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Wei W, Ma S, Fu B, Song R, Guo H. Human-specific insights into candidate genes and boosted discoveries of novel loci illuminate roles of neuroglia in reading disorders. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12899. [PMID: 38752599 PMCID: PMC11097622 DOI: 10.1111/gbb.12899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
Reading disorders (RD) are human-specific neuropsychological conditions associated with decoding printed words and/or reading comprehension. So far only a handful of candidate genes segregated in families and 42 loci from genome-wide association study (GWAS) have been identified that jointly provided little clues of pathophysiology. Leveraging human-specific genomic information, we critically assessed the RD candidates for the first time and found substantial human-specific features within. The GWAS candidates (i.e., population signals) were distinct from the familial counterparts and were more likely pleiotropic in neuropsychiatric traits and to harbor human-specific regulatory elements (HSREs). Candidate genes associated with human cortical morphology indeed showed human-specific expression in adult brain cortices, particularly in neuroglia likely regulated by HSREs. Expression levels of candidate genes across human brain developmental stages showed a clear pattern of uplifted expression in early brain development crucial to RD development. Following the new insights and loci pleiotropic in cognitive traits, we identified four novel genes from the GWAS sub-significant associations (i.e., FOXO3, MAPT, KMT2E and HTT) and the Semaphorin gene family with functional priors (i.e., SEMA3A, SEMA3E and SEMA5B). These novel genes were related to neuronal plasticity and disorders, mostly conserved the pattern of uplifted expression in early brain development and had evident expression in cortical neuroglial cells. Our findings jointly illuminated the association of RD with neuroglia regulation-an emerging hotspot in studying neurodevelopmental disorders, and highlighted the need of improving RD phenotyping to avoid jeopardizing future genetic studies of RD.
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Affiliation(s)
- Wen‐Hua Wei
- Centre for Biostatistics, Division of Population Health, Health Services Research and Primary CareThe University of ManchesterManchesterUK
| | - Shaowei Ma
- Hebei Key Laboratory of Children's Cognition and Digital Education and School of Foreign LanguagesLangfang Normal UniversityLangfangChina
| | - Bo Fu
- School of Data ScienceFudan UniversityShanghaiChina
| | - Ranran Song
- Department of Maternal and Child Health and MOE (Ministry of Education) Key Laboratory of Environment and Health, School of Public Health, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Hui Guo
- Centre for Biostatistics, Division of Population Health, Health Services Research and Primary CareThe University of ManchesterManchesterUK
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2
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List JM. Open Problems in Computational Historical Linguistics. OPEN RESEARCH EUROPE 2024; 3:201. [PMID: 38357681 PMCID: PMC10864822 DOI: 10.12688/openreseurope.16804.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/30/2024] [Indexed: 02/16/2024]
Abstract
Problems constitute the starting point of all scientific research. The essay reflects on the different kinds of problems that scientists address in their research and discusses a list of 10 problems for the field of computational historical linguistics, that was proposed throughout 2019 in a series of blog posts (see http://phylonetworks.blogspot.com/). In contrast to problems identified in different contexts, these problems were considered to be solvable, but no solution could be proposed back then. By discussing the problems in the light of developments that have been made in the field during the past five years, a modified list is proposed that takes new insights into account but also finds that the majority of the problems has not yet been solved.
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Affiliation(s)
- Johann-Mattis List
- Chair of Multilingual Computational Linguistics, University of Passau, Passau, Bavaria, 94032, Germany
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
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3
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Maleszka R. Reminiscences on the honeybee genome project and the rise of epigenetic concepts in insect science. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38196200 DOI: 10.1111/imb.12888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
The sequencing of the honeybee genome in 2006 was an important technological and logistic achievement experience. But what benefits have flown from the honeybee genome project? What does the annotated genomic assembly mean for the study of behavioural complexity and organismal function in honeybees? Here, I discuss several lines of research that have arisen from this project and highlight the rapidly expanding studies on insect epigenomics, emergent properties of royal jelly, the mechanism of nutritional control of development and the contribution of epigenomic regulation to the evolution of sociality. I also argue that the term 'insect epigenetics' needs to be carefully redefined to reflect the diversity of epigenomic toolkits in insects and the impact of lineage-specific innovations on organismal outcomes. The honeybee genome project helped pioneer advances in social insect molecular biology, and fuelled breakthrough research into the role of flexible epigenomic control systems in linking genotype to phenotype.
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Affiliation(s)
- Ryszard Maleszka
- Research School of Biology, Australian National University, Canberra, ACT, Australia
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4
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Abstract
Brain development in humans is achieved through precise spatiotemporal genetic control, the mechanisms of which remain largely elusive. Recently, integration of technological advances in human stem cell-based modelling with genome editing has emerged as a powerful platform to establish causative links between genotypes and phenotypes directly in the human system. Here, we review our current knowledge of complex genetic regulation of each key step of human brain development through the lens of evolutionary specialization and neurodevelopmental disorders and highlight the use of human stem cell-derived 2D cultures and 3D brain organoids to investigate human-enriched features and disease mechanisms. We also discuss opportunities and challenges of integrating new technologies to reveal the genetic architecture of human brain development and disorders.
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Affiliation(s)
- Yi Zhou
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Vaglietti S, Villeri V, Dell’Oca M, Marchetti C, Cesano F, Rizzo F, Miller D, LaPierre L, Pelassa I, Monje FJ, Colnaghi L, Ghirardi M, Fiumara F. PolyQ length-based molecular encoding of vocalization frequency in FOXP2. iScience 2023; 26:108036. [PMID: 37860754 PMCID: PMC10582585 DOI: 10.1016/j.isci.2023.108036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
The transcription factor FOXP2, a regulator of vocalization- and speech/language-related phenotypes, contains two long polyQ repeats (Q1 and Q2) displaying marked, still enigmatic length variation across mammals. We found that the Q1/Q2 length ratio quantitatively encodes vocalization frequency ranges, from the infrasonic to the ultrasonic, displaying striking convergent evolution patterns. Thus, species emitting ultrasonic vocalizations converge with bats in having a low ratio, whereas species vocalizing in the low-frequency/infrasonic range converge with elephants and whales, which have higher ratios. Similar, taxon-specific patterns were observed for the FOXP2-related protein FOXP1. At the molecular level, we observed that the FOXP2 polyQ tracts form coiled coils, assembling into condensates and fibrils, and drive liquid-liquid phase separation (LLPS). By integrating evolutionary and molecular analyses, we found that polyQ length variation related to vocalization frequency impacts FOXP2 structure, LLPS, and transcriptional activity, thus defining a novel form of polyQ length-based molecular encoding of vocalization frequency.
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Affiliation(s)
- Serena Vaglietti
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Veronica Villeri
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Marco Dell’Oca
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Chiara Marchetti
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Federico Cesano
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Francesca Rizzo
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 518057, China
| | - Dave Miller
- Cascades Pika Watch, Oregon Zoo, Portland, OR 97221, USA
| | - Louis LaPierre
- Deptartment of Natural Science, Lower Columbia College, Longview, WA 98632, USA
| | - Ilaria Pelassa
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Francisco J. Monje
- Department of Neurophysiology and Neuropharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Luca Colnaghi
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Mirella Ghirardi
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Ferdinando Fiumara
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
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6
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de Sousa AA, Beaudet A, Calvey T, Bardo A, Benoit J, Charvet CJ, Dehay C, Gómez-Robles A, Gunz P, Heuer K, van den Heuvel MP, Hurst S, Lauters P, Reed D, Salagnon M, Sherwood CC, Ströckens F, Tawane M, Todorov OS, Toro R, Wei Y. From fossils to mind. Commun Biol 2023; 6:636. [PMID: 37311857 PMCID: PMC10262152 DOI: 10.1038/s42003-023-04803-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/04/2023] [Indexed: 06/15/2023] Open
Abstract
Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology's approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.
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Affiliation(s)
| | - Amélie Beaudet
- Laboratoire de Paléontologie, Évolution, Paléoécosystèmes et Paléoprimatologie (PALEVOPRIM), UMR 7262 CNRS & Université de Poitiers, Poitiers, France.
- University of Cambridge, Cambridge, UK.
| | - Tanya Calvey
- Division of Clinical Anatomy and Biological Anthropology, University of Cape Town, Cape Town, South Africa.
| | - Ameline Bardo
- UMR 7194, CNRS-MNHN, Département Homme et Environnement, Musée de l'Homme, Paris, France
- Skeletal Biology Research Centre, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Julien Benoit
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Christine J Charvet
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Colette Dehay
- University of Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, F-69500, Bron, France
| | | | - Philipp Gunz
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Katja Heuer
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et Théorique, F-75015, Paris, France
| | | | - Shawn Hurst
- University of Indianapolis, Indianapolis, IN, USA
| | - Pascaline Lauters
- Institut royal des Sciences naturelles, Direction Opérationnelle Terre et Histoire de la Vie, Brussels, Belgium
| | - Denné Reed
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | - Mathilde Salagnon
- CNRS, CEA, IMN, GIN, UMR 5293, Université Bordeaux, Bordeaux, France
- PACEA UMR 5199, CNRS, Université Bordeaux, Pessac, France
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Felix Ströckens
- C. & O. Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mirriam Tawane
- Ditsong National Museum of Natural History, Pretoria, South Africa
| | - Orlin S Todorov
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Roberto Toro
- Institut Pasteur, Université Paris Cité, Unité de Neuroanatomie Appliquée et Théorique, F-75015, Paris, France
| | - Yongbin Wei
- Beijing University of Posts and Telecommunications, Beijing, China
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7
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Bornschein U, Zeberg H, Enard W, Hevers W, Pääbo S. Functional dissection of two amino acid substitutions unique to the human FOXP2 protein. Sci Rep 2023; 13:3747. [PMID: 36879029 PMCID: PMC9988825 DOI: 10.1038/s41598-023-30663-3] [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: 08/01/2022] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
The transcription factor forkhead box P2 (FOXP2) is involved in the development of language and speech in humans. Two amino acid substitutions (T303N, N325S) occurred in the human FOXP2 after the divergence from the chimpanzee lineage. It has previously been shown that when they are introduced into the FOXP2 protein of mice they alter striatal synaptic plasticity by increasing long-term depression in medium spiny neurons. Here we introduce each of these amino acid substitutions individually into mice and analyze their effects in the striatum. We find that long-term depression in medium spiny neurons is increased in mice carrying only the T303N substitution to the same extent as in mice carrying both amino acid substitutions. In contrast, the N325S substitution has no discernable effects.
