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The metabarcoding of vertebrate DNA found in invertebrate-derived DNA (iDNA) has proven a powerful tool for monitoring biodiversity. To date, iDNA has primarily been used to detect the presence/absence of particular taxa using metabarcoding, though recent efforts demonstrated the potential utility of these data for estimating relative animal abundance. Here, we test whether iDNA can also be used to reconstruct complete mammalian mitogenomes and therefore bring the field closer to population-level analyses. Specifically, we used mitogenomic hybridization capture coupled with high-throughput sequencing to analyze individual (N = 7) or pooled (N = 5) fly-derived DNA extracts, and individual (N = 7) or pooled (N = 1) leech-derived DNA extracts, which were known a priori to contain primate DNA. All sources of iDNA showed their ability to generate large amounts of mammalian mitogenomic information and deeper sequencing of libraries is predicted to allow for even more complete recovery of primate mitogenomes from most samples (90%). Sixty percent of these iDNA extracts allowed for the recovery of (near) complete mammalian mitochondrial genomes (hereafter mitogenomes) that proved useable for phylogenomic analyses. These findings contribute to paving the way for iDNA-based population mitogenomic studies of terrestrial mammals. © 2023 The Authors. Environmental DNA published by John Wiley & Sons Ltd.

The selection pressures that drove dramatic encephalisation processes through the mammal lineage remain elusive, as does knowledge of brain structure reorganisation through this process. In particular, considerable structural brain changes are present across the primate lineage, culminating in the complex human brain that allows for unique behaviours such as language and sophisticated tool use. To understand this evolution, a diverse sample set of humans' closest relatives with varying socio-ecologies is needed. However, current brain banks predominantly curate brains from primates that died in zoological gardens. We try to address this gap by establishing a field pipeline mitigating the challenges associated with brain extractions of wild primates in their natural habitat. The success of our approach is demonstrated by our ability to acquire a novel brain sample of deceased primates with highly variable socio-ecological exposure and a particular focus on wild chimpanzees. Methods in acquiring brain tissue from wild settings are comprehensively explained, highlighting the feasibility of conducting brain extraction procedures under strict biosafety measures by trained veterinarians in field sites. Brains are assessed at a fine-structural level via high-resolution MRI and state-of-the-art histology. Analyses confirm that excellent tissue quality of primate brains sourced in the field can be achieved with a comparable tissue quality of brains acquired from zoo-living primates. Our field methods are noninvasive, here defined as not harming living animals, and may be applied to other mammal systems than primates. In sum, the field protocol and methodological pipeline validated here pose a major advance for assessing the influence of socio-ecology on medium to large mammal brains, at both macro- and microstructural levels as well as aiding with the functional annotation of brain regions and neuronal pathways via specific behaviour assessments.

The selection pressures that drove dramatic encephalisation processes through the mammal lineage remain elusive, as does knowledge of brain structure reorganisation through this process. In particular, considerable structural brain changes are present across the primate lineage, culminating in the complex human brain that allows for unique behaviours such as language and sophisticated tool use. To understand this evolution, a diverse sample set of humans' closest relatives with varying socio-ecologies is needed. However, current brain banks predominantly curate brains from primates that died in zoological gardens. We try to address this gap by establishing a field pipeline mitigating the challenges associated with brain extractions of wild primates in their natural habitat.The success of our approach is demonstrated by our ability to acquire a novel brain sample of deceased primates with highly variable socio-ecological exposure and a particular focus on wild chimpanzees. Methods in acquiring brain tissue from wild settings are comprehensively explained, highlighting the feasibility of conducting brain extraction procedures under strict biosafety measures by trained veterinarians in field sites.Brains are assessed at a fine-structural level via high-resolution MRI and state-of-the-art histology. Analyses confirm that excellent tissue quality of primate brains sourced in the field can be achieved with a comparable tissue quality of brains acquired from zoo-living primates.Our field methods are noninvasive, here defined as not harming living animals, and may be applied to other mammal systems than primates. In sum, the field protocol and methodological pipeline validated here pose a major advance for assessing the influence of socio-ecology on medium to large mammal brains, at both macro- and microstructural levels as well as aiding with the functional annotation of brain regions and neuronal pathways via specific behaviour assessments

