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Williams AC, Hill LJ. Nicotinamide as Independent Variable for Intelligence, Fertility, and Health: Origin of Human Creative Explosions? Int J Tryptophan Res 2019; 12:1178646919855944. [PMID: 31258332 PMCID: PMC6585247 DOI: 10.1177/1178646919855944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 12/28/2022] Open
Abstract
Meat and nicotinamide acquisition was a defining force during the 2-million-year evolution of the big brains necessary for, anatomically modern, Homo sapiens to survive. Our next move was down the food chain during the Mesolithic 'broad spectrum', then horticultural, followed by the Neolithic agricultural revolutions and progressively lower average 'doses' of nicotinamide. We speculate that a fertility crisis and population bottleneck around 40 000 years ago, at the time of the Last Glacial Maximum, was overcome by Homo (but not the Neanderthals) by concerted dietary change plus profertility genes and intense sexual selection culminating in behaviourally modern Homo sapiens. Increased reliance on the 'de novo' synthesis of nicotinamide from tryptophan conditioned the immune system to welcome symbionts, such as TB (that excrete nicotinamide), and to increase tolerance of the foetus and thereby fertility. The trade-offs during the warmer Holocene were physical and mental stunting and more infectious diseases and population booms and busts. Higher nicotinamide exposure could be responsible for recent demographic and epidemiological transitions to lower fertility and higher longevity, but with more degenerative and auto-immune disease.
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Affiliation(s)
- Adrian C Williams
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lisa J Hill
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
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52
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Shultz DR, Montrey M, Shultz TR. Comparing fitness and drift explanations of Neanderthal replacement. Proc Biol Sci 2019; 286:20190907. [PMID: 31185865 DOI: 10.1098/rspb.2019.0907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
There is a general consensus among archaeologists that replacement of Neanderthals by anatomically modern humans in Europe occurred around 40-35 ka. However, the causal mechanism for this replacement continues to be debated. Proposed models have featured either fitness advantages in favour of anatomically modern humans or invoked neutral drift under various preconditions. Searching for specific fitness advantages in the archaeological record has proven difficult, as these may be obscured, absent or subject to interpretation. To bridge this gap, we rigorously compare the system-level properties of fitness- and drift-based explanations of Neanderthal replacement. Our stochastic simulations and analytical predictions show that, although both fitness and drift can produce replacement, they present important differences in (i) required initial conditions, (ii) reliability, (iii) time to replacement, and (iv) path to replacement (population histories). These results present useful opportunities for comparison with archaeological and genetic data. We find greater agreement between the available empirical evidence and the system-level properties of replacement by differential fitness, rather than by neutral drift.
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Affiliation(s)
- Daniel R Shultz
- 1 Department of Anthropology, McGill University , Montreal, Quebec , Canada.,2 Department of History, McGill University , Montreal, Quebec , Canada
| | - Marcel Montrey
- 3 Department of Psychology, McGill University , Montreal, Quebec , Canada
| | - Thomas R Shultz
- 3 Department of Psychology, McGill University , Montreal, Quebec , Canada.,4 School of Computer Science, McGill University , Montreal, Quebec , Canada
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53
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Banerjee N, Polushina T, Bettella F, Steen VM, Andreassen OA, Le Hellard S. Analysis of differentially methylated regions in great apes and extinct hominids provides support for the evolutionary hypothesis of schizophrenia. Schizophr Res 2019; 206:209-216. [PMID: 30545758 DOI: 10.1016/j.schres.2018.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 10/12/2018] [Accepted: 11/22/2018] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The persistence of schizophrenia in human populations separated by geography and time led to the evolutionary hypothesis that proposes schizophrenia as a by-product of the higher cognitive abilities of modern humans. To explore this hypothesis, we used here an evolutionary epigenetics approach building on differentially methylated regions (DMRs) of the genome. METHODS We implemented a polygenic enrichment testing pipeline using the summary statistics of genome-wide association studies (GWAS) of schizophrenia and 12 other phenotypes. We investigated the enrichment of association of these traits across genomic regions with variable methylation between modern humans and great apes (orangutans, chimpanzees and gorillas; great ape DMRs) and between modern humans and recently extinct hominids (Neanderthals and Denisovans; hominid DMRs). RESULTS Regions that are hypo-methylated in humans compared to great apes show enrichment of association with schizophrenia only if the major histocompatibility complex (MHC) region is included. With the MHC region removed from the analysis, only a modest enrichment for SNPs of low effect persists. The INRICH pipeline confirms this finding after rigorous permutation and bootstrapping procedures. CONCLUSION The analyses of regions with differential methylation changes in humans and great apes do not provide compelling evidence of enrichment of association with schizophrenia, in contrast to our previous findings on more recent methylation differences between modern humans, Neanderthals and Denisovans. Our results further support the evolutionary hypothesis of schizophrenia and indicate that the origin of some of the genetic susceptibility factors of schizophrenia may lie in recent human evolution.
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Affiliation(s)
- Niladri Banerjee
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Tatiana Polushina
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Francesco Bettella
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
| | - Vidar M Steen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Ole A Andreassen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
| | - Stephanie Le Hellard
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
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54
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Renaud G, Schubert M, Sawyer S, Orlando L. Authentication and Assessment of Contamination in Ancient DNA. Methods Mol Biol 2019; 1963:163-194. [PMID: 30875054 DOI: 10.1007/978-1-4939-9176-1_17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.
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Affiliation(s)
- Gabriel Renaud
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Susanna Sawyer
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, Toulouse, France.
