Baboons Research Articles

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.

Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.

A Comprehensive Overview of Baboon Phylogenetic History.

Baboons (genus Papio) are an intriguing study system to investigate complex evolutionary processes and the evolution of social systems. An increasing number of studies over the last 20 years has shown that considerable incongruences exist between phylogenies based on morphology, mitochondrial, and nuclear sequence data of modern baboons, and hybridization and introgression have been suggested as the main drivers of these patterns. Baboons, therefore, present an excellent opportunity to study these phenomena and their impact on speciation. Advances both in geographic and genomic coverage provide increasing details on the complexity of the phylogeography of baboons. Here, we compile the georeferenced genetic data of baboons and review the current knowledge on baboon phylogeny, discuss the evolutionary processes that may have shaped the patterns that we observe today, and propose future avenues for research.

Baboon perspectives on the ecology and behavior of early human ancestors

For more than 70 y researchers have looked to baboons (monkeys of the genus Papio) as a source of hypotheses about the ecology and behavior of early hominins (early human ancestors and their close relatives). This approach has undergone a resurgence in the last decade as a result of rapidly increasing knowledge from experimental and field studies of baboons and from archeological and paleontological studies of hominins. The result is a rich array of analogies, scenarios, and other stimuli to thought about the ecology and behavior of early hominins. The main intent here is to illustrate baboon perspectives on early hominins, with emphasis on recent developments. This begins with a discussion of baboons and hominins as we know them currently and explains the reasons for drawing comparisons between them. These include occupation of diverse environments, combination of arboreal and terrestrial capabilities, relatively large body size, and sexual dimorphism. The remainder of the paper illustrates the main points with a small number of examples drawn from diverse areas of interest: diet (grasses and fish), danger (leopards and crocodiles), social organization (troops and multilevel societies), social relationships (male–male, male–female, female–female), communication (possible foundations of language), cognition (use of social information, comparison of self to others), and bipedalism (a speculative developmental hypothesis about the neurological basis). The conclusion is optimistic about the future of baboon perspectives on early hominins.

Symetryczna wyprzeniowa i zgięciowa osutka polekowa (zespół pawiana) wywołana kotrimoksazolem

Symetryczna wyprzeniowa i zgięciowa osutka polekowa (zespół pawiana) wywołana kotrimoksazolem

Social bonds, social status and survival in wild baboons: A tale of two sexes: Social effects on survival in baboons

Social bonds, social status and survival in wild baboons: A tale of two sexes: Social effects on survival in baboons

Mycobacterium tuberculosis in a Primagam negative wild caught captive olive baboon (Papio anubis) in Ethiopia

A free-roaming wild olive baboon (Papio anubis) was caught in the compound of a hospital and kept in captivity pending reintroduction to the wild. The animal had a sporadic dry cough but was TB negative on the blood-based assay PRIMAGAM (IFN-γ test). Six years later, the animal was found dead without any prior clinical signs. The lungs were severely affected. Laboratory analysis included Ziehl-Neelsen staining, GenExpert, culture, deletion typing and spoligotyping. M. tuberculosis was isolated. The spoligotype was SIT 53 (lineage 4) and no Rifampicin resistance was detected. This case report raised challenges on accurate diagnosis of TB in Non-Human Primates in Ethiopia, the question of latency in baboon and the lack of spread of a highly virulent TB strain in the Non-Human Primate colony. It also highlighted the potential role of TB transmission between Non-Human Primates and people in Ethiopia with impacts as well on public health as on primate conservation. Key words: Baboon; diagnostics; Ethiopia; Mycobacterium tuberculosis; tuberculosis

On the evolution of baboon greeting rituals.

To balance the trade-offs of male co-residence, males living in multi-male groups may exchange ritualized greetings. Although these non-aggressive signals are widespread in the animal kingdom, the repertoire described in the genus Papio is exceptional, involving potentially harmful behaviours such as genital fondling. Such greetings are among the most striking male baboon social interactions, yet their function remains disputed. Drawing on the comprehensive analysis from our own research on wild Guinea baboons, combined with a survey of the literature into other baboon species, we review the form and function of male-male ritualized greetings and their relation to the various social systems present in this genus. These ritualized signals differ between species in their occurrence, form and function. While ritualized greetings are rare in species with the most intense contest competition, the complexity of and risk involved in greeting rituals increase with the degree of male-male tolerance and cooperation. The variety of societies found in this genus, combined with its role as a model for human socioecological evolution, sheds light on the evolution of ritualized behaviour in non-human primates and rituals in humans. This article is part of the theme issue 'Ritual renaissance: new insights into the most human of behaviours'.

Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry

BackgroundBaboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-throughput “poly-Detect” method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data.ResultsWe identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings.ConclusionsOur discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting.

Insights into the evolution of social systems and species from baboon studies.

Baboons, members of the genus Papio, comprise six closely related species distributed throughout sub-Saharan Africa and southwest Arabia. The species exhibit more ecological flexibility and a wider range of social systems than many other primates. This article summarizes our current knowledge of the natural history of baboons and highlights directions for future research. We suggest that baboons can serve as a valuable model for complex evolutionary processes, such as speciation and hybridization. The evolution of baboons has been heavily shaped by climatic changes and population expansion and fragmentation in the African savanna environment, similar to the processes that acted during human evolution. With accumulating long-term data, and new data from previously understudied species, baboons are ideally suited for investigating the links between sociality, health, longevity and reproductive success. To achieve these aims, we propose a closer integration of studies at the proximate level, including functional genomics, with behavioral and ecological studies.

Species-specific effects of climate change on the distribution of suitable baboon habitats – Ecological niche modeling of current and Last Glacial Maximum conditions

Baboons (genus Papio) have been proposed as a possible analogous phylogeographic model for intra-African dispersal of hominins during the Pleistocene. Previous studies of the genus reveal complex evolutionary dynamics including introgressive hybridization and, as for hominins, it has been hypothesized that past climate change has been a major driver in their evolutionary history. However, how historical climate changes affected the distribution and extent of baboon habitats is not clear. We therefore employed three ecological niche modeling algorithms (maximum entropy model: MaxEnt; general additive model: GAM; gradient boosting model: GBM) to map suitable habitat of baboons at both genus and species levels under two extreme late-Quaternary climates: current (warm period) and Last Glacial Maximum (LGM, cold period). The three model algorithms predicted habitat suitabilities for the baboon species with high accuracy, as indicated by AUC values of 0.83–0.85 at genus level and ≥0.90 for species. The results suggest that climate change from LGM to current affected the distribution and extent of suitable habitats for the genus Papio only slightly (>80% of the habitat remained suitable). However, and in contrast to our expectation for ecological generalists, individual species have been differentially affected. While P. ursinus and P. anubis lost some of their suitable habitats (net loss 25.5% and 13.3% respectively), P. kindae and P. papio gained large portions (net gain >62%), and P. cynocephalus and P. hamadryas smaller portions (net gain >20%). Overlap among the specific realized climate niches remained small, suggesting only slight overlap of suitable habitat among species. Results of our study further suggest that shifts of suitable habitats could have led to isolation and reconnection of populations which most likely affected gene flow among them. The impact of historic climate changes on baboon habitats might have been similar for other savanna living species, such as hominins.

Baboons’ gut makeup is determined mostly by soil, not genetics

Baboons’ gut makeup is determined mostly by soil, not genetics

Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony.

Baboons (genus Papio) are broadly studied in the wild and in captivity. They are widely used as a nonhuman primate model for biomedical studies, and the Southwest National Primate Research Center (SNPRC) at Texas Biomedical Research Institute has maintained a large captive baboon colony for more than 50 yr. Unlike other model organisms, however, the genomic resources for baboons are severely lacking. This has hindered the progress of studies using baboons as a model for basic biology or human disease. Here, we describe a data set of 100 high-coverage whole-genome sequences obtained from the mixed colony of olive (P. anubis) and yellow (P. cynocephalus) baboons housed at the SNPRC. These data provide a comprehensive catalog of common genetic variation in baboons, as well as a fine-scale genetic map. We show how the data can be used to learn about ancestry and admixture and to correct errors in the colony records. Finally, we investigated the consequences of inbreeding within the SNPRC colony and found clear evidence for increased rates of infant mortality and increased homozygosity of putatively deleterious alleles in inbred individuals.

Listen: Pig-heart transplants in baboons work for longer than ever before

Improvements to process keep animals with transplanted tickers alive for three times longer. Improvements to process keep animals with transplanted tickers alive for three times longer.

