1
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Çokoğlu SS, Koptekin D, Fidan FR, Somel M. Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise. Evol Appl 2024; 17:e13743. [PMID: 38957308 PMCID: PMC11217591 DOI: 10.1111/eva.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 05/29/2024] [Accepted: 06/08/2024] [Indexed: 07/04/2024] Open
Abstract
The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.
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Affiliation(s)
| | - Dilek Koptekin
- Department of BiologyMiddle East Technical UniversityAnkaraTurkey
| | | | - Mehmet Somel
- Department of BiologyMiddle East Technical UniversityAnkaraTurkey
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2
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Borodko DD, Zhenilo SV, Sharko FS. Search for differentially methylated regions in ancient and modern genomes. Vavilovskii Zhurnal Genet Selektsii 2023; 27:820-828. [PMID: 38213708 PMCID: PMC10777292 DOI: 10.18699/vjgb-23-95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 01/13/2024] Open
Abstract
Currently, active research is focused on investigating the mechanisms that regulate the development of various pathologies and their evolutionary dynamics. Epigenetic mechanisms, such as DNA methylation, play a significant role in evolutionary processes, as their changes have a faster impact on the phenotype compared to mutagenesis. In this study, we attempted to develop an algorithm for identifying differentially methylated regions associated with metabolic syndrome, which have undergone methylation changes in humans during the transition from a hunter-gatherer to a sedentary lifestyle. The application of existing whole-genome bisulfite sequencing methods is limited for ancient samples due to their low quality and fragmentation, and the approach to obtaining DNA methylation profiles differs significantly between ancient hunter-gatherer samples and modern tissues. In this study, we validated DamMet, an algorithm for reconstructing ancient methylomes. Application of DamMet to Neanderthal and Denisovan genomes showed a moderate level of correlation with previously published methylation profiles and demonstrated an underestimation of methylation levels in the reconstructed profiles by an average of 15-20 %. Additionally, we developed a new Python-based algorithm that allows for the comparison of methylomes in ancient and modern samples, despite the absence of methylation profiles in modern bone tissue within the context of obesity. This analysis involves a two-step data processing approach, where the first step involves the identification and filtration of tissue-specific methylation regions, and the second step focuses on the direct search for differentially methylated regions in specific areas associated with the researcher's target condition. By applying this algorithm to test data, we identified 38 differentially methylated regions associated with obesity, the majority of which were located in promoter regions. The pipeline demonstrated sufficient efficiency in detecting these regions. These results confirm the feasibility of reconstructing DNA methylation profiles in ancient samples and comparing them with modern methylomes. Furthermore, possibilities for further methodological development and the implementation of a new step for studying differentially methylated positions associated with evolutionary processes are discussed.
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Affiliation(s)
- D D Borodko
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - S V Zhenilo
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - F S Sharko
- Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
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3
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DNA methylation-based profiling of horse archaeological remains for age-at-death and castration. iScience 2023; 26:106144. [PMID: 36843848 PMCID: PMC9950528 DOI: 10.1016/j.isci.2023.106144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/02/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take advantage of the availability of a DNA methylation clock based on 31,836 CpG sites and dental age markers in horses to assess age predictions in 84 ancient remains. We evaluate our approach using whole-genome sequencing data and develop a capture assay providing reliable estimates for only a fraction of the cost. We also leverage DNA methylation patterns to assess castration practice in the past. Our work opens for a deeper characterization of past husbandry and ritual practices and holds the potential to reveal age mortality profiles in ancient societies, once extended to human remains.