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55
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Liu Z, Wang Z, Jia E, Ouyang T, Pan M, Lu J, Ge Q, Bai Y. Analysis of genome-wide in cell free DNA methylation: progress and prospect. Analyst 2019; 144:5912-5922. [DOI: 10.1039/c9an00935c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this work, we focus on the detection methods of cfDNA methylation based on NGS and the latest progress.
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Affiliation(s)
- Zhiyu Liu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Zexin Wang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Erteng Jia
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Tinglan Ouyang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Min Pan
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Jiafeng Lu
- Center of Reproduction and Genetics
- Affiliated Suzhou Hospital of Nanjing Medical University
- Suzhou Municipal Hospital
- Suzhou 215002
- China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
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56
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Insights from epigenetic studies on human health and evolution. Curr Opin Genet Dev 2018; 53:36-42. [DOI: 10.1016/j.gde.2018.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/01/2018] [Accepted: 06/08/2018] [Indexed: 12/28/2022]
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57
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Social Structure Facilitated the Evolution of Care-giving as a Strategy for Disease Control in the Human Lineage. Sci Rep 2018; 8:13997. [PMID: 30262928 PMCID: PMC6160448 DOI: 10.1038/s41598-018-31568-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/21/2018] [Indexed: 01/18/2023] Open
Abstract
Humans are the only species to have evolved cooperative care-giving as a strategy for disease control. A synthesis of evidence from the fossil record, paleogenomics, human ecology, and disease transmission models, suggests that care-giving for the diseased evolved as part of the unique suite of cognitive and socio-cultural specializations that are attributed to the genus Homo. Here we demonstrate that the evolution of hominin social structure enabled the evolution of care-giving for the diseased. Using agent-based modeling, we simulate the evolution of care-giving in hominin networks derived from a basal primate social system and the three leading hypotheses of ancestral human social organization, each of which would have had to deal with the elevated disease spread associated with care-giving. We show that (1) care-giving is an evolutionarily stable strategy in kin-based cooperatively breeding groups, (2) care-giving can become established in small, low density groups, similar to communities that existed before the increases in community size and density that are associated with the advent of agriculture in the Neolithic, and (3) once established, care-giving became a successful method of disease control across social systems, even as community sizes and densities increased. We conclude that care-giving enabled hominins to suppress disease spread as social complexity, and thus socially-transmitted disease risk, increased.
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58
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Danchin E, Pocheville A, Rey O, Pujol B, Blanchet S. Epigenetically facilitated mutational assimilation: epigenetics as a hub within the inclusive evolutionary synthesis. Biol Rev Camb Philos Soc 2018. [PMCID: PMC6378602 DOI: 10.1111/brv.12453] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
After decades of debate about the existence of non‐genetic inheritance, the focus is now slowly shifting towards dissecting its underlying mechanisms. Here, we propose a new mechanism that, by integrating non‐genetic and genetic inheritance, may help build the long‐sought inclusive vision of evolution. After briefly reviewing the wealth of evidence documenting the existence and ubiquity of non‐genetic inheritance in a table, we review the categories of mechanisms of parent–offspring resemblance that underlie inheritance. We then review several lines of argument for the existence of interactions between non‐genetic and genetic components of inheritance, leading to a discussion of the contrasting timescales of action of non‐genetic and genetic inheritance. This raises the question of how the fidelity of the inheritance system can match the rate of environmental variation. This question is central to understanding the role of different inheritance systems in evolution. We then review and interpret evidence indicating the existence of shifts from inheritance systems with low to higher transmission fidelity. Based on results from different research fields we propose a conceptual hypothesis linking genetic and non‐genetic inheritance systems. According to this hypothesis, over the course of generations, shifts among information systems allow gradual matching between the rate of environmental change and the inheritance fidelity of the corresponding response. A striking conclusion from our review is that documented shifts between types of inherited non‐genetic information converge towards epigenetics (i.e. inclusively heritable molecular variation in gene expression without change in DNA sequence). We then interpret the well‐documented mutagenicity of epigenetic marks as potentially generating a final shift from epigenetic to genetic encoding. This sequence of shifts suggests the existence of a relay in inheritance systems from relatively labile ones to gradually more persistent modes of inheritance, a relay that could constitute a new mechanistic basis for the long‐proposed, but still poorly documented, hypothesis of genetic assimilation. A profound difference between the genocentric and the inclusive vision of heredity revealed by the genetic assimilation relay proposed here lies in the fact that a given form of inheritance can affect the rate of change of other inheritance systems. To explore the consequences of such inter‐connection among inheritance systems, we briefly review published theoretical models to build a model of genetic assimilation focusing on the shift in the engraving of environmentally induced phenotypic variation into the DNA sequence. According to this hypothesis, when environmental change remains stable over a sufficient number of generations, the relay among inheritance systems has the potential to generate a form of genetic assimilation. In this hypothesis, epigenetics appears as a hub by which non‐genetically inherited environmentally induced variation in traits can become genetically encoded over generations, in a form of epigenetically facilitated mutational assimilation. Finally, we illustrate some of the major implications of our hypothetical framework, concerning mutation randomness, the central dogma of molecular biology, concepts of inheritance and the curing of inherited disorders, as well as for the emergence of the inclusive evolutionary synthesis.
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Affiliation(s)
- Etienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
| | - Arnaud Pocheville
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
- Department of Philosophy and Charles Perkins Centre; University of Sydney; Sydney NSW 2006 Australia
| | - Olivier Rey
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321; 09200 Moulis France
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier; F-66860 Perpignan France
| | - Benoit Pujol
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
| | - Simon Blanchet
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321; 09200 Moulis France
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59
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Estrada O, Breen J, Richards SM, Cooper A. Ancient plant DNA in the genomic era. NATURE PLANTS 2018; 4:394-396. [PMID: 29915330 DOI: 10.1038/s41477-018-0187-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Oscar Estrada
- Australian Centre for Ancient DNA, University of Adelaide, South Australia, Australia
| | - James Breen
- Robinson Research Institute, University of Adelaide, South Australia, Australia.
