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Torfs JRR, Eens M, Laméris DW, Stevens JMG, Verspeek J, Guery JP, Staes N. Visually assessed body condition shows high heritability in a pedigreed great ape population. Am J Primatol 2023; 85:e23540. [PMID: 37507232 DOI: 10.1002/ajp.23540] [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: 02/09/2023] [Revised: 06/28/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Body condition, a measure for relative fat mass, is associated with primate health, fitness, and overall welfare. Body condition is often influenced by dietary factors, age, and/or sex, but several body condition measures (body weight, weight-to-height ratios, and so on) also show high heritability across primate species, indicating a role of genetic effects. Although different measures for body condition exist, many require direct handling of animals, which is invasive, time-consuming, and expensive, making them impractical in wild and captive settings. Therefore, noninvasive visual body condition score (BCS) systems were developed for various animal species, including macaques and chimpanzees, to visually assess relative fat mass. Here we evaluate the utility of a visual BCS system in bonobos by assessing (1) inter-rater reliability, (2) links with body mass, a traditional hands-on measure of condition, and (3) the factors driving individual variation in BCS. We adapted the chimpanzee BCS system to rate 76 bonobos in 11 European zoos (92% of the adult population). Inter-rater reliability was high (s* = 0.948), BCSs were positively associated with body mass (β = 0.075) and not predicted by diet, sex, or age, nor were they associated with a higher abundance of obesity-related diseases. Instead, BCSs showed high levels of heritability (h2 = 0.637), indicating that a majority of body condition variation in bonobos is attributable to genetic similarity of the individuals. This is in line with reported h2 -values for traditional body condition measures in primates and provides support for the reliability of visual BCS systems in great apes. The results of this study emphasize an often unanticipated role of genetics in determining primate body fat and health that has implications for the management of captive primates. Application of this tool in wild populations would aid to unravel environmental from genetic drivers of body condition variation in primates.
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Affiliation(s)
- Jonas R R Torfs
- Behavioural Ecology and Ecophysiology Research Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Zoo Antwerp Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Marcel Eens
- Behavioural Ecology and Ecophysiology Research Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Daan W Laméris
- Behavioural Ecology and Ecophysiology Research Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Zoo Antwerp Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Jeroen M G Stevens
- SALTO Agro- and Biotechnology, Odisee University College, Sint-Niklaas, Belgium
| | - Jonas Verspeek
- Behavioural Ecology and Ecophysiology Research Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Zoo Antwerp Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | | | - Nicky Staes
- Behavioural Ecology and Ecophysiology Research Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Zoo Antwerp Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
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2
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Tamagnini D, Michaud M, Meloro C, Raia P, Soibelzon L, Tambusso PS, Varela L, Maiorano L. Conical and sabertoothed cats as an exception to craniofacial evolutionary allometry. Sci Rep 2023; 13:13571. [PMID: 37604901 PMCID: PMC10442348 DOI: 10.1038/s41598-023-40677-6] [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: 05/18/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
Among evolutionary trends shaping phenotypic diversity over macroevolutionary scales, CREA (CRaniofacial Evolutionary Allometry) describes a tendency, among closely related species, for the smaller-sized of the group to have proportionally shorter rostra and larger braincases. Here, we used a phylogenetically broad cranial dataset, 3D geometric morphometrics, and phylogenetic comparative methods to assess the validity and strength of CREA in extinct and living felids. To test for the influence of biomechanical constraints, we quantified the impact of relative canine height on cranial shape evolution. Our results provided support to CREA at the family level. Yet, whereas felines support the rule, big cats, like Pantherinae and Machairodontinae, conform weakly if not at all with CREA predictions. Our findings suggest that Machairodontinae constitute one of the first well-supported exceptions to this biological rule currently known, probably in response to the biomechanical demands and developmental changes linked with their peculiar rostral adaptations. Our results suggest that the acquisition of extreme features concerning biomechanics, evo-devo constraints, and/or ecology is likely to be associated with peculiar patterns of morphological evolution, determining potential exceptions to common biological rules, for instance, by inducing variations in common patterns of evolutionary integration due to heterochronic changes under ratchet-like evolution.
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Affiliation(s)
- Davide Tamagnini
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", Zoology Building, Viale dell'Università 32, 00185, Rome, Italy.