In tropical forests, anthropogenic activities are major drivers of the destruction and degradation of natural habitats, causing severe biodiversity loss. African colobine monkeys (Colobinae) are mainly folivore and strictly arboreal primates that require large forests to subsist, being among the most vulnerable of all nonhuman primates. The Western red colobus Piliocolobus badius and the King colobus Colobus polykomos inhabit highly fragmented West African forests, including the Cantanhez Forests National Park (CFNP) in Guinea-Bissau. Both species are also found in the largest and best-preserved West African forest?the Taï National Park (TNP) in Ivory Coast. Colobine monkeys are hunted for bushmeat in both protected areas, but these exhibit contrasting levels of forest fragmentation, thus offering an excellent opportunity to investigate the importance of well-preserved forests for the maintenance of evolutionary potential in these arboreal primates. We estimated genetic diversity, population structure, and demographic history by using microsatellite loci and mitochondrial DNA. We then compared the genetic patterns of the colobines from TNP with the ones previously obtained for CFNP and found contrasting genetic patterns. Contrary to the colobines from CFNP that showed very low genetic diversity and a strong population decline, the populations in TNP still maintain high levels of genetic diversity and we found no clear signal of population decrease in Western red colobus and a limited decrease in King colobus. These results suggest larger and historically more stable populations in TNP compared to CFNP. We cannot exclude the possibility that the demographic effects resulting from the recent increase of bushmeat hunting are not yet detectable in TNP using genetic data. Nevertheless, the fact that the TNP colobus populations are highly genetically diverse and maintain large effective population sizes suggests that well-preserved forests are crucial for the maintenance of populations, species, and probably for the evolutionary potential in colobines.

It is becoming increasingly obvious that we only know a fraction of the human virome. The development of next-generation sequencing (NGS) technologies has dramatically increased our ability to hunt viruses. Yet, the small genomes and low copy numbers characteristic of most viruses make undirected (shotgun) hunts a relatively inefficient strategy. Here, we propose to speed-up the rate of double-stranded DNA (dsDNA) virus discovery by combining NGS with evolutionary thinking. dsDNA viruses are thought to have co-diverged with their hosts. As this applies to the hominine lineages (gorillas, humans, chimpanzees, and bonobos), it is theoretically possible to estimate the phylogenetic position of cryptic human viruses by identifying co-divergent viral lineages infecting non-human hominines. Where these lineages do not comprise a human-infecting counterpart, a yet-unknown human virus may be hiding. The first phase of this project will consist in the high-throughput characterization of dsDNA viruses (herpesviruses, papillomaviruses, and polyomaviruses) infecting wild gorillas, chimpanzees, and bonobos. For this, we will use an exhaustive collection of fecal samples (in terms of hominine species/sub-species diversity) and apply a discovery strategy combining in-solution capture and NGS. This strategy has been developed in the ancient DNA field but has a very broad applicability; it will constitute a nice addendum to the institute technical portfolio. Thanks to the massive amount of information collected, we will be able to reconstruct the evolutionary history of many dsDNA virus lineages and to identify those where a human virus would be expected but is still unknown. This will pave the way to the second phase of the project which will consist in a pre-oriented dsDNA human virus hunt based on the use of specific PCR systems implemented in multiplex. We expect that this project will generate an unprecedented amount of data on the processes at play along dsDNA virus evolution (co-divergence versus cross-species transmission), help determine the directionality, frequency, and timing of cross-species transmission events between hominines and unveil the existence of yet-to-be-discovered human viruses.

