Application of machine learning to quantify forest cover loss in the Congo Basin and its implications for large mammal habitat suitability

Machine learning (ML) models are a powerful tool for land use and land cover (LULC) mapping. In the African tropics, and particularly in the Congo Basin, there is a need to better assess the performance and reliability of ML-based LULC classification using coarse-resolution satellite images. In the context of ongoing climate change and socioeconomically-driven forest disturbances, it is important to understand and quantify the extent of forest cover loss in the Congo Basin, as well as the impact of this loss on suitable habitat for key wildlife species. In this dissertation, I address these key issues in three manuscript-based chapters. In Chapter 2, I compared the classification performance of four ML algorithms (k-nearest neighbor (kNN), support vector machines (SVM), artificial neural networks (ANN), and random forests (RF)) for LULC mapping within a tropical region in Central Africa (the Mayo Rey department of northern Cameroon). All four classification algorithms produced high accuracy (overall classification accuracy > 80%), with the RF model (> 90% classification accuracy) outperforming the other algorithms. In Chapter 3, I used the RF model, together with the Idrissi TerrSet land change modeler, to map and project LULCC for the Congo Basin under historical and future scenarios of socioeconomic impacts and climate change. I found that over 352642 km2 of dense forests have been lost in this region between 1990 and 2020, with projected continued loss of about 174860 - 204161 km2 by the year 2050. In Chapter 4, I produced spatially explicit species distribution models to map habitat suitability for great apes (chimpanzees and gorillas) and elephants within the Dzanga Sangha Protected Areas (DSPA) of the Congo Basin. I found that priority habitat areas for the three mammal species mostly occurred and overlapped spatially within the DSPA national parks. However, priority habitat areas for the three species declined by 4, 4.5 and 9.8 percentage points respectively between 2015 and 2020, mostly due to increased human pressures. This research provides a new understanding of the extend and implications of forest cover loss in the Congo Basin, highlighting the critical conservation challenges that remain in this region

Discovery of Novel Herpes Simplexviruses in Wild Gorillas, Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2

Viruses closely related to human pathogens can reveal the origins of human infectious diseases. Human herpes simplexvirus type 1 (HSV-1) and type 2 (HSV-2) are hypothesized to have arisen via host-virus codivergence and crossspecies transmission. We report the discovery of novel herpes simplexviruses during a large-scale screening of fecal samples from wild gorillas, bonobos, and chimpanzees. Phylogenetic analysis indicates that, contrary to expectation, simplexviruses from these African apes are all more closely related to HSV-2 than to HSV-1. Molecular clock-based hypothesis testing suggests the divergence between HSV-1 and the African great ape simplexviruses likely represents a codivergence event between humans and gorillas. The simplexviruses infecting African great apes subsequently experienced multiple cross-species transmission events over the past 3 My, the most recent of which occurred between humans and bonobos around 1 Ma. These findings revise our understanding of the origins of human herpes simplexviruses and suggest that HSV-2 is one of the earliest zoonotic pathogens

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° (approximately 5.19 km2 grid cells) and a temporal resolution of between 1000 and 4000 years. Using our model, we mapped habitat stability over time using three approaches, comparing our modeled 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 approximately 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 behavioral, ecological, and genetic diversity with additional data. This methodology can be applied to other species and geographic areas when sufficient data are available

Population dynamics and genetic connectivity in recent chimpanzee history

Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (<Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees

Recent genetic connectivity and clinal variation in chimpanzees

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated. Lester and colleagues use faecal samples and genetic analyses to investigate the genetic connectivity across chimpanzees. Their results indicate that the global pattern of genetic diversity in chimpanzees is largely characterized by a pattern of isolation by distance with several isolated populations exhibiting strong local differentiation