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4
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A study of strong nucleosomes in the human genome. iScience 2022; 25:104593. [PMID: 35789840 PMCID: PMC9249913 DOI: 10.1016/j.isci.2022.104593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/03/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022] Open
Abstract
Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, nucleosomes are highly dynamic and susceptible to experimental conditions, resulting in extreme variability across nucleosome maps, which complicates the generation of accurate nucleosome organization data. We mapped nucleosomes from different individuals using improved MNase-seq. The improvements included setting different digestion levels (low, medium, high) and naked DNA correction to remove the noise caused by experimental manipulation and comparing maps to obtain the accurate position and occupancy of strong nucleosomes (SNs) in the whole genome. In addition, the characteristics of SNs were further excavated. SNs were enriched in Alu elements and near the centromere of Chr12. SNs contain some specific sequences, and the GC content of SNs is different from that of dynamic nucleosomes. The findings suggest that nucleosome location in the genome and the DNA sequence may affect nucleosome stability. Naked DNA correction improved the accuracy of nucleosome map in partial digestion Level of MNase digestion has effects on nucleosome organization A type of strong nucleosomes (SNs) exist across different nucleosome maps Nucleosome stability may be related to its location and the DNA sequence
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5
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Suchan T, Chauvey L, Poullet M, Tonasso‐Calvière L, Schiavinato S, Clavel P, Clavel B, Lepetz S, Seguin‐Orlando A, Orlando L. Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA. Mol Ecol Resour 2022; 22:2262-2274. [DOI: 10.1111/1755-0998.13619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Tomasz Suchan
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
- W. Szafer Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Lorelei Chauvey
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Marine Poullet
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Laure Tonasso‐Calvière
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Stéphanie Schiavinato
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Pierre Clavel
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Benoit Clavel
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE) Muséum National d’Histoire Naturelle CNRS CP 55 rue Buffon Paris France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE) Muséum National d’Histoire Naturelle CNRS CP 55 rue Buffon Paris France
| | - Andaine Seguin‐Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT) Université Paul Sabatier Faculté de Santé 37 allées Jules Guesde, Bâtiment A 31000 Toulouse France
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6
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Epigenomic Modifications in Modern and Ancient Genomes. Genes (Basel) 2022; 13:genes13020178. [PMID: 35205223 PMCID: PMC8872240 DOI: 10.3390/genes13020178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/26/2022] Open
Abstract
Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.
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7
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Suchan T, Kusliy MA, Khan N, Chauvey L, Tonasso-Calvière L, Schiavinato S, Southon J, Keller M, Kitagawa K, Krause J, Bessudnov AN, Bessudnov AA, Graphodatsky AS, Valenzuela-Lamas S, Wilczyński J, Pospuła S, Tunia K, Nowak M, Moskal-delHoyo M, Tishkin AA, Pryor AJE, Outram AK, Orlando L. Performance and automation of ancient DNA capture with RNA hyRAD probes. Mol Ecol Resour 2021; 22:891-907. [PMID: 34582623 PMCID: PMC9291508 DOI: 10.1111/1755-0998.13518] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 01/23/2023]
Abstract
DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.
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Affiliation(s)
- Tomasz Suchan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Mariya A Kusliy
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.,Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - John Southon
- Earth System Science Department, University of California, Irvine, Irvine, California, USA
| | - Marcel Keller
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Keiko Kitagawa
- SFB 1070 ResourceCultures, University of Tübingen, Tübingen, Germany.,Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Alexander A Bessudnov
- Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Silvia Valenzuela-Lamas
- Institución Milà i Fontanals de Humanidades, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Sylwia Pospuła
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Krzysztof Tunia
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Marek Nowak
- Institute of Archaeology, Jagiellonian University, Kraków, Poland
| | | | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | | | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
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8
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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9
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Barbier J, Vaillant C, Volff JN, Brunet FG, Audit B. Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution. Genes (Basel) 2021; 12:genes12060851. [PMID: 34205881 PMCID: PMC8228248 DOI: 10.3390/genes12060851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.
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Affiliation(s)
- Jérémy Barbier
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Cédric Vaillant
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Correspondence: (J.-N.V.); (B.A.)
| | - Frédéric G. Brunet
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
| | - Benjamin Audit
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
- Correspondence: (J.-N.V.); (B.A.)
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Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France. Curr Biol 2021; 31:1072-1083.e10. [PMID: 33434506 DOI: 10.1016/j.cub.2020.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022]
Abstract
The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4-8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage.16 This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.
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11
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Mathov Y, Batyrev D, Meshorer E, Carmel L. Harnessing epigenetics to study human evolution. Curr Opin Genet Dev 2020; 62:23-29. [PMID: 32574964 DOI: 10.1016/j.gde.2020.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 11/27/2022]
Abstract
Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates.
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Affiliation(s)
- Yoav Mathov
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190400, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190400, Israel
| | - Daniel Batyrev
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190400, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190400, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190400, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190400, Israel.