- Museum of Zoology, Sapienza Museum Centre, University of Rome "La Sapienza", Rome, Italy.
| | - Margot Michaud
- Evolution & Diversity Dynamics Lab, University of Liège, Liege, Belgium
| | - Carlo Meloro
- School of Biological and Environmental Sciences, Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Pasquale Raia
- Dipartimento di Scienze della Terra, dell'Ambiente e delle Risorse, University of Naples Federico II, Naples, Italy
| | - Leopoldo Soibelzon
- División Paleontología Vertebrados, Museo de La Plata, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, 1900, La Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnicas (CONICET), Godoy Cruz 2290, C1425FQB, CABA, Argentina
| | - P Sebastián Tambusso
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
- Departamento de Canelones, Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500, Sauce, Uruguay
| | - Luciano Varela
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
- Departamento de Canelones, Servicio Académico Universitario y Centro de Estudios Paleontológicos (SAUCE-P), Universidad de la República, Santa Isabel s/n, 91500, Sauce, Uruguay
| | - Luigi Maiorano
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome "La Sapienza", Zoology Building, Viale dell'Università 32, 00185, Rome, Italy
- Museum of Zoology, Sapienza Museum Centre, University of Rome "La Sapienza", Rome, Italy
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3
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Le Maître A, Guy F, Merceron G, Kostopoulos DS. Morphology of the Bony Labyrinth Supports the Affinities of Paradolichopithecus with the Papionina. INT J PRIMATOL 2022; 44:209-236. [PMID: 36817734 PMCID: PMC9931825 DOI: 10.1007/s10764-022-00329-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
Discoveries in recent decades indicate that the large papionin monkeys Paradolipopithecus and Procynocephalus are key members of the Late Pliocene - Early Pleistocene mammalian faunas of Eurasia. However, their taxonomical status, phylogenetic relationships, and ecological profile remain unclear. Here we investigate the two latter aspects through the study of the inner ear anatomy, as revealed by applying micro-CT scan imaging techniques on the cranium LGPUT DFN3-150 of Paradolichopithecus from the lower Pleistocene (2.3 Ma) fossil site Dafnero-3 in Northwestern Greece. Using geometric morphometric methods, we quantified shape variation and the allometric and phylogenetic signals in extant cercopithecines (n = 80), and explored the morphological affinities of the fossil specimen with extant taxa. LGPUT DFN3-150 has a large centroid size similar to that of baboons and their relatives. It shares several shape features with Macacina and Cercopithecini, which we interpret as probable retention of a primitive morphology. Overall, its inner ear morphology is more consistent with a stem Papionini more closely related to Papionina than Macacina, or to a basal crown Papionina. Our results, along with morphometrical and ecological features from previous studies, call into question the traditional hypothesis of a Paradolichopithecus-Macacina clade, and provide alternative perspectives in the study of Eurasian primate evolution during the late Neogene-Quaternary. Supplementary Information The online version contains supplementary material available at 10.1007/s10764-022-00329-4.
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Affiliation(s)
- Anne Le Maître
- Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- PALEVOPRIM - UMR 7262 CNRS INEE, Université de Poitiers, Poitiers, France
| | - Franck Guy
- PALEVOPRIM - UMR 7262 CNRS INEE, Université de Poitiers, Poitiers, France
| | - Gildas Merceron
- PALEVOPRIM - UMR 7262 CNRS INEE, Université de Poitiers, Poitiers, France
| | - Dimitris S Kostopoulos
- Laboratory of Geology and Palaeontology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Hardin AM, Knigge RP, Duren DL, Williams-Blangero S, Subedi J, Mahaney MC, Sherwood RJ. Genetic influences on dentognathic morphology in the Jirel population of Nepal. Anat Rec (Hoboken) 2022; 305:2137-2157. [PMID: 34981668 PMCID: PMC9250551 DOI: 10.1002/ar.24857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022]
Abstract
Patterns of genetic variation and covariation impact the evolution of the craniofacial complex and contribute to clinically significant malocclusions in modern human populations. Previous quantitative genetic studies have estimated the heritabilities and genetic correlations of skeletal and dental traits in humans and nonhuman primates, but none have estimated these quantitative genetic parameters across the dentognathic complex. A large and powerful pedigree from the Jirel population of Nepal was leveraged to estimate heritabilities and genetic correlations in 62 maxillary and mandibular arch dimensions, incisor and canine lengths, and post-canine tooth crown areas (N ≥ 739). Quantitative genetic parameter estimation was performed using maximum likelihood-based variance decomposition. Residual heritability estimates were significant for all traits, ranging from 0.269 to 0.898. Genetic correlations were positive for all trait pairs. Principal components analyses of the phenotypic and genetic correlation matrices indicate an overall size effect across all measurements on the first principal component. Additional principal components demonstrate positive relationships between post-canine tooth crown areas and arch lengths and negative relationships between post-canine tooth crown areas and arch widths, and between arch lengths and arch widths. Based on these findings, morphological variation in the human dentognathic complex may be constrained by genetic relationships between dental dimensions and arch lengths, with weaker genetic correlations between these traits and arch widths allowing for variation in arch shape. The patterns identified are expected to have impacted the evolution of the dentognathic complex and its genetic architecture as well as the prevalence of dental crowding in modern human populations.
