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Davies TW, Gunz P, Spoor F, Alemseged Z, Gidna A, Hublin JJ, Kimbel WH, Kullmer O, Plummer WP, Zanolli C, Skinner MM. Dental morphology in Homo habilis and its implications for the evolution of early Homo. Nat Commun 2024; 15:286. [PMID: 38177110 PMCID: PMC10767101 DOI: 10.1038/s41467-023-44375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/11/2023] [Indexed: 01/06/2024] Open
Abstract
The phylogenetic position of Homo habilis is central to debates over the origin and early evolution of the genus Homo. A large portion of the species hypodigm consists of dental remains, but they have only been studied at the often worn enamel surface. We investigate the morphology of the H. habilis enamel-dentine junction (EDJ), which is preserved in cases of moderate tooth wear and known to carry a strong taxonomic signal. Geometric morphometrics is used to characterise dentine crown shape and size across the entire mandibular and maxillary tooth rows, compared with a broad comparative sample (n = 712). We find that EDJ morphology in H. habilis is for the most part remarkably primitive, supporting the hypothesis that the H. habilis hypodigm has more in common with Australopithecus than later Homo. Additionally, the chronologically younger specimen OH 16 displays a suite of derived features; its inclusion in H. habilis leads to excessive levels of variation.
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Affiliation(s)
- Thomas W Davies
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- School of Anthropology and Conservation, University of Kent, Canterbury, UK.
| | - Philipp Gunz
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fred Spoor
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Centre for Human Evolution Research, Natural History Museum, London, UK
| | - Zeresenay Alemseged
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | - Agness Gidna
- Department of Cultural Heritage, Ngorongoro Conservation Area Authority, P. O. Box 1, Ngorongoro Crater, Arusha, Tanzania
| | - Jean-Jacques Hublin
- Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - William H Kimbel
- Institute of Human Origins, and School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Ottmar Kullmer
- Palaeobiology and Environment workgroup, Institute of Ecology, Evolution, and Diversity, Goethe University, Frankfurt, Germany
- Division of Palaeoanthropology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - William P Plummer
- School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Clément Zanolli
- Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600, Pessac, France
| | - Matthew M Skinner
- School of Anthropology and Conservation, University of Kent, Canterbury, UK
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg, South Africa
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Rathmann H, Perretti S, Porcu V, Hanihara T, Scott GR, Irish JD, Reyes-Centeno H, Ghirotto S, Harvati K. Inferring human neutral genetic variation from craniodental phenotypes. PNAS NEXUS 2023; 2:pgad217. [PMID: 37457893 PMCID: PMC10338903 DOI: 10.1093/pnasnexus/pgad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
There is a growing consensus that global patterns of modern human cranial and dental variation are shaped largely by neutral evolutionary processes, suggesting that craniodental features can be used as reliable proxies for inferring population structure and history in bioarchaeological, forensic, and paleoanthropological contexts. However, there is disagreement on whether certain types of data preserve a neutral signature to a greater degree than others. Here, we address this unresolved question and systematically test the relative neutrality of four standard metric and nonmetric craniodental data types employing an extensive computational genotype-phenotype comparison across modern populations from around the world. Our computation draws on the largest existing data sets currently available, while accounting for geographically structured environmental variation, population sampling uncertainty, disparate numbers of phenotypic variables, and stochastic variation inherent to a neutral model of evolution. Our results reveal that the four data types differentially capture neutral genomic variation, with highest signals preserved in dental nonmetric and cranial metric data, followed by cranial nonmetric and dental metric data. Importantly, we demonstrate that combining all four data types together maximizes the neutral genetic signal compared with using them separately, even with a limited number of phenotypic variables. We hypothesize that this reflects a lower level of genetic integration through pleiotropy between, compared to within, the four data types, effectively forming four different modules associated with relatively independent sets of loci. Therefore, we recommend that future craniodental investigations adopt holistic combined data approaches, allowing for more robust inferences about underlying neutral genetic variation.
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Affiliation(s)
| | - Silvia Perretti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Valentina Porcu
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara 252-0374, Japan
| | - G Richard Scott
- Department of Anthropology, University of Nevada, Reno, NV 89557, USA
| | - Joel D Irish
- Research Centre in Evolutionary Anthropology and Palaeoecology, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
- The Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg WITS 2050, South Africa
| | - Hugo Reyes-Centeno
- Department of Anthropology, University of Kentucky, Lexington, KY 40506, USA
- William S. Webb Museum of Anthropology, University of Kentucky, Lexington, KY 40504, USA
- DFG Center for Advanced Studies ‘Words, Bones, Genes, Tools’, University of Tübingen, Tübingen 72070, Germany
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
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Schroeder L, Ackermann RR. Moving beyond the adaptationist paradigm for human evolution, and why it matters. J Hum Evol 2023; 174:103296. [PMID: 36527977 DOI: 10.1016/j.jhevol.2022.103296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 12/23/2022]
Abstract
The Journal of Human Evolution (JHE) was founded 50 years ago when much of the foundation for how we think about human evolution was in place or being put in place, providing the main framework for how we consider our origins today. Here, we will explore historical developments, including early JHE outputs, as they relate to our understanding of the relationship between phenotypic variation and evolutionary process, and use that as a springboard for considering our current understanding of these links as applied to human evolution. We will focus specifically on how the study of variation itself has shifted us away from taxonomic and adaptationist perspectives toward a richer understanding of the processes shaping human evolutionary history, using literature searches and specific test cases to highlight this. We argue that natural selection, gene exchange, genetic drift, and mutation should not be considered individually when considering the production of hominin diversity. In this context, we offer suggestions for future research directions and reflect on this more complex understanding of human evolution and its broader relevance to society. Finally, we end by considering authorship demographics and practices in the last 50 years within JHE and how a shift in these demographics has the potential to reshape the science of human evolution going forward.