- University of Adelaide Bioinformatics Hub, School of Biological Sciences, University of Adelaide, South Australia, Australia.
| | - Stephen M Richards
- Australian Centre for Ancient DNA, University of Adelaide, South Australia, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, University of Adelaide, South Australia, Australia
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60
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Dannemann M, Racimo F. Something old, something borrowed: admixture and adaptation in human evolution. Curr Opin Genet Dev 2018; 53:1-8. [PMID: 29894925 DOI: 10.1016/j.gde.2018.05.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/21/2018] [Accepted: 05/24/2018] [Indexed: 01/09/2023]
Abstract
The sequencing of ancient DNA from archaic humans-Neanderthals and Denisovans-has revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Was the introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full. Here, we review the recent literature characterizing introgressed DNA and the likely biological consequences for their modern human carriers. We focus particularly on archaic human haplotypes that were beneficial to modern humans as they expanded across the globe, and on ways to understand how populations harboring these haplotypes evolved over time.
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Affiliation(s)
- Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
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61
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62
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Banerjee N, Polushina T, Bettella F, Giddaluru S, Steen VM, Andreassen OA, Le Hellard S. Recently evolved human-specific methylated regions are enriched in schizophrenia signals. BMC Evol Biol 2018; 18:63. [PMID: 29747567 PMCID: PMC5946405 DOI: 10.1186/s12862-018-1177-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 04/11/2018] [Indexed: 01/10/2023] Open
Abstract
Background One explanation for the persistence of schizophrenia despite the reduced fertility of patients is that it is a by-product of recent human evolution. This hypothesis is supported by evidence suggesting that recently-evolved genomic regions in humans are involved in the genetic risk for schizophrenia. Using summary statistics from genome-wide association studies (GWAS) of schizophrenia and 11 other phenotypes, we tested for enrichment of association with GWAS traits in regions that have undergone methylation changes in the human lineage compared to Neanderthals and Denisovans, i.e. human-specific differentially methylated regions (DMRs). We used analytical tools that evaluate polygenic enrichment of a subset of genomic variants against all variants. Results Schizophrenia was the only trait in which DMR SNPs showed clear enrichment of association that passed the genome-wide significance threshold. The enrichment was not observed for Neanderthal or Denisovan DMRs. The enrichment seen in human DMRs is comparable to that for genomic regions tagged by Neanderthal Selective Sweep markers, and stronger than that for Human Accelerated Regions. The enrichment survives multiple testing performed through permutation (n = 10,000) and bootstrapping (n = 5000) in INRICH (p < 0.01). Some enrichment of association with height was observed at the gene level. Conclusions Regions where DNA methylation modifications have changed during recent human evolution show enrichment of association with schizophrenia and possibly with height. Our study further supports the hypothesis that genetic variants conferring risk of schizophrenia co-occur in genomic regions that have changed as the human species evolved. Since methylation is an epigenetic mark, potentially mediated by environmental changes, our results also suggest that interaction with the environment might have contributed to that association. Electronic supplementary material The online version of this article (10.1186/s12862-018-1177-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Niladri Banerjee
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Tatiana Polushina
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Francesco Bettella
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Sudheer Giddaluru
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Vidar M Steen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ole A Andreassen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Stephanie Le Hellard
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway. .,Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway. .,Department of Clinical Medicine, Laboratory Building, Haukeland University Hospital, N-5021, Bergen, Norway.
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63
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Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MHS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience 2018; 6:1-13. [PMID: 28854615 PMCID: PMC5570000 DOI: 10.1093/gigascience/gix049] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/20/2017] [Indexed: 12/30/2022] Open
Abstract
Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction–amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
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Affiliation(s)
- Sarah Siu Tze Mak
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | | | - Shanlin Liu
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Mikkel-Holger S Sinding
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Natural History Museum, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway.,The Qimmeq Project, University of Greenland, Manutooq 1, PO Box 1061, 3905 Nuussuaq, Greenland
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | | | - Shujin Fu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mietje Germonpré
- OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, ul. Kulakovskogo 48, 677980 Yakutsk, Russia
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Thomas Sicheritz-Pontén
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen 518083, China
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, 6102 Perth, Australia.,Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
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Palumbo D, Affinito O, Monticelli A, Cocozza S. DNA Methylation variability among individuals is related to CpGs cluster density and evolutionary signatures. BMC Genomics 2018; 19:229. [PMID: 29606093 PMCID: PMC5880022 DOI: 10.1186/s12864-018-4618-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/23/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In recent years, epigenetics has gained a central role in the understanding of the process of natural selection. It is now clear how environmental impacts on the methylome could promote methylation variability with direct effects on disease etiology as well as phenotypic and genotypic variations in evolutionary processes. To identify possible factors influencing inter-individual methylation variability, we studied methylation values standard deviation of 166 healthy individuals searching for possible associations with genomic features and evolutionary signatures. RESULTS We analyzed methylation variability values in relation to CpG cluster density and we found a strong association between them (p-value < 2.2 × 10- 16). Furthermore, we found that genes related to CpGs with high methylation variability values were enriched for immunological pathways; instead, those associated with low ones were enriched for pathways related to basic cellular functions. Finally, we found an association between methylation variability values and signals of both ancient (p-value < 2.2 × 10- 16) and recent selective pressure (p-value < 1 × 10- 4). CONCLUSION Our results indicate the presence of an intricate interplay between genetics, epigenetic code and evolutionary constraints in humans.