Evolution of DNA Methylation in Papio Baboons.

Changes in gene regulation have long been thought to play an important role in primate evolution. However, although a number of studies have compared genome-wide gene expression patterns across primate species, fewer have investigated the gene regulatory mechanisms that underlie such patterns, or the relative contribution of drift versus selection. Here, we profiled genome-scale DNA methylation levels in blood samples from five of the six extant species of the baboon genus Papio (4-14 individuals per species). This radiation presents the opportunity to investigate DNA methylation divergence at both shallow and deeper timescales (0.380-1.4 My). In contrast to studies in human populations, but similar to studies in great apes, DNA methylation profiles clearly mirror genetic and geographic structure. Divergence in DNA methylation proceeds fastest in unannotated regions of the genome and slowest in regions of the genome that are likely more constrained at the sequence level (e.g., gene exons). Both heuristic approaches and Ornstein-Uhlenbeck models suggest that DNA methylation levels at a small set of sites have been affected by positive selection, and that this class is enriched in functionally relevant contexts, including promoters, enhancers, and CpG islands. Our results thus indicate that the rate and distribution of DNA methylation changes across the genome largely mirror genetic structure. However, at some CpG sites, DNA methylation levels themselves may have been a target of positive selection, pointing to loci that could be important in connecting sequence variation to fitness-related traits.

Baboon vocal repertoires and the evolution of primate vocal diversity

A remarkable and derived trait of humans is the faculty for language, and considerable research effort has been devoted to understanding the evolution of speech. In contrast to spoken language, which constitutes a (learned) symbolic communication system, the acoustic structure of nonhuman primate vocalizations is largely genetically fixed. Yet, appreciable differences between different genera and species may exist. Environmental conditions, sexual selection, and characteristics of the social system have been invoked to explain these differences. Here, we studied the acoustic variation of call types and vocal repertoires in the genus Papio. Because the genus comprises both stable groups as well as multi-level societies, and reveals striking variation in the degree of aggressiveness from south to north, it constitutes a promising model to assess the link between social system characteristics and vocal communication. We found that, the vocal repertoires of the different species were composed of the same general call types. A quantitative analysis of the acoustic features of the grunts and loud calls of chacma (Papio ursinus), olive (P. anubis), and Guinea (P. papio) baboons showed subtle acoustic differences within call types, however. Social system characteristics did not map onto acoustic variation. We found no correlation between the structure of grunts and geographic distance; the same was true for female loud calls. Only for male loud calls from three populations, call structure varied with geographic distance. Our findings corroborate the view that the structure of nonhuman primate vocalizations is highly conserved, despite the differences in social systems. Apparently, variation in rate and intensity of occurrence of signals, probably due to different behavioral dispositions in species, are sufficient to allow for plasticity at the level of the social relationships, mating patterns, and social organization.

Greetings in male Guinea baboons and the function of rituals in complex social groups

Ritualized greetings, defined as exchanges of non-aggressive signals, are common among males living in multi-male groups and are thought to balance the trade-offs of male co-residence. While ritualized greetings are widespread in the animal kingdom, the behavioral repertoire described in the genus Papio is exceptional, as it involves potentially harmful behaviors such as genital fondling. Although greetings are one of the most striking male social interactions in baboons, their function is still disputed. We investigated the function of male–male ritualized greeting behavior in wild Guinea baboons. This species lives in multilevel societies where several ‘units’ comprising a primary male, females with young, and occasionally a secondary male form a ‘party’, and two to three parties form a gang. Adult males maintain affiliative relationships with preferred male partners whom they support in coalitions, regardless of kinship. We examined the social behavior of 24 adolescent and adult males (∼900 h focal observations) in the Niokolo-Koba National Park, Senegal, to test whether greetings reflect relationship quality or function to buffer tension. Greetings were ten times more frequent than aggression and twice as frequent as affiliation. Neither dyadic aggression nor tense context predicted greeting rate, discounting the buffering hypothesis. Greetings occurred almost exclusively between males of the same party, even when other parties were around. Within parties, spatially tolerant partners greeted more frequently but dyads did not greet due to proximity prior to the greeting. Although affiliation did not predict overall greeting rate, intense and potentially costly greetings were more likely between males with stronger affiliative relationships. Greetings in Guinea baboons appear to signal commitment among party members, test relationships among spatially tolerant partners, and accentuate relationship strength among highly affiliated males. Although ritualized baboon greetings lack the symbolic component of human rituals, they appear to serve similar functions, specifically to strengthen in-group affiliation and promote cooperation.