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Affiliation(s)
- Ulrich Bornschein
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.,Department of Pharmacology and Physiology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Wolfgang Enard
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.,Faculty of Biology, Ludwig Maximilian University, 82152, Martinsried, Germany
| | - Wulf Hevers
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.,Okinawa Institute of Science and Technology, Onna-Son, Japan
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8
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Zhang X, Fang B, Huang YF. Transcription factor binding sites are frequently under accelerated evolution in primates. Nat Commun 2023; 14:783. [PMID: 36774380 PMCID: PMC9922303 DOI: 10.1038/s41467-023-36421-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 01/31/2023] [Indexed: 02/13/2023] Open
Abstract
Recent comparative genomic studies have identified many human accelerated elements (HARs) with elevated substitution rates in the human lineage. However, it remains unknown to what extent transcription factor binding sites (TFBSs) are under accelerated evolution in humans and other primates. Here, we introduce two pooling-based phylogenetic methods with dramatically enhanced sensitivity to examine accelerated evolution in TFBSs. Using these new methods, we show that more than 6000 TFBSs annotated in the human genome have experienced accelerated evolution in Hominini, apes, and Old World monkeys. Although these TFBSs individually show relatively weak signals of accelerated evolution, they collectively are more abundant than HARs. Also, we show that accelerated evolution in Pol III binding sites may be driven by lineage-specific positive selection, whereas accelerated evolution in other TFBSs might be driven by nonadaptive evolutionary forces. Finally, the accelerated TFBSs are enriched around developmental genes, suggesting that accelerated evolution in TFBSs may drive the divergence of developmental processes between primates.
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Affiliation(s)
- Xinru Zhang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA. .,Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Bohao Fang
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, Boston, MA, 02135, USA
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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9
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Zamorano-Abramson J, Michon M, Hernández-Lloreda MV, Aboitiz F. Multimodal imitative learning and synchrony in cetaceans: A model for speech and singing evolution. Front Psychol 2023; 14:1061381. [PMID: 37138983 PMCID: PMC10150787 DOI: 10.3389/fpsyg.2023.1061381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/13/2023] [Indexed: 05/05/2023] Open
Abstract
Multimodal imitation of actions, gestures and vocal production is a hallmark of the evolution of human communication, as both, vocal learning and visual-gestural imitation, were crucial factors that facilitated the evolution of speech and singing. Comparative evidence has revealed that humans are an odd case in this respect, as the case for multimodal imitation is barely documented in non-human animals. While there is evidence of vocal learning in birds and in mammals like bats, elephants and marine mammals, evidence in both domains, vocal and gestural, exists for two Psittacine birds (budgerigars and grey parrots) and cetaceans only. Moreover, it draws attention to the apparent absence of vocal imitation (with just a few cases reported for vocal fold control in an orangutan and a gorilla and a prolonged development of vocal plasticity in marmosets) and even for imitation of intransitive actions (not object related) in monkeys and apes in the wild. Even after training, the evidence for productive or "true imitation" (copy of a novel behavior, i.e., not pre-existent in the observer's behavioral repertoire) in both domains is scarce. Here we review the evidence of multimodal imitation in cetaceans, one of the few living mammalian species that have been reported to display multimodal imitative learning besides humans, and their role in sociality, communication and group cultures. We propose that cetacean multimodal imitation was acquired in parallel with the evolution and development of behavioral synchrony and multimodal organization of sensorimotor information, supporting volitional motor control of their vocal system and audio-echoic-visual voices, body posture and movement integration.
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Affiliation(s)
- José Zamorano-Abramson
- Centro de Investigación en Complejidad Social, Facultad de Gobierno, Universidad del Desarrollo, Santiago, Chile
- Grupo UCM de Psicobiología Social, Evolutiva y Comparada, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: José Zamorano-Abramson,
| | - Maëva Michon
- Centro de Estudios en Neurociencia Humana y Neuropsicología, Facultad de Psicología, Universidad Diego Portales, Santiago, Chile
- Laboratory for Cognitive and Evolutionary Neuroscience, Department of Psychiatry, Faculty of Medicine, Interdisciplinary Center for Neuroscience, Pontificia Universidad Católica de, Santiago, Chile
- Maëva Michon,
| | - Ma Victoria Hernández-Lloreda
- Grupo UCM de Psicobiología Social, Evolutiva y Comparada, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Psicobiología y Metodología de las Ciencias del Comportamiento, Facultad de Psicología, Campus de Somosaguas, Universidad Complutense de Madrid, Madrid, Spain
| | - Francisco Aboitiz
- Laboratory for Cognitive and Evolutionary Neuroscience, Department of Psychiatry, Faculty of Medicine, Interdisciplinary Center for Neuroscience, Pontificia Universidad Católica de, Santiago, Chile
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10
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Upregulation of Glutaminyl Cyclase Contributes to ERS-Induced Apoptosis in PC12 Cells. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4154697. [PMID: 36479306 PMCID: PMC9722295 DOI: 10.1155/2022/4154697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/22/2022] [Accepted: 10/17/2022] [Indexed: 11/30/2022]
Abstract
Glutaminyl cyclase (QC) is responsible for converting the N-terminal glutaminyl and glutamyl of the proteins into pyroglutamate (pE) through cyclization. It has been confirmed that QC catalyzes the formation of neurotoxic pE-modified Aβ in the brain of AD patients. But the effects of upregulated QC in diverse diseases have not been much clear until recently. Here, RNA sequencing was applied to identify differentially expressed genes (DEGs) in PC12 cells with QC overexpressing or knockdown. A total of 697 DEGs were identified in QC overexpressing cells while only 77 in QC knockdown cells. Multiple bioinformatic approaches revealed that the DEGs in QC overexpressing group were enriched in endoplasmic reticulum stress (ERS) related signaling pathways. The gene expression patterns of 23 DEGs were confirmed by RT-qPCR, in which the genes related to ERS showed the highest consistency. We also revealed the protein levels of GRP78, PERK, CHOP, and PARP-1, and caspase family was significantly upregulated by overexpressing QC. Moreover, overexpressing QC significantly increased apoptosis of PC12 cells in a time dependent manner. However, no significant alteration was observed in QC knockdown cells. Therefore, our study indicated that upregulated QC could induce ERS and apoptosis, which consequently trigger diseases by catalyzing the generation of pE-modified mediators.
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11
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Newton T. Psychology: Where history, culture, and biology meet. THEORY & PSYCHOLOGY 2022. [DOI: 10.1177/09593543221131782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This article argues that the same epistemological assumptions cannot be confidently applied in the transition from the biological to the social arenas of psychology, as a consequence of the sociocultural instability resulting from human linguistic and technological flair. To illustrate this contention, reference is made to historicist theses within critical and sociocultural psychology, the work of Ian Hacking and Norbert Elias, the centrality of language and technology to sociocultural instability, and the illustrative issues raised by cultural neuroscience and replication studies.
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12
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Ma S, Skarica M, Li Q, Xu C, Risgaard RD, Tebbenkamp AT, Mato-Blanco X, Kovner R, Krsnik Ž, de Martin X, Luria V, Martí-Pérez X, Liang D, Karger A, Schmidt DK, Gomez-Sanchez Z, Qi C, Gobeske KT, Pochareddy S, Debnath A, Hottman CJ, Spurrier J, Teo L, Boghdadi AG, Homman-Ludiye J, Ely JJ, Daadi EW, Mi D, Daadi M, Marín O, Hof PR, Rasin MR, Bourne J, Sherwood CC, Santpere G, Girgenti MJ, Strittmatter SM, Sousa AM, Sestan N. Molecular and cellular evolution of the primate dorsolateral prefrontal cortex. Science 2022; 377:eabo7257. [PMID: 36007006 PMCID: PMC9614553 DOI: 10.1126/science.abo7257] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The granular dorsolateral prefrontal cortex (dlPFC) is an evolutionary specialization of primates that is centrally involved in cognition. We assessed more than 600,000 single-nucleus transcriptomes from adult human, chimpanzee, macaque, and marmoset dlPFC. Although most cell subtypes defined transcriptomically are conserved, we detected several that exist only in a subset of species as well as substantial species-specific molecular differences across homologous neuronal, glial, and non-neural subtypes. The latter are exemplified by human-specific switching between expression of the neuropeptide somatostatin and tyrosine hydroxylase, the rate-limiting enzyme in dopamine production in certain interneurons. The above molecular differences are also illustrated by expression of the neuropsychiatric risk gene FOXP2, which is human-specific in microglia and primate-specific in layer 4 granular neurons. We generated a comprehensive survey of the dlPFC cellular repertoire and its shared and divergent features in anthropoid primates.
