Background: Comparative data from non-human primates provide insight into the processes that shap... more Background: Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, nonhuman primates. Results: Contrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates. Conclusions: Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.
The great apes are in deep trouble. Their habitats are being logged rapidly, their numbers are dw... more The great apes are in deep trouble. Their habitats are being logged rapidly, their numbers are dwindling, and conservation solutions are spotty and unproven. There is a dire need for better oversight, more monitoring, greater habitat protection, less consumerism, and incentives for locals to preserve the great apes and their habitat. Moreover, we are running out of time. According to Conservation International, three great apes-the Cross River gorilla, the eastern lowland gorilla, and the Sumatran orangutan-are among the 25 most endangered primates. Great ape conservation is inextricably linked to the economic status of the humans who share their habitat. With abject poverty prevailing in 16 of the 23 countries where great apes live, many find financial gain through logging and trade or slaughter of apes and other species. Practical conservation solutions are needed, and one step toward this is a clear understanding of the present status of each of the great apes in their ranges. The World Atlas of Great Apes and Their Conservation is a remarkably comprehensive and very timely contribution. This volume is the result of collaboration among editors Julian Caldecott and Lera Miles, a host of notable primatologists and conservation-minded contributors, and an afterword by Russell Mittermeier, director of Conservation International. The editors are affiliated with the United Nations Environment Program (UNEP) which launched the Great Ape Survival Project (GRASP) in 2001. GRASP is made up of governments of great ape range countries, UN bodies, nongovernmental organizations (NGOs), civilians, and private-sector interests concerned with great ape conservation. GRASP's mission is to help all great ape range countries work together to develop a coherent global strategy for great ape conservation and raise the funds to implement it. The goal of the atlas is to raise awareness about the plight of the great apes, to spur global action for great ape conservation, and to provide a database of information for researchers and activists who can advocate for change where it is most needed. Toward these goals, this hefty, beautifully illustrated book is divided into four sections. The first section focuses on human interest in the great apes (both historical and evolutionary), and is followed by a section on extant great ape natural history. A third section is devoted to challenges, both past
This dataset contains all data used in the two studies included in "PICAN-PI..." by Nut... more This dataset contains all data used in the two studies included in "PICAN-PI..." by Nute, et al, other than the original raw sequences. That includes: 1) Supplementary information for the Manuscript, including all the graphics that were created, 2) 16S Reference Alignment, Phylogeny and Taxonomic Annotation used by SEPP, and 3) Data used in the manuscript as input for the graphics generation (namely, SEPP outputs and sequence multiplicities).
We examined a purported lemur (Eulemur fulvus rufus  E. albocollaris) hybrid zone at Andringitra... more We examined a purported lemur (Eulemur fulvus rufus  E. albocollaris) hybrid zone at Andringitra, Madagascar, using sequences from five genes (one mitochondrial gene (d-loop) and four nuclear introns (hemopexin, malic enzyme, ceruloplasmin, and microsatellite 26 flanking region)), from 60 individuals (E. albocollaris (n = 16), E.f. rufus (n = 14), E. collaris (n = 9), and purported hybrids from Andringitra (n = 21)). Diagnostic (d-loop and microsatellite 26) and private sites (all other genes) were found in all gene regions for E. albocollaris and E.f. rufus. Also, private sites were found for the purported hybrid population in two gene regions (d-loop and ceruloplasmin). When the putative hybrids were examined for diagnostic and private markers, 18 of 21 were found to contain markers from both E. albocollaris and E.f. rufus populations. The remaining three individuals were found to contain only markers for E. albocollaris. These results indicate that the population at Andringitra is a hybrid population between E. albocollaris and E.f. rufus.
Sulawesi endemic Macaca maura is included in the IUCN Red List as Endangered due to anthropogenic... more Sulawesi endemic Macaca maura is included in the IUCN Red List as Endangered due to anthropogenic disturbance and fragmentation of its habitat. Residual populations have a scattered distribution in the karst forests of south Sulawesi. Here the dissolution of limestone layers has created a multi-level landscape hardly accessible for ground predators and humans. In this study, we aimed to obtain better knowledge on the ecological flexibility of M. maura in the use of such a complex habitat, and its consequences on health status. Since all data published on M. maura were obtained from a single group (group B), an additional group (G) was habituated to human presence. We analysed 50 vegetation plots (10 × 20 metres) to discriminate structural features in terms of feeding options (e.g. key food species diversity, density and DBH) and anthropogenic disturbance (e.g. human trails and solid litter). We then correlated these data with habitat use and helminth infection. We collected 74 faecal samples from 18 different adult individuals belonging to both groups. Vegetation analysis suggested that there were 2 suitable habitats: a Ground Forest (e.g. higher abundance of key food species) and a Karst Tower Forest (e.g. lower presence of human trails and solid litter). Gastrointestinal investigation revealed a positive correlation between the prevalence of Trichuris sp. and time devoted to ground food-related activities in all individuals (Spearman correlation, rs = 0.665, p = 0.003). Moreover, behavioural data confirmed that group B, the larger study group of the area, spent most of its activity time in the Ground Forest (N group B = 33 ± 1; N group G = 18 ± 1; χ 2 = 134.30, d.f. = 1, p < 0.001). Since resource availability and predation risk can influence foraging decisions and, ultimately, space use, the "group size effect" might explain the significantly higher proportion of time spent by group B in the Ground Forest. Consequently, due to the Trichuris faecal-oral contamination life-cycle, the chance of infecting individuals based on their feeding habits might be described according to the "soil-transmitted helminthiasis hypothesis".
