Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP)

Paleoclimate reconstructions have enhanced our understanding of how past climates have shaped present-day biodiversity. We hypothesize that the geographic extent of Pleistocene forest refugia and suitable habitat fluctuated significantly in time during the late Quaternary for chimpanzees (Pan troglodytes). Using bioclimatic variables representing monthly temperature and precipitation estimates, past human population density data and an extensive database of georeferenced presence points, we built a model of changing habitat suitability for chimpanzees at fine spatio-temporal scales dating back to the Last Interglacial (120,000 BP). Our models cover a spatial resolution of 0.0467 degrees (approximately 5.19 km2 grid cells) and a temporal resolution of between1,000–4,000 years . Using our model, we mapped habitat stability over time using three approaches, comparing our modelled stability estimates to existing knowledge of Afrotropical refugia, as well as contemporary patterns of major keystone tropical food resources used by chimpanzees, figs (Moraceae) and palms (Arecacae). Results show habitat stability congruent with known glacial refugia across Africa, suggesting their extents may have been underestimated for chimpanzees, with potentially up to ~60,000 km2 of previously unrecognized glacial refugia. The refugia we highlight coincide with higher species richness for figs and palms. Our results provide spatio-temporally explicit insights into the role of refugia across the chimpanzee range, forming the empirical foundation for developing and testing hypotheses about behavioural, ecological and genetic diversity with additional data. This methodology can be applied to other species and geographic areas when sufficient data are available.

Methods
This is a large species distribution modelling project based on chimpanzee occurrence data from the IUCN SSC APES database (http://apesportal.eva.mpg.de/) and paleoclimate data dating back to the Last Interglacial from Bell et al. 2017 (https://onlinelibrary.wiley.com/doi/10.1111/mec.14260). 

The DRYAD package here contains two files (Barratt_et_al_2021_AJP_data.zip and Barratt_et_al_2021_AJP_scripts.zip) to:

0 - generate pseudoabsence points prior to modelling

1- run large ensemble SDMs

2- summarize and plot variable importance across models

3 - generate stability estimates across time (static, dynamic stability and co-efficient of variation)

4 - plot these stability estimates

5 - calculate and plot SDM habitat suitability correlations across sensitivity analyses and with chimpanzee food plant species richness

6 - plot an animated GIF image of the changing habitat suitability through time (0-120 kya, 62 paleoclimate snapshots)

7 - quantify modelled estimates of refugia against previously published results to give numbers and % of refugial areas recovered