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Affiliation(s)
- Lauren Schroeder
- Department of Anthropology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada; Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa.
| | - Rebecca Rogers Ackermann
- Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa; Department of Archaeology, University of Cape Town, Rondebosch, 7701, South Africa.
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Teeth, prenatal growth rates, and the evolution of human-like pregnancy in later Homo. Proc Natl Acad Sci U S A 2022; 119:e2200689119. [PMID: 36191229 PMCID: PMC9564099 DOI: 10.1073/pnas.2200689119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Evidence of how gestational parameters evolved is essential to understanding this fundamental stage of human life. Until now, these data seemed elusive given the skeletal bias of the fossil record. We demonstrate that dentition provides a window into the life of neonates. Teeth begin to form in utero and are intimately associated with gestational development. We measured the molar dentition for 608 catarrhine primates and collected data on prenatal growth rate (PGR) and endocranial volume (ECV) for 19 primate genera from the literature. We found that PGR and ECV are highly correlated (R2 = 0.93, P < 0.001). Additionally, we demonstrated that molar proportions are significantly correlated with PGR (P = 0.004) and log-transformed ECV (P = 0.001). From these correlations, we developed two methods for reconstructing PGR in the fossil record, one using ECV and one using molar proportions. Dental proportions reconstruct hominid ECV (R2 = 0.81, P < 0.001), a result that can be extrapolated to PGR. As teeth dominate fossil assemblages, our findings greatly expand our ability to investigate life history in the fossil record. Fossil ECVs and dental measurements from 13 hominid species both support significantly increasing PGR throughout the terminal Miocene and Plio-Pleistocene, reflecting known evolutionary changes. Together with pelvic and endocranial morphology, reconstructed PGRs indicate the need for increasing maternal energetics during pregnancy over the last 6 million years, reaching a human-like PGR (i.e., more similar to humans than to other extant apes) and ECV in later Homo less than 1 million years ago.
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Monson TA, Brasil MF, Mahaney MC, Schmitt CA, Taylor CE, Hlusko LJ. Keeping 21st Century Paleontology Grounded: Quantitative Genetic Analyses and Ancestral State Reconstruction Re-Emphasize the Essentiality of Fossils. BIOLOGY 2022; 11:biology11081218. [PMID: 36009845 PMCID: PMC9404954 DOI: 10.3390/biology11081218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 02/06/2023]
Abstract
Simple Summary Over the last two decades of biological research, our understanding of how genes determine dental development and variation has expanded greatly. Here, we explore how this new knowledge can be applied to the fossil record of cercopithecid monkeys. We compare a traditional paleontological method for assessing dental size variation with measurement approaches derived from quantitative genetics and developmental biology. We find that these new methods for assessing dental variation provide novel insight to the evolution of the cercopithecid monkey dentition, different from the insight provided by traditional size measurements. When we explore the variation of these traits in the cercopithecid fossil record, we find that the variation is outside the range predicted based on extant variation alone. Our 21st century biological approach to paleontology reveals that we have even more to learn from fossils than previously recognized. Abstract Advances in genetics and developmental biology are revealing the relationship between genotype and dental phenotype (G:P), providing new approaches for how paleontologists assess dental variation in the fossil record. Our aim was to understand how the method of trait definition influences the ability to reconstruct phylogenetic relationships and evolutionary history in the Cercopithecidae, the Linnaean Family of monkeys currently living in Africa and Asia. We compared the two-dimensional assessment of molar size (calculated as the mesiodistal length of the crown multiplied by the buccolingual breadth) to a trait that reflects developmental influences on molar development (the inhibitory cascade, IC) and two traits that reflect the genetic architecture of postcanine tooth size variation (defined through quantitative genetic analyses: MMC and PMM). All traits were significantly influenced by the additive effects of genes and had similarly high heritability estimates. The proportion of covariate effects was greater for two-dimensional size compared to the G:P-defined traits. IC and MMC both showed evidence of selection, suggesting that they result from the same genetic architecture. When compared to the fossil record, Ancestral State Reconstruction using extant taxa consistently underestimated MMC and PMM values, highlighting the necessity of fossil data for understanding evolutionary patterns in these traits. Given that G:P-defined dental traits may provide insight to biological mechanisms that reach far beyond the dentition, this new approach to fossil morphology has the potential to open an entirely new window onto extinct paleobiologies. Without the fossil record, we would not be able to grasp the full range of variation in those biological mechanisms that have existed throughout evolution.
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Affiliation(s)
- Tesla A. Monson
- Department of Anthropology, Western Washington University, 516 High Street, Bellingham, WA 98225, USA
| | - Marianne F. Brasil
- Berkeley Geochronology Center, 2455 Ridge Road, Berkeley, CA 94709, USA
- Human Evolution Research Center, Valley Life Sciences Building, University of California Berkeley, MC-3140, Berkeley, CA 94720, USA
| | - Michael C. Mahaney
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Christopher A. Schmitt
- Department of Anthropology, Boston University, 232 Bay State Road, Boston, MA 02115, USA
| | - Catherine E. Taylor
- Human Evolution Research Center, Valley Life Sciences Building, University of California Berkeley, MC-3140, Berkeley, CA 94720, USA
| | - Leslea J. Hlusko
- Human Evolution Research Center, Valley Life Sciences Building, University of California Berkeley, MC-3140, Berkeley, CA 94720, USA
- National Center for Research on Human Evolution (CENIEH), Paseo Sierra de Atapuerca 3, 09002 Burgos, Spain
- Correspondence:
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