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Affiliation(s)
- Domenico Palumbo
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples “Federico II”, Naples, Italy
| | - Ornella Affinito
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples “Federico II”, Naples, Italy
| | - Antonella Monticelli
- Institute for Experimental Endocrinology and Oncology (IEOS) “Gaetano Salvatore”, CNR, Naples, Italy
| | - Sergio Cocozza
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples “Federico II”, Naples, Italy
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65
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Zhang W, Yang D, Zhao J, Hou L, Sessler JL, Yang XJ, Wu B. Controlling the Recognition and Reactivity of Alkyl Ammonium Guests Using an Anion Coordination-Based Tetrahedral Cage. J Am Chem Soc 2018; 140:5248-5256. [DOI: 10.1021/jacs.8b01488] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Wenyao Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069, China
| | - Dong Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069, China
| | - Jie Zhao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069, China
| | - Lekai Hou
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069, China
| | - Jonathan L. Sessler
- Center for Supramolecular Chemistry and Catalysis, Shanghai University, Shanghai 200444, China
| | - Xiao-Juan Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069, China
| | - Biao Wu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710069, China
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67
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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68
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Colwell M, Drown M, Showel K, Drown C, Palowski A, Faulk C. Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements. Epigenetics 2018; 13:49-60. [PMID: 29372669 PMCID: PMC5836973 DOI: 10.1080/15592294.2017.1411447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/14/2017] [Accepted: 11/27/2017] [Indexed: 01/14/2023] Open
Abstract
Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.
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Affiliation(s)
- Mathia Colwell
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Melissa Drown
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Kelly Showel
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Chelsea Drown
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Amanda Palowski
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
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69
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70
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Llamas B, Willerslev E, Orlando L. Human evolution: a tale from ancient genomes. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0484. [PMID: 27994125 DOI: 10.1098/rstb.2015.0484] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/21/2022] Open
Abstract
The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for ADNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Wellcome Genome Campus Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark .,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, CNRS UMR 5288, 31000 Toulouse, France
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71
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Affiliation(s)
- Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052
| | - Aida Gómez-Robles
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
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72
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Abstract
Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more. We demonstrate this approach by showing that hunger-related DNA methylation changes are found in ancient hunter-gatherers. The strategy we present here opens a window to reconstruct previously inaccessible aspects of the lives of past individuals.
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Affiliation(s)
- David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Anat Malul
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
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73
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Der Sarkissian C, Pichereau V, Dupont C, Ilsøe PC, Perrigault M, Butler P, Chauvaud L, Eiríksson J, Scourse J, Paillard C, Orlando L. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past. Mol Ecol Resour 2017; 17:835-853. [PMID: 28394451 DOI: 10.1111/1755-0998.12679] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 03/24/2017] [Accepted: 04/03/2017] [Indexed: 02/05/2023]
Abstract
Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Vianney Pichereau
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | | | - Peter C Ilsøe
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Mickael Perrigault
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | - Paul Butler
- CGES, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, UK
| | - Laurent Chauvaud
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | - Jón Eiríksson
- Institute of Earth Sciences, University of Iceland, Askja, Reykjavík, Iceland
| | - James Scourse
- CGES, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, UK
| | - Christine Paillard
- Lemar UMR6539 CNRS/UBO/IRD/Ifremer, Université de Brest, IUEM, Plouzané, France
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
- Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, Toulouse, France
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74
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Enhancing our brains: Genomic mechanisms underlying cortical evolution. Semin Cell Dev Biol 2017; 76:23-32. [PMID: 28864345 DOI: 10.1016/j.semcdb.2017.08.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/24/2017] [Indexed: 12/31/2022]
Abstract
Our most distinguishing higher cognitive functions are controlled by the cerebral cortex. Comparative studies detail abundant anatomical and cellular features unique to the human developing and adult neocortex. Emerging genomic studies have further defined vast differences distinguishing developing human neocortices from related primates. These human-specific changes can affect gene function and/or expression, and result from structural variations such as chromosomal deletions and duplications, or from point mutations in coding and noncoding regulatory regions. Here, we review this rapidly growing field which aims to identify and characterize genetic loci unique to the human cerebral cortex. We catalog known human-specific genomic changes distinct from other primates, including those whose function has been interrogated in animal models. We also discuss how new model systems and technologies such as single cell RNA sequencing, primate iPSCs, and gene editing, are enabling the field to gain unprecedented resolution into function of these human-specific changes. Some neurological disorders are thought to uniquely present in humans, thus reinforcing the need to comprehensively understand human-specific gene expression in the developing brain.
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75
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Abstract
The Modern Evolutionary Synthesis (MS) forged in the mid-twentieth century was built on a notion of heredity that excluded soft inheritance, the inheritance of the effects of developmental modifications. However, the discovery of molecular mechanisms that generate random and developmentally induced epigenetic variations is leading to a broadening of the notion of biological heredity that has consequences for ideas about evolution. After presenting some old challenges to the MS that were raised, among others, by Karl Popper, I discuss recent research on epigenetic inheritance, which provides experimental and theoretical support for these challenges. There is now good evidence that epigenetic inheritance is ubiquitous and is involved in adaptive evolution and macroevolution. I argue that the many evolutionary consequences of epigenetic inheritance open up new research areas and require the extension of the evolutionary synthesis beyond the current neo-Darwinian model.