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190400, Israel.
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12
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Poullet M, Orlando L. Assessing DNA Sequence Alignment Methods for Characterizing Ancient Genomes and Methylomes. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00105] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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13
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Museum Epigenomics: Charting the Future by Unlocking the Past. Trends Ecol Evol 2020; 35:295-300. [DOI: 10.1016/j.tree.2019.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/05/2019] [Accepted: 12/13/2019] [Indexed: 02/03/2023]
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14
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Liu Y, Weyrich LS, Llamas B. More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment. Mol Biol Evol 2020; 37:307-319. [PMID: 31638147 DOI: 10.1093/molbev/msz231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.
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Affiliation(s)
- Yichen Liu
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
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15
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Wagner S, Plomion C, Orlando L. Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Rubi TL, Knowles LL, Dantzer B. Museum epigenomics: Characterizing cytosine methylation in historic museum specimens. Mol Ecol Resour 2019; 20:1161-1170. [DOI: 10.1111/1755-0998.13115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/23/2019] [Accepted: 11/01/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Tricia L. Rubi
- Department of Psychology University of Michigan Ann Arbor MI USA
- Department of Biology University of Victoria Victoria BC Canada
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Ben Dantzer
- Department of Psychology University of Michigan Ann Arbor MI USA
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
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17
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Renaud G, Hanghøj K, Korneliussen TS, Willerslev E, Orlando L. Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples. Genetics 2019; 212:587-614. [PMID: 31088861 PMCID: PMC6614887 DOI: 10.1534/genetics.119.302057] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/01/2019] [Indexed: 11/18/2022] Open
Abstract
Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6× and down to 7-8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.
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Affiliation(s)
- Gabriel Renaud
- Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark
| | - Kristian Hanghøj
- Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, France
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark
- Department of Zoology, University of Cambridge, CB2 3EJ, UK
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- The Danish Institute for Advanced Study at The University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ludovic Orlando
- Lundbeck Foundation GeoGenetics Center, Globe Institute, University of Copenhagen, 1350K, Denmark
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, France
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18
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The Promise of Paleogenomics Beyond Our Own Species. Trends Genet 2019; 35:319-329. [PMID: 30954285 DOI: 10.1016/j.tig.2019.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/18/2019] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.
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19
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Smith O, Nicholson WV, Kistler L, Mace E, Clapham A, Rose P, Stevens C, Ware R, Samavedam S, Barker G, Jordan D, Fuller DQ, Allaby RG. A domestication history of dynamic adaptation and genomic deterioration in Sorghum. NATURE PLANTS 2019; 5:369-379. [PMID: 30962527 DOI: 10.1038/s41477-019-0397-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 02/28/2019] [Indexed: 05/20/2023]
Abstract
The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated episodes of introgression. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia. These data indicate no evidence for the effects of a domestication bottleneck, but instead reveal a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially to shape architectural and nutritional domestication traits and to facilitate adaptation to the local environment. Later introgression between sorghum races allowed the exchange of adaptive traits and achieved mutual genomic rescue through an ameliorated mutation load. These results reveal a model of domestication in which genomic adaptation and deterioration were not focused on the initial stages of domestication but occurred throughout the history of cultivation.
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Affiliation(s)
- Oliver Smith
- School of Life Sciences, University of Warwick, Coventry, UK
- Natural History Museum of Denmark, Copenhagen, Denmark
| | - William V Nicholson
- School of Life Sciences, University of Warwick, Coventry, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Logan Kistler
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, D.C., USA
| | - Emma Mace
- Department of Agriculture, Fisheries and Forestry Queensland (DAFFQ), Warwick, Queensland, Australia
| | - Alan Clapham
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Pamela Rose
- The Austrian Archaeological Institute, Cairo Branch, Zamalek, Cairo, Egypt
| | | | - Roselyn Ware
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Siva Samavedam
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Guy Barker
- School of Life Sciences, University of Warwick, Coventry, UK
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, Queensland, Australia
| | | | - Robin G Allaby
- School of Life Sciences, University of Warwick, Coventry, UK.
