1
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Taurozzi AJ, Rüther PL, Patramanis I, Koenig C, Sinclair Paterson R, Madupe PP, Harking FS, Welker F, Mackie M, Ramos-Madrigal J, Olsen JV, Cappellini E. Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel. Nat Protoc 2024; 19:2085-2116. [PMID: 38671208 DOI: 10.1038/s41596-024-00975-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/12/2024] [Indexed: 04/28/2024]
Abstract
In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient DNA preservation in the same areas. Accordingly, their amino acid sequences currently represent the only source of genetic information available to pursue phylogenetic inference involving species that went extinct too long ago to be amenable for ancient DNA analysis. Here we present a complete workflow, including sample preparation, mass spectrometric data acquisition and computational analysis, to recover and interpret million-year-old dental enamel protein sequences. During sample preparation, the proteolytic digestion step, usually an integral part of conventional bottom-up proteomics, is omitted to increase the recovery of the randomly degraded peptides spontaneously generated by extensive diagenetic hydrolysis of ancient proteins over geological time. Similarly, we describe other solutions we have adopted to (1) authenticate the endogenous origin of the protein traces we identify, (2) detect and validate amino acid variation in the ancient protein sequences and (3) attempt phylogenetic inference. Sample preparation and data acquisition can be completed in 3-4 working days, while subsequent data analysis usually takes 2-5 days. The workflow described requires basic expertise in ancient biomolecules analysis, mass spectrometry-based proteomics and molecular phylogeny. Finally, we describe the limits of this approach and its potential for the reconstruction of evolutionary relationships in paleontology and paleoanthropology.
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Affiliation(s)
| | - Patrick L Rüther
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Palesa P Madupe
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Florian Simon Harking
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Meaghan Mackie
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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2
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Psonis N, Vassou D, Nafplioti A, Tabakaki E, Pavlidis P, Stamatakis A, Poulakakis N. Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes. Forensic Sci Int Genet 2024; 71:103060. [PMID: 38796876 DOI: 10.1016/j.fsigen.2024.103060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/29/2024]
Abstract
In the Battle of Crete during the World War II occupation of Greece, the German forces faced substantial civilian resistance. To retribute the numerous German losses, a series of mass executions took place in numerous places in Crete; a common practice reported from Greece and elsewhere. In Adele, a village in the regional unit of Rethymnon, 18 male civilians were executed and buried in a burial pit at the Sarakina site. In this study, the first one conducted for a conflict that occurred in Greece, we identified for humanitarian purposes the 18 skulls of the Sarakina victims, following a request from the local community of Adele. The molecular identification of historical human remains via ancient DNA approaches and low coverage whole genome sequencing has only recently been introduced. Here, we performed genome skimming on the living relatives of the victims, as well as high throughput historical DNA analysis on the skulls to infer the kinship degrees among the victims via genetic relatedness analyses. We also conducted targeted anthropological analysis to successfully complete the identification of all Sarakina victims. We demonstrate that our methodological approach constitutes a potentially highly informative forensic tool to identify war victims. It can hence be applied to analogous studies on degraded DNA, thus, paving the path for systematic war victim identification in Greece and beyond.
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Affiliation(s)
- Nikolaos Psonis
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece.
| | - Despoina Vassou
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece
| | - Argyro Nafplioti
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece
| | - Eugenia Tabakaki
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Irakleio 70013, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio 70013, Greece
| | - Alexandros Stamatakis
- Institute of Computer Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Irakleio 70013, Greece; Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Nikos Poulakakis
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece; Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio 70013, Greece
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3
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Tretmanis JM, Jay F, Avila-Árcos MC, Huerta-Sanchez E. Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560049. [PMID: 37808674 PMCID: PMC10557694 DOI: 10.1101/2023.09.28.560049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing quality. We also develop a software tool that simulates aDNA taking into account the features of aDNA as well as the evolutionary history of the population. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (~ 400 generations in the past) as long as contamination and read depth are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resulting in the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations.
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Affiliation(s)
| | - Flora Jay
- Interdisciplinary Laboratory of Numerical Sciences, Université Paris-Saclay
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4
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Thorburn DMJ, Sagonas K, Binzer-Panchal M, Chain FJJ, Feulner PGD, Bornberg-Bauer E, Reusch TBH, Samonte-Padilla IE, Milinski M, Lenz TL, Eizaguirre C. Origin matters: Using a local reference genome improves measures in population genomics. Mol Ecol Resour 2023; 23:1706-1723. [PMID: 37489282 DOI: 10.1111/1755-0998.13838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 06/02/2023] [Indexed: 07/26/2023]
Abstract
Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and FST ), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.