Dear Editor, The bacterium Treponema pallidum (TP) causes human syphilis (subsp. pallidum; TPA), bejel (subsp. endemicum; TEN), and yaws (subsp. pertenue; TPE) (1). Although syphilis has reached a worldwide distribution (2), bejel and yaws have remained endemic diseases. Bejel affects individuals in dry areas of Sahelian Africa and Saudi Arabia, whereas yaws affects those living in the humid tropics (1). Yaws is currently reported as endemic in 14 countries, and an additional 84 countries have a known history of yaws but lack recent epidemiological data (3,4). Although this disease was subject to global eradication efforts in the mid-20th century, it later reemerged in West Africa, Southern Asia, and the Pacific region (5). New large-scale treatment options triggered the ongoing second eradication campaign, the goal of which is to eradicate yaws globally by 2020 (5).\ud \ud References:\ud (1) Giacani, L. & Lukehart, S.A. The endemic treponematoses. Clin. Microbiol. Rev. 27, 89–115 (2014).\ud (2) Arora, N. et al. Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster. Nat. Microbiol. 2, 16245 (2016).\ud (3) Marks, M. Yaws: towards the WHO eradication target. Trans. R Soc. Trop. Med. Hyg. 110, 319–320 (2016).\ud (4) World Health Organization. Eradication of yaws: procedures for verification and certification of interruption of transmission (World Health Organization, Geneva, 2018).\ud (5) Asiedu, K., Fitzpatrick, C. & Jannin, J. Eradication of yaws: historical efforts and achieving WHO’s 2020 target. PLoS Negl. Trop. Dis. 8, e3016 (2014).

Nuts are high in energetic and nutritional value, but the kernel inside is difficult to access. In the Taï forest, it is estimated that chimpanzees (Pan troglodytes verus) can eat 6–10 times as many nuts with the help of a tool as to when they crack them with their own teeth. However, sympatric-living terrestrial monkeys never crack nuts using tools. So this begs the question, why not? In this chapter, we report on the foraging behaviour of the sooty mangabeys (Cercocebus atys atys). A quick synopsis goes as follows: they observe nut-cracking chimpanzees at a distance of 5–10 metres, relish in the leftovers of the freshly cracked nuts, and then continue to follow the chimpanzees to different nut-cracking sites. With this information, we go on to consider the underlying reasons for the absence of nut-cracking in sooty mangabeys, with a particular focus on cognitive limitations, and then discuss the implications of field observations for studies on imitation in the laboratory.

Despite appealing support for theories that argue that social complexity is the main force driving primate brain-size evolution, it is still unclear how great apes were able to afford the evolution of larger and more expensive brains than sympatric species. Comparative phylogenetic studies suggest that the costs of evolutionary brain enlargement were overcome by a permanent increase in net energy intake, renewing interest in the role of ecological complexity in primate brain-size evolution. As relatively larger-brained primates, like chimpanzees, show less seasonality in their net energy intake than smaller-brained species, larger brains are proposed to provide a ‘cognitive behavioural flexibility’ that facilitates the consumption of nutritious foods during periods of food scarcity (cognitive buffer hypothesis). To date, it remains unclear what this cognitive flexibility entails. In this chapter, I will provide evidence for a variety of mechanisms of temporal cognition that chimpanzees employ to gain first access to newly ripened, energy-rich fruit in a competitive and complex rainforest environment.

Determining individual health status is of great importance for a better understanding of life history trade-offs between growth, reproduction, and maintenance. However, existing immunological methods are invasive and therefore not suitable for investigating health status in wild populations. Thus, there is an urgent need for non-invasive methods to assess the immune status of animals. Neopterin is involved in the cell-mediated pathway of the immune response (Th1–type), secreted during the activation of monocytes and macrophages. We investigated if urinary neopterin could serve as a biomarker of health status in bonobos and chimpanzees. First, we performed a chemical validation of a commercial neopterin enzyme immune assay (EIA) for bonobo and chimpanzee urine. We then examined if urinary neopterin levels in bonobos increase during the acute period of respiratory infections. We found that neopterin levels can be reliably measured in urine of the two species with a commercial EIA. Stability experiments revealed considerable changes in urinary neopterin levels in relation to multiple freeze–thaw cycles and extended exposure to room temperature. Exposure to sunlight led to a degradation of urinary neopterin, whereas sample storage up to two years did not affect urinary neopterin levels. There was no detectable diurnal variation in neopterin levels, and levels remained very stable across several days in healthy individuals. While urinary neopterin levels were independent of sex, nonadult individuals had higher urinary neopterin levels than adults. Most importantly, there was a significant increase in urinary neopterin levels during a period of respiratory infection. Our results demonstrate that regular urine sample collection would allow for the monitoring of individual health status and disease progression with minimal disturbance of the subjects. In combination with behavioral, life history, and endocrinological parameters, the method can be used to investigate questions related to immunocompetence handicaps or life history trade-offs.

