Assessing Host-Virus Codivergence for Close Relatives of Merkel Cell Polyomavirus Infecting African Great Apes

It has long been hypothesized that polyomaviruses (PyV; family Polyomaviridae) codiverged with their animal hosts. In contrast, recent analyses suggested that codivergence may only marginally influence the evolution of PyV. We reassess this question by focusing on a single lineage of PyV infecting hominine hosts, the Merkel cell polyomavirus (MCPyV) lineage. By characterizing the genetic diversity of these viruses in seven African great ape taxa, we show that they exhibit very strong host specificity. Reconciliation analyses identify more codivergence than noncodivergence events. In addition, we find that a number of host and PyV divergence events are synchronous. Collectively, our results support codivergence as the dominant process at play during the evolution of the MCPyV lineage. More generally, our results add to the growing body of evidence suggesting an ancient and stable association of PyV and their animal hosts

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

Social Perceptions of Forest Ecosystem Services in the Democratic Republic of Congo

The forests of the Albertine Rift are known for their high biodiversity and the important ecosystem services they provide to millions of inhabitants. However, their conservation and the maintenance of ecosystem service delivery is a challenge, particularly in the Democratic Republic of the Congo. Our research investigates how livelihood strategy and ethnicity affects local perceptions of forest ecosystem services. We collected data through 25 focus-group discussions in villages from distinct ethnic groups, including farmers (Tembo, Shi, and Nyindu) and hunter-gatherers (Twa). Twa identify more food-provisioning services and rank bush meat and honey as the most important. They also show stronger place attachment to the forest than the farmers, who value other ecosystem services, but all rank microclimate regulation as the most important. Our findings help assess ecosystem services trade-offs, highlight the important impacts of restricted access to forests resources for Twa, and point to the need for developing alternative livelihood strategies for these communities

Population dynamics and genetic connectivity in recent chimpanzee history

The European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 864203) (to T.M.-B.). BFU2017-86471-P (MINECO/FEDER, UE) (to T.M.-B.). “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M) (to T.M.-B.). Howard Hughes International Early Career (to T.M.-B.). NIH 1R01HG010898-01A1 (to T.M.-B.). Secretaria d’Universitats i Recerca and CERCA Program del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880) (to T.M.-B.). UCL’s Wellcome Trust ISSF3 award 204841/Z/16/Z (to A.M.A. and J.M.S.). Generalitat de Catalunya (2017 SGR-1040) (to M. Llorente). Wellcome Trust Investigator Award 202802/Z/16/Z (to D.A.H.). The Pan African Program: The Cultured Chimpanzee (PanAf) is generously funded by the Max Planck Society, the Max Planck Society Innovation Fund, and the Heinz L. Krekeler Foundation.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.Publisher PDFPeer reviewe

Author Correction: Environmental variability supports chimpanzee behavioural diversity

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21010-z

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

Environmental variability supports chimpanzee behavioural diversity.

Funder: Max-Planck-Gesellschaft (Max Planck Society); doi: https://doi.org/10.13039/501100004189Funder: Heinz L. Krekeler FoundationLarge brains and behavioural innovation are positively correlated, species-specific traits, associated with the behavioural flexibility animals need for adapting to seasonal and unpredictable habitats. Similar ecological challenges would have been important drivers throughout human evolution. However, studies examining the influence of environmental variability on within-species behavioural diversity are lacking despite the critical assumption that population diversification precedes genetic divergence and speciation. Here, using a dataset of 144 wild chimpanzee (Pan troglodytes) communities, we show that chimpanzees exhibit greater behavioural diversity in environments with more variability - in both recent and historical timescales. Notably, distance from Pleistocene forest refugia is associated with the presence of a larger number of behavioural traits, including both tool and non-tool use behaviours. Since more than half of the behaviours investigated are also likely to be cultural, we suggest that environmental variability was a critical evolutionary force promoting the behavioural, as well as cultural diversification of great apes

Extent of biodiversity surveys and ranges for endemic species in the Albertine Rift

This article contains data on the estimated ranges of endemic species in the Albertine Rift both currently and under future climate change related to the research article entitled “Conservation of the endemic species of the Albertine Rift under future climate change” (Ayebare et al., 2018) [1]. Biodiversity surveys focused mainly on 5 taxa: birds, mammals, reptiles, amphibians and plants. A combination of line transects, point counts, recce walks, camera traps, visual encounter surveys, qualitative surveys and appropriate capture methods (mist nets, Sherman traps, pitfall traps) were used to survey the different taxa and provide point location data for each species. The biodiversity surveys were conducted by the Wildlife Conservation Society starting in the late 1990s. Additional species data were sourced from individual researchers and institutions.The current and future species ranges were estimated using the Maximum Entropy ‘(Maxent)’ species distribution modeling algorithm. The areas of suitable habitat (current and future) of 162 endemic species for 5 taxa (birds (40), mammals (33), plants (49), reptiles (11), amphibians (29), the extent of occurrence (EOO), area of occupancy (AOO), percentage range contraction due to climate change and to agriculture conversion of suitable habitat for each species are given in Table S1. Threshold geotiffs are also provided for each species modeled and made available at www.albertinerift.org. Keywords: Biodiversity surveys, Albertine Rift, Endemic species ranges, Climate change, Habitat los