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Affiliation(s)
- Doko-Miles J Thorburn
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Kostas Sagonas
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mahesh Binzer-Panchal
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Uppsala University, Uppsala, Sweden
| | - Frederic J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Irene E Samonte-Padilla
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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5
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Papalini S, Di Vittori V, Pieri A, Allegrezza M, Frascarelli G, Nanni L, Bitocchi E, Bellucci E, Gioia T, Pereira LG, Susek K, Tenaillon M, Neumann K, Papa R. Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies. PLANTS (BASEL, SWITZERLAND) 2023; 12:3452. [PMID: 37836192 PMCID: PMC10575153 DOI: 10.3390/plants12193452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums, and in other archival collections. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, herbarium specimens offered a new source for studying phenological traits in plants and for disentangling biogeography and evolutionary scenarios of species. More recently, advances in molecular technologies went in parallel with the decreasing costs of next-generation sequencing (NGS) approaches, which paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and ancient samples, such as herbarium specimens, this research field is still relatively unexplored due to the need for improving strategies for aDNA manipulation and exploitation from ancient samples. The higher susceptibility of aDNA to degradation and contamination during herbarium conservation and manipulation and the occurrence of biochemical postmortem damage can result in a more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical herbarium plant materials, such as best practices for aDNA extraction, amplification, and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of herbarium specimens for their exploitation in plant evolutionary studies.
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Affiliation(s)
- Simone Papalini
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Alice Pieri
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Marina Allegrezza
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy;
| | - Luis Guasch Pereira
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology (CRF-INIA-CSIC), 28805 Alcalá de Henares, Madrid, Spain;
| | - Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland;
| | - Maud Tenaillon
- Génétique Quantitative et Evolution–Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, 91190 Gif-sur-Yvette, France;
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany;
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (S.P.); (A.P.); (M.A.); (G.F.); (L.N.); (E.B.); (E.B.)
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6
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Ortiz D, Pekár S, Bilat J, Shafaie S, Alvarez N, Gauthier J. Dynamic evolution of size and colour in the highly specialized Zodarion ant-eating spiders. Proc Biol Sci 2023; 290:20230797. [PMID: 37554037 PMCID: PMC10410226 DOI: 10.1098/rspb.2023.0797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023] Open
Abstract
Ecological specialists constitute relevant case studies for understanding the mechanisms, potential and limitations of evolution. The species-rich and strictly myrmecophagous spiders of the genus Zodarion show diversified defence mechanisms, including myrmecomorphy of different ant species and nocturnality. Through Hybridization Capture Using RAD Probes (hyRAD), a phylogenomic technique designed for sequencing poorly preserved specimens, we reconstructed a phylogeny of Zodarion using 52 (approx. a third of the nominal) species that cover its phylogenetic and distributional diversity. We then estimated the evolution of body size and colour, traits that have diversified noticeably and are linked to defence mechanisms, across the group. Our genomic matrix of 300 loci led to a well-supported phylogenetic hypothesis that uncovered two main clades inside Zodarion. Ancestral state estimation revealed the highly dynamic evolution of body size and colour across the group, with multiple transitions and convergences in both traits, which we propose is likely indicative of multiple transitions in ant specialization across the genus. Our study will allow the informed targeted selection of Zodarion taxa of special interest for research into the group's remarkable adaptations to ant specialization. It also exemplifies the utility of hyRAD for phylogenetic studies using museum material.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Julia Bilat
- Geneva Natural History Museum, Geneva, Switzerland
| | - Sepideh Shafaie
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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7
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Marsh WA, Brace S, Barnes I. Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data. BMC Genomics 2023; 24:111. [PMID: 36918761 PMCID: PMC10015695 DOI: 10.1186/s12864-023-09198-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and yet the identification and interpretation of kin relationships in prehistoric human groups is difficult. In recent years, the advent of archaeogenetic techniques have offered a fresh approach, and when combined with more traditional osteological and interpretive archaeological methods, allows for improved interpretation of the burial practices, cultural behaviours, and societal stratification in ancient societies. Although archaeogenetic techniques are developing at pace, questions remain as to their accuracy, particularly when applied to the low coverage datasets that results from the sequencing of DNA derived from highly degraded ancient material. RESULTS The performance of six of the most commonly used kinship identifcation software methods was explored at a range of low and ultra low genome coverages. An asymmetrical response was observed across packages, with decreased genome coverage resulting in differences in both direction and degree of change of calculated kinship scores and thus pairwise relatedness estimates are dependant on both package used and genome coverage. Methods reliant upon genotype likelihoods methods (lcMLkin, NGSrelate and NGSremix) show a decreased level of prediction at coverage below 1x, although were consistent in the particular relationships identified at these coverages when compared to the pseudohaploid reliant methods tested (READ, the Kennett 2017 method and TKGWV2.0). The three pseudohaploid methods show predictive potential at coverages as low as 0.05x, although the accuracy of the relationships identified is questionable given the increase in the number of relationships identifIed at the low coverage (type I errors). CONCLUSION Two pseudohaploid methods (READ and Kennett 2017) show relatively consistent inference of kin relationships at low coverage (0.5x), with READ only showing a significant performance drop off at ultralow coverages (< 0.2x). More generally, our results reveal asymmetrical kinship classifications in some software packages even at high coverages, highlighting the importance of applying multiple methods to authenticate kin relationships in ancient material, along with the continuing need to develop laboratory methods that maximise data output for downstream analyses.