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Affiliation(s)
- Anna M. Hardin
- Biology Department, Western Oregon University
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
| | - Ryan P. Knigge
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
- Department of Integrative Biology and Physiology, University of Minnesota Medical School
| | - Dana L. Duren
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
| | - Sarah Williams-Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley
| | | | - Michael C. Mahaney
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley
| | - Richard J. Sherwood
- Craniofacial Research Center, Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine
- Department of Orthopaedic Surgery, University of Missouri School of Medicine
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Housman G, Briscoe E, Gilad Y. Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model. PLoS Genet 2022; 18:e1010073. [PMID: 35263340 PMCID: PMC8936463 DOI: 10.1371/journal.pgen.1010073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 03/21/2022] [Accepted: 02/02/2022] [Indexed: 01/10/2023] Open
Abstract
The evolution of complex skeletal traits in primates was likely influenced by both genetic and environmental factors. Because skeletal tissues are notoriously challenging to study using functional genomic approaches, they remain poorly characterized even in humans, let alone across multiple species. The challenges involved in obtaining functional genomic data from the skeleton, combined with the difficulty of obtaining such tissues from nonhuman apes, motivated us to consider an alternative in vitro system with which to comparatively study gene regulation in skeletal cell types. Specifically, we differentiated six human (Homo sapiens) and six chimpanzee (Pan troglodytes) induced pluripotent stem cell lines (iPSCs) into mesenchymal stem cells (MSCs) and subsequently into osteogenic cells (bone cells). We validated differentiation using standard methods and collected single-cell RNA sequencing data from over 100,000 cells across multiple samples and replicates at each stage of differentiation. While most genes that we examined display conserved patterns of expression across species, hundreds of genes are differentially expressed (DE) between humans and chimpanzees within and across stages of osteogenic differentiation. Some of these interspecific DE genes show functional enrichments relevant in skeletal tissue trait development. Moreover, topic modeling indicates that interspecific gene programs become more pronounced as cells mature. Overall, we propose that this in vitro model can be used to identify interspecific regulatory differences that may have contributed to skeletal trait differences between species. Primates display a range of skeletal morphologies and susceptibilities to skeletal diseases, but the molecular basis of these phenotypic differences is unclear. Studies of gene expression variation in primate skeletal tissues are extremely restricted due to the ethical and practical challenges associated with collecting samples. Nevertheless, the ability to study gene regulation in primate skeletal tissues is crucial for understanding how the primate skeleton has evolved. We therefore developed a comparative primate skeletal cell culture model that allows us to access a spectrum of human and chimpanzee cell types as they differentiate from stem cells into bone cells. While most gene expression patterns are conserved across species, we also identified hundreds of differentially expressed genes between humans and chimpanzees within and across stages of differentiation. We also classified cells by osteogenic stage and identified additional interspecific differentially expressed genes which may contribute to skeletal trait differences. We anticipate that this model will be extremely useful for exploring questions related to gene regulation variation in primate bone biology and development.