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Affiliation(s)
- Eva Jablonka
- The Cohn Institute for the History and Philosophy of Science and Ideas, Tel-Aviv University, Tel-Aviv 69978, Israel
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76
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Mozzi A, Forni D, Cagliani R, Pozzoli U, Clerici M, Sironi M. Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders. Sci Rep 2017; 7:6116. [PMID: 28733602 PMCID: PMC5522412 DOI: 10.1038/s41598-017-06440-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/13/2017] [Indexed: 01/11/2023] Open
Abstract
In addition to high intelligence, humans evolved specialized social-cognitive skills, which are specifically affected in children with autism spectrum disorder (ASD). Genes affected in ASD represent suitable candidates to study the evolution of human social cognition. We performed an evolutionary analysis on 68 genes associated to neurodevelopmental disorders; our data indicate that genetic diversity was shaped by distinct selective forces, including natural selection and introgression from archaic hominins. We discuss the possibility that segregation distortion during spermatogenesis accounts for a subset of ASD mutations. Finally, we detected modern-human-specific alleles in DYRK1A and TCF4. These variants are located within regions that display chromatin features typical of transcriptional enhancers in several brain areas, strongly suggesting a regulatory role. These SNPs thus represent candidates for association with neurodevelopmental disorders, and await experimental validation in future studies.
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Affiliation(s)
- Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy.
| | - Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20090, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, 20100, Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
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77
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Time to Spread Your Wings: A Review of the Avian Ancient DNA Field. Genes (Basel) 2017; 8:genes8070184. [PMID: 28718817 PMCID: PMC5541317 DOI: 10.3390/genes8070184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/27/2017] [Accepted: 07/10/2017] [Indexed: 01/16/2023] Open
Abstract
Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.
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78
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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79
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The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 2017; 204:423-434. [PMID: 27729493 DOI: 10.1534/genetics.116.194860] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/17/2016] [Indexed: 12/21/2022] Open
Abstract
The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.
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80
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Pérez-Criado L, Rosas A. Evolutionary anatomy of the Neandertal ulna and radius in the light of the new El Sidrón sample. J Hum Evol 2017; 106:38-53. [PMID: 28434539 DOI: 10.1016/j.jhevol.2017.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 01/11/2023]
Abstract
This paper aims to improve our understanding of the phylogenetic trait polarity related to hominin forearm evolution, in particular those traits traditionally defined as "Neandertal features." To this aim, twelve adult and adolescent fragmented forelimb elements (including ulnae and radii) of Homo neanderthalensis recovered from the site of El Sidrón (Asturias, Spain) were examined comparatively using three-dimensional geometric and traditional morphometrics. Mean centroid size and shape comparisons, principal components analysis, and phylogenetic signal analysis were undertaken. Our investigations revealed that the proximal region of the ulna discriminated best between Neandertals and modern humans, with fewer taxonomically-informative features in the distal ulna and radius. Compared to modern humans, the divergent features in the Neandertal ulna are an increase in olecranon breadth (a derived trait), lower coronoid length (primitive), and anterior orientation of the trochlear notch (primitive). In the Neandertal radius, we observe a larger neck length (primitive), medial orientation of the radial tubercle (secondarily primitive), and a curved diaphysis (secondarily primitive). Anatomically, we identified three units of evolutionary change: 1) the olecranon and its fossa, 2) the coronoid-radius neck complex, and 3) the tubercle and radial diaphysis. Based on our data, forearm evolution followed a mosaic pattern in which some features were inherited from a pre-Homo ancestor, others originated in some post-ergaster and pre-antecessor populations, and other characters emerged in the specific Homo sapiens and H. neanderthalensis lineages, sometimes appearing as secondarily primitive. Future investigations might consider the diverse phylogenetic origin of apomorphies while at the same time seeking to elucidate their functional meaning.
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Affiliation(s)
- Laura Pérez-Criado
- Group of Paleoanthropology MNCN-CSIC, Department of Paleobiology, Museo Nacional de Ciencias Naturales-CSIC, Calle José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Antonio Rosas
- Group of Paleoanthropology MNCN-CSIC, Department of Paleobiology, Museo Nacional de Ciencias Naturales-CSIC, Calle José Gutiérrez Abascal 2, 28006 Madrid, Spain
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81
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Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sánchez E, Nielsen R. Archaic Adaptive Introgression in TBX15/WARS2. Mol Biol Evol 2017; 34:509-524. [PMID: 28007980 PMCID: PMC5430617 DOI: 10.1093/molbev/msw283] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.
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Affiliation(s)
- Fernando Racimo
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Matteo Fumagalli
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
| | - Amy Ko
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | | | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
- Department of Statistics, University of California Berkeley, Berkeley, CA
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
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82
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Epigenome-wide association studies for cancer biomarker discovery in circulating cell-free DNA: technical advances and challenges. Curr Opin Genet Dev 2017; 42:48-55. [DOI: 10.1016/j.gde.2017.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 01/12/2017] [Accepted: 01/27/2017] [Indexed: 12/18/2022]
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83
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Xu CJ, Bonder MJ, Söderhäll C, Bustamante M, Baïz N, Gehring U, Jankipersadsing SA, van der Vlies P, van Diemen CC, van Rijkom B, Just J, Kull I, Kere J, Antó JM, Bousquet J, Zhernakova A, Wijmenga C, Annesi-Maesano I, Sunyer J, Melén E, Li Y, Postma DS, Koppelman GH. The emerging landscape of dynamic DNA methylation in early childhood. BMC Genomics 2017; 18:25. [PMID: 28056824 PMCID: PMC5217260 DOI: 10.1186/s12864-016-3452-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/21/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND DNA methylation has been found to associate with disease, aging and environmental exposure, but it is unknown how genome, environment and disease influence DNA methylation dynamics in childhood. RESULTS By analysing 538 paired DNA blood samples from children at birth and at 4-5 years old and 726 paired samples from children at 4 and 8 years old from four European birth cohorts using the Illumina Infinium Human Methylation 450 k chip, we have identified 14,150 consistent age-differential methylation sites (a-DMSs) at epigenome-wide significance of p < 1.14 × 10-7. Genes with an increase in age-differential methylation were enriched in pathways related to 'development', and were more often located in bivalent transcription start site (TSS) regions, which can silence or activate expression of developmental genes. Genes with a decrease in age-differential methylation were involved in cell signalling, and enriched on H3K27ac, which can predict developmental state. Maternal smoking tended to decrease methylation levels at the identified da-DMSs. We also found 101 a-DMSs (0.71%) that were regulated by genetic variants using cis-differential Methylation Quantitative Trait Locus (cis-dMeQTL) mapping. Moreover, a-DMS-associated genes during early development were significantly more likely to be linked with disease. CONCLUSION Our study provides new insights into the dynamic epigenetic landscape of the first 8 years of life.