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Affiliation(s)
- William A Marsh
- Natural History Museum, Cromwell Road, SW7 5BD, London, England. .,BioArCh, University of York, YO10 5NG, York, England.
| | - Selina Brace
- Natural History Museum, Cromwell Road, SW7 5BD, London, England
| | - Ian Barnes
- Natural History Museum, Cromwell Road, SW7 5BD, London, England
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Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review. Genes (Basel) 2023; 14:genes14020303. [PMID: 36833230 PMCID: PMC9957072 DOI: 10.3390/genes14020303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/25/2023] Open
Abstract
Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.
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Henriksen RA, Zhao L, Korneliussen TS. NGSNGS: next-generation simulator for next-generation sequencing data. Bioinformatics 2023; 39:6994180. [PMID: 36661298 PMCID: PMC9891242 DOI: 10.1093/bioinformatics/btad041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
SUMMARY With the rapid expansion of the capabilities of the DNA sequencers throughout the different sequencing generations, the quantity of generated data has likewise increased. This evolution has also led to new bioinformatical methods, for which in silico data have become crucial when verifying the accuracy of a model or the robustness of a genomic analysis pipeline. Here, we present a multithreaded next-generation simulator for next-generation sequencing data (NGSNGS), which simulates reads faster than currently available methods and programs. NGSNGS can simulate reads with platform-specific characteristics based on nucleotide quality score profiles as well as including a post-mortem damage model which is relevant for simulating ancient DNA. The simulated sequences are sampled (with replacement) from a reference DNA genome, which can represent a haploid genome, polyploid assemblies or even population haplotypes and allows the user to simulate known variable sites directly. The program is implemented in a multithreading framework and is factors faster than currently available tools while extending their feature set and possible output formats. AVAILABILITY AND IMPLEMENTATION The method and associated programs are released as open-source software, code and user manual are available at https://github.com/RAHenriksen/NGSNGS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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10
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Popli D, Peyrégne S, Peter BM. KIN: a method to infer relatedness from low-coverage ancient DNA. Genome Biol 2023; 24:10. [PMID: 36650598 PMCID: PMC9843908 DOI: 10.1186/s13059-023-02847-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness of a pair of individuals from the identical-by-descent segments they share. KIN accurately classifies up to 3rd-degree relatives using at least 0.05x sequence coverage and differentiates siblings from parent-child pairs. It incorporates additional models to adjust for contamination and detect inbreeding, which improves classification accuracy.
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Affiliation(s)
- Divyaratan Popli
- grid.419518.00000 0001 2159 1813 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stéphane Peyrégne
- grid.419518.00000 0001 2159 1813 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin M. Peter
- grid.419518.00000 0001 2159 1813 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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11
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De Sanctis B, Money D, Pedersen MW, Durbin R. A theoretical analysis of taxonomic binning accuracy. Mol Ecol Resour 2022; 22:2208-2219. [PMID: 35285150 DOI: 10.1111/1755-0998.13608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 11/28/2022]
Abstract
Many metagenomic and environmental DNA studies require the taxonomic assignment of individual reads or sequences by aligning reads to a reference database, known as taxonomic binning. When a read aligns to more than one reference sequence, it is often classified based on sequence similarity. This step can assign reads to incorrect taxa, at a rate which depends both on the assignment algorithm and on underlying population genetic and database parameters. In particular, as we move towards using environmental DNA to study eukaryotic taxa subject to regular recombination, we must take into account issues concerning gene tree discordance. Though accuracy is often compared across algorithms using a fixed data set, the relative impact of these population genetic and database parameters on accuracy has not yet been quantified. Here, we develop both a theoretical and simulation framework in the simplified case of two reference species, and compute binning accuracy over a wide range of parameters, including sequence length, species-query divergence time, divergence times of the reference species, reference database completeness, sample age and effective population size. We consider two assignment methods and contextualize our results using parameters from a recent ancient environmental DNA study, comparing them to the commonly used discriminative k-mer-based method Clark (Current Biology, 31, 2021, 2728; BMC Genomics, 16, 2015, 1). Our results quantify the degradation in assignment accuracy as the samples diverge from their closest reference sequence, and with incompleteness of reference sequences. We also provide a framework in which others can compute expected accuracy for their particular method or parameter set. Code is available at https://github.com/bdesanctis/binning-accuracy.
