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Foley RA, Mirazón Lahr M. Ghosts of extinct apes: genomic insights into African hominid evolution. Trends Ecol Evol 2024; 39:456-466. [PMID: 38302324 DOI: 10.1016/j.tree.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024]
Abstract
We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.
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Affiliation(s)
- Robert A Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK.
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK
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Pougnault L, Levréro F, Leroux M, Paulet J, Bombani P, Dentressangle F, Deruti L, Mulot B, Lemasson A. Social pressure drives "conversational rules" in great apes. Biol Rev Camb Philos Soc 2021; 97:749-765. [PMID: 34873806 DOI: 10.1111/brv.12821] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 01/07/2023]
Abstract
In the last decade, two hypotheses, one on the evolution of animal vocal communication in general and the other on the origins of human language, have gained ground. The first hypothesis argues that the complexity of communication co-evolved with the complexity of sociality. Species forming larger groups with complex social networks have more elaborate vocal repertoires. The second hypothesis posits that the core of communication is represented not only by what can be expressed by an isolated caller, but also by the way that vocal interactions are structured, language being above all a social act. Primitive forms of conversational rules based on a vocal turn-taking principle are thought to exist in primates. To support and bring together these hypotheses, more comparative studies of socially diverse species at different levels of the primate phylogeny are needed. However, the majority of available studies focus on monkeys, primates that are distant from the human lineage. Great apes represent excellent candidates for such comparative studies because of their phylogenetic proximity to humans and their varied social lives. We propose that studying vocal turn-taking in apes could address several major gaps regarding the social relevance of vocal turn-taking and the evolutionary trajectory of this behaviour among anthropoids. Indeed, how the social structure of a species may influence the vocal interaction patterns observed among group members remains an open question. We gathered data from the literature as well as original unpublished data (where absent in the literature) on four great ape species: chimpanzees Pan troglodytes, bonobos Pan paniscus, western lowland gorillas Gorilla gorilla gorilla and Bornean orang-utans Pongo pygmaeus. We found no clear-cut relationship between classical social complexity metrics (e.g. number of group members, interaction rates) and vocal complexity parameters (e.g. repertoire size, call rates). Nevertheless, the nature of the society (i.e. group composition, diversity and valence of social bonds) and the type of vocal interaction patterns (isolated calling, call overlap, turn-taking-based vocal exchanges) do appear to be related. Isolated calling is the main vocal pattern found in the species with the smallest social networks (orang-utan), while the other species show vocal interactions that are structured according to temporal rules. A high proportion of overlapping vocalisations is found in the most competitive species (chimpanzee), while vocal turn-taking predominates in more tolerant bonobos and gorillas. Also, preferentially interacting individuals and call types used to interact are not randomly distributed. Vocal overlap ('chorusing') and vocal exchange ('conversing') appear as possible social strategies used to advertise/strengthen social bonds. Our analyses highlight that: (i) vocal turn-taking is also observed in non-human great apes, revealing universal rules for conversing that may be deeply rooted in the primate lineage; (ii) vocal interaction patterns match the species' social lifestyle; (iii) although limited to four species here, adopting a targeted comparative approach could help to identify the multiple and subtle factors underlying social and vocal complexity. We believe that vocal interaction patterns form the basis of a promising field of investigation that may ultimately improve our understanding of the socially driven evolution of communication.
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Affiliation(s)
- Loïc Pougnault
- Univ Rennes, Normandie Univ, CNRS, EthoS (Éthologie animale et humaine) - UMR 6552, 263 avenue du Général Leclerc, Rennes, 35042, France.,Université de Lyon/Saint-Etienne, CNRS, Equipe Neuro-Ethologie Sensorielle, ENES/CRNL, UMR5292, INSERM UMR_S 1028, 23 rue Paul Michelon, Saint-Etienne, 42023, France.,ZooParc de Beauval & Beauval Nature, Avenue du Blanc, Saint Aignan, 41110, France
| | - Florence Levréro
- Université de Lyon/Saint-Etienne, CNRS, Equipe Neuro-Ethologie Sensorielle, ENES/CRNL, UMR5292, INSERM UMR_S 1028, 23 rue Paul Michelon, Saint-Etienne, 42023, France
| | - Maël Leroux
- Department of Comparative Linguistics, University of Zürich, Thurgauerstrasse 30, Zürich-Oerlikon, 8050, Switzerland.,Budongo Conservation Field Station, Masindi, Uganda.,Center for the Interdisciplinary Study of Language Evolution (ISLE), University of Zürich, Plattenstrasse 54, Zürich, 8032, Switzerland
| | - Julien Paulet
- Univ Rennes, Normandie Univ, CNRS, EthoS (Éthologie animale et humaine) - UMR 6552, 263 avenue du Général Leclerc, Rennes, 35042, France
| | - Pablo Bombani
- NGO Mbou-Mon-Tour, Nkala, Territoire de Bolodo, Maï-Ndombe, Democratic Republic of the Congo
| | - Fabrice Dentressangle
- Université de Lyon/Saint-Etienne, CNRS, Equipe Neuro-Ethologie Sensorielle, ENES/CRNL, UMR5292, INSERM UMR_S 1028, 23 rue Paul Michelon, Saint-Etienne, 42023, France
| | - Laure Deruti
- Université de Lyon/Saint-Etienne, CNRS, Equipe Neuro-Ethologie Sensorielle, ENES/CRNL, UMR5292, INSERM UMR_S 1028, 23 rue Paul Michelon, Saint-Etienne, 42023, France
| | - Baptiste Mulot
- ZooParc de Beauval & Beauval Nature, Avenue du Blanc, Saint Aignan, 41110, France
| | - Alban Lemasson
- Univ Rennes, Normandie Univ, CNRS, EthoS (Éthologie animale et humaine) - UMR 6552, 263 avenue du Général Leclerc, Rennes, 35042, France.,Institut Universitaire de France, 1 rue Descartes, Paris, 75231, France
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Khan N, de Manuel M, Peyregne S, Do R, Prufer K, Marques-Bonet T, Varki N, Gagneux P, Varki A. Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins. Genome Biol Evol 2021; 12:1040-1050. [PMID: 32556248 PMCID: PMC7379906 DOI: 10.1093/gbe/evaa125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface “self-associated molecular patterns” that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2–3 Ma, possibly contributing to the origins of the genus Homo. The mutation likely altered human self-associated molecular patterns, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some gene-encoding Sia-sensing proteins suggested a “hotspot” in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human–Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal–human divergence ∼0.6 Ma. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, Natural Killer(NK) cells, and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6 and 2 Ma, potentially affecting human evolution.
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Affiliation(s)
- Naazneen Khan
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Stephane Peyregne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Raymond Do
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Kay Prufer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain
| | - Nissi Varki
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Pascal Gagneux
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
| | - Ajit Varki
- Glycobiology Research and Training Center, Department of Medicine, University of California San Diego.,Center for Academic Research and Training in Anthropogeny (CARTA),University of California San Diego
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