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Affiliation(s)
- Genevieve Housman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Emilie Briscoe
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Yoav Gilad
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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6
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Ghosh S, Kasher M, Malkina I, Livshits G. Is craniofacial morphology and body composition related by common genes: Comparative analysis of two ethnically diverse populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:249-261. [PMID: 34297355 DOI: 10.1002/ajpa.24373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/18/2023]
Abstract
OBJECTIVES The overarching hypothesis of the present paper is that ethnically and/or genetically diverse human populations may exhibit similarity in correlations between various aspects of human phenotypes due to the morphological integration process during the ontogenetic stages. To test this we investigated whether an association between craniofacial (CF) features and body composition (BC) variations is present in humans and the extent to which such possible associations are comparable in different populations. Furthermore, the paper examines the contribution of common genetic (additive) and shared familial environmental factors in assessing the correlation between CF and BC characteristics in humans. MATERIALS AND METHODS Two pedigree-based samples were collected from two distinct populations, including India (Santhal) and Europe (Chuvash). Canonical correlation analysis was used to compare the association between CF and BC characteristics in the two studied samples. The contribution of genetic and familial environmental factors on the correlation between CF and BC features was analyzed through variance decomposition analysis by implementing the Mendelian Analysis package (MAN). RESULTS Our study suggests that CF morphology is significantly (p < 0.001) associated with BC variation in both samples. CF characteristics and BC phenotypes revealed a consistent trend in both samples where condensed and broad CF morphology was significantly associated with increased fat accumulation, with slight variations between the Santhal and Chuvash samples. Despite the variations observed between the samples, the heritability estimates were impressively equivalent for traits like total facial height (55.6%Santhal vs.56.1%Chuvash ) and nasal index (42.8%Santhal vs. 43.3%Chuvash ). DISCUSSION The genetic contribution of CF morphology appeared to be extensive and the contribution of common genetic and shared family environmental correlations between CF and BC measures were suggestively substantial. Accordingly, these correlations were consistently observed across ethnically diverse populations, despite drastic morphological differences between the samples under comparison.
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Affiliation(s)
- Sudipta Ghosh
- Department of Anthropology, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Melody Kasher
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Ida Malkina
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Gregory Livshits
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.,Adelson School of Medicine, Ariel University, Ariel, Israel
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Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Siodi L, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. Gut microbiome heritability is nearly universal but environmentally contingent. Science 2021; 373:181-186. [PMID: 34244407 PMCID: PMC8377764 DOI: 10.1126/science.aba5483] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022]
Abstract
Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
- Research Center, Montreal Heart Institute, Montréal, Quebec H1T 1C8, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Neil Gottel
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jacob B Gordon
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
- The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Kenya
| | | | | | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
| | - Jack A Gilbert
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
- Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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8
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Villamil CI. The role of developmental rate, body size, and positional behavior in the evolution of covariation and evolvability in the cranium of strepsirrhines and catarrhines. J Hum Evol 2021; 151:102941. [PMID: 33482561 DOI: 10.1016/j.jhevol.2020.102941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/30/2022]
Abstract
Recent studies on hominin craniofacial evolution have focused on phenotypic integration or covariation among traits. Covariation is thought to significantly affect evolutionary trajectories, shaping the ways in which hominins and other primates could have evolved. However, the ways in which covariation itself evolves are not well understood. This study aims to investigate the role of phylogeny, development, body size, and positional behavior in shaping the strength of covariation in strepsirrhine and catarrhine primate crania (n = 1009, representing 11 genera). These factors may have been catalysts for change in the magnitude of covariation, and they have changed significantly during primate evolution and particularly hominin evolution. Modern humans in particular have slow developmental trajectories, large bodies, and a unique form of locomotion in the form of orthograde bipedalism. Variance of eigenvalues, mean integration, mean evolvability, and mean conditional evolvability was estimated and their relationship to the various factors described earlier was assessed using phylogenetic and nonphylogenetic analyses. Results indicate that some phylogenetic signal is present, but it is not equivalent across integration statistics or cranial regions. In particular, these results suggest that closely related species are more similar than more distantly related species in evolvability of the cranial base and integration of the face. Two divergent patterns were also identified, in which covariation and evolvability of the cranial base are linked to developmental rate, but those of the face are linked to body size. Neither locomotion nor posture appears related to covariation or evolvability of the primate cranium. These results suggest that overall low covariation observed in the hominin cranium may be a result of separate trends in different cranial regions.
