Biology subjects

Dieguez, P.

Publications and source records attributed to Dieguez, P..

6 recordsLinked to original sources

bioRxiv2026

Non-invasive genomic sampling uncovers novel connectivities and origins of confiscated gorillas

BackgroundGorillas are a group of African great apes with two species and four subspecies that are currently critically endangered or endangered. Previous studies that analysed the genetics of wild gorillas from non-invasive samples, such as faeces or hair, analysed short mitochondrial or nuclear markers, which may not reflect the wider nuclear genome. Recent technical advances in target capture hybridisation, enrich the endogenous DNA content of non-invasive samples, allowing contiguous genomic regions to be sequenced. ResultsHere, we generated georeferenced genetic data from faecal and hair samples of 280 wild gorillas, sampled from three of the four gorilla subspecies, across large parts of their present-day distributions. With this expanded representation of gorilla genetic diversity in the wild, we detected three population clusters in western lowland gorillas, with the Sangha River and its affluents acting as significant barriers to gene flow. We reconstructed patterns of past population connectivity between western lowland gorillas in the north-eastern distribution range and Cross River gorillas, which may have been facilitated by a migration corridor also used by the Central and Nigeria-Cameroon chimpanzee subspecies. Finally, we predicted the geographic origins of wild-born gorillas, achieving a mean prediction error of 65 km, with a population-level resolution for mountain gorillas and some populations of western lowland gorillas. ConclusionOur work characterises fine-scale population structure in western lowland gorillas, which will be informative for future conservation strategies. This proof of concept in predicting geographic locations of wild gorillas, will be useful for future applications to geolocalise trafficked or rescued gorillas.

evolutionary biology↗

bioRxiv2026

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

Bonobos (Pan paniscus), an endangered species, have for decades been genetically understudied, partly due to difficulties in obtaining high-quality samples. The study of their genome is important not only for understanding their evolution, but also for improving conservation efforts, including population management, diversity and inbreeding assessment, and tracking rescued individuals to combat illegal wildlife trafficking. Here, we use chromosome 21 target capture data from 156 non-invasively collected faecal samples from wild bonobos to perform a comprehensive analysis of their population structure. We confirm the existence of three previously suggested subpopulations identified here as Western, Central and Eastern bonobos which are defined by natural barriers of gene flow such as the Lomami River. By estimating levels of inbreeding, diversity and differentiation, we find support for isolation of mainly Western and Eastern populations and add information on the dispersal routes of their ancestors. We infer split times and separation of these populations and apply a genetic framework to geolocalize samples of unknown origin, showing that locations of their potential origin can be estimated with a precision of up to a median of [~]50 km. Our study provides valuable insight into the evolution and population structure of bonobos and reveals how rivers act as strong barriers between populations. It also offers resources for conservation efforts and highlights the need to monitor bonobo populations more closely, in particular isolated ones. ImpactBonobos have been difficult to study genetically due to their remote forest habitat and endangered status. Here we used non-invasive sampling and chromosome 21 target capture sequencing to perform the most detailed analysis to date of their population structure. We find three main subpopulations and genetic differentiation influenced by river barriers, especially with populations found on the Eastern side of the Lomami river. This data will be useful for identifying the geographic origin of confiscated samples and thus aid bonobo conservation efforts.

bioinformatics↗

bioRxiv2024

Local genetic adaptation to habitat in wild chimpanzees

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees. One-Sentence SummaryChimpanzees show evidence of local genetic adaptation to habitat, particularly to pathogens, such as malaria, in forests.

evolutionary biology↗

bioRxiv2020

Chimpanzee (Pan troglodytes verus) density and environmental gradients at their biogeographical range edge

Identifying ecological gradients at the range edge of a species is an essential step in revealing the underlying mechanisms and constraints that limit the species geographic range. We aimed to describe the patterns of variation in chimpanzee (Pan troglodytes verus) density and habitat characteristics perpendicular to the northern edge of their range and to investigate potential environmental mechanisms underlying chimpanzee distribution in a savanna-mosaic habitat. We estimated chimpanzee densities at six sites forming a 126 km latitudinal gradient at the biogeographical range edge of the western chimpanzee in the savanna-mosaic habitats of southeastern Senegal. To accompany these data, we used systematically placed vegetation plots to characterize the habitats at each site for habitat heterogeneity, tree density and size, floral assemblages, among other variables. We found that both biotic and abiotic factors are potential determinants of the chimpanzee range limit in this ecoregion. Specifically, chimpanzee-occupied landscapes at the limit had smaller available floral assemblages, less habitat heterogeneity, and contained fewer closed canopy habitats in which chimpanzees could seek refuge from high temperatures than landscapes farther from the range limit. This pattern was accompanied by a decline in chimpanzee density with increasing proximity to the range limit. Our results provide several indications of the potential limits of food species diversity, thermal refuge, and water availability to the chimpanzee niche and the implications of these limits for chimpanzee biogeography, especially in the face of climate change predictions, as well as to species distributional modeling more generally.