Background: Comparative data from non-human primates provide insight into the processes that shap... more Background: Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, nonhuman primates. Results: Contrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates. Conclusions: Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.
The great apes are in deep trouble. Their habitats are being logged rapidly, their numbers are dw... more The great apes are in deep trouble. Their habitats are being logged rapidly, their numbers are dwindling, and conservation solutions are spotty and unproven. There is a dire need for better oversight, more monitoring, greater habitat protection, less consumerism, and incentives for locals to preserve the great apes and their habitat. Moreover, we are running out of time. According to Conservation International, three great apes-the Cross River gorilla, the eastern lowland gorilla, and the Sumatran orangutan-are among the 25 most endangered primates. Great ape conservation is inextricably linked to the economic status of the humans who share their habitat. With abject poverty prevailing in 16 of the 23 countries where great apes live, many find financial gain through logging and trade or slaughter of apes and other species. Practical conservation solutions are needed, and one step toward this is a clear understanding of the present status of each of the great apes in their ranges. The World Atlas of Great Apes and Their Conservation is a remarkably comprehensive and very timely contribution. This volume is the result of collaboration among editors Julian Caldecott and Lera Miles, a host of notable primatologists and conservation-minded contributors, and an afterword by Russell Mittermeier, director of Conservation International. The editors are affiliated with the United Nations Environment Program (UNEP) which launched the Great Ape Survival Project (GRASP) in 2001. GRASP is made up of governments of great ape range countries, UN bodies, nongovernmental organizations (NGOs), civilians, and private-sector interests concerned with great ape conservation. GRASP's mission is to help all great ape range countries work together to develop a coherent global strategy for great ape conservation and raise the funds to implement it. The goal of the atlas is to raise awareness about the plight of the great apes, to spur global action for great ape conservation, and to provide a database of information for researchers and activists who can advocate for change where it is most needed. Toward these goals, this hefty, beautifully illustrated book is divided into four sections. The first section focuses on human interest in the great apes (both historical and evolutionary), and is followed by a section on extant great ape natural history. A third section is devoted to challenges, both past
This dataset contains all data used in the two studies included in "PICAN-PI..." by Nut... more This dataset contains all data used in the two studies included in "PICAN-PI..." by Nute, et al, other than the original raw sequences. That includes: 1) Supplementary information for the Manuscript, including all the graphics that were created, 2) 16S Reference Alignment, Phylogeny and Taxonomic Annotation used by SEPP, and 3) Data used in the manuscript as input for the graphics generation (namely, SEPP outputs and sequence multiplicities).
We examined a purported lemur (Eulemur fulvus rufus  E. albocollaris) hybrid zone at Andringitra... more We examined a purported lemur (Eulemur fulvus rufus  E. albocollaris) hybrid zone at Andringitra, Madagascar, using sequences from five genes (one mitochondrial gene (d-loop) and four nuclear introns (hemopexin, malic enzyme, ceruloplasmin, and microsatellite 26 flanking region)), from 60 individuals (E. albocollaris (n = 16), E.f. rufus (n = 14), E. collaris (n = 9), and purported hybrids from Andringitra (n = 21)). Diagnostic (d-loop and microsatellite 26) and private sites (all other genes) were found in all gene regions for E. albocollaris and E.f. rufus. Also, private sites were found for the purported hybrid population in two gene regions (d-loop and ceruloplasmin). When the putative hybrids were examined for diagnostic and private markers, 18 of 21 were found to contain markers from both E. albocollaris and E.f. rufus populations. The remaining three individuals were found to contain only markers for E. albocollaris. These results indicate that the population at Andringitra is a hybrid population between E. albocollaris and E.f. rufus.
Sulawesi endemic Macaca maura is included in the IUCN Red List as Endangered due to anthropogenic... more Sulawesi endemic Macaca maura is included in the IUCN Red List as Endangered due to anthropogenic disturbance and fragmentation of its habitat. Residual populations have a scattered distribution in the karst forests of south Sulawesi. Here the dissolution of limestone layers has created a multi-level landscape hardly accessible for ground predators and humans. In this study, we aimed to obtain better knowledge on the ecological flexibility of M. maura in the use of such a complex habitat, and its consequences on health status. Since all data published on M. maura were obtained from a single group (group B), an additional group (G) was habituated to human presence. We analysed 50 vegetation plots (10 × 20 metres) to discriminate structural features in terms of feeding options (e.g. key food species diversity, density and DBH) and anthropogenic disturbance (e.g. human trails and solid litter). We then correlated these data with habitat use and helminth infection. We collected 74 faecal samples from 18 different adult individuals belonging to both groups. Vegetation analysis suggested that there were 2 suitable habitats: a Ground Forest (e.g. higher abundance of key food species) and a Karst Tower Forest (e.g. lower presence of human trails and solid litter). Gastrointestinal investigation revealed a positive correlation between the prevalence of Trichuris sp. and time devoted to ground food-related activities in all individuals (Spearman correlation, rs = 0.665, p = 0.003). Moreover, behavioural data confirmed that group B, the larger study group of the area, spent most of its activity time in the Ground Forest (N group B = 33 ± 1; N group G = 18 ± 1; χ 2 = 134.30, d.f. = 1, p < 0.001). Since resource availability and predation risk can influence foraging decisions and, ultimately, space use, the "group size effect" might explain the significantly higher proportion of time spent by group B in the Ground Forest. Consequently, due to the Trichuris faecal-oral contamination life-cycle, the chance of infecting individuals based on their feeding habits might be described according to the "soil-transmitted helminthiasis hypothesis".
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