in cells where there were at least two surveys separated by at least 30 days, we show least squares regression lines (red, yellow and green lines within cells) between number of nests or nest groups and time. In the other cells we show the average number of nests as a horizontal line. Regression lines were colored according to the correlation coefficient (rho) between number of nests or nest groups and time, with colors grading from red (rho = -1) over yellow (rho = 0) to green (rho = 1). Horizontal lines were colored grading from red (no nests or nest groups) over yellow (half the maximum number of nests or nest groups) to green (maximum number of nests or nest groups). The grey shading of the background reflects habitat suitability for great apes (with darker tones indicating more suitable habitat). Note that to the west of the road (NR2; blue line) most cells had either low or clearly decreasing ape nest densities, whereas to the east of the road neighboring cells showed strikingly differing patterns. In each panel, the depicted area equals that within the rectangle shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154505#pone.0154505.g002" target="_blank">Fig 2</a>.</p

Proportions of simulated outbreaks from a given cell (filled red) affecting other cells in its vicinity.

<p>Cells affected at least once are depicted by colored circles whereby the redder the circle, the larger the proportion of simulations leading to the respective cell eventually being affected. Note that a large proportion of the cells were affected by only a small proportion of the simulations. Also note that in none of the simulations did the epidemic cross the NR2 road heading from northeast through the center of the area. The grey shading of the background reflects habitat suitability for great apes (with darker tones indicating more suitable habitat).</p

Proportion of protected areas with conservation activities between 1990 and 1999 across different African regions.

<p>The number of protected areas with available information on presence and absence of any conservation activity (research, tourism and law enforcement guards) over the considered period were in total 105.</p

Threats impact levels to 98 tropical African protected areas at a continental and regional scale.

<p>Clockwise from top: Africa (a), Central Africa (b), East Africa (c) and West Africa (d).</p

Influence of law enforcement activities and PA size on threat levels in 90 PAs.

<p>In bold are highlighted significant values (p <i><0.05</i>). See abbreviations in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114154#pone-0114154-t002" target="_blank">Tab 2</a>. AIC, Akaike's Information Criterion; AICw, Akaike Information Criterion weight; Rank, model rank from the smallest to the largest AIC value; k, number of variables including the intercept.</p><p>Influence of law enforcement activities and PA size on threat levels in 90 PAs.</p

Regional distribution of the protected areas (PAs) in tropical Africa considered in the analyses.

<p>The regions are coloured in different grey scale colours. Light grey represents West Africa, including 54 protected areas; medium grey represents Central Africa, including 31 protected areas; dark grey represents East Africa, including 14 protected areas. On the left-side bottom corner a MODIS NDVI image of Africa, with a red quadrant highlighting the tropical area considered in the study.</p