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Welcome to Celia Lacomme who just obtained her PhD bursary to work on the effect of anthropogenic diet on chacma baboon’s microbiome and health

In the course of their evolution, just as humans have colonized every corner and biome of our planet, chacma baboons (Papio ursinus) have explored a wide variety of territories in southern Africa (from Namibia to Mozambique to South Africa). This non-human primate species is indeed present in savannahs, low and high grasslands, coastal and mountain forests, as well as in more extreme environments such as high-altitude mountains (>3,280 m in South Africa) or deserts (Namibian Desert, Karoo in South Africa). Their presence in such a diversity of environments reflects their incredible ability to adapt to different and variable natural conditions. Over the course of their history, chacma baboons have been confronted with the arrival of human populations that have resulted in significant modifications to the landscape that have become increasingly fragmented. Faced with this fragmentation of the natural landscapes, chacma baboons, like other animal species, began to colonize increasingly anthropized environments. It is well known that these anthropogenic alterations are major factors affecting primate populations worldwide, including in Africa. Through the colonization of these increasingly anthropized environments, chacma baboons have faced new conditions that differ from their natural environments, including exposure to as a first factor a new human modified diet, but also then new pathogens, and different hazards, to name but a few. Then, this transition from a natural environment to an increasingly anthropized environment raises a key question: What are the consequences of this transition from a natural diet to an anthropogenic diet, characterized as rich in carbohydrates and fats, on the gut microbiome and health of chacma baboons?
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PhD opportunity on the impact of urban diet on chacma baboons microbiome, health and behavior

In the course of their evolution, just as humans have colonized every corner and biome of our planet, chacma baboons (Papio ursinus) have explored a wide variety of territories in southern Africa (from Namibia to Mozambique to South Africa). This non-human primate species is indeed present in savannahs, low and high grasslands, coastal and mountain forests, as well as in more extreme environments such as high-altitude mountains (>3,280 m in South Africa) or deserts (Namibian Desert, Karoo in South Africa). Their presence in such a diversity of environments reflects their incredible ability to adapt to different and variable natural conditions. Over the course of their history, chacma baboons have been confronted with the arrival of human populations that have resulted in significant modifications to the landscape that have become increasingly fragmented. Faced with this fragmentation of the natural landscapes, chacma baboons, like other animal species, began to colonize increasingly anthropized environments. It is well known that these anthropogenic alterations are major factors affecting primate populations worldwide, including in Africa. Through the colonization of these increasingly anthropized environments, chacma baboons have faced new conditions that differ from their natural environments, including exposure to as a first factor a new human modified diet, but also then new pathogens, and different hazards, to name but a few. Then, this transition from a natural environment to an increasingly anthropized environment raises a key question: What are the consequences of this transition from a natural diet to an anthropogenic diet, characterized as rich in carbohydrates and fats, on the gut microbiome and health of chacma baboons? Link to apply to the doctoral competition E2M2 Lyon, France : https://e2m2.universite-lyon.fr/medias/fichier/sujete2m2-2023-virginierougeronfrancais_1683033723130-pdf?ID_FICHE=99693 To get more details about the project and apply, please contact: virginie.rougeron@cnrs.fr
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PhD offer on chacma baboon evolution and adaptation in South Africa

The goal of this PhD project will be to get a better understanding of the evolution, history and adaptation of chacma baboons in different environments (i.e. biomes). From modern tissue and ancient (archeological) remains collected in different biomes in South Africa, full genomic information will be generated using high throughput sequencing strategies. To do so, the PhD student will have to extract all modern samples for their DNAs, that will be sent for sequencing (bench laboratory work). For archeological remains, all remains will be treated in a dedicated ancient DNA laboratory (Orlando Ludovic Laboratory, France). Sequences obtained will be then analyzed using sets of bio-informatics and population genetics tools. This will allow the student to elucidate the evolutionary origin and history of chacma baboons as well as to look for their key genetic adaptations in specific environments. This project will allow to get new information about the genetic basis of chacma baboons adaptation that enable these wild animals to become successful species in a large diversity of environments, which is a key question in the study of animal biology and conservation. Candidates should have a MSc Honours degree (or equivalent), formation in molecular biology (experience in a laboratory will be a plus), genetics and bioinformatics (expected very good experience in different bioinformatic languages) as well as a valid driver’s licence. Preference will be given to South African students. Students will be based at the Nelson Mandela University’s George Campus. A bursary of R120 000 per year is offered for a period of 3 years (Mars 2023 – February 2026). Candidate are expected to apply to NRF and PJRS bursaries from 2023. Supervisors: Virginie Rougeron (Research Associate at NMU, CRCN at CNRS) and Franck Prugnolle (Research Associate at NMU and DR1 at CNRS), both evolutionary biologists and geneticists, will be the main co-supervisors of this PhD thesis. Michael Fontaine (CR CNRS), specialist in genomics and evolutionary adaptation of organisms in conservation, will co-supervised the student. Contact: virginie.rougeron@cnrs.fr
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Molecular laboratory setting up started

We are very happy that the setting up of the future molecular laboratories started. This is a long process but the goal will be to get good infracstucture to start all the genetic, conservation genetic and environment genetic work directly from our place. We hope the lab will be ready within the next three months.
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Answer to Sharp et al. The origin of Plasmodium vivax: science or story telling?

We thank Sharp et al. (2021) for pointing out the mistakes in the schematic phylogeny presented in Fig. 1 that appeared during the multiple editing of the phylogeny. We indeed agree that Plasmodium gonderi should be basal to the Asian primate Plasmodium (subgenus Plasmodium) and that P. carteri should be between P. vivax-like/P. vivax and P. cynomolgi and not be basal to P. cynomolgi/P. vivax-P. vivax-like. The phylogenies of Figs 1 and 2 have now been redrawn to correct these two points. Fortunately, this does not change what was written in the text and the take home messages of the article. Regarding the fact that Sharp et al. (2021) said that we are blind to the evidence regarding the P. vivax origin, we strongly disagree. We really think that the current evidence is not sufficient yet to conclude regarding the origin of the parasite. We do not say so because we are in favor of one or the other hypothesis (out-of-Africa or out-of-Asia), but simply because the scientific evidence is still not strong enough to draw any clear conclusion. In our review, we explain what we see as the problems/bias/contradictions in the data (from phylogenetics and population genetics), so would not go through those again here.
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