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Affiliation(s)
- Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mario Skarica
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Qian Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Chuan Xu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ryan D. Risgaard
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Xoel Mato-Blanco
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), MELIS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Rothem Kovner
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Željka Krsnik
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Xabier de Martin
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), MELIS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Xavier Martí-Pérez
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), MELIS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Dan Liang
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA, USA
| | - Danielle K. Schmidt
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachary Gomez-Sanchez
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Cai Qi
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Kevin T. Gobeske
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sirisha Pochareddy
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ashwin Debnath
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Cade J. Hottman
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Joshua Spurrier
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Neurology, Yale School of Medicine, New Haven, CT 06536, USA
| | - Leon Teo
- Australian Regenerative Medicine Institute, 15 Innovation Walk, Monash University, Clayton VIC, 3800, Australia
| | - Anthony G. Boghdadi
- Australian Regenerative Medicine Institute, 15 Innovation Walk, Monash University, Clayton VIC, 3800, Australia
| | - Jihane Homman-Ludiye
- Australian Regenerative Medicine Institute, 15 Innovation Walk, Monash University, Clayton VIC, 3800, Australia
| | - John J. Ely
- MAEBIOS, Alamogordo, NM 88310, USA
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
| | - Etienne W. Daadi
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Da Mi
- Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Marcel Daadi
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
- Department of Cell Systems & Anatomy, Radiology, Long School of Medicine, UT Health San Antonio
- NeoNeuron LLC, Palo Alto, CA 94306, USA
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE1 1UL, UK
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London SE1 1UL, UK
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - James Bourne
- Australian Regenerative Medicine Institute, 15 Innovation Walk, Monash University, Clayton VIC, 3800, Australia
| | - Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), MELIS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Matthew J. Girgenti
- Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA
- National Center for PTSD, US Department of Veterans Affairs, White River Junction, VT, USA
| | - Stephen M. Strittmatter
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Neurology, Yale School of Medicine, New Haven, CT 06536, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - André M.M. Sousa
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Departments of Genetics and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
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13
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Akter M, Khan SF, Sajib AA, Rima FS. A comprehensive in silico analysis of the deleterious nonsynonymous SNPs of human FOXP2 protein. PLoS One 2022; 17:e0272625. [PMID: 35944036 PMCID: PMC9362936 DOI: 10.1371/journal.pone.0272625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
FOXP2 encodes the forkhead transcription factor that plays a significant role in language development. Single nucleotide polymorphisms in FOXP2 have been linked to speech- language disorder, autism, cancer and schizophrenia. So, scrutinizing the functional SNPs to better understand their association in disease is an uphill task. The purpose of the current study was to identify the missense SNPs which have detrimental structural and functional effects on the FOXP2 protein. Multiple computational tools were employed to investigate the deleterious role of non-synonymous SNPs. Five variants as Y531H, L558P, R536G and R553C were found to be associated with diseases and located at the forkhead domain of the FOXP2 protein. Molecular docking analysis of FOXP2 DNA binding domain with its most common target sequence 5’-CAAATT-3’ predicted that R553C and L558P mutant variants destabilize protein structure by changing protein-DNA interface interactions and disruption of hydrogen bonds that may reduce the specificity and affinity of the binding. Further experimental investigations may need to verify whether this kind of structural and functional variations dysregulate protein activities and induce formation of disease.
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Affiliation(s)
- Mahmuda Akter
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Sumaiya Farah Khan
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Fahmida Sultana Rima
- Department of Biochemistry and Biotechnology, University of Barishal, Barishal, Bangladesh
- * E-mail:
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14
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Harnish SM, Diedrichs VA, Bartlett CW. EARLY CONSIDERATIONS OF GENETICS IN APHASIA REHABILITATION: A NARRATIVE REVIEW. APHASIOLOGY 2022; 37:835-853. [PMID: 37346093 PMCID: PMC10281715 DOI: 10.1080/02687038.2022.2043234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/14/2022] [Indexed: 06/23/2023]
Abstract
Background Early investigations linking language and genetics were focused on the evolution of human communication in populations with developmental speech and language disorders. Recently, studies suggest that genes may also modulate recovery from post-stroke aphasia. Aims Our goal is to review current literature related to the influence of genetics on post-stroke recovery, and the implications for aphasia rehabilitation. We describe candidate genes implicated by empirical findings and address additional clinical considerations. Main Contribution We describe existing evidence and mechanisms supporting future investigations into how genetic factors may modulate aphasia recovery and propose that two candidate genes, brain derived neurotrophic factor (BDNF) and apolipoprotein E (APOE), may be important considerations for future research assessing response to aphasia treatment. Evidence suggests that BDNF is important for learning, memory, and neuroplasticity. APOE influences cognitive functioning and memory in older individuals and has also been implicated in neural repair. Moreover, recent data suggest an interaction between specific alleles of the BDNF and APOE genes in influencing episodic memory. Conclusions Genetic influences on recovery from aphasia have been largely unexplored in the literature despite evidence that genetic factors influence behaviour and recovery from brain injury. As researchers continue to explore prognostic factors that may influence response to aphasia treatment, it is time for genetic factors to be considered as a source of variability. As the field moves in the direction of personalized medicine, eventually allied health professionals may utilize genetic profiles to inform treatment decisions and education for patients and care partners.
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Affiliation(s)
- Stacy M Harnish
- Department of Speech and Hearing Science, The Ohio State University
| | | | - Christopher W Bartlett
- Battelle Center for Mathematical Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital and Department of Pediatrics, College of Medicine, The Ohio State University
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15
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Palaniyappan L, Du J, Zhang J, Feng J. Reply to: "Historical pursuits of the language pathway hypothesis of schizophrenia". NPJ SCHIZOPHRENIA 2021; 7:54. [PMID: 34753936 PMCID: PMC8578441 DOI: 10.1038/s41537-021-00183-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Lena Palaniyappan
- Department of Psychiatry and Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
- Lawson Health Research Institute, London, Ontario, Canada
| | - Jingnan Du
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, 200030, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
| | - Jie Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China.
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China.
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL, UK.
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16
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Navarro L, Martinón-Torres F, Salas A. Sensogenomics and the Biological Background Underlying Musical Stimuli: Perspectives for a New Era of Musical Research. Genes (Basel) 2021; 12:1454. [PMID: 34573436 PMCID: PMC8472585 DOI: 10.3390/genes12091454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/01/2021] [Accepted: 09/13/2021] [Indexed: 01/03/2023] Open
Abstract
What is the actual impact of music on the human being and the scope for scientific research in this realm? Compared to other areas, the study of the relationship between music and human biology has received limited attention. At the same time, evidence of music's value in clinical science, neuroscience, and social science keeps increasing. This review article synthesizes the existing knowledge of genetics related to music. While the success of genomics has been demonstrated in medical research, with thousands of genes that cause inherited diseases or a predisposition to multifactorial disorders identified, much less attention has been paid to other human traits. We argue for the development of a new discipline, sensogenomics, aimed at investigating the impact of the sensorial input on gene expression and taking advantage of new, discovery-based 'omic' approaches that allow for the exploration of the whole transcriptome of individuals under controlled experiments and circumstances.
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Affiliation(s)
- Laura Navarro
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, 15706 Santiago de Compostela, Spain;
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de San-tiago (SERGAS), Galicia, 15706 Santiago de Compostela, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Universidad de Santiago de Compostela (USC), Galicia, 15706 Santiago de Compostela, Spain;
| | - Federico Martinón-Torres
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Universidad de Santiago de Compostela (USC), Galicia, 15706 Santiago de Compostela, Spain;
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia, 15706 Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, 15706 Santiago de Compostela, Spain;
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de San-tiago (SERGAS), Galicia, 15706 Santiago de Compostela, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Universidad de Santiago de Compostela (USC), Galicia, 15706 Santiago de Compostela, Spain;
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17
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von Merten S, Pfeifle C, Künzel S, Hoier S, Tautz D. A humanized version of Foxp2 affects ultrasonic vocalization in adult female and male mice. GENES BRAIN AND BEHAVIOR 2021; 20:e12764. [PMID: 34342113 DOI: 10.1111/gbb.12764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/02/2021] [Accepted: 07/31/2021] [Indexed: 01/03/2023]
Abstract
The transcription factor FoxP2 is involved in setting up the neuronal circuitry for vocal learning in mammals and birds and is thought to have played a special role in the evolution of human speech and language. It has been shown that an allele with a humanized version of the murine Foxp2 gene changes the ultrasonic vocalization of mouse pups compared to pups of the wild-type inbred strain. Here we tested if this humanized allele would also affect the ultrasonic vocalization of adult female and male mice. In a previous study, in which only male vocalization was considered and the mice were recorded under a restricted spatial and temporal regime, no difference in adult vocalization between genotypes was found. Here, we use a different test paradigm in which both female and male vocalizations are recorded in extended social contact. We found differences in temporal, spectral and syntactical parameters between the genotypes in both sexes, and between sexes. Mice carrying the humanized Foxp2 allele were using higher frequencies and more complex syllable types than mice of the corresponding wildtype inbred strain. Our results support the notion that the humanized Foxp2 allele has a differential effect on mouse ultrasonic vocalization. As mice carrying the humanized version of the Foxp2 gene show effects opposite to those of mice carrying disrupted or mutated alleles of this gene, we conclude that this mouse line represents an important model for the study of human speech and language evolution.
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Affiliation(s)
- Sophie von Merten
- CESAM - Centro de Estudos do Ambiente e do Mar, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.,Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Christine Pfeifle
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Künzel
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Svenja Hoier
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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18
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den Hoed J, Devaraju K, Fisher SE. Molecular networks of the FOXP2 transcription factor in the brain. EMBO Rep 2021; 22:e52803. [PMID: 34260143 PMCID: PMC8339667 DOI: 10.15252/embr.202152803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/19/2021] [Accepted: 06/23/2021] [Indexed: 01/06/2023] Open
Abstract
The discovery of the FOXP2 transcription factor, and its implication in a rare severe human speech and language disorder, has led to two decades of empirical studies focused on uncovering its roles in the brain using a range of in vitro and in vivo methods. Here, we discuss what we have learned about the regulation of FOXP2, its downstream effectors, and its modes of action as a transcription factor in brain development and function, providing an integrated overview of what is currently known about the critical molecular networks.
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Affiliation(s)
- Joery den Hoed
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- International Max Planck Research School for Language SciencesMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Karthikeyan Devaraju
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Simon E Fisher
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- Donders Institute for Brain, Cognition and BehaviourRadboud UniversityNijmegenThe Netherlands
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19
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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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20
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Richerson PJ, Gavrilets S, de Waal FBM. Modern theories of human evolution foreshadowed by Darwin's Descent of Man. Science 2021; 372:372/6544/eaba3776. [PMID: 34016754 DOI: 10.1126/science.aba3776] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/15/2021] [Indexed: 12/17/2022]
Abstract
Charles Darwin's The Descent of Man, published 150 years ago, laid the grounds for scientific studies into human origins and evolution. Three of his insights have been reinforced by modern science. The first is that we share many characteristics (genetic, developmental, physiological, morphological, cognitive, and psychological) with our closest relatives, the anthropoid apes. The second is that humans have a talent for high-level cooperation reinforced by morality and social norms. The third is that we have greatly expanded the social learning capacity that we see already in other primates. Darwin's emphasis on the role of culture deserves special attention because during an increasingly unstable Pleistocene environment, cultural accumulation allowed changes in life history; increased cognition; and the appearance of language, social norms, and institutions.
