1
|
Santiago MFM, Raulo A. Finding common connections. eLife 2023; 12:e89468. [PMID: 37358559 DOI: 10.7554/elife.89468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Ecological associations among gut bacteria are largely consistent across hosts in a population of wild baboons.
Collapse
Affiliation(s)
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Computing, University of Turku, Turku, Finland
| |
Collapse
|
2
|
Roche KE, Bjork JR, Dasari MR, Grieneisen L, Jansen D, Gould TJ, Gesquiere LR, Barreiro LB, Alberts SC, Blekhman R, Gilbert JA, Tung J, Mukherjee S, Archie EA. Universal gut microbial relationships in the gut microbiome of wild baboons. eLife 2023; 12:e83152. [PMID: 37158607 PMCID: PMC10292843 DOI: 10.7554/elife.83152] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/08/2023] [Indexed: 05/10/2023] Open
Abstract
Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing the overall direction and strength of these relationships is essential to learn how ecology scales up to affect microbiome assembly, dynamics, and host health. However, whether bacterial relationships are generalizable across hosts or personalized to individual hosts is debated. Here, we apply a robust, multinomial logistic-normal modeling framework to extensive time series data (5534 samples from 56 baboon hosts over 13 years) to infer thousands of correlations in bacterial abundance in individual baboons and test the degree to which bacterial abundance correlations are 'universal'. We also compare these patterns to two human data sets. We find that, most bacterial correlations are weak, negative, and universal across hosts, such that shared correlation patterns dominate over host-specific correlations by almost twofold. Further, taxon pairs that had inconsistent correlation signs (either positive or negative) in different hosts always had weak correlations within hosts. From the host perspective, host pairs with the most similar bacterial correlation patterns also had similar microbiome taxonomic compositions and tended to be genetic relatives. Compared to humans, universality in baboons was similar to that in human infants, and stronger than one data set from human adults. Bacterial families that showed universal correlations in human infants were often universal in baboons. Together, our work contributes new tools for analyzing the universality of bacterial associations across hosts, with implications for microbiome personalization, community assembly, and stability, and for designing microbiome interventions to improve host health.
Collapse
Affiliation(s)
- Kimberly E Roche
- Program in Computational Biology and Bioinformatics, Duke UniversityDurhamUnited States
| | - Johannes R Bjork
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and HepatologyGroningenNetherlands
- University of Groningen and University Medical Center Groningen, Department of GeneticsGroningenNetherlands
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Mauna R Dasari
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan CampusKelownaCanada
| | - David Jansen
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Trevor J Gould
- Department of Ecology, Evolution, and Behavior, University of MinnesotaMinneapolisUnited States
| | | | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of ChicagoChicagoUnited States
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
- Committee on Immunology, University of ChicagoChicagoUnited States
| | - Susan C Alberts
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke University Population Research Institute, Duke UniversityDurhamUnited States
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
| | - Jack A Gilbert
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San DiegoSan DiegoUnited States
| | - Jenny Tung
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke University Population Research Institute, Duke UniversityDurhamUnited States
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke UniversityDurhamUnited States
- Departments of Statistical Science, Mathematics, Computer Science, and Bioinformatics & Biostatistics, Duke UniversityDurhamUnited States
- Center for Scalable Data Analytics and Artificial Intelligence, University of LeipzigLeipzigGermany
- Max Plank Institute for Mathematics in the Natural SciencesLeipzigGermany
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| |
Collapse
|
3
|
Becker Y, Claidière N, Margiotoudi K, Marie D, Roth M, Nazarian B, Anton JL, Coulon O, Meguerditchian A. Broca area homologue's asymmetry reflects gestural communication lateralisation in monkeys (Papio anubis). eLife 2022; 11:70521. [PMID: 35108197 PMCID: PMC8846582 DOI: 10.7554/elife.70521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 02/01/2022] [Indexed: 11/23/2022] Open
Abstract
Manual gestures and speech recruit a common neural network, involving Broca’s area in the left hemisphere. Such speech-gesture integration gave rise to theories on the critical role of manual gesturing in the origin of language. Within this evolutionary framework, research on gestural communication in our closer primate relatives has received renewed attention for investigating its potential language-like features. Here, using in vivo anatomical MRI in 50 baboons, we found that communicative gesturing is related to Broca homologue’s marker in monkeys, namely the ventral portion of the Inferior Arcuate sulcus (IA sulcus). In fact, both direction and degree of gestural communication’s handedness – but not handedness for object manipulation are associated and correlated with contralateral depth asymmetry at this exact IA sulcus portion. In other words, baboons that prefer to communicate with their right hand have a deeper left-than-right IA sulcus, than those preferring to communicate with their left hand and vice versa. Interestingly, in contrast to handedness for object manipulation, gestural communication’s lateralisation is not associated to the Central sulcus depth asymmetry, suggesting a double dissociation of handedness’ types between manipulative action and gestural communication. It is thus not excluded that this specific gestural lateralisation signature within the baboons’ frontal cortex might reflect a phylogenetical continuity with language-related Broca lateralisation in humans.