Introduction: The reservoir(s) and ecology of Ebola viruses (EBV) remains largely unknown, but previous detection of viral RNA and anti-EBV antibodies in bats suggests that they may play a role in zoonotic transmission. Objectives: Gain insight into the circulation of EBV in bat populations in West and Central Africa by testing for the presence of antibodies against different EBV, using high throughput technology. Materials and methods: Bats were captured across 7 regions in Cameroon and 4 in Guinea, and released immediately after collection of dried blood spots and biological data. Here we used a multiplex immunoassay with Luminex® technology for antibody detection against NP, GP and VP40 antigens for Zaire (EBOV), Sudan (SUDV), Bundibugyo (BDBV) and Reston (RESTV) EBV. In the absence of positive controls, cut-off values were determined using the change-point analysis method with bootstrapping (10 000 times). A sample was considered positive if the detected antibodies level was over the estimated cut-off for both NP and GP antigens. Results: We studied 1796 bats (Cameroon, n=1365 and Guinea, n=431) belonging to 10 genera of the frugivorous family Pteropodidae (n=641) and 12 genera of 6 insectivorous families (n=1155). Based on the change-point analysis, 0,2% (3/1796) of bats were positive for EBOV (E. helvum, n=1; M. angolensis, n=1 and Mops sp., n=1) and 0,1% (1/1796) for SUDV (R. aegyptiacus). A total of 7,9% (142/1796) reacted to at least one EBV antigen, mainly GP. These bats belonged mainly (97%) to 8 frugivorous species and one insectivorous genus (Mops). Conclusion: we confirm the presence of antibodies in 2 frugivorous bat species and 1 insectivorous genus previously found to be seropositive, as well as for the first time in M. angolensis, a frugivorous species. Using a stringent method of interpretation (change-point analysis), prevalence of EBV antibodies can be underestimated. More studies are needed to evaluate the extend of EBV in bats in areas at risk for EBV outbreaks in Africa and complementary less conservative methods to define cut-offs could be used for comparison in order to reflect natural circulation or exposure to Filoviruses.

The existence and genetic make-up of most primate retroviruses was revealed by studies of bushmeat and fecal samples from unhabituated primate communities. For these, detailed data on intra- and within-species contact rates are generally missing, which makes identification of factors influencing transmission a challenging task. Here we present an assessment of 12 years of research on primate retroviruses in the Tai National Park area, Cote d'Ivoire. We discuss insights gained into the prevalence, within- and cross-species transmission of primate retroviruses (including towards local human populations) and the importance of virus-host interactions in determining cross-species transmission risk. Finally we discuss how retroviruses ecology and evolution may change in a shifting environment and identify avenues for future research.

The authors describe genital alterations and detailed histologic findings in baboons naturally infected with Treponema pallidum. The disease causes moderate to severe genital ulcerations in a population of olive baboons (Papio hamadryas anubis) at Lake Manyara National Park in Tanzania. In a field survey in 2007, 63 individuals of all age classes, both sexes, and different grades of infection were chemically immobilized and sampled. Histology and molecular biological tests were used to detect and identify the organism responsible: a strain similar to T pallidum ssp pertenue, the cause of yaws in humans. Although treponemal infections are not a new phenomenon in nonhuman primates, the infection described here appears to be strictly associated with the anogenital region and results in tissue alterations matching those found in human syphilis infections (caused by T pallidum ssp pallidum), despite the causative pathogen’s greater genetic similarity to human yaws-causing strains.