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Affiliation(s)
- Peter J Richerson
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Sergey Gavrilets
- Department of Ecology and Evolutionary Biology, Department of Mathematics, National Institute for Mathematical and Biological Synthesis, Center for the Dynamics of Social Complexity, University of Tennessee, Knoxville, TN 37996, USA.
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21
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Beccacece L, Abondio P, Cilli E, Restani D, Luiselli D. Human Genomics and the Biocultural Origin of Music. Int J Mol Sci 2021; 22:5397. [PMID: 34065521 PMCID: PMC8160972 DOI: 10.3390/ijms22105397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/03/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
Music is an exclusive feature of humankind. It can be considered as a form of universal communication, only partly comparable to the vocalizations of songbirds. Many trends of research in this field try to address music origins, as well as the genetic bases of musicality. On one hand, several hypotheses have been made on the evolution of music and its role, but there is still debate, and comparative studies suggest a gradual evolution of some abilities underlying musicality in primates. On the other hand, genome-wide studies highlight several genes associated with musical aptitude, confirming a genetic basis for different musical skills which humans show. Moreover, some genes associated with musicality are involved also in singing and song learning in songbirds, suggesting a likely evolutionary convergence between humans and songbirds. This comprehensive review aims at presenting the concept of music as a sociocultural manifestation within the current debate about its biocultural origin and evolutionary function, in the context of the most recent discoveries related to the cross-species genetics of musical production and perception.
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Affiliation(s)
- Livia Beccacece
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Paolo Abondio
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna—Ravenna Campus, 48121 Ravenna, Italy; (E.C.); (D.R.)
| | - Donatella Restani
- Department of Cultural Heritage, University of Bologna—Ravenna Campus, 48121 Ravenna, Italy; (E.C.); (D.R.)
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna—Ravenna Campus, 48121 Ravenna, Italy; (E.C.); (D.R.)
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22
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Jovanovic VM, Sarfert M, Reyna-Blanco CS, Indrischek H, Valdivia DI, Shelest E, Nowick K. Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. Front Genet 2021; 12:662239. [PMID: 34079582 PMCID: PMC8166252 DOI: 10.3389/fgene.2021.662239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/19/2021] [Indexed: 01/09/2023] Open
Abstract
Gene regulatory factors (GRFs), such as transcription factors, co-factors and histone-modifying enzymes, play many important roles in modifying gene expression in biological processes. They have also been proposed to underlie speciation and adaptation. To investigate potential contributions of GRFs to primate evolution, we analyzed GRF genes in 27 publicly available primate genomes. Genes coding for zinc finger (ZNF) proteins, especially ZNFs with a Krüppel-associated box (KRAB) domain were the most abundant TFs in all genomes. Gene numbers per TF family differed between all species. To detect signs of positive selection in GRF genes we investigated more than 3,000 human GRFs with their more than 70,000 orthologs in 26 non-human primates. We implemented two independent tests for positive selection, the branch-site-model of the PAML suite and aBSREL of the HyPhy suite, focusing on the human and great ape branch. Our workflow included rigorous procedures to reduce the number of false positives: excluding distantly similar orthologs, manual corrections of alignments, and considering only genes and sites detected by both tests for positive selection. Furthermore, we verified the candidate sites for selection by investigating their variation within human and non-human great ape population data. In order to approximately assign a date to positively selected sites in the human lineage, we analyzed archaic human genomes. Our work revealed with high confidence five GRFs that have been positively selected on the human lineage and one GRF that has been positively selected on the great ape lineage. These GRFs are scattered on different chromosomes and have been previously linked to diverse functions. For some of them a role in speciation and/or adaptation can be proposed based on the expression pattern or association with human diseases, but it seems that they all contributed independently to human evolution. Four of the positively selected GRFs are KRAB-ZNF proteins, that induce changes in target genes co-expression and/or through arms race with transposable elements. Since each positively selected GRF contains several sites with evidence for positive selection, we suggest that these GRFs participated pleiotropically to phenotypic adaptations in humans.
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Affiliation(s)
- Vladimir M Jovanovic
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany.,Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Melanie Sarfert
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany
| | - Carlos S Reyna-Blanco
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Henrike Indrischek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Dulce I Valdivia
- Evolutionary Genomics Laboratory and Genome Topology and Regulation Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-Irapuato), Irapuato, Mexico
| | - Ekaterina Shelest
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, United Kingdom
| | - Katja Nowick
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany
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23
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Gopalan S, Atkinson EG, Buck LT, Weaver TD, Henn BM. Inferring archaic introgression from hominin genetic data. Evol Anthropol 2021; 30:199-220. [PMID: 33951239 PMCID: PMC8360192 DOI: 10.1002/evan.21895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 08/03/2020] [Accepted: 03/29/2021] [Indexed: 01/05/2023]
Abstract
Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Elizabeth G Atkinson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Stanley Center for Psychiatric Research, Broad Institute, Boston, Massachusetts, USA
| | - Laura T Buck
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Timothy D Weaver
- Department of Anthropology, University of California, Davis, California, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Anthropology, University of California, Davis, California, USA.,UC Davis Genome Center, University of California, Davis, California, USA
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24
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Dumas G, Malesys S, Bourgeron T. Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition. Genome Res 2021; 31:484-496. [PMID: 33441416 PMCID: PMC7919455 DOI: 10.1101/gr.262113.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022]
Abstract
The human brain differs from that of other primates, but the genetic basis of these differences remains unclear. We investigated the evolutionary pressures acting on almost all human protein-coding genes (N = 11,667; 1:1 orthologs in primates) based on their divergence from those of early hominins, such as Neanderthals, and non-human primates. We confirm that genes encoding brain-related proteins are among the most strongly conserved protein-coding genes in the human genome. Combining our evolutionary pressure metrics for the protein-coding genome with recent data sets, we found that this conservation applied to genes functionally associated with the synapse and expressed in brain structures such as the prefrontal cortex and the cerebellum. Conversely, several genes presenting signatures commonly associated with positive selection appear as causing brain diseases or conditions, such as micro/macrocephaly, Joubert syndrome, dyslexia, and autism. Among those, a number of DNA damage response genes associated with microcephaly in humans such as BRCA1, NHEJ1, TOP3A, and RNF168 show strong signs of positive selection and might have played a role in human brain size expansion during primate evolution. We also showed that cerebellum granule neurons express a set of genes also presenting signatures of positive selection and that may have contributed to the emergence of fine motor skills and social cognition in humans. This resource is available online and can be used to estimate evolutionary constraints acting on a set of genes and to explore their relative contributions to human traits.
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Affiliation(s)
- Guillaume Dumas
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris 75015, France
- Department of Psychiatry, Université de Montreal, CHU Sainte-Justine Hospital, Montreal H3T 1C5, Quebec, Canada
| | - Simon Malesys
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris 75015, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris 75015, France
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25
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Franchini LF. Genetic Mechanisms Underlying Cortical Evolution in Mammals. Front Cell Dev Biol 2021; 9:591017. [PMID: 33659245 PMCID: PMC7917222 DOI: 10.3389/fcell.2021.591017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
The remarkable sensory, motor, and cognitive abilities of mammals mainly depend on the neocortex. Thus, the emergence of the six-layered neocortex in reptilian ancestors of mammals constitutes a fundamental evolutionary landmark. The mammalian cortex is a columnar epithelium of densely packed cells organized in layers where neurons are generated mainly in the subventricular zone in successive waves throughout development. Newborn cells move away from their site of neurogenesis through radial or tangential migration to reach their specific destination closer to the pial surface of the same or different cortical area. Interestingly, the genetic programs underlying neocortical development diversified in different mammalian lineages. In this work, I will review several recent studies that characterized how distinct transcriptional programs relate to the development and functional organization of the neocortex across diverse mammalian lineages. In some primates such as the anthropoids, the neocortex became extremely large, especially in humans where it comprises around 80% of the brain. It has been hypothesized that the massive expansion of the cortical surface and elaboration of its connections in the human lineage, has enabled our unique cognitive capacities including abstract thinking, long-term planning, verbal language and elaborated tool making capabilities. I will also analyze the lineage-specific genetic changes that could have led to the modification of key neurodevelopmental events, including regulation of cell number, neuronal migration, and differentiation into specific phenotypes, in order to shed light on the evolutionary mechanisms underlying the diversity of mammalian brains including the human brain.
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Affiliation(s)
- Lucía Florencia Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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26
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Atkinson EG, Maihofer AX, Kanai M, Martin AR, Karczewski KJ, Santoro ML, Ulirsch JC, Kamatani Y, Okada Y, Finucane HK, Koenen KC, Nievergelt CM, Daly MJ, Neale BM. Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power. Nat Genet 2021; 53:195-204. [PMID: 33462486 PMCID: PMC7867648 DOI: 10.1038/s41588-020-00766-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022]
Abstract
Admixed populations are routinely excluded from genomic studies due to concerns over population structure. Here, we present a statistical framework and software package, Tractor, to facilitate the inclusion of admixed individuals in association studies by leveraging local ancestry. We test Tractor with simulated and empirical two-way admixed African-European cohorts. Tractor generates accurate ancestry-specific effect-size estimates and P values, can boost genome-wide association study (GWAS) power and improves the resolution of association signals. Using a local ancestry-aware regression model, we replicate known hits for blood lipids, discover novel hits missed by standard GWAS and localize signals closer to putative causal variants.