Collapse
Affiliation(s)
- Yannick Becker
- UMR7290, Laboratoire de Psychologie Cognitive, CNRS, Aix-Marseille University, Marseille, France
| | - Nicolas Claidière
- UMR7290, Laboratoire de Psychologie Cognitive, CNRS, Aix-Marseille University, Marseille, France
| | - Konstantina Margiotoudi
- UMR7290, Laboratoire de Psychologie Cognitive, CNRS, Aix-Marseille University, Marseille, France
| | - Damien Marie
- UMR7290, Laboratoire de Psychologie Cognitive, CNRS, Aix-Marseille University, Marseille, France
| | - Muriel Roth
- Centre IRMf Institut de Neurosciences de la Timone, CNRS, Aix-Marseille University, Marseille, France
| | - Bruno Nazarian
- Centre IRM Institut de Neurosciences de la Timone, CNRS, Aix-Marseille University, Marseille, France
| | - Jean-Luc Anton
- Centre IRM Institut de Neurosciences de la Timone, CNRS, Aix-Marseille University, Marseille, France
| | - Olivier Coulon
- Institut de Neurosciences de la Timone, CNRS, Aix-Marseille University, Marseille, France
| | - Adrien Meguerditchian
- Laboratoire de Psychologie Cognitive, CNRS, Aix-Marseille University, Marseille, France
| |
Collapse
|
4
|
Ryan CP, Kuzawa CW. The temporary cost of dominance. eLife 2021; 10:68790. [PMID: 33929318 PMCID: PMC8087441 DOI: 10.7554/elife.68790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 11/29/2022] Open
Abstract
In a population of wild baboons, a new way to assess biological age reveals a surprising effect of social hierarchy.
Collapse
Affiliation(s)
- Calen P Ryan
- Department of Anthropology, Northwestern University, Evanston, United States
| | - Christopher W Kuzawa
- Department of Anthropology, Northwestern University, Evanston, United States.,Institute for Policy Research, Northwestern University, Evanston, United States
| |
Collapse
|
5
|
Anderson JA, Johnston RA, Lea AJ, Campos FA, Voyles TN, Akinyi MY, Alberts SC, Archie EA, Tung J. High social status males experience accelerated epigenetic aging in wild baboons. eLife 2021; 10:e66128. [PMID: 33821798 PMCID: PMC8087445 DOI: 10.7554/elife.66128] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/18/2021] [Indexed: 12/14/2022] Open
Abstract
Aging, for virtually all life, is inescapable. However, within populations, biological aging rates vary. Understanding sources of variation in this process is central to understanding the biodemography of natural populations. We constructed a DNA methylation-based age predictor for an intensively studied wild baboon population in Kenya. Consistent with findings in humans, the resulting 'epigenetic clock' closely tracks chronological age, but individuals are predicted to be somewhat older or younger than their known ages. Surprisingly, these deviations are not explained by the strongest predictors of lifespan in this population, early adversity and social integration. Instead, they are best predicted by male dominance rank: high-ranking males are predicted to be older than their true ages, and epigenetic age tracks changes in rank over time. Our results argue that achieving high rank for male baboons - the best predictor of reproductive success - imposes costs consistent with a 'live fast, die young' life-history strategy.