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20
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Hanghøj K, Renaud G, Albrechtsen A, Orlando L. DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage. Gigascience 2019; 8:giz025. [PMID: 31004132 PMCID: PMC6474913 DOI: 10.1093/gigascience/giz025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/07/2019] [Accepted: 02/27/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons. FINDINGS Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data. It builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post-mortem cytosine deamination rates at both methylated and unmethylated sites. To validate DamMet, we extended gargammel, a sequence simulator for ancient DNA data, by introducing methylation-dependent features of post-mortem DNA decay. This new simulator provides direct validation of DamMet predictions. Additionally, the methylation levels inferred by DamMet were found to be correlated to those inferred by epiPALEOMIX and both on par and directly comparable to those measured from whole-genome bisulphite sequencing experiments of fresh tissues. CONCLUSIONS DamMet provides genuine estimates for local DNA methylation levels in ancient individual genomes. The returned estimates are directly cross-sample comparable, and the software is available as an open-source C++ program hosted at https://gitlab.com/KHanghoj/DamMet along with a manual and tutorial.
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Affiliation(s)
- Kristian Hanghøj
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse III, Paul Sabatier (UPS), 31000 Toulouse, France
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Anders Albrechtsen
- Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark, Øster voldgade 5-7, 1350k
| | - Ludovic Orlando
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse III, Paul Sabatier (UPS), 31000 Toulouse, France
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21
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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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22
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23
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24
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Teasdale MD, Fiddyment S, Vnouček J, Mattiangeli V, Speller C, Binois A, Carver M, Dand C, Newfield TP, Webb CC, Bradley DG, Collins MJ. The York Gospels: a 1000-year biological palimpsest. ROYAL SOCIETY OPEN SCIENCE 2017. [PMID: 29134095 DOI: 10.5061/dryad.1p390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.
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Affiliation(s)
- Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Jiří Vnouček
- BioArCh, University of York, York YO10 5DD, UK
- Department of Preservation, The Royal Library, København K DK-1016, Denmark
| | | | | | - Annelise Binois
- Department of Archaeology, University of Paris 1 Panthéon-Sorbonne, 3 rue Michelet, 75006 Paris, France
| | - Martin Carver
- Department of Archaeology, University of York, York YO10 5DD, UK
| | - Catherine Dand
- Borthwick Institute for Archives, University of York, York YO10 5DD, UK
| | - Timothy P Newfield
- Departments of History and Biology, Georgetown University, 37th and O Streets NW, ICC 600, Washington, DC 20057, USA
| | | | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew J Collins
- BioArCh, University of York, York YO10 5DD, UK
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
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25
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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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26
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Teasdale MD, Fiddyment S, Vnouček J, Mattiangeli V, Speller C, Binois A, Carver M, Dand C, Newfield TP, Webb CC, Bradley DG, Collins MJ. The York Gospels: a 1000-year biological palimpsest. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170988. [PMID: 29134095 PMCID: PMC5666278 DOI: 10.1098/rsos.170988] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/22/2017] [Indexed: 05/10/2023]
Abstract
Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.
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Affiliation(s)
- Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Authors for correspondence: Matthew D. Teasdale e-mail: ;
| | - Sarah Fiddyment
- BioArCh, University of York, York YO10 5DD, UK
- Authors for correspondence: Sarah Fiddyment e-mail:
| | - Jiří Vnouček
- BioArCh, University of York, York YO10 5DD, UK
- Department of Preservation, The Royal Library, København K DK-1016, Denmark
| | | | | | - Annelise Binois
- Department of Archaeology, University of Paris 1 Panthéon-Sorbonne, 3 rue Michelet, 75006 Paris, France
| | - Martin Carver
- Department of Archaeology, University of York, York YO10 5DD, UK
| | - Catherine Dand
- Borthwick Institute for Archives, University of York, York YO10 5DD, UK
| | - Timothy P. Newfield
- Departments of History and Biology, Georgetown University, 37th and O Streets NW, ICC 600, Washington, DC 20057, USA
| | | | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew J. Collins
- BioArCh, University of York, York YO10 5DD, UK
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
- Authors for correspondence: Matthew J. Collins e-mail:
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27
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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: 33] [Impact Index Per Article: 4.7] [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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