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Affiliation(s)
- Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Daniel Money
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
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12
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Erven JAM, Çakirlar C, Bradley DG, Raemaekers DCM, Madsen O. Imputation of Ancient Whole Genome Sus scrofa DNA Introduces Biases Toward Main Population Components in the Reference Panel. Front Genet 2022; 13:872486. [PMID: 35903348 PMCID: PMC9315352 DOI: 10.3389/fgene.2022.872486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
Sequencing ancient DNA to high coverage is often limited by sample quality and cost. Imputing missing genotypes can potentially increase information content and quality of ancient data, but requires different computational approaches than modern DNA imputation. Ancient imputation beyond humans has not been investigated. In this study we report results of a systematic evaluation of imputation of three whole genome ancient Sus scrofa samples from the Early and Late Neolithic (∼7,100-4,500 BP), to test the utility of imputation. We show how issues like genetic architecture and, reference panel divergence, composition and size affect imputation accuracy. We evaluate a variety of imputation methods, including Beagle5, GLIMPSE, and Impute5 with varying filters, pipelines, and variant calling methods. We achieved genotype concordance in most cases reaching above 90%; with the highest being 98% with ∼2,000,000 variants recovered using GLIMPSE. Despite this high concordance the sources of diversity present in the genotypes called in the original high coverage genomes were not equally imputed leading to biases in downstream analyses; a trend toward genotypes most common in the reference panel is observed. This demonstrates that the current reference panel does not possess the full diversity needed for accurate imputation of ancient Sus, due to missing variations from Near Eastern and Mesolithic wild boar. Imputation of ancient Sus scrofa holds potential but should be approached with caution due to these biases, and suggests that there is no universal approach for imputation of non-human ancient species.
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Affiliation(s)
- J. A. M. Erven
- Groningen Institute of Archaeology, University of Groningen, Groningen, Netherlands
| | - C. Çakirlar
- Groningen Institute of Archaeology, University of Groningen, Groningen, Netherlands
| | - D. G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - D. C. M. Raemaekers
- Groningen Institute of Archaeology, University of Groningen, Groningen, Netherlands
| | - O. Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
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13
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Ausmees K, Sanchez-Quinto F, Jakobsson M, Nettelblad C. An empirical evaluation of genotype imputation of ancient DNA. G3 (BETHESDA, MD.) 2022; 12:6575448. [PMID: 35482488 PMCID: PMC9157144 DOI: 10.1093/g3journal/jkac089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
Abstract
With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.
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Affiliation(s)
- Kristiina Ausmees
- Department of Information Technology, Uppsala University, Uppsala 751 05, Sweden
| | - Federico Sanchez-Quinto
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.,Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Carl Nettelblad
- Department of Information Technology, Uppsala University, Uppsala 751 05, Sweden
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14
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Abstract
Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.
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Affiliation(s)
- Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Pille Hallast
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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15
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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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16
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Hahn EE, Alexander MR, Grealy A, Stiller J, Gardiner DM, Holleley CE. Unlocking inaccessible historical genomes preserved in formalin. Mol Ecol Resour 2021; 22:2130-2147. [PMID: 34549888 DOI: 10.1111/1755-0998.13505] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/27/2022]
Abstract
Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine sample processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically diverse specimens collected between 1962 and 2006 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3× nuclear genome coverage from formalin-preserved tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out-performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. Here, we demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and nondestructive assessment criteria. Sequencing of formalin-preserved specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.
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Affiliation(s)
- Erin E Hahn
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Marina R Alexander
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Alicia Grealy
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
| | - Jiri Stiller
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, St Lucia, Qld, Australia
| | - Donald M Gardiner
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, St Lucia, Qld, Australia
| | - Clare E Holleley
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT, Australia
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17
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Sarno S, Cilli E, Serventi P, De Fanti S, Corona A, Fontani F, Traversari M, Ferri G, Fariselli AC, Luiselli D. Insights into Punic genetic signatures in the southern necropolis of Tharros (Sardinia). Ann Hum Biol 2021; 48:247-259. [PMID: 34459340 DOI: 10.1080/03014460.2021.1937699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Phoenician and Punic expansions have been protagonists of intense trade networks and settlements in the Mediterranean Sea. AIMS The maternal genetic variability of ancient Punic samples from the Sardinian necropolis of Tharros was analysed, with the aim to explore genetic interactions and signatures of past population events. SUBJECTS AND METHODS The mtDNA HVS-I and coding region SNPs were analysed in 14 Punic samples and 74 modern individuals from Cabras and Belvì (for which the HVS-II region was also analysed). The results were compared with 5,590 modern Euro-Mediterranean sequences and 127 ancient samples. RESULTS While contemporary groups fall within the genetic variability of other modern Sardinians, our Punic samples reveal proximity to present-day North-African and Iberian populations. Furthermore, Cabras and Belvì cluster mainly with pre-Phoenician groups, while samples from Tharros project with other Punic Sardinian individuals. CONCLUSION This study provides the first preliminary insights into the population dynamics of the Punic site of Tharros. While the number of currently available samples does not allow definitive investigation of the connection with indigenous Sardinian groups, our results seem to confirm internal migratory phenomena in the central-western Mediterranean and female participation in the Punic mobility.