Collapse
Affiliation(s)
- Jordan A Anderson
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Rachel A Johnston
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Amanda J Lea
- Department of Biology, Duke UniversityDurhamUnited States
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton UniversityPrincetonUnited States
- Department of Ecology and Evolution, Princeton UniversityPrincetonUnited States
| | - Fernando A Campos
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Anthropology, University of Texas at San AntonioSan AntonioUnited States
| | - Tawni N Voyles
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Mercy Y Akinyi
- Institute of Primate Research, National Museums of KenyaNairobiKenya
| | - Susan C Alberts
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Department of Biology, Duke UniversityDurhamUnited States
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Department of Biology, Duke UniversityDurhamUnited States
- Duke Population Research Institute, Duke UniversityDurhamUnited States
- Canadian Institute for Advanced ResearchTorontoCanada
| |
Collapse
|
6
|
Dominy NJ, Ikram S, Moritz GL, Wheatley PV, Christensen JN, Chipman JW, Koch PL. Mummified baboons reveal the far reach of early Egyptian mariners. eLife 2020; 9:60860. [PMID: 33319742 PMCID: PMC7738181 DOI: 10.7554/elife.60860] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
The Red Sea was witness to important events during human history, including the first long steps in a trade network (the spice route) that would drive maritime technology and shape geopolitical fortunes for thousands of years. Punt was a pivotal early node in the rise of this enterprise, serving as an important emporium for luxury goods, including sacred baboons (Papio hamadryas), but its location is disputed. Here, we use geospatial variation in the oxygen and strontium isotope ratios of 155 baboons from 77 locations to estimate the geoprovenance of mummified baboons recovered from ancient Egyptian temples and tombs. Five Ptolemaic specimens of P. anubis (404–40 BC) showed evidence of long-term residency in Egypt prior to mummification, consistent with a captive breeding program. Two New Kingdom specimens of P. hamadryas were sourced to a region that encompasses much of present-day Ethiopia, Eritrea, and Djibouti, and portions of Somalia and Yemen. This result is a testament to the tremendous reach of Egyptian seafaring during the 2nd millennium BC. It also corroborates the balance of scholarly conjecture on the location of Punt. Strontium is a chemical element that can act as a geographic fingerprint: its composition differs between locations, and as it enters the food chain, it can help to retrace the life history of extant or past animals. In particular, strontium in teeth – which stop to develop early – can reveal where an individual was born; strontium in bone and hair, on the other hand, can show where it lived just before death. Together, these analyses may hold the key to archaeological mysteries, such as the location of a long-lost kingdom revered by ancient Egyptians. For hundreds of years, the Land of Punt was one of Egypt’s strongest trading partners, and a place from which to import premium incense and prized monkeys. Travellers could reach Punt by venturing south and east of Egypt, suggesting that the kingdom occupied the southern Red Sea region. Yet its exact location is still highly debated. To investigate, Dominy et al. examined the mummies of baboons present in ancient Egyptian tombs, and compared the strontium compositions of the bones, hair and teeth of these remains with the ones found in baboons living in various regions across Africa. This shed a light on the origins of the ancient baboons: while some were probably raised in captivity in Egypt, others were born in modern Ethiopia, Eritrea, Djibouti, Somalia and Yemen – areas already highlighted as potential locations for the Land of Punt. The work by Dominy et al. helps to better understand the ancient trade routes that shaped geopolitical fortunes for millennia. It also highlights the need for further archaeological research in Eritrea and Somalia, two areas which are currently understudied.
Collapse
Affiliation(s)
- Nathaniel J Dominy
- Departments of Anthropology and Biological Sciences, Dartmouth College, Hanover, United States
| | - Salima Ikram
- Department of Sociology, Egyptology, and Anthropology, American University in Cairo, New Cairo, Egypt
| | - Gillian L Moritz
- Departments of Anthropology and Biological Sciences, Dartmouth College, Hanover, United States
| | - Patrick V Wheatley
- Center for Isotope Geochemistry, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - John N Christensen
- Center for Isotope Geochemistry, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Paul L Koch
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, Santa Cruz, United States
| |
Collapse
|
7
|
Zipple MN, Archie EA, Tung J, Altmann J, Alberts SC. Intergenerational effects of early adversity on survival in wild baboons. eLife 2019; 8:e47433. [PMID: 31549964 PMCID: PMC6759315 DOI: 10.7554/elife.47433] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/06/2019] [Indexed: 01/09/2023] Open
Abstract
Early life adversity can affect an individual's health, survival, and fertility for many years after the adverse experience. Whether early life adversity also imposes intergenerational effects on the exposed individual's offspring is not well understood. We fill this gap by leveraging prospective, longitudinal data on a wild, long-lived primate. We find that juveniles whose mothers experienced early life adversity exhibit high mortality before age 4, independent of the juvenile's own experience of early adversity. These juveniles often preceded their mothers in death by 1 to 2 years, indicating that high adversity females decline in their ability to raise offspring near the end of life. While we cannot exclude direct effects of a parent's environment on offspring quality (e.g., inherited epigenetic changes), our results are completely consistent with a classic parental effect, in which the environment experienced by a parent affects its future phenotype and therefore its offspring's phenotype.
Collapse
Affiliation(s)
| | - Elizabeth A Archie
- Department of Biological SciencesUniversity of Notre DameSouth BendUnited States
- Institute of Primate Research, National Museums of KenyaNairobiKenya
| | - Jenny Tung
- Department of BiologyDuke UniversityDurhamUnited States
- Institute of Primate Research, National Museums of KenyaNairobiKenya
- Department of Evolutionary AnthropologyDuke UniversityDurhamUnited States
- Duke Population Research InstituteDuke UniversityDurhamUnited States
| | - Jeanne Altmann
- Institute of Primate Research, National Museums of KenyaNairobiKenya
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonUnited States
| | - Susan C Alberts
- Department of BiologyDuke UniversityDurhamUnited States
- Institute of Primate Research, National Museums of KenyaNairobiKenya
- Department of Evolutionary AnthropologyDuke UniversityDurhamUnited States
- Duke Population Research InstituteDuke UniversityDurhamUnited States
| |
Collapse
|