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Affiliation(s)
- Catalina I Villamil
- School of Chiropractic, Universidad Central Del Caribe, PO Box 60327, Bayamón, PR, 00960-6032, USA; Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY, 10003, USA; New York Consortium in Evolutionary Primatology, New York, NY, 10024, USA.
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Abstract
Teeth have been studied for decades and continue to reveal information relevant to human evolution. Studies have shown that many traits of the outer enamel surface evolve neutrally and can be used to infer human population structure. However, many of these traits are unavailable in archaeological and fossil individuals due to processes of wear and taphonomy. Enamel-dentine junction (EDJ) morphology, the shape of the junction between the enamel and the dentine within a tooth, captures important information about tooth development and vertebrate evolution and is informative because it is subject to less wear and thus preserves more anatomy in worn or damaged specimens, particularly in mammals with relatively thick enamel like hominids. This study looks at the molar EDJ across a large sample of human populations. We assessed EDJ morphological variation in a sample of late Holocene modern humans (n = 161) from archaeological populations using μ-CT biomedical imaging and geometric morphometric analyses. Global variation in human EDJ morphology was compared to the statistical expectations of neutral evolution and "Out of Africa" dispersal modeling of trait evolution. Significant correlations between phenetic variation and neutral genetic variation indicate that EDJ morphology has evolved neutrally in humans. While EDJ morphology reflects population history, its global distribution does not follow expectations of the Out of Africa dispersal model. This study increases our knowledge of human dental variation and contributes to our understanding of dental development more broadly, with important applications to the investigation of population history and human genetic structure.
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10
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Elton S, Dunn J. Baboon biogeography, divergence, and evolution: Morphological and paleoecological perspectives. J Hum Evol 2020; 145:102799. [DOI: 10.1016/j.jhevol.2020.102799] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 11/30/2022]
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11
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Housman G, Quillen EE, Stone AC. Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:34-49. [PMID: 32170728 DOI: 10.1002/ajpa.24041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Epigenetic mechanisms influence the development and maintenance of complex phenotypes and may also contribute to the evolution of species-specific phenotypes. With respect to skeletal traits, little is known about the gene regulation underlying these hard tissues or how tissue-specific patterns are associated with bone morphology or vary among species. To begin exploring these topics, this study evaluates one epigenetic mechanism, DNA methylation, in skeletal tissues from five nonhuman primate species which display anatomical and locomotor differences representative of their phylogenetic groups. MATERIALS AND METHODS First, we test whether intraspecific variation in skeletal DNA methylation is associated with intraspecific variation in femur morphology. Second, we identify interspecific differences in DNA methylation and assess whether these lineage-specific patterns may have contributed to species-specific morphologies. Specifically, we use the Illumina Infinium MethylationEPIC BeadChip to identify DNA methylation patterns in femur trabecular bone from baboons (n = 28), macaques (n = 10), vervets (n = 10), chimpanzees (n = 4), and marmosets (n = 6). RESULTS Significant differentially methylated positions (DMPs) were associated with a subset of morphological variants, but these likely have small biological effects and may be confounded by other variables associated with morphological variation. Conversely, several species-specific DMPs were identified, and these are found in genes enriched for functions associated with complex skeletal traits. DISCUSSION Overall, these findings reveal that while intraspecific epigenetic variation is not readily associated with skeletal morphology differences, some interspecific epigenetic differences in skeletal tissues exist and may contribute to evolutionarily distinct phenotypes. This work forms a foundation for future explorations of gene regulation and skeletal trait evolution in primates.
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Affiliation(s)
- Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
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Pérez-Ben CM, Báez AM, Schoch RR. Morphological evolution of the skull roof in temnospondyl amphibians mirrors conservative ontogenetic patterns. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Addressing the patterns of ontogenetic allometry is relevant to understand morphological diversification because allometry might constrain evolution to specific directions of change in shape but also facilitate phenotypic differentiation along lines of least evolutionary resistance. Temnospondyl amphibians are a suitable group to address these issues from a deep-time perspective because different growth stages are known for numerous Palaeozoic and Mesozoic species. Herein we examine the patterns of ontogenetic allometry in the skull roof of 15 temponspondyl species and their relationship with adult morphological evolution. Using geometric morphometrics, we assessed ontogenetic and evolutionary allometries of this cranial part and the distribution of adult shapes in the morphospace to investigate whether these patterns relate to each other and/or to lifestyle and phylogeny. We found conspicuous stereotyped ontogenetic changes of the skull roof which are mirrored at the evolutionary level and consistency of the adult shape with phylogeny rather than lifestyle. These results suggest that the evolution of adult cranial shape was significantly biased by development towards pathways patterned by ontogenetic change in shape. The retrieved conserved patterns agree with a widespread evolutionary craniofacial trend found in amniotes, suggesting that they might have originated early in tetrapod evolutionary history or even earlier.