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Affiliation(s)
- Elizabeth G Atkinson
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Adam X Maihofer
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marcos L Santoro
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departamento de Psiquiatria, Universidade Federal de São Paulo, São Paulo, Brazil
- Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jacob C Ulirsch
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Hilary K Finucane
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karestan C Koenen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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27
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Zhuo X, Du AY, Pehrsson EC, Li D, Wang T. Epigenomic differences in the human and chimpanzee genomes are associated with structural variation. Genome Res 2021; 31:279-290. [PMID: 33303495 PMCID: PMC7849402 DOI: 10.1101/gr.263491.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022]
Abstract
Structural variation (SV), including insertions and deletions (indels), is a primary mechanism of genome evolution. However, the mechanism by which SV contributes to epigenome evolution is poorly understood. In this study, we characterized the association between lineage-specific indels and epigenome differences between human and chimpanzee to investigate how SVs might have shaped the epigenetic landscape. By intersecting medium-to-large human-chimpanzee indels (20 bp-50 kb) with putative promoters and enhancers in cranial neural crest cells (CNCCs) and repressed regions in induced pluripotent cells (iPSCs), we found that 12% of indels overlap putative regulatory and repressed regions (RRRs), and 15% of these indels are associated with lineage-biased RRRs. Indel-associated putative enhancer and repressive regions are approximately 1.3 times and approximately three times as likely to be lineage-biased, respectively, as those not associated with indels. We found a twofold enrichment of medium-sized indels (20-50 bp) in CpG island (CGI)-containing promoters than expected by chance. Lastly, from human-specific transposable element insertions, we identified putative regulatory elements, including NR2F1-bound putative CNCC enhancers derived from SVAs and putative iPSC promoters derived from LTR5s. Our results show that different types of indels are associated with specific epigenomic diversity between human and chimpanzee.
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Affiliation(s)
- Xiaoyu Zhuo
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Alan Y Du
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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28
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Endo S, Motomura K, Tsuhako M, Kakazu Y, Nakamura M, M. Otaki J. Search for Human-Specific Proteins Based on Availability Scores of Short Constituent Sequences: Identification of a WRWSH Protein in Human Testis. Comput Biol Chem 2020. [DOI: 10.5772/intechopen.89653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Little is known about protein sequences unique in humans. Here, we performed alignment-free sequence comparisons based on the availability (frequency bias) of short constituent amino acid (aa) sequences (SCSs) in proteins to search for human-specific proteins. Focusing on 5-aa SCSs (pentats), exhaustive comparisons of availability scores among the human proteome and other nine mammalian proteomes in the nonredundant (nr) database identified a candidate protein containing WRWSH, here called FAM75, as human-specific. Examination of various human genome sequences revealed that FAM75 had genomic DNA sequences for either WRWSH or WRWSR due to a single nucleotide polymorphism (SNP). FAM75 and its related protein FAM205A were found to be produced through alternative splicing. The FAM75 transcript was found only in humans, but the FAM205A transcript was also present in other mammals. In humans, both FAM75 and FAM205A were expressed specifically in testis at the mRNA level, and they were immunohistochemically located in cells in seminiferous ducts and in acrosomes in spermatids at the protein level, suggesting their possible function in sperm development and fertilization. This study highlights a practical application of SCS-based methods for protein searches and suggests possible contributions of SNP variants and alternative splicing of FAM75 to human evolution.
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29
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Dussex N, Kutschera VE, Wiberg RAW, Parker DJ, Hunt GR, Gray RD, Rutherford K, Abe H, Fleischer RC, Ritchie MG, Rutz C, Wolf JBW, Gemmell NJ. A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows. Mol Ecol 2020; 30:973-986. [PMID: 33305388 DOI: 10.1111/mec.15775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 12/30/2022]
Abstract
Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.
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Affiliation(s)
- Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Department of Bioinformatics and Genetics, Centre for Palaeogenetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Verena E Kutschera
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - R Axel W Wiberg
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.,Department of Environmental Sciences, Evolutionary Biology, University of Basel, Basel, Switzerland
| | - Darren J Parker
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Gavin R Hunt
- University of Auckland, Science Centre 302, Auckland, New Zealand
| | - Russell D Gray
- University of Auckland, Science Centre 302, Auckland, New Zealand.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hideaki Abe
- Department of Anatomy, University of Otago, Dunedin, New Zealand.,Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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30
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Picard L, Ganivet Q, Allatif O, Cimarelli A, Guéguen L, Etienne L. DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes. Nucleic Acids Res 2020; 48:e103. [PMID: 32941639 PMCID: PMC7544217 DOI: 10.1093/nar/gkaa680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptive evolution has shaped major biological processes. Finding the protein-coding genes and the sites that have been subjected to adaptation during evolutionary time is a major endeavor. However, very few methods fully automate the identification of positively selected genes, and widespread sources of genetic innovations such as gene duplication and recombination are absent from most pipelines. Here, we developed DGINN, a highly-flexible and public pipeline to Detect Genetic INNovations and adaptive evolution in protein-coding genes. DGINN automates, from a gene's sequence, all steps of the evolutionary analyses necessary to detect the aforementioned innovations, including the search for homologs in databases, assignation of orthology groups, identification of duplication and recombination events, as well as detection of positive selection using five methods to increase precision and ranking of genes when a large panel is analyzed. DGINN was validated on nineteen genes with previously-characterized evolutionary histories in primates, including some engaged in host-pathogen arms-races. Our results confirm and also expand results from the literature, including novel findings on the Guanylate-binding protein family, GBPs. This establishes DGINN as an efficient tool to automatically detect genetic innovations and adaptive evolution in diverse datasets, from the user's gene of interest to a large gene list in any species range.
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Affiliation(s)
- Lea Picard
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
- Laboratoire de Biologie et Biométrie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Quentin Ganivet
- Laboratoire de Biologie et Biométrie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Omran Allatif
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Andrea Cimarelli
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Laurent Guéguen
- Laboratoire de Biologie et Biométrie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne, France
- Swedish Collegium for Advanced Study, Uppsala, Sweden
| | - Lucie Etienne
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
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31
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Breyl M. Triangulating Neanderthal cognition: A tale of not seeing the forest for the trees. WILEY INTERDISCIPLINARY REVIEWS. COGNITIVE SCIENCE 2020; 12:e1545. [PMID: 32918796 DOI: 10.1002/wcs.1545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 01/20/2023]
Abstract
The inference of Neanderthal cognition, including their cultural and linguistic capabilities, has persisted as a fiercely debated research topic for decades. This lack of consensus is substantially based on inherent uncertainties in reconstructing prehistory out of indirect evidence as well as other methodological limitations. Further factors include systemic difficulties within interdisciplinary discourse, data artifacts, historic research biases, and the sheer scope of the relevant research. Given the degrees of freedom in interpretation ensuing from these complications, any attempt to find approximate answers to the yet unsettled pertinent discourse may not rest on single studies, but instead a careful and comprehensive interdisciplinary synthesis of findings. Triangulating Neanderthals' cognition by considering the plethora of data, diverse perspectives and aforementioned complexities present within the literature constitutes the currently most reliable pathway to tentative conclusions. While some uncertainties remain, such an approach paints the picture of an extensive shared humanity between anatomically modern humans and Neanderthals. This article is categorized under: Cognitive Biology > Evolutionary Roots of Cognition Linguistics > Evolution of Language.
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Affiliation(s)
- Michael Breyl
- Germanistik, Komparatistik, Nordistik, Deutsch als Fremdsprache, Ludwig-Maximilians-University of Munich (LMU), Munich, Germany
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32
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di Porzio U. A bigger brain for a more complex environment. Rev Neurosci 2020; 31:/j/revneuro.ahead-of-print/revneuro-2020-0041/revneuro-2020-0041.xml. [PMID: 32924383 DOI: 10.1515/revneuro-2020-0041] [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: 05/24/2020] [Accepted: 07/04/2020] [Indexed: 11/15/2022]
Abstract
The environment increased complexity required more neural functions to develop in the hominin brains, and the hominins adapted to the complexity by developing a bigger brain with a greater interconnection between its parts. Thus, complex environments drove the growth of the brain. In about two million years during hominin evolution, the brain increased three folds in size, one of the largest and most complex amongst mammals, relative to body size. The size increase has led to anatomical reorganization and complex neuronal interactions in a relatively small skull. At birth, the human brain is only about 20% of its adult size. That facilitates the passage through the birth canal. Therefore, the human brain, especially cortex, develops postnatally in a rich stimulating environment with continuous brain wiring and rewiring and insertion of billions of new neurons. One of the consequence is that in the newborn brain, neuroplasticity is always turned "on" and it remains active throughout life, which gave humans the ability to adapt to complex and often hostile environments, integrate external experiences, solve problems, elaborate abstract ideas and innovative technologies, store a lot of information. Besides, hominins acquired unique abilities as music, language, and intense social cooperation. Overwhelming ecological, social, and cultural challenges have made the human brain so unique. From these events, as well as the molecular genetic changes that took place in those million years, under the pressure of natural selection, derive the distinctive cognitive abilities that have led us to complex social organizations and made our species successful.
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Affiliation(s)
- Umberto di Porzio
- Developmental Neurobiology Laboratory, Institute of Genetics and Biophysics, CNR, Via Pietro Castellino 111, 80128 Naples, Italy
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33
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den Hoed J, Fisher SE. Genetic pathways involved in human speech disorders. Curr Opin Genet Dev 2020; 65:103-111. [PMID: 32622339 DOI: 10.1016/j.gde.2020.05.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/08/2020] [Accepted: 05/08/2020] [Indexed: 12/12/2022]
Abstract
Rare genetic variants that disrupt speech development provide entry points for deciphering the neurobiological foundations of key human capacities. The value of this approach is illustrated by FOXP2, a transcription factor gene that was implicated in speech apraxia, and subsequently investigated using human cell-based systems and animal models. Advances in next-generation sequencing, coupled to de novo paradigms, facilitated discovery of etiological variants in additional genes in speech disorder cohorts. As for other neurodevelopmental syndromes, gene-driven studies show blurring of boundaries between diagnostic categories, with some risk genes shared across speech disorders, intellectual disability and autism. Convergent evidence hints at involvement of regulatory genes co-expressed in early human brain development, suggesting that etiological pathways could be amenable for investigation in emerging neural models such as cerebral organoids.