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Affiliation(s)
- Stefania Sarno
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Patrizia Serventi
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Sara De Fanti
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Interdepartmental Centre "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)", University of Bologna, Bologna, Italy
| | - Andrea Corona
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Dipartimento di Scienze del Sistema Nervoso e del Comportamento, Università di Pavia, Pavia, Italy
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Mirko Traversari
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Gianmarco Ferri
- Department of Diagnostic and Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
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18
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Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-Del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proc Biol Sci 2021; 288:20211252. [PMID: 34428961 PMCID: PMC8385357 DOI: 10.1098/rspb.2021.1252] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Marianne Dehasque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Petter Larsson
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Špela Lemež
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana N Meleg
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,'Emil Racoviță' Institute of Speleology of the Romanian Academy, Calea 13 Septembrie, nr. 13, 050711, Sector 5, Bucharest, Romania.,Emil. G. Racoviță Institute, Babeș-Bolyai University, Clinicilor 5-7, 400006 Cluj-Napoca, Romania
| | - Johannes Måsviken
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Ancient DNA Unit, SciLifeLab, Stockholm and Uppsala, Sweden
| | - Jovanka Studerus
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Mário Vicente
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Peter D Heintzman
- The Arctic University Museum of Norway, The Arctic University of Norway, 9037 Tromsø, Norway
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19
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Smith AD, Kamiński MJ, Kanda K, Sweet AD, Betancourt JL, Holmgren CA, Hempel E, Alberti F, Hofreiter M. Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing. Sci Rep 2021; 11:12635. [PMID: 34135378 PMCID: PMC8209150 DOI: 10.1038/s41598-021-91896-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.
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Affiliation(s)
- Aaron D Smith
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA.
| | - Marcin J Kamiński
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
- Zoological Museum, Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warszawa, Poland
| | - Kojun Kanda
- USDA Systematic Entomology Laboratory, C/O Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Andrew D Sweet
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Arkansas State University, State University, AR, 72467, USA
| | | | - Camille A Holmgren
- Department of Geography and Planning, SUNY Buffalo State College, Buffalo, NY, USA
| | - Elisabeth Hempel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Museum Für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Federica Alberti
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Reiss-Engelhorn-Museen, Mannheim, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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20
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Straube N, Lyra ML, Paijmans JLA, Preick M, Basler N, Penner J, Rödel MO, Westbury MV, Haddad CFB, Barlow A, Hofreiter M. Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Mol Ecol Resour 2021; 21:2299-2315. [PMID: 34036732 DOI: 10.1111/1755-0998.13433] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023]
Abstract
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.
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Affiliation(s)
- Nicolas Straube
- University Museum of Bergen, Bergen, Norway.,SNSB Bavarian State Collection of Zoology, München, Germany
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.,Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Johanna L A Paijmans
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michaela Preick
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nikolas Basler
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johannes Penner
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Chair of Wildlife Ecology and Management, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Célio F B Haddad
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil
| | - Axel Barlow
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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21
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Seixas FA, Edelman NB, Mallet J. Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus. Genome Biol Evol 2021; 13:6207971. [PMID: 33792688 PMCID: PMC8290116 DOI: 10.1093/gbe/evab069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Heliconius butterflies (Lepidoptera: Nymphalidae) are a group of 48 neotropical species widely studied in evolutionary research. Despite the wealth of genomic data generated in past years, chromosomal level genome assemblies currently exist for only two species, Heliconius melpomene and Heliconius erato, each a representative of one of the two major clades of the genus. Here, we use these reference genomes to improve the contiguity of previously published draft genome assemblies of 16 Heliconius species. Using a reference-assisted scaffolding approach, we place and order the scaffolds of these genomes onto chromosomes, resulting in 95.7-99.9% of their genomes anchored to chromosomes. Genome sizes are somewhat variable among species (270-422 Mb) and in one small group of species (Heliconius hecale, Heliconius elevatus, and Heliconius pardalinus) expansions in genome size are driven mainly by repetitive sequences that map to four small regions in the H. melpomene reference genome. Genes from these repeat regions show an increase in exon copy number, an absence of internal stop codons, evidence of constraint on nonsynonymous changes, and increased expression, all of which suggest that at least some of the extra copies are functional. Finally, we conducted a systematic search for inversions and identified five moderately large inversions fixed between the two major Heliconius clades. We infer that one of these inversions was transferred by introgression between the lineages leading to the erato/sara and burneyi/doris clades. These reference-guided assemblies represent a major improvement in Heliconius genomic resources that enable further genetic and evolutionary discoveries in this genus.