ecology↗

bioRxiv2020

Late Quaternary habitat suitability models for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP)

AimPaleoclimate reconstructions have enhanced our understanding of how past climates may have shaped present-day biodiversity. We hypothesize that habitat stability in historical Afrotropical refugia played a major role in the habitat suitability and persistence of chimpanzees (Pan troglodytes) during the late Quaternary. We aimed to build a dynamic model of changing habitat suitability for chimpanzees at fine spatio-temporal scales to provide a new resource for understanding their ecology, behaviour and evolution. LocationAfrotropics. TaxonChimpanzee (Pan troglodytes), including all four subspecies (P. t. verus, P. t. ellioti, P. t. troglodytes, P. t. schweinfurthii). MethodsWe used downscaled bioclimatic variables representing monthly temperature and precipitation estimates, historical human population density data and an extensive database of georeferenced presence points to infer chimpanzee habitat suitability at 62 paleoclimatic time periods across the Afrotropics based on ensemble species distribution models. We mapped habitat stability over time using an approach that accounts for dispersal between time periods, and compared our modelled stability estimates to existing knowledge of Afrotropical refugia. Our models cover a spatial resolution of 0.0467 degrees (approximately 5.19 km2 grid cells) and a temporal resolution of every 1,000-4,000 years dating back to the Last Interglacial (120,000 BP). ResultsOur results show high habitat stability concordant with known historical forest refugia across Africa, but suggest that their extents are underestimated for chimpanzees. We provide the first fine-grained dynamic map of historical chimpanzee habitat suitability since the Last Interglacial which is suspected to have influenced a number of ecological-evolutionary processes, such as the emergence of complex patterns of behavioural and genetic diversity. Main ConclusionsWe provide a novel resource that can be used to reveal spatio-temporally explicit insights into the role of refugia in determining chimpanzee behavioural, ecological and genetic diversity. This methodology can be applied to other taxonomic groups and geographic areas where sufficient data are available.

ecology↗

bioRxiv2019

Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue

BackgroundIncreasing evidence suggests many non-human primate (NHP) species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue (TPE), the bacterium causing yaws in humans. In humans, yaws is characterized by lesions of the extremities and face, while Treponema pallidum subsp. pallidum (TPA) causes venereal syphilis and is characterized by primary lesions on the genital, anal or oral mucosae, and has not been detected in NHPs. Due to a paucity of genetic data, it remains unclear whether other Treponema pallidum (TP) subspecies found in humans also occur in NHP and how the genomic diversity of TPE lineages that do occur in NHPs is distributed across hosts and space. MethodologyWe observed a combination of yaws- and syphilis-like symptoms in sooty mangabeys (Cercocebus atys atys) in Tai National Park (TNP), Cote dIvoire and collected swabs and biopsies from symptomatic animals. We also collected NHP bones from eight species from TNP, as well as from 19 species at 12 field sites across sub-Saharan Africa. Samples were screened for TP DNA using PCRs. In-solution hybridization capture coupled with high throughput sequencing was used to sequence TP genomes from positive samples. Principal findingsWe generated four nearly complete TP genomes from biopsies and swabs and five partial genomes from bones. Phylogenomic analyses revealed that both syphilis- and yaws-like lesions of sooty mangabeys within a single social group in TNP were caused by TPE. All TPE genomes determined from these sooty mangabeys were different and exhibited divergence levels not observed in TPE from a single species at any other field site where the disease seems to be epizootic. In general, simian TPE isolates did not form monophyletic clades based on host species or the type of symptoms caused by an isolate, but rather clustered based on geography. ConclusionsThere is a large diversity of TPE strains infecting NHPs in TNP. Our observations within a single social group of sooty mangabeys do not support the epizootic spread of a single clone, but rather points towards frequent independent introductions of the bacterium, which can cause syphilis- and yaws-like lesions. On a larger scale, the geographic clustering of TPE genomes might be compatible with cross-species transmission of TPE within ecosystems or environmental exposure leading to acquisition of closely related strains. Authors summaryIndividuals in several populations of wild non-human primates (NHP) in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue (TPE), a pathogen causing yaws disease in humans. In humans, yaws is characterized by skin lesions of the extremities and face. In contrast, Treponema pallidum subsp. pallidum, which causes venereal syphilis in humans, has not been observed in NHPs. We describe a combination of yaws- and syphilis-like symptoms in a sooty mangabey (Cercocebus atys atys) social group in Tai National Park (TNP), Cote dIvoire. We sampled lesioned animals and collected and tested NHP bones from field sites across sub-Saharan Africa. We were able to reconstruct four genomes from swabs/biopsies and five partial genomes from bone samples. Phylogenomic analyses revealed that syphilis-like lesions and yaws-like lesions in TNP were caused by a large diversity of TPE strains. Additionally, simian TPE isolates did not form monophyletic clades based on the host species or the types of symptoms caused by an isolate, but rather clustered by geographic origin. This is suggestive of cross-species transmission of TPE within ecosystems or environmental exposure leading to acquisition of closely related strains.

genomics↗