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Affiliation(s)
- Joery den Hoed
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands; International Max Planck Research School for Language Sciences, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands.
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34
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The cognitive and speech genes are jointly shaped by both positive and relaxed selection in the human lineage. Genomics 2020; 112:2922-2927. [PMID: 32387504 DOI: 10.1016/j.ygeno.2020.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 04/17/2020] [Accepted: 05/05/2020] [Indexed: 11/22/2022]
Abstract
The emergence of a coordinated network of cognitive and speech genes in the human lineage performing overlapping functions is a great evolutionary puzzle. Prior studies on the speech gene FOXP2 are inconclusive on the nature of selection operating on this gene in the human lineage. Here, I show that the evolution of FOXP2 is accelerated in the human lineage due to relaxation of purifying selection (relaxed selection). Five potential genes associated with human-specific intelligence and speech genes have evolved under the impact of positive selection and three genes including FOXP2 have undergone relaxation of purifying selection in the human lineage. Overall, three evolutionary processes namely positive selection, relaxation of purifying selection and neutral evolution have contributed for the genomic evolution of extraordinary cognitive ability and speech in the hominin lineage. The cognitive and speech genes subjected to natural selection in the human lineage have demonstrated a coevolutionary trend.
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Hejase HA, Dukler N, Siepel A. From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection. Trends Genet 2020; 36:243-258. [PMID: 31954511 PMCID: PMC7177178 DOI: 10.1016/j.tig.2019.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/15/2019] [Accepted: 12/11/2019] [Indexed: 01/01/2023]
Abstract
Methods to detect signals of natural selection from genomic data have traditionally emphasized the use of simple summary statistics. Here, we review a new generation of methods that consider combinations of conventional summary statistics and/or richer features derived from inferred gene trees and ancestral recombination graphs (ARGs). We also review recent advances in methods for population genetic simulation and ARG reconstruction. Finally, we describe opportunities for future work on a variety of related topics, including the genetics of speciation, estimation of selection coefficients, and inference of selection on polygenic traits. Together, these emerging methods offer promising new directions in the study of natural selection.
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Affiliation(s)
- Hussein A Hejase
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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36
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Dalvie S, Maihofer AX, Coleman JRI, Bradley B, Breen G, Brick LA, Chen CY, Choi KW, Duncan LE, Guffanti G, Haas M, Harnal S, Liberzon I, Nugent NR, Provost AC, Ressler KJ, Torres K, Amstadter AB, Bryn Austin S, Baker DG, Bolger EA, Bryant RA, Calabrese JR, Delahanty DL, Farrer LA, Feeny NC, Flory JD, Forbes D, Galea S, Gautam A, Gelernter J, Hammamieh R, Jett M, Junglen AG, Kaufman ML, Kessler RC, Khan A, Kranzler HR, Lebois LAM, Marmar C, Mavissakalian MR, McFarlane A, Donnell MO, Orcutt HK, Pietrzak RH, Risbrough VB, Roberts AL, Rothbaum AO, Roy-Byrne P, Ruggiero K, Seligowski AV, Sheerin CM, Silove D, Smoller JW, Stein MB, Teicher MH, Ursano RJ, Van Hooff M, Winternitz S, Wolff JD, Yehuda R, Zhao H, Zoellner LA, Stein DJ, Koenen KC, Nievergelt CM. Genomic influences on self-reported childhood maltreatment. Transl Psychiatry 2020; 10:38. [PMID: 32066696 PMCID: PMC7026037 DOI: 10.1038/s41398-020-0706-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 11/28/2019] [Accepted: 12/11/2019] [Indexed: 12/27/2022] Open
Abstract
Childhood maltreatment is highly prevalent and serves as a risk factor for mental and physical disorders. Self-reported childhood maltreatment appears heritable, but the specific genetic influences on this phenotype are largely unknown. The aims of this study were to (1) identify genetic variation associated with self-reported childhood maltreatment, (2) estimate SNP-based heritability (h2snp), (3) assess predictive value of polygenic risk scores (PRS) for childhood maltreatment, and (4) quantify genetic overlap of childhood maltreatment with mental and physical health-related phenotypes, and condition the top hits from our analyses when such overlap is present. Genome-wide association analysis for childhood maltreatment was undertaken, using a discovery sample from the UK Biobank (UKBB) (n = 124,000) and a replication sample from the Psychiatric Genomics Consortium-posttraumatic stress disorder group (PGC-PTSD) (n = 26,290). h2snp for childhood maltreatment and genetic correlations with mental/physical health traits were calculated using linkage disequilibrium score regression. PRS was calculated using PRSice and mtCOJO was used to perform conditional analysis. Two genome-wide significant loci associated with childhood maltreatment (rs142346759, p = 4.35 × 10-8, FOXP1; rs10262462, p = 3.24 × 10-8, FOXP2) were identified in the discovery dataset but were not replicated in PGC-PTSD. h2snp for childhood maltreatment was ~6% and the PRS derived from the UKBB was significantly predictive of childhood maltreatment in PGC-PTSD (r2 = 0.0025; p = 1.8 × 10-15). The most significant genetic correlation of childhood maltreatment was with depressive symptoms (rg = 0.70, p = 4.65 × 10-40), although we show evidence that our top hits may be specific to childhood maltreatment. This is the first large-scale genetic study to identify specific variants associated with self-reported childhood maltreatment. Speculatively, FOXP genes might influence externalizing traits and so be relevant to childhood maltreatment. Alternatively, these variants may be associated with a greater likelihood of reporting maltreatment. A clearer understanding of the genetic relationships of childhood maltreatment, including particular abuse subtypes, with a range of phenotypes, may ultimately be useful in in developing targeted treatment and prevention strategies.
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Affiliation(s)
- Shareefa Dalvie
- SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa.
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - Jonathan R I Coleman
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
- King's College London, NIHR BRC at the Maudsley, London, UK
| | - Bekh Bradley
- Atlanta VA Health Care System, Mental Health Service Line, Decatur, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Gerome Breen
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
- King's College London, NIHR BRC at the Maudsley, London, UK
| | - Leslie A Brick
- Alpert Medical School of Brown University, Providence, RI, USA
| | - Chia-Yen Chen
- Massachusetts General Hospital, Analytic and Translational Genetics Unit, Boston, MA, USA
- Massachusetts General Hospital, Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Boston, MA, USA
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Karmel W Choi
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA
| | - Laramie E Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Guia Guffanti
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Magali Haas
- Cohen Veterans Bioscience, Cambridge, MA, USA
| | - Supriya Harnal
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Israel Liberzon
- Department of Psychiatry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicole R Nugent
- Alpert Medical School of Brown University, Providence, RI, USA
- Bradley/Hasbro Children's Research Center of Rhode Island Hospital, Providence, RI, USA
| | | | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Katy Torres
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - Ananda B Amstadter
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - S Bryn Austin
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- Harvard School of Public Health, Department of Social and Behavioral Sciences, Boston, MA, USA
- Boston Children's Hospital, Division of Adolescent and Young Adult Medicine, Boston, MA, USA
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA, USA
| | - Dewleen G Baker
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Psychiatry Service, San Diego, CA, USA
| | - Elizabeth A Bolger
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Richard A Bryant
- Department of Psychology, University of New South Wales, Sydney, NSW, Australia
| | | | - Douglas L Delahanty
- Department of Psychological Sciences, Kent State University, Kent, OH, USA
- Research and Sponsored Programs, Kent State University, Kent, OH, USA
| | - Lindsay A Farrer
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Norah C Feeny
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Janine D Flory
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Forbes
- Department of Psychiatry, University of Melbourne, Melbourne, VIC, Australia
| | - Sandro Galea
- Department of Psychological and Brain Sciences, Boston University, Boston, MA, USA
| | - Aarti Gautam
- US Army Medical Research and Materiel Command, Fort Detrick, MD, USA
| | - Joel Gelernter
- US Department of Veterans Affairs, Department of Psychiatry, West Haven, CT, USA
- VA Connecticut Healthcare Center, West Haven, CT, USA
- Department of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Rasha Hammamieh
- US Army Medical Research and Materiel Command, USACEHR, Fort Detrick, MD, USA
| | - Marti Jett
- US Army Medical Research and Materiel Command, USACEHR, Fort Detrick, MD, USA
| | - Angela G Junglen
- Department of Psychological Sciences, Kent State University, Kent, OH, USA
| | - Milissa L Kaufman
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Ronald C Kessler
- Harvard Medical School, Department of Health Care Policy, Boston, MA, USA
| | - Alaptagin Khan
- McLean Hospital, Belmont, MA, USA
- Harvard Medical School, Department of Health Care Policy, Boston, MA, USA
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
| | - Lauren A M Lebois
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Charles Marmar
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| | | | - Alexander McFarlane
- University of Adelaide, Centre for Traumatic Stress Studies, Adelaide, SA, Australia
| | - Meaghan O' Donnell
- Department of Psychiatry, University of Melbourne, Melbourne, VIC, Australia
| | - Holly K Orcutt
- Department of Psychology, Northern Illinois University, DeKalb, IL, USA
| | - Robert H Pietrzak
- U.S. Department of Veterans Affairs National Center for Posttraumatic Stress Disorder, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Victoria B Risbrough
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - Andrea L Roberts
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alex O Rothbaum
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Peter Roy-Byrne
- Department of Psychiatry, University of Washington, Seattle, WA, USA
| | - Ken Ruggiero
- Department of Nursing and Department of Psychiatry, Medical University of South Carolina, Charleston, SC, USA
| | - Antonia V Seligowski
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Christina M Sheerin
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Richmond, VA, USA
| | - Derrick Silove
- Department of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Jordan W Smoller
- Massachusetts General Hospital, Analytic and Translational Genetics Unit, Boston, MA, USA
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Psychiatry Service, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Million Veteran Program, San Diego, CA, USA
| | - Martin H Teicher
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Robert J Ursano
- Department of Psychiatry, Uniformed Services University, Bethesda, MD, USA
| | - Miranda Van Hooff
- University of Adelaide, Centre for Traumatic Stress Studies, Adelaide, SA, Australia
| | - Sherry Winternitz
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | | | - Rachel Yehuda
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Mental Health, James J. Peters VA Medical Center, Bronx, NY, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale University, New Haven, CT, USA
| | - Lori A Zoellner
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Dan J Stein
- SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Karestan C Koenen
- Massachusetts General Hospital, Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Boston, MA, USA
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Harvard School of Public Health, Department of Epidemiology, Boston, MA, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
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Zhou Q, Wang C, Zhu Y, Wu Q, Jiang Y, Huang Y, Hu Y. Key Genes And Pathways Controlled By E2F1 In Human Castration-Resistant Prostate Cancer Cells. Onco Targets Ther 2019; 12:8961-8976. [PMID: 31802906 PMCID: PMC6827506 DOI: 10.2147/ott.s217347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 09/18/2019] [Indexed: 12/17/2022] Open
Abstract
Background Treatment of castration-resistant prostate cancer (CRPC) is an enormous challenge. As E2F transcription factor 1 (E2F1) is an essential factor in CRPC, this study investigated the genes and pathways controlled by E2F1 and their effects on cellular behavior in CRPC. Methods In vitro assays were used to evaluate cellular proliferation, apoptosis, and behavior. Cellular expression was quantified by RNA sequencing (RNA-seq). Gene co-expression was assessed using the GeneMANIA database, and correlations were analyzed with the GEPIA server. Altered pathways of differentially expressed genes (DEGs) were revealed by functional annotation. Module analysis was performed using the STRING database and hub genes were filtered with the Cytoscape software. Some DEGs were validated by real-time quantitative PCR (RT-qPCR). Results Knockdown of E2F1 significantly inhibited proliferation and accelerated apoptosis in PC3 cells but not in DU145 cells. Invasion and migration were reduced for both cell lines. A total of 1811 DEGs were identified in PC3 cells and 27 DEGs in DU145 cells exhibiting E2F1 knockdown. Ten overlapping DEGs, including TMOD2 and AIF1L, were identified in both knockdown cell lines and were significantly enriched for association with actin filament organization pathways. TMOD2 and KREMEN2 were genes co-expressed with E2F1; six overlapping DEGs were positively correlated with transcription factor E2F1. DEGs of the PC3 and DU145 groups were associated with multiple pathways. Five DEGs that overlapped between the two cell lines and three hub DEGs from PC3 cells were validated by RT-qPCR. Conclusion The results of this study suggest that E2F1 has a critical role in regulating actin filaments, as indicated by the change in expression level of several genes, including TMOD2 and AIF1L, in CRPC. This extends our understanding of the cellular responses affected by E2F1 in CRPC.
