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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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D'Atanasio E, Risi F, Ravasini F, Montinaro F, Hajiesmaeil M, Bonucci B, Pistacchia L, Amoako-Sakyi D, Bonito M, Onidi S, Colombo G, Semino O, Destro Bisol G, Anagnostou P, Metspalu M, Tambets K, Trombetta B, Cruciani F. The genomic echoes of the last Green Sahara on the Fulani and Sahelian people. Curr Biol 2023; 33:5495-5504.e4. [PMID: 37995693 DOI: 10.1016/j.cub.2023.10.075] [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: 05/04/2023] [Revised: 09/28/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
The population history of the Sahara/Sahelian belt is understudied, despite previous work highlighting complex dynamics.1,2,3,4,5,6,7 The Sahelian Fulani, i.e., the largest nomadic pastoral population in the world,8 represent an interesting case because they show a non-negligible proportion of an Eurasian genetic component, usually explained by recent admixture with northern Africans.1,2,5,6,7,9,10,11,12 Nevertheless, their origins are largely unknown, although several hypotheses have been proposed, including a possible link to ancient peoples settled in the Sahara during its last humid phase (Green Sahara, 12,000-5,000 years before present [BP]).13,14,15 To shed light about the Fulani ancient genetic roots, we produced 23 high-coverage (30×) whole genomes from Fulani individuals from 8 Sahelian countries, plus 17 samples from other African groups and 3 from Europeans as controls, for a total of 43 new whole genomes. These data have been compared with 814 published modern whole genomes2,16,17,18 and with relevant published ancient sequences (> 1,800 samples).19 These analyses showed some evidence that the non-sub-Saharan genetic ancestry component of the Fulani might have also been shaped by older events,1,5,6 possibly tracing the Fulani origins to unsampled ancient Green Saharan population(s). The joint analysis of modern and ancient samples allowed us to shed light on the genetic ancestry composition of such ancient Saharans, suggesting a similarity with Late Neolithic Moroccans and possibly pointing to a link with the spread of cattle herding. We also identified two different Fulani clusters whose admixture pattern may be informative about the historical Fulani movements and their later involvement in the western African empires.
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Affiliation(s)
- Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy.
| | - Flavia Risi
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Montinaro
- Department of Biology, University of Bari, 70121 Bari, Italy; Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Mogge Hajiesmaeil
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Letizia Pistacchia
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy; Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Daniel Amoako-Sakyi
- Department of Microbiology and Immunology, University of Cape Coast, Cape Coast, Ghana
| | - Maria Bonito
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Sara Onidi
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Giovanni Destro Bisol
- Department of Enviromental Biology, Sapienza University of Rome, 00185 Rome, Italy; Istituto Italiano di Antropologia, 00185 Rome, Italy
| | - Paolo Anagnostou
- Department of Enviromental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | | | - Beniamino Trombetta
- Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Fulvio Cruciani
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy; Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy.
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Garnås E. Perspective: Darwinian Applications to Nutrition-The Value of Evolutionary Insights to Teachers and Students. Adv Nutr 2022; 13:1431-1439. [PMID: 35675225 PMCID: PMC9526857 DOI: 10.1093/advances/nmac063] [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: 04/06/2022] [Revised: 05/13/2022] [Accepted: 05/30/2022] [Indexed: 01/28/2023] Open
Abstract
Evolutionary biology informs us that the living world is a product of evolution, guided by the Darwinian mechanism of natural selection. This recognition has been fruitfully employed in a number of issues in health and nutrition sciences; however, it has not been incorporated into education. Nutrition and dietetics students generally learn very little or nothing on the subject of evolution, despite the fact that evolution is the process by which our genetically determined physiological traits and needs were shaped. In the present Perspective article, 3 examples of topics (inflammatory diseases, nutrition transition, and food intolerance) that can benefit from evolutionary information and reasoning are given, with relevant lines of research and inquiry provided throughout. It is argued that the application of evolutionary science to these and other areas of nutrition education can facilitate a deeper and more coherent teaching and learning experience. By recognizing and reframing nutrition as an aspect and discipline of biology, grounded in the fundamental principle of adaptation, revelatory light is shed on physiological states and responses, contentious and unresolved issues, genomic, epigenomic, and microbiomic features, and optimal nutrient status and intakes.
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Affiliation(s)
- Eirik Garnås
- Institute of Health, Oslo New University College, Oslo, Norway
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Forni D, Cagliani R, Clerici M, Pozzoli U, Sironi M. You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations. Mol Biol Evol 2020; 37:442-454. [PMID: 31593241 DOI: 10.1093/molbev/msz227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise FST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based FST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations.
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Affiliation(s)
- Diego Forni
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Lecco, Italy
| | - Rachele Cagliani
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Lecco, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Uberto Pozzoli
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Lecco, Italy
| | - Manuela Sironi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Lecco, Italy
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