Posterior distributions for the past (<i>N</i>₁) and present (<i>N</i>₀) effective population sizes using MSVAR 1.3.

<p>This is shown here for one of the investigated site (Sabangau) in Central Kalimantan and pooled samples analyses from the same region represented on a log₁₀ scale. The solid lines correspond to the posterior distribution obtained by independent MCMC runs. Dashed lines correspond to the different priors used for <i>N</i>₀ and <i>N</i>_1.</p

Test of the most likely period associated with orang-utan population decline.

<p>Natural logarithms of the Bayes Factors (BF) have been computed to determine during which of the important phases the populations started to decrease. a) The BF values of parameter <i>T</i> (time since the beginning of the population collapse) for all orang-utan populations were computed for each 500 year time steps and are plotted for last 50,000 years. The BF value of 3 is plotted as horizontal dash line. The vertical dash lines corresponds to the dates of forest exploitation (FE) ∼ 0.2 kya, arrival of first farmers (F) ∼ 5 kya, and arrival of hunter gatherers (HG) ∼ 40 kya. Note that LK Lot2 is Lower Kinabatangan Lot2 population. b) As 5a), and plotted for the last 5 kya. c) H1 to H4 represents four different hypotheses tested, each corresponding to one of the four factors and time periods that may have led to orang-utan population collapse (discussed in the text). Phase H4 is most ancient and corresponds to time period between 100–40 kya (before the arrival of hunter gatherers (HG) and the time when major climatic and vegetational changes associated with the Pleistocene glaciations occurred). Phase H3 corresponds to the time period after the arrival of HG. Phase H2 corresponds to the time period after the arrival of first farmers (F) and before recent forest exploitation (FE) occurred. Phase H1 is most recent and corresponds to time period of the last 200 years when major forest exploitation occurred in Borneo. Thus, the BF represents the weighted evidence in favor of each phase against the cumulative evidence of all other phases taken together. The dashed horizontal line corresponds to a BF of 3, suggesting that phase H2 has more support than H1, H3, and H4 (see results). d) H2 phase (5,000 years from present) has been divided into two periods: H2.1 and H2.2 which corresponds to the time period just before the recent forest exploitation and after the arrival of the first farmers. The dashed horizontal line corresponds to a BF of 3 and suggesting that phase H2.1 has more support than H1 and H2.2.</p

since the population collapse using MSVAR 1.3.

<p>The posterior distribution for the time since orang-utan populations (all) collapse started is represented on a logarithmic scale. The different coloured vertical dashed line corresponds to: forest exploitation (FE in red), arrival of farmers (F in blue), and arrival of hunter gatherers (HG in green). The most extreme 95% quantile of the posterior distribution is shown as a black vertical dashed line. The prior is shown as dashed line, its median being 100,000 y ago.</p

Bornean orang-utan sampling sites.

<p>The sample sizes for each site are as follows: DV = Danum Valley (<i>n</i> = 20), LK = Lower Kinabatangan (<i>n</i> = 26), TU = Tuanan (<i>n</i> = 29), SL = Sungai Lading (<i>n</i> = 26), SA = Sabangau (<i>n</i> = 19), and GP = Gunung Palung (<i>n</i> = 6).</p

Demographic collapse detected using MSVAR 0.4.

<p>Posterior distributions of the effective population size change, log (<i>N</i>₀/<i>N</i>₁). This is shown here for one of the investigated site (Sabangau) in Central Kalimantan and pooled samples analyses from the same region. Note that for illustrative purposes only two plots are shown (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049429#pone.0049429.s001" target="_blank">Figure S1</a> for the other regions). Solid lines (multiple independent runs) correspond to the linear population size change model. Dashed lines (multiple independent runs) correspond to the exponential population size model. Log (<i>N</i>₀/<i>N</i>₁) represents the ratio of present (<i>N</i>₀) to past (<i>N</i>₁) population size. The dotted vertical line corresponds to the absence of population size change, log (<i>N</i>₀/<i>N</i>₁) = 0. The prior distribution is shown for comparison (flat dotted line). The vertical dashed line corresponds to the 95% quantile of the posterior distribution.</p

Contributions of contextual layers to orang-utan Maxent model.

<p>Note: validation model values are the mean, min-max values from a 10 fold validation model ran with the same data in Maxent.</p

This figure shows the results of the jackknife procedure on the full Maxent model.

<p>This figure shows the results of the jackknife procedure on the full Maxent model.</p

Overview maps of forest cover and orang-utan data points in combination with the orang-utan distribution and land use types.

<p>a) Remaining forest cover in 2010. The sample of 558 orang-utan points used to model habitat is shown. b) Concessions and protected areas in 2010, c) The modelled orang-utan spatial distribution. d) Orang-utan distribution and overlap with protected areas and concessions.</p

Contextual layers used for the generation of the orang-utan distribution.

<p>Note: Layer correlations (Using ENMTools <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049142#pone.0049142-Warren1" target="_blank">[84]</a>) were lower than 0.5 except for elevation with slope and rugosity. All three layers were maintained in the final analyses since they are of different importance for orang-utans.</p

Orang-utan distribution area in protected areas and concessions.

<p>Note: Areas in this Table are expressed in km². IOPP: industrial Oil Palm Plantation; ITP: Industrial Timber Plantation.</p><p>For Sabah data on oil palm plantations concessions were not available.</p