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Affiliation(s)
- Qingniao Zhou
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China.,Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Chengbang Wang
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China.,Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yuanyuan Zhu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Qunying Wu
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China.,Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yonghua Jiang
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yuanjie Huang
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
| | - Yanling Hu
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China.,Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China.,Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, People's Republic of China
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38
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Abstract
FOXP2 mutations cause a speech and language disorder, raising interest in potential roles of this gene in human evolution. A new study re-evaluates genomic variation at the human FOXP2 locus but finds no evidence of recent adaptive evolution.
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Affiliation(s)
- Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands.
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40
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Zaidel DW. Coevolution of language and symbolic meaning: Co-opting meaning underlying the initial arts in early human culture. WILEY INTERDISCIPLINARY REVIEWS. COGNITIVE SCIENCE 2019; 11:e1520. [PMID: 31502423 DOI: 10.1002/wcs.1520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/19/2019] [Accepted: 08/22/2019] [Indexed: 12/28/2022]
Abstract
Many of language's components, including communicating symbolic meaning, have neurobiological roots that go back millions of years in evolutionary time. The intersection with the human social survival strategy spawned additional adaptive meaning systems. Under conditions threatening survival in socially oriented human groups, extra-language meaning systems co-opted and adapted to facilitate unity, including the early formats of the arts. They would have percolated into cultural practice for this social purpose and ultimately survival. With evolutionary pressures tapping into biologically inherited, physiologically functioning sensory-motor pathways, anchored specifically in rhythm cognition and motor synchrony output, initial art practice conveyed symbolic group cohesion through communal, all-inclusive synchronously moving dance formations and rhythmically produced vocal or percussion sounds. As with the sounds of language in the deep past, and numerous other cultural behaviors, such nonmaterial early art formats would not have left marks in the archeological record but their evolutionary driven practice would have contributed to adaptive genetic factors woven into brain-behavior evolution. Their practice is likely to have well predated unearthed art-related objects. Consolidation of evidence and notions from language evolution, genetics, human physiology, comparative animal communication, archeology, and climate history in the distant past of early humans in Africa supports the evolutionary driven practice of initial nonmaterial art formats conveying symbolic expressions optimizing group survival. This article is categorized under: Cognitive Biology > Evolutionary Roots of Cognition Linguistics > Evolution of Language Psychology > Comparative Psychology.
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Affiliation(s)
- Dahlia W Zaidel
- Department of Psychology, University of California, Los Angeles (UCLA), Los Angeles, California
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Schreiweis C, Irinopoulou T, Vieth B, Laddada L, Oury F, Burguière E, Enard W, Groszer M. Mice carrying a humanized Foxp2 knock-in allele show region-specific shifts of striatal Foxp2 expression levels. Cortex 2019; 118:212-222. [DOI: 10.1016/j.cortex.2019.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/07/2018] [Accepted: 01/08/2019] [Indexed: 12/31/2022]
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Burunat E. Love is a physiological motivation (like hunger, thirst, sleep or sex). Med Hypotheses 2019; 129:109225. [PMID: 31371074 DOI: 10.1016/j.mehy.2019.05.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/17/2019] [Accepted: 05/12/2019] [Indexed: 10/26/2022]
Abstract
The multitude of terms associated with love has given rise to a false perception of love. In this paper, only maternal and romantic love are considered. Love is usually regarded as a feeling, motivation, addiction, passion, and, above all, an emotion. This confusion has consequences in the lives of human beings, leading not only to divorces, suicides, femicides but possibly also to a number of mental illnesses and suffering. Therefore, it is crucial to first clarify what is meant by emotion, motivation and love. This work aims to finally place love within the category of physiological motivations, such as hunger, thirst, sleep, or sex, on the basis that love is also essential for human survival, especially in childhood. Love is presented from an evolutionary perspective. Some other similarities between love and other physiological motivations are pointed out, such as its importance for appropriate human development, both its ontogeny and its permanence, and the long-lasting consequences of abuse and neglect. There are summarized reasons that account for this, such as the fact that physiological motivations are essential for survival and that love is an essential motivation for the survival of human offspring. Other reasons are that minimum changes in the quantity and quality of love alters development, that there can be a variety of neurophysiological and behavioural states within a motivation, and that motivations (also love) appear and change throughout development. Also, motivations and love sometimes may lead to an addictive behaviour. Finally, it is recognized that once physiological motivations (and love) appear, they become permanent. In a third section, some potential social, cultural, clinical and scientific consequences of the proposed consideration of love as a motivation are discussed. Accordingly, love's recognition as a motivation in the clinical field would imply a better understanding of its disorders and its inclusion in classifications manuals such as The Diagnostic and Statistical Manual of Mental Disorders (DSM), or in the International Classification of Diseases (ICD). Considering love as a motivation rather than an emotion could also impact the results of scientific research (an example is included). A comprehensive understanding of these questions could potentially allow for a new therapeutic approach in the treatment of mental illness, while offering an all-inclusive evolutionary explanation of cultural phenomena such as the origin and diffusion of both language and art. Love should be understood as a physiological motivation, like hunger, sleep or sex, and not as an emotion as it is commonly considered.
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Affiliation(s)
- Enrique Burunat
- School of Health Sciences/School of Psychology, Department of Clinical Psychology, Psychobiology and Methodology, University of La Laguna, P.O. Box 456, 38200 Santa Cruz de Tenerife, Canary Islands, Spain.
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Caporale AL, Gonda CM, Franchini LF. Transcriptional Enhancers in the FOXP2 Locus Underwent Accelerated Evolution in the Human Lineage. Mol Biol Evol 2019; 36:2432-2450. [PMID: 31359064 DOI: 10.1093/molbev/msz173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/26/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Unique human features such as complex language are the result of molecular evolutionary changes that modified developmental programs of our brain. The human-specific evolution of the forkhead box P2 (FOXP2) gene coding region has been linked to the emergence of speech and language in the human kind. However, little is known about how the expression of FOXP2 is regulated and if its regulatory machinery evolved in a lineage-specific manner in humans. In order to identify FOXP2 regulatory regions containing human-specific changes we used databases of human accelerated non-coding sequences or HARs. We found that the topologically associating domain (TAD) determined using developing human cerebral cortex containing the FOXP2 locus includes two clusters of 12 HARs, placing the locus occupied by FOXP2 among the top regions showing fast acceleration rates in non-coding regions in the human genome. Using in vivo enhancer assays in zebrafish, we found that at least five FOXP2-HARs behave as transcriptional enhancers throughout different developmental stages. In addition, we found that at least two FOXP2-HARs direct the expression of the reporter gene EGFP to foxP2 expressing regions and cells. Moreover, we uncovered two FOXP2-HARs showing reporter expression gain of function in the nervous system when compared with the chimpanzee ortholog sequences. Our results indicate that regulatory sequences in the FOXP2 locus underwent a human-specific evolutionary process suggesting that the transcriptional machinery controlling this gene could have also evolved differentially in the human lineage.