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Affiliation(s)
- Fernando A Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut, USA
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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22
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Diroma MA, Modi A, Lari M, Sineo L, Caramelli D, Vai S. New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples. Front Genet 2021; 12:619950. [PMID: 33679884 PMCID: PMC7930628 DOI: 10.3389/fgene.2021.619950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Polizzello (Sicily, Italy). The pipeline includes several modules from well-established tools for aDNA analysis and a recently released variant caller, which was specifically conceived for mtDNA, applied for the first time to aDNA data. Through a fine-tuned filtering on variant allele sequencing features, we were able to accurately reconstruct nearly complete (>88%) mtDNA genome for almost all the analyzed samples (27 out of 30), depending on the degree of preservation and the sequencing throughput, and to get a reliable set of variants allowing haplogroup prediction. Additionally, we provide guidelines to deal with possible artifact sources, including nuclear mitochondrial sequence (NumtS) contamination, an often-neglected issue in ancient mtDNA surveys. Potential heteroplasmy levels were also estimated, although most variants were likely homoplasmic, and validated by data simulations, proving that new sequencing technologies and software are sensitive enough to detect partially mutated sites in ancient genomes and discriminate true variants from artifacts. A thorough functional annotation of detected and filtered mtDNA variants was also performed for a comprehensive evaluation of these ancient samples.
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Affiliation(s)
- Maria Angela Diroma
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Alessandra Modi
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Luca Sineo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
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23
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Environmental palaeogenomic reconstruction of an Ice Age algal population. Commun Biol 2021; 4:220. [PMID: 33594237 PMCID: PMC7887274 DOI: 10.1038/s42003-021-01710-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA. Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.
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24
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Garrett Vieira F, Samaniego Castruita JA, Gilbert MTP. Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction. Ecol Evol 2020; 10:12700-12709. [PMID: 33304488 PMCID: PMC7713980 DOI: 10.1002/ece3.6925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 01/20/2023] Open
Abstract
Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.
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Affiliation(s)
- Filipe Garrett Vieira
- Section for Evolutionary GenomicsThe GLOBE InstituteFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - José Alfredo Samaniego Castruita
- Section for Evolutionary GenomicsThe GLOBE InstituteFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary GenomicsThe GLOBE InstituteFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- University MuseumNorwegian University of Science and TechnologyTrondheimNorway
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25
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Feuerborn TR, Palkopoulou E, van der Valk T, von Seth J, Munters AR, Pečnerová P, Dehasque M, Ureña I, Ersmark E, Lagerholm VK, Krzewińska M, Rodríguez-Varela R, Götherström A, Dalén L, Díez-Del-Molino D. Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets. BMC Genomics 2020; 21:844. [PMID: 33256612 PMCID: PMC7708127 DOI: 10.1186/s12864-020-07229-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/16/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. RESULTS Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. CONCLUSIONS We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
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Affiliation(s)
- Tatiana R Feuerborn
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Centre for Palaeogenetics, Stockholm, Sweden.
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Tom van der Valk
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, Uppsala University, Uppsala, Sweden
| | | | - Marianne Dehasque
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Irene Ureña
- Department of Animal Breeding, INIA, Madrid, Spain
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Ricardo Rodríguez-Varela
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
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26
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Parker C, Rohrlach AB, Friederich S, Nagel S, Meyer M, Krause J, Bos KI, Haak W. A systematic investigation of human DNA preservation in medieval skeletons. Sci Rep 2020; 10:18225. [PMID: 33106554 PMCID: PMC7588426 DOI: 10.1038/s41598-020-75163-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022] Open
Abstract
Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.
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Affiliation(s)
- Cody Parker
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Adam B Rohrlach
- Max Planck Institute for the Science of Human History, Jena, Germany
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA, Australia
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie, Sachsen-Anhalt, Halle (Saale), Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany.
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27
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Martiniano R, Garrison E, Jones ER, Manica A, Durbin R. Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph. Genome Biol 2020; 21:250. [PMID: 32943086 PMCID: PMC7499850 DOI: 10.1186/s13059-020-02160-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 08/27/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for aDNA and compare with existing methods. RESULTS We use vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants and compare with the same data aligned with bwa to the human linear reference genome. Using vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias but can have lower sensitivity than vg, particularly for indels. CONCLUSIONS Our findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analyzing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.