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Affiliation(s)
- Cheng-Jian Xu
- Department of Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. .,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Mariona Bustamante
- ISGlobal, Centre for Research in Environmental Epidemiology, Barcelona, Spain.,Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Nour Baïz
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France
| | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Soesma A Jankipersadsing
- Department of Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pieter van der Vlies
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bianca van Rijkom
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jocelyne Just
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France.,Department of Allergology-Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Inger Kull
- Department of Clinical Science and Education, Stockholm South General Hospital, Karolinska Institutet, and Sachs' Children's Hospital, SE-118 83, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Folkhälsan Institute of Genetics and Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Josep Maria Antó
- ISGlobal, Centre for Research in Environmental Epidemiology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- University Hospital, Montpellier, France.,MACVIA-France, Contre les Maladies Chroniques pour un VIeillissement Actif en France, European Innovation Partnership on Active and Healthy Ageing Reference Site, Paris, France.,INSERM, VIMA: Ageing and chronic diseases. Epidemiological and public health approaches, U1168, Paris, France.,UVSQ, UMR-S 1168, Université Versailles St-Quentin-en-Yvelines, Versailles, France
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France
| | - Jordi Sunyer
- ISGlobal, Centre for Research in Environmental Epidemiology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Erik Melén
- Department of Paediatric Pulmonology and Paediatric Allergy, Beatrix Children's Hospital, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yang Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Dirkje S Postma
- Department of Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard H Koppelman
- Department of Paediatric Pulmonology and Paediatric Allergy, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, GRIAC Research Institute, Groningen, The Netherlands
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84
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Xu L, Fang G, Li S. Supramolecular catalysis in the methylation of meta-phenylene ethynylene foldamer containing N,N-dimethylaminopyridine. RSC Adv 2017. [DOI: 10.1039/c7ra00710h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DFT investigations show that the methylation reaction of N,N-dimethylaminopyridine (DMAP)-modified meta-phenylene ethynylene foldamer can be catalyzed by the noncovalent interactions between the foldamer and the methyl sulfonate esters.
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Affiliation(s)
- Lina Xu
- Key Laboratory of Carbon Materials of Zhejiang Province
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou 325035
- China
| | - Guoyong Fang
- Key Laboratory of Carbon Materials of Zhejiang Province
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou 325035
- China
| | - Shuhua Li
- Institute of Theoretical and Computational Chemistry
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
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85
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MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci 2016; 5:329-351. [PMID: 27813680 DOI: 10.1146/annurev-animal-022516-022747] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.
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Affiliation(s)
- David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland; .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; .,Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 31000 Toulouse, France
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86
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Bell CG. Insights in human epigenomic dynamics through comparative primate analysis. Genomics 2016; 108:115-125. [DOI: 10.1016/j.ygeno.2016.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 08/03/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022]
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87
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Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX. Mol Biol Evol 2016; 33:3284-3298. [PMID: 27624717 PMCID: PMC5100044 DOI: 10.1093/molbev/msw184] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.
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Affiliation(s)
- Kristian Hanghøj
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Danish National High-Throughput DNA Sequencing Center, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Madsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark .,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, Toulouse, France
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88
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Benítez-Burraco A, Lattanzi W, Murphy E. Language Impairments in ASD Resulting from a Failed Domestication of the Human Brain. Front Neurosci 2016; 10:373. [PMID: 27621700 PMCID: PMC5002430 DOI: 10.3389/fnins.2016.00373] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/02/2016] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorders (ASD) are pervasive neurodevelopmental disorders entailing social and cognitive deficits, including marked problems with language. Numerous genes have been associated with ASD, but it is unclear how language deficits arise from gene mutation or dysregulation. It is also unclear why ASD shows such high prevalence within human populations. Interestingly, the emergence of a modern faculty of language has been hypothesized to be linked to changes in the human brain/skull, but also to the process of self-domestication of the human species. It is our intention to show that people with ASD exhibit less marked domesticated traits at the morphological, physiological, and behavioral levels. We also discuss many ASD candidates represented among the genes known to be involved in the “domestication syndrome” (the constellation of traits exhibited by domesticated mammals, which seemingly results from the hypofunction of the neural crest) and among the set of genes involved in language function closely connected to them. Moreover, many of these genes show altered expression profiles in the brain of autists. In addition, some candidates for domestication and language-readiness show the same expression profile in people with ASD and chimps in different brain areas involved in language processing. Similarities regarding the brain oscillatory behavior of these areas can be expected too. We conclude that ASD may represent an abnormal ontogenetic itinerary for the human faculty of language resulting in part from changes in genes important for the “domestication syndrome” and, ultimately, from the normal functioning of the neural crest.