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Affiliation(s)
- Alfredo Leandro Caporale
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Catalina M Gonda
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lucía Florencia Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Fröhlich M, Sievers C, Townsend SW, Gruber T, van Schaik CP. Multimodal communication and language origins: integrating gestures and vocalizations. Biol Rev Camb Philos Soc 2019; 94:1809-1829. [PMID: 31250542 DOI: 10.1111/brv.12535] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022]
Abstract
The presence of divergent and independent research traditions in the gestural and vocal domains of primate communication has resulted in major discrepancies in the definition and operationalization of cognitive concepts. However, in recent years, accumulating evidence from behavioural and neurobiological research has shown that both human and non-human primate communication is inherently multimodal. It is therefore timely to integrate the study of gestural and vocal communication. Herein, we review evidence demonstrating that there is no clear difference between primate gestures and vocalizations in the extent to which they show evidence for the presence of key language properties: intentionality, reference, iconicity and turn-taking. We also find high overlap in the neurobiological mechanisms producing primate gestures and vocalizations, as well as in ontogenetic flexibility. These findings confirm that human language had multimodal origins. Nonetheless, we note that in great apes, gestures seem to fulfil a carrying (i.e. predominantly informative) role in close-range communication, whereas the opposite holds for face-to-face interactions of humans. This suggests an evolutionary shift in the carrying role from the gestural to the vocal stream, and we explore this transition in the carrying modality. Finally, we suggest that future studies should focus on the links between complex communication, sociality and cooperative tendency to strengthen the study of language origins.
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Affiliation(s)
- Marlen Fröhlich
- Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christine Sievers
- Department of Philosophy and Media Studies, Philosophy Seminar, University of Basel, Holbeinstrasse 12, 4051, Basel, Switzerland
| | - Simon W Townsend
- Department of Comparative Linguistics, University of Zurich, Plattenstrasse 54, 8032, Zurich, Switzerland.,Department of Psychology, University of Warwick, University Road, CV4 7AL, Coventry, UK
| | - Thibaud Gruber
- Swiss Center for Affective Sciences, CISA, University of Geneva, Chemin des Mines 9, 1202, Geneva, Switzerland.,Department of Zoology, University of Oxford, 11a Mansfield Road, OX1 3SZ, Oxford, UK
| | - Carel P van Schaik
- Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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Suzuki IK. Molecular drivers of human cerebral cortical evolution. Neurosci Res 2019; 151:1-14. [PMID: 31175883 DOI: 10.1016/j.neures.2019.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/10/2023]
Abstract
One of the most important questions in human evolutionary biology is how our ancestor has acquired an expanded volume of the cerebral cortex, which may have significantly impacted on improving our cognitive abilities. Recent comparative approaches have identified developmental features unique to the human or hominid cerebral cortex, not shared with other animals including conventional experimental models. In addition, genomic, transcriptomic, and epigenomic signatures associated with human- or hominid-specific processes of the cortical development are becoming identified by virtue of technical progress in the deep nucleotide sequencing. This review discusses ontogenic and phylogenetic processes of the human cerebral cortex, followed by the introduction of recent comprehensive approaches identifying molecular mechanisms potentially driving the evolutionary changes in the cortical development.
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Affiliation(s)
- Ikuo K Suzuki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan; VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KULeuven, 3000 Leuven, Belgium; Université Libre de Bruxelles (U.L.B.), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium.
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47
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Beyond Critical Period Learning: Striatal FoxP2 Affects the Active Maintenance of Learned Vocalizations in Adulthood. eNeuro 2019; 6:eN-CFN-0071-19. [PMID: 31001575 PMCID: PMC6469881 DOI: 10.1523/eneuro.0071-19.2019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 01/06/2023] Open
Abstract
In humans, mutations in the transcription factor forkhead box P2 (FOXP2) result in language disorders associated with altered striatal structure. Like speech, birdsong is learned through social interactions during maturational critical periods, and it relies on auditory feedback during initial learning and on-going maintenance. Hearing loss causes learned vocalizations to deteriorate in adult humans and songbirds. In the adult songbird brain, most FoxP2-enriched regions (e.g., cortex, thalamus) show a static expression level, but in the striatal song control nucleus, area X, FoxP2 is regulated by singing and social context: when juveniles and adults sing alone, its levels drop, and songs are more variable. When males sing to females, FoxP2 levels remain high, and songs are relatively stable: this “on-line” regulation implicates FoxP2 in ongoing vocal processes, but its role in the auditory-based maintenance of learned vocalization has not been examined. To test this, we overexpressed FoxP2 in both hearing and deafened adult zebra finches and assessed effects on song sung alone versus songs directed to females. In intact birds singing alone, no changes were detected between songs of males expressing FoxP2 or a GFP construct in area X, consistent with the marked stability of mature song in this species. In contrast, songs of males overexpressing FoxP2 became more variable and were less preferable to females, unlike responses to songs of GFP-expressing control males. In deafened birds, song deteriorated more rapidly following FoxP2 overexpression relative to GFP controls. Together, these experiments suggest that behavior-driven FoxP2 expression and auditory feedback interact to precisely maintain learned vocalizations.
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Feng C, Forthman KL, Kuplicki R, Yeh HW, Stewart JL, Paulus MP. Neighborhood affluence is not associated with positive and negative valence processing in adults with mood and anxiety disorders: A Bayesian inference approach. Neuroimage Clin 2019; 22:101738. [PMID: 30870735 PMCID: PMC6416773 DOI: 10.1016/j.nicl.2019.101738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/09/2019] [Accepted: 02/27/2019] [Indexed: 10/27/2022]
Abstract
Survey-based studies show that neighborhood disadvantage is associated with community reported mental health problems. However, fewer studies have examined whether neighborhood characteristics have measurable impact on mental health status of individuals in general and whether neighborhood characteristics impact positive/negative valence processing at both behavioral and brain levels. This study addressed these questions by investigating effects of census-based neighborhood affluence on self-reported symptoms, brain functions, and structures associated with positive/negative valence processing in a sample of individuals with mood and anxiety disorders (n = 262). Employing a Bayesian inference approach, our investigation demonstrates that neighborhood affluence fails to be associated with positive/negative valence processing measured across multiple modalities, with the only effects of neighborhood affluence identified in trait anxiety scores. These findings highlight that while community-based relationships between neighborhood characteristics and mental health problems are strong, it is much less clear that these characteristics have a measurable impact on the individual.
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Affiliation(s)
- Chunliang Feng
- Laureate Institute for Brain Research, Tulsa, OK, United States of America
| | - Katherine L Forthman
- Laureate Institute for Brain Research, Tulsa, OK, United States of America; University of Tulsa, Tulsa, OK, United States of America
| | - Rayus Kuplicki
- Laureate Institute for Brain Research, Tulsa, OK, United States of America
| | - Hung-Wen Yeh
- Laureate Institute for Brain Research, Tulsa, OK, United States of America
| | - Jennifer L Stewart
- Laureate Institute for Brain Research, Tulsa, OK, United States of America
| | - Martin P Paulus
- Laureate Institute for Brain Research, Tulsa, OK, United States of America.
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49
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Abstract
During the course of evolution the human brain has increased in size and complexity, ultimately these differences are the result of changes at the genetic level. Identifying and characterizing molecular evolution requires an understanding of both the genetic underpinning of the system as well as the comparative genetic tools to identify signatures of selection. This chapter aims to describe our current understanding of the genetics of human brain evolution. Primarily this is the story of the evolution of the human brain since our last common ape ancestor, but where relevant we will also discuss changes that are unique to the primate brain (compared to other mammals) or various other lineages in the evolution of humans more generally. It will focus on genetic changes that both directly affected the development and function of the brain as well as those that have indirectly influenced brain evolution through both prenatal and postnatal environment. This review is not meant to be exhaustive, but rather to begin to construct a general framework for understanding the full array of data being generated.
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Affiliation(s)
- Eric J Vallender
- University of Mississippi Medical Center, Jackson, MS, United States; Tulane National Primate Research Center, Covington, LA, United States.
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50
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Castells-Nobau A, Eidhof I, Fenckova M, Brenman-Suttner DB, Scheffer-de Gooyert JM, Christine S, Schellevis RL, van der Laan K, Quentin C, van Ninhuijs L, Hofmann F, Ejsmont R, Fisher SE, Kramer JM, Sigrist SJ, Simon AF, Schenck A. Conserved regulation of neurodevelopmental processes and behavior by FoxP in Drosophila. PLoS One 2019; 14:e0211652. [PMID: 30753188 PMCID: PMC6372147 DOI: 10.1371/journal.pone.0211652] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/30/2022] Open
Abstract
FOXP proteins form a subfamily of evolutionarily conserved transcription factors involved in the development and functioning of several tissues, including the central nervous system. In humans, mutations in FOXP1 and FOXP2 have been implicated in cognitive deficits including intellectual disability and speech disorders. Drosophila exhibits a single ortholog, called FoxP, but due to a lack of characterized mutants, our understanding of the gene remains poor. Here we show that the dimerization property required for mammalian FOXP function is conserved in Drosophila. In flies, FoxP is enriched in the adult brain, showing strong expression in ~1000 neurons of cholinergic, glutamatergic and GABAergic nature. We generate Drosophila loss-of-function mutants and UAS-FoxP transgenic lines for ectopic expression, and use them to characterize FoxP function in the nervous system. At the cellular level, we demonstrate that Drosophila FoxP is required in larvae for synaptic morphogenesis at axonal terminals of the neuromuscular junction and for dendrite development of dorsal multidendritic sensory neurons. In the developing brain, we find that FoxP plays important roles in α-lobe mushroom body formation. Finally, at a behavioral level, we show that Drosophila FoxP is important for locomotion, habituation learning and social space behavior of adult flies. Our work shows that Drosophila FoxP is important for regulating several neurodevelopmental processes and behaviors that are related to human disease or vertebrate disease model phenotypes. This suggests a high degree of functional conservation with vertebrate FOXP orthologues and established flies as a model system for understanding FOXP related pathologies.
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Affiliation(s)
- Anna Castells-Nobau
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ilse Eidhof
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Michaela Fenckova
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Jolanda M. Scheffer-de Gooyert
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sheren Christine
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rosa L. Schellevis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kiran van der Laan
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christine Quentin
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Lisa van Ninhuijs
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Falko Hofmann
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Radoslaw Ejsmont
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute of Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Jamie M. Kramer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stephan J. Sigrist
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Anne F. Simon
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- * E-mail:
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