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Affiliation(s)
- Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, CB3 0DH UK
| | - Erik Garrison
- Wellcome Sanger Institute, Cambridge, CB10 1SA UK
- Genomics Institute, University of California, Santa Cruz, CA 95064 USA
| | - Eppie R. Jones
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ UK
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, CB3 0DH UK
- Wellcome Sanger Institute, Cambridge, CB10 1SA UK
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28
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Peyrégne S, Peter BM. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biol 2020; 21:246. [PMID: 32933569 PMCID: PMC7490890 DOI: 10.1186/s13059-020-02123-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/27/2020] [Indexed: 12/31/2022] Open
Abstract
Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
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29
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Dommain R, Andama M, McDonough MM, Prado NA, Goldhammer T, Potts R, Maldonado JE, Nkurunungi JB, Campana MG. The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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30
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Peyrégne S, Prüfer K. Present-Day DNA Contamination in Ancient DNA Datasets. Bioessays 2020; 42:e2000081. [PMID: 32648350 DOI: 10.1002/bies.202000081] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/20/2020] [Indexed: 01/06/2023]
Abstract
Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
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31
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Rifkin RF, Vikram S, Ramond JB, Rey-Iglesia A, Brand TB, Porraz G, Val A, Hall G, Woodborne S, Le Bailly M, Potgieter M, Underdown SJ, Koopman JE, Cowan DA, Van de Peer Y, Willerslev E, Hansen AJ. Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome. MICROBIOME 2020; 8:62. [PMID: 32375874 PMCID: PMC7204047 DOI: 10.1186/s40168-020-00832-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/18/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. METHODS Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. RESULTS Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. CONCLUSIONS Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.
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Affiliation(s)
- Riaan F Rifkin
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK.
| | - Surendra Vikram
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Jean-Baptiste Ramond
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Tina B Brand
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Guillaume Porraz
- CNRS, UMR 7041 ArScAn-AnTET, Université Paris-Nanterre, Paris, France
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
| | - Aurore Val
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Grant Hall
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Stephan Woodborne
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
- iThemba LABS, Braamfontein Johannesburg, South Africa
| | - Matthieu Le Bailly
- University of Bourgogne France-Comte, CNRS UMR 6249 Chrono-environment, Besancon, France
| | - Marnie Potgieter
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Simon J Underdown
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
| | - Jessica E Koopman
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Don A Cowan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Yves Van de Peer
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- VIB Centre for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Eske Willerslev
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Anders J Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark.
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32
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Pre-Columbian zoonotic enteric parasites: An insight into Puerto Rican indigenous culture diets and life styles. PLoS One 2020; 15:e0227810. [PMID: 31999735 PMCID: PMC6992007 DOI: 10.1371/journal.pone.0227810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 12/30/2019] [Indexed: 11/19/2022] Open
Abstract
The pre-Columbian Huecoid and Saladoid cultures were agricultural ethnic groups that supplemented their diets by fishing, hunting and scavenging. Archaeological deposits associated to these cultures contained a variety of faunal osseous remains that hinted at the cultures' diets. The present study identified zoonotic parasites that may have infected these two cultures as a result of their diets. We used metagenomic sequencing and microscopy data from 540-1,400 year old coprolites as well as the zooarchaeological data to recreate the possible interactions between zoonotic parasites and their hosts. Microscopy revealed Diphyllobothrium spp. and Dipylidium caninum eggs along with unidentified cestode and trematode eggs. DNA sequencing together with functional prediction and phylogenetic inference identified reads of Cryptosporidium spp., Giardia intestinalis and Schistosoma spp. The complimentary nature of the molecular, microscopy and zooarchaeology data provided additional insight into the detected zoonotic parasites' potential host range. Network modeling revealed that rodents and canids living in close proximity to these cultures were most likely the main source of these zoonotic parasite infections.