Correction: Disrupted dispersal and its genetic consequences: Comparing protected and threatened baboon populations (Papio papio) in West Africa.

[This corrects the article DOI: 10.1371/journal.pone.0194189.].

What Is (Not) a Baboon?

The term “baboon” is the common name used for a subset of terrestrial Cercopithecines with large bodies and protruding snouts. Although the application of the term has changed considerably over the years, we argue that common names, such as “baboon,” should reflect the current state of phylogenetic knowledge. This practice promotes a broader understanding of taxonomic diversity that can impact decisions related to ecotourism, wildlife management, and conservation. Thus, we argue that “baboon” should be used only for members of the genus Papio.

Identification and Molecular Characterization of Alpha Papillomavirus from Male Olive Baboons (Papio anubis) Maintained in a Captive Colony

Papillomaviruses (PVs) are ubiquitous highly diverse group of circular double stranded DNA viruses. Nearly all the human papillomavirus (HPVs) that cause cancer are clustered in Alphapapillomavirus (αPV) genera and have a common ancestor. The aim of the study was to isolate and perform molecular characterization of alphapapilloma virus from male olive baboons (Papio anubis) that are maintained in a captive colony at the Institute of Primate Research, Nairobi, Kenya and establish their evolutionary relationship with known strains responsible for various species causing cervical cancer in human. Twenty (n=20) different genital swabs from sexually active male olive baboons were collected. Positive samples for αPV by nested PCR were 9/20 (45%). The nested PCR primers targeted a conserved region of L1 major capsid gene and aided in generating amplicons of 134bp. Only three amplicons with good quality bands (1C, 2C, and 4C) were further sequenced and analysed using MEGA X, Clustal W algorithm and DnaSP 5.10.01 software. Phylogenetic analysis through Neighbour-joining method indicated a close evolutionary relationship between subtype 2C and Human papillomavirus (AB745694) which is associated with human cervical cancer. Subtype 2C was found to be more close to 1C than 4C and other sequences of JF304764, EU490515, EF558839, AB745694, FJ598133 as well as EF591300 blasted from NCBI and treated as outgroup. On analysis of genetic diversity using DnaSP software, sequences of subtype 2C and 4C were found to harbour synonymous SNPs at position four and eight respectively hence indicating that the region is more conserved. Male olive baboon harbor αPV and may be a good model for study of the pathogenesis of HPV and also for testing therapeutic agents that target αPVs in both humans and non-human primates.

Antimicrobial Susceptibility Patterns of Escherichia coli Isolated from Olive Baboon ( Papio anubis ) Gut

Background: Antimicrobial resistance is widely acknowledged as a global health problem that has resulted in devastating emerging and re-emerging conditions which are difficult to manage due to limited or unavailable intervention options. It is deepened by the fact that genes encoding for antimicrobial resistance can be transferred horizontally by mobile genetic elements. Escherichia coli is primarily a gut microbial flora in warm-blooded animals including non-human primates that can acquire any of these gene elements from other resistant bacterial strains resulting in their transmission between humans and animals. This study aimed to determine antimicrobial susceptibility of E. coli against commonly used agents as well as production of extended spectrum β-lactamases. Methods: E. coli was isolated from stool samples that were collected from sixty-two captive and sixty-two wild baboons using culture-based methods. The isolates were subjected to fourteen antimicrobial agents followed by characterization of three putative resistance genes; blaCTX-M, blaTEM and blaSHV using polymerase chain reaction. Results: E. coli isolates from both groups of animals were resistant to all antimicrobial agents except Ciprofloxacin. Prevalence of Ampicillin resistance was high in E. coli isolated from both captive (32.3%) and wild (35.5%) baboons. There was higher prevalence of ESBLs in E. coli isolated from wild (17.7%) than captive (14.5%) baboons. Conclusion: As reservoirs of ESBL producing E. coli type, baboons could play a potential role in antibiotic resistant plasmids transmission to the environment and other animals including humans.