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Affiliation(s)
- Celeste M Pérez-Ben
- CONICET. Departamento de Ciencias Geológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ana M Báez
- CONICET. Departamento de Ciencias Geológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’, Buenos Aires, Argentina
| | - Rainer R Schoch
- Staaliches Museum für Naturkunde, Stuttgart, Baden-Württemberg, Germany
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13
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Joganic JL, Heuzé Y. Allometry and advancing age significantly structure craniofacial variation in adult female baboons. J Anat 2019; 235:217-232. [PMID: 31070786 PMCID: PMC6637449 DOI: 10.1111/joa.13005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2019] [Indexed: 11/29/2022] Open
Abstract
Primate craniofacial growth is traditionally assumed to cease upon maturation or at least be negligible, whereas bony remodeling is typically associated with advanced adult age and, in particular, tooth loss. Therefore, size and shape of the craniofacial skeleton of young and middle-aged adults should be stable. However, research on both modern and historic human samples suggests that portions of the CFS exhibit age-related changes in mature individuals, both related to and independent of tooth loss. These results demonstrate that the age-category 'adult' is heterogeneous, containing individuals demonstrating post-maturational age-related variation, but the topic remains understudied outside of humans and in the cranial vault and base. Our research quantifies variation in a sample of captive adult female baboons (n = 97) in an effort to understand how advancing age alters the mature CFS. Craniometric landmarks and sliding semilandmarks were collected from computed tomography (CT) scans of adult baboons aged 7-32 years old. To determine whether craniofacial morphology is sensitive to aging mechanisms and whether any such effects are differentially distributed throughout the cranium, geometric morphometric techniques were employed to compare the shapes of various cranial regions among individuals of increasing age. Unexpectedly, the biggest form differences were observed between young and middle-aged adults, rather than between adults with full dentitions and those with some degree of tooth loss. Shape variation was greatest in masticatory and nuchal musculature attachment areas. Our results indicate that the craniofacial skeleton changes form during adulthood in baboons, raising interesting questions about the molecular and biological mechanisms governing these changes.
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Affiliation(s)
- Jessica L. Joganic
- CNRSMCCPACEAUMR5199University of BordeauxPessacFrance
- Department of AnthropologyWashington University in St. LouisSt. LouisMOUSA
| | - Yann Heuzé
- CNRSMCCPACEAUMR5199University of BordeauxPessacFrance
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14
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15
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Wang Y, Chen F, Wang J, Zhao Y, Liu F. Two novel homozygous mutations in NPHP1 lead to late onset end-stage renal disease: a case report of an adult nephronophthisis in a Chinese intermarriage family. BMC Nephrol 2019; 20:173. [PMID: 31096956 PMCID: PMC6524295 DOI: 10.1186/s12882-019-1372-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/06/2019] [Indexed: 02/05/2023] Open
Abstract
Background Nephronophthisis (NPHP) is an autosomal recessive hereditary disease with highly variable clinical characteristics for which 20 genes (NPHP1–20) have been identified. NPHP1 is the major subtype leading to pediatric end-stage renal disease (ESRD). Reports of adult NPHP1 are rare. Case presentation Here, we report a 27-year-old male from a Chinese intermarriage family who was diagnosed as NPHP from clinical presentations and molecular genetic analysis by whole-exome sequencing. The genetic investigation revealed a novel homozygous nonsense mutation, p. E697X,37 and a novel homozygous missense mutation, p. F691 L, in the NPHP1 gene. His parents and fraternal twin harbored heterozygous mutations of the two loci and had no renal symptoms. His elder sister developed ESRD and died at 23 years of age. Conclusions The report indicated that adult NPHP should be taken into consideration for adults with ESRD of uncertain cause. The genotype-phenotype correlation requires further investigation.