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Affiliation(s)
| | - Wanda Lattanzi
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore Rome, Italy
| | - Elliot Murphy
- Division of Psychology and Language Sciences, University College London London, UK
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89
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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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90
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91
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Gokhman D, Meshorer E, Carmel L. Epigenetics: It's Getting Old. Past Meets Future in Paleoepigenetics. Trends Ecol Evol 2016; 31:290-300. [DOI: 10.1016/j.tree.2016.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 01/08/2023]
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92
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Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS, Chisholm RL, Crosslin DR, Hebbring SJ, Jarvik GP, Kullo IJ, Li R, Pathak J, Ritchie MD, Roden DM, Verma SS, Tromp G, Prato JD, Bush WS, Akey JM, Denny JC, Capra JA. The phenotypic legacy of admixture between modern humans and Neandertals. Science 2016; 351:737-41. [PMID: 26912863 DOI: 10.1126/science.aad2149] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many modern human genomes retain DNA inherited from interbreeding with archaic hominins, such as Neandertals, yet the influence of this admixture on human traits is largely unknown. We analyzed the contribution of common Neandertal variants to over 1000 electronic health record (EHR)-derived phenotypes in ~28,000 adults of European ancestry. We discovered and replicated associations of Neandertal alleles with neurological, psychiatric, immunological, and dermatological phenotypes. Neandertal alleles together explained a significant fraction of the variation in risk for depression and skin lesions resulting from sun exposure (actinic keratosis), and individual Neandertal alleles were significantly associated with specific human phenotypes, including hypercoagulation and tobacco use. Our results establish that archaic admixture influences disease risk in modern humans, provide hypotheses about the effects of hundreds of Neandertal haplotypes, and demonstrate the utility of EHR data in evolutionary analyses.
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Affiliation(s)
- Corinne N Simonti
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | | | - David S Carrell
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David R Crosslin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Scott J Hebbring
- Center for Human Genetics, Marshfield Clinic, Marshfield, WI, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Iftikhar J Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Rongling Li
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jyotishman Pathak
- Division of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Marylyn D Ritchie
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA. Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
| | - Dan M Roden
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA. Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA. Department of Medicine, Vanderbilt University, Nashville, TN, USA. Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Shefali S Verma
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Gerard Tromp
- Weis Center for Research, Geisinger Health System, Danville, PA, USA. Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Science, Stellenbosch University, Tygerberg, South Africa
| | - Jeffrey D Prato
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - William S Bush
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Joshua C Denny
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA. Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA. Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - John A Capra
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA. Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA. Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA
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93
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Zhang M, Wang CC, Yang C, Meng H, Agbagwa IO, Wang LX, Wang Y, Yan S, Ren S, Sun Y, Pei G, Liu X, Liu J, Jin L, Li H, Sun Y. Epigenetic Pattern on the Human Y Chromosome Is Evolutionarily Conserved. PLoS One 2016; 11:e0146402. [PMID: 26760298 PMCID: PMC4711989 DOI: 10.1371/journal.pone.0146402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/02/2015] [Indexed: 11/19/2022] Open
Abstract
DNA methylation plays an important role for mammalian development. However, it is unclear whether the DNA methylation pattern is evolutionarily conserved. The Y chromosome serves as a powerful tool for the study of human evolution because it is transferred between males. In this study, based on deep-rooted pedigrees and the latest Y chromosome phylogenetic tree, we performed epigenetic pattern analysis of the Y chromosome from 72 donors. By comparing their respective DNA methylation level, we found that the DNA methylation pattern on the Y chromosome was stable among family members and haplogroups. Interestingly, two haplogroup-specific methylation sites were found, which were both genotype-dependent. Moreover, the African and Asian samples also had similar DNA methylation pattern with a remote divergence time. Our findings indicated that the DNA methylation pattern on the Y chromosome was conservative during human male history.
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Affiliation(s)
- Minjie Zhang
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuan-Chao Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Caiyun Yang
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Meng
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ikechukwu O. Agbagwa
- Department of Plant Science & Biotechnology, University of Port Harcourt, Port Harcourt, Nigeria
| | - Ling-Xiang Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yingzhi Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Shi Yan
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Shancheng Ren
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Yinghao Sun
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Gang Pei
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Xin Liu
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiang Liu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
- * E-mail: (YLS); (HL); (LJ)
| | - Hui Li
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
- * E-mail: (YLS); (HL); (LJ)
| | - Yingli Sun
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- * E-mail: (YLS); (HL); (LJ)
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94
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Benítez-Burraco A, Uriagereka J. The Immune Syntax Revisited: Opening New Windows on Language Evolution. Front Mol Neurosci 2016; 8:84. [PMID: 26793054 PMCID: PMC4707268 DOI: 10.3389/fnmol.2015.00084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/14/2015] [Indexed: 01/29/2023] Open
Abstract
Recent research has added new dimensions to our understanding of classical evolution, according to which evolutionary novelties result from gene mutations inherited from parents to offspring. Language is surely one such novelty. Together with specific changes in our genome and epigenome, we suggest that two other (related) mechanisms may have contributed to the brain rewiring underlying human cognitive evolution and, specifically, the changes in brain connectivity that prompted the emergence of our species-specific linguistic abilities: the horizontal transfer of genetic material by viral and non-viral vectors and the brain/immune system crosstalk (more generally, the dialogue between the microbiota, the immune system, and the brain).