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Affiliation(s)
- Yiting Wang
- Division of Nephrology, West China Hospital of Sichuan University, No. 37, Guoxue Alley, Chengdu, 610041, Sichuan Province, China
| | - Feng Chen
- Division of Nephrology, West China Hospital of Sichuan University, No. 37, Guoxue Alley, Chengdu, 610041, Sichuan Province, China
| | - Jiali Wang
- Division of Nephrology, West China Hospital of Sichuan University, No. 37, Guoxue Alley, Chengdu, 610041, Sichuan Province, China
| | - Yingwang Zhao
- Division of Nephrology, West China Hospital of Sichuan University, No. 37, Guoxue Alley, Chengdu, 610041, Sichuan Province, China
| | - Fang Liu
- Division of Nephrology, West China Hospital of Sichuan University, No. 37, Guoxue Alley, Chengdu, 610041, Sichuan Province, China.
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16
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Hardin AM. Genetic contributions to dental dimensions in brown-mantled tamarins (Saguinus fuscicollis) and rhesus macaques (Macaca mulatta). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 168:292-302. [PMID: 30508220 PMCID: PMC6328332 DOI: 10.1002/ajpa.23744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVES The use of dental metrics in phylogenetic reconstructions of fossil primates assumes variation in tooth size is highly heritable. Quantitative genetic studies in humans and baboons have estimated high heritabilities for dental traits, providing a preliminary view of the variability of dental trait heritability in nonhuman primate species. To expand upon this view, the heritabilities and evolvabilities of linear dental dimensions are estimated in brown-mantled tamarins (Saguinus fuscicollis) and rhesus macaques (Macaca mulatta). MATERIALS AND METHODS Quantitative genetic analyses were performed on linear dental dimensions collected from 302 brown-mantled tamarins and 364 rhesus macaques. Heritabilities were estimated in SOLAR using pedigrees from each population, and evolvabilities were calculated manually. RESULTS Tamarin heritability estimates range from 0.19 to 0.99, and 25 of 26 tamarin estimates are significantly different from zero. Macaque heritability estimates range from 0.08 to 1.00, and 25 out of 28 estimates are significantly different from zero. DISCUSSION Dental dimensions are highly heritable in captive brown-mantled tamarins and free-ranging rhesus macaques. The range of heritability estimates in these populations is broadly similar to those of baboons and humans. Evolvability tends to increase with heritability, although evolvability is high relative to heritability in some dimensions. Estimating evolvability helps to contextualize differences in heritability, and the observed relationship between evolvability and heritability in dental dimensions requires further investigation.
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Affiliation(s)
- Anna M Hardin
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri
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Hlusko LJ. Recent insights into the evolution of quantitative traits in non-human primates. Curr Opin Genet Dev 2018; 53:15-20. [PMID: 29913352 DOI: 10.1016/j.gde.2018.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/25/2018] [Accepted: 05/31/2018] [Indexed: 10/28/2022]
Abstract
The past few years of genetic research on primate quantitative trait variation have been notable in the diversity of phenotypes explored, ranging from classic skeletal measurements to behavior, through to levels of gene expression, and with observations from both captive and wild populations. These studies demonstrate the importance of captive pedigreed breeding colonies, populations that can be matched to their wild counterparts to enable comparison of genetic architectures. Non-human primate genotype:phenotype maps are essential for placing human variation within an evolutionary framework as well as for gaining insight to human biology. While the demographic history of most primates has been fairly stable since the Late Pleistocene, humans experienced a dramatic population expansion that increased the number of rare, mildly deleterious mutations. These rare genetic variants complicate the genotype:phenotype association because they account for a disproportionate amount of the genetic variance and are harder to detect. The similar physiologies of our closest living relatives may prove to be key for overcoming the hurdles posed by humans' peculiar demographic explosion.
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Affiliation(s)
- Leslea J Hlusko
- Human Evolution Research Center, Department of Integrative Biology, University of California Berkeley, 3040 Valley Life Science Bldg, MC-3140, Berkeley, CA 94720, USA.
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