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Affiliation(s)
| | - Juan Uriagereka
- Department of Linguistics, University of Maryland College Park, MD, USA
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95
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Giuliani C, Cilli E, Bacalini MG, Pirazzini C, Sazzini M, Gruppioni G, Franceschi C, Garagnani P, Luiselli D. Inferring chronological age from DNA methylation patterns of human teeth. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:585-95. [PMID: 26667772 DOI: 10.1002/ajpa.22921] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Current methods to determine chronological age from modern and ancient remains rely on both morphological and molecular approaches. However, low accuracy and the lack of standardized protocols make the development of alternative methods for the estimation of individual's age even more urgent for several research fields, such as biological anthropology, biodemography, forensics, evolutionary genetics, and ancient DNA studies. Therefore, the aim of this study is to identify genomic regions whose DNA methylation level correlates with age in modern teeth. METHODS We used MALDI-TOF mass spectrometry to analyze DNA methylation levels of specific CpGs located in the ELOVL2, FHL2, and PENK genes. We considered methylation data from cementum, dentin and pulp of 21 modern teeth (from 17 to 77 years old) to construct a mathematical model able to exploit DNA methylation values to predict age of the individuals. RESULTS The median difference between the real age and that estimated using DNA methylation values is 1.20 years (SD = 1.9) if DNA is recovered from both cementum and pulp of the same modern teeth, 2.25 years (SD = 2.5) if DNA is recovered from dental pulp, 2.45 years (SD = 3.3) if DNA is extracted from cementum and 7.07 years (SD = 7.0) when DNA is recovered from dentin only. DISCUSSION We propose for the first time the evaluation of DNA methylation at ELOVL2, FHL2, and PENK genes as a powerful tool to predict age in modern teeth for anthropological applications. Future studies are needed to apply this method also to historical and relatively ancient human teeth.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy
| | - Marco Sazzini
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
| | - Giorgio Gruppioni
- Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy.,IRCCS Institute of Neurological Sciences, Bologna, 40139, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy.,Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
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96
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Abstract
A fundamental initiative for evolutionary biologists is to understand the molecular basis underlying phenotypic diversity. A long-standing hypothesis states that species-specific traits may be explained by differences in gene regulation rather than differences at the protein level. Over the past few years, evolutionary studies have shifted from mere sequence comparisons to integrative analyses in which gene regulation is key to understanding species evolution. DNA methylation is an important epigenetic modification involved in the regulation of numerous biological processes. Nevertheless, the evolution of the human methylome and the processes driving such changes are poorly understood. Here, we review the close interplay between Cytosine-phosphate-Guanine (CpG) methylation and the underlying genome sequence, as well as its evolutionary impact. We also summarize the latest advances in the field, revisiting the main literature on human and nonhuman primates. We hope to encourage the scientific community to address the many challenges posed by the field of comparative epigenomics.
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97
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Silver DL. Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex. Bioessays 2015; 38:162-71. [PMID: 26642006 DOI: 10.1002/bies.201500108] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The cerebral cortex controls our most distinguishing higher cognitive functions. Human-specific gene expression differences are abundant in the cerebral cortex, yet we have only begun to understand how these variations impact brain function. This review discusses the current evidence linking non-coding regulatory DNA changes, including enhancers, with neocortical evolution. Functional interrogation using animal models reveals converging roles for our genome in key aspects of cortical development including progenitor cell cycle and neuronal signaling. New technologies, including iPS cells and organoids, offer potential alternatives to modeling evolutionary modifications in a relevant species context. Several diseases rooted in the cerebral cortex uniquely manifest in humans compared to other primates, thus highlighting the importance of understanding human brain differences. Future studies of regulatory loci, including those implicated in disease, will collectively help elucidate key cellular and genetic mechanisms underlying our distinguishing cognitive traits.
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Affiliation(s)
- Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.,Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.,Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
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98
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Thayer ZM, Non AL. Anthropology Meets Epigenetics: Current and Future Directions. AMERICAN ANTHROPOLOGIST 2015. [DOI: 10.1111/aman.12351] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Zaneta M. Thayer
- Department of Anthropology; University of Colorado Denver; Denver CO 80217-3364
| | - Amy L. Non
- Department of Anthropology; University of California San Diego La Jolla; CA 92093-0532
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99
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Gamba C, Hanghøj K, Gaunitz C, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Bradley DANIELG, Orlando L. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Mol Ecol Resour 2015; 16:459-69. [DOI: 10.1111/1755-0998.12470] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/17/2015] [Accepted: 09/20/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Cristina Gamba
- Centre for GeoGenetics; Natural History Museum of Denmark; Øster Voldgade 5-7 1350K Copenhagen Denmark
| | - Kristian Hanghøj
- Centre for GeoGenetics; Natural History Museum of Denmark; Øster Voldgade 5-7 1350K Copenhagen Denmark
| | - Charleen Gaunitz
- Centre for GeoGenetics; Natural History Museum of Denmark; Øster Voldgade 5-7 1350K Copenhagen Denmark
| | - Ahmed H. Alfarhan
- Zoology Department; College of Science; King Saud University; Riyadh 11451 Saudi Arabia
| | - Saleh A. Alquraishi
- Zoology Department; College of Science; King Saud University; Riyadh 11451 Saudi Arabia
| | | | - DANIEL G. Bradley
- Smurfit Institute of Genetics; Trinity College Dublin; College Green, Dublin 2 Ireland
| | - Ludovic Orlando
- Centre for GeoGenetics; Natural History Museum of Denmark; Øster Voldgade 5-7 1350K Copenhagen Denmark
- Université de Toulouse; CNRS UMR 5288; Université Paul Sabatier (UPS); 37 allées Jules Guesde 31000 Toulouse France
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100
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Campbell K, Hofreiter M. Resurrecting phenotypes from ancient DNA sequences: promises and perspectives. CAN J ZOOL 2015. [DOI: 10.1139/cjz-2014-0337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller’s sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these “living” processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology.
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Affiliation(s)
- K.L. Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - M. Hofreiter
- Faculty of Mathematics and Life Sciences, Institute of Biochemistry and Biology, Unit of General Zoology–Evolutionary Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany
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