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Gelabert P, Sandoval-Velasco M, Serres A, de Manuel M, Renom P, Margaryan A, Stiller J, de-Dios T, Fang Q, Feng S, Mañosa S, Pacheco G, Ferrando-Bernal M, Shi G, Hao F, Chen X, Petersen B, Olsen RA, Navarro A, Deng Y, Dalén L, Marquès-Bonet T, Zhang G, Antunes A, Gilbert MTP, Lalueza-Fox C. Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet. Curr Biol 2019; 30:108-114.e5. [PMID: 31839456 DOI: 10.1016/j.cub.2019.10.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/03/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022]
Abstract
As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. The cause of its extinction remains contentious: besides excessive mortality associated to habitat destruction and active hunting, their survival could have been negatively affected by its range having become increasingly patchy [2] or by the exposure to poultry pathogens [3, 4]. In addition, the Carolina parakeet showed a predilection for cockleburs, an herbaceous plant that contains a powerful toxin, carboxyatractyloside, or CAT [5], which did not seem to affect them but made the birds notoriously toxic to most predators [3]. To explore the demographic history of this bird, we generated the complete genomic sequence of a preserved specimen held in a private collection in Espinelves (Girona, Spain), as well as of a close extant relative, Aratinga solstitialis. We identified two non-synonymous genetic changes in two highly conserved proteins known to interact with CAT that could underlie a specific dietary adaptation to this toxin. Our genomic analyses did not reveal evidence of a dramatic past demographic decline in the Carolina parakeet; also, its genome did not exhibit the long runs of homozygosity that are signals of recent inbreeding and are typically found in endangered species. As such, our results suggest its extinction was an abrupt process and thus likely solely attributable to human causes.
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Affiliation(s)
- Pere Gelabert
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Aitor Serres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Pere Renom
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ashot Margaryan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Shenzhen 518083, China
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Shenzhen 518083, China
| | - Santi Mañosa
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Facultat de Biologia, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Manuel Ferrando-Bernal
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guolin Shi
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Fei Hao
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Xianqing Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Semeling Road, 08100 Kedah, Malaysia
| | - Remi-André Olsen
- ScieLifeLab, Department of Biochemistry and Biophysics, Stockholm University, Frescativägen 40, SE-17121 Solna, Sweden
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08036 Barcelona, Spain
| | - Yuan Deng
- BGI-Shenzhen, Beishan Industrial Zone, Building 11, Shenzhen 518083, China
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 40, 10405 Stockholm, Sweden
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08036 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, c. de les Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; NTNU University Museum, Erling Skakkes gate 47c, 7012 Trondheim, Norway.
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain.
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Abstract
Motivation The study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling. Results I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals. Availability and implementation The C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kay Prüfer
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Günther T, Nettelblad C. The presence and impact of reference bias on population genomic studies of prehistoric human populations. PLoS Genet 2019; 15:e1008302. [PMID: 31348818 PMCID: PMC6685638 DOI: 10.1371/journal.pgen.1008302] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/07/2019] [Accepted: 07/10/2019] [Indexed: 11/18/2022] Open
Abstract
Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.
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Affiliation(s)
- Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Carl Nettelblad
- Division of Scientific Computing, Department of Information Technology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Kawash JK, Smith SD, Karaiskos S, Grigoriev A. ARIADNA: machine learning method for ancient DNA variant discovery. DNA Res 2018; 25:619-627. [PMID: 30215675 PMCID: PMC6289774 DOI: 10.1093/dnares/dsy029] [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: 02/11/2018] [Accepted: 08/15/2018] [Indexed: 12/30/2022] Open
Abstract
Ancient DNA (aDNA) studies often rely on standard methods of mutation calling, optimized for high-quality contemporary DNA but not for excessive contamination, time- or environment-related damage of aDNA. In the absence of validated datasets and despite showing extreme sensitivity to aDNA quality, these methods have been used in many published studies, sometimes with additions of arbitrary filters or modifications, designed to overcome aDNA degradation and contamination problems. The general lack of best practices for aDNA mutation calling may lead to inaccurate results. To address these problems, we present ARIADNA (ARtificial Intelligence for Ancient DNA), a novel approach based on machine learning techniques, using specific aDNA characteristics as features to yield improved mutation calls. In our comparisons of variant callers across several ancient genomes, ARIADNA consistently detected higher-quality genome variants with fast runtimes, while reducing the false positive rate compared with other approaches.
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Affiliation(s)
- Joseph K Kawash
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Sean D Smith
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Spyros Karaiskos
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Andrey Grigoriev
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
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de Filippo C, Meyer M, Prüfer K. Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences. BMC Biol 2018; 16:121. [PMID: 30359256 PMCID: PMC6202837 DOI: 10.1186/s12915-018-0581-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/27/2018] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short. RESULTS Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~ 430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17-150%. This allows us to place a third specimen from the site on the Neandertal lineage. CONCLUSIONS Our method maximizes the sequence data amenable to genetic analysis from highly degraded ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.
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Affiliation(s)
- Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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Serventi P, Panicucci C, Bodega R, De Fanti S, Sarno S, Fondevila Alvarez M, Brisighelli F, Trombetta B, Anagnostou P, Ferri G, Vazzana A, Delpino C, Gruppioni G, Luiselli D, Cilli E. Iron Age Italic population genetics: the Piceni from Novilara (8th-7th century BC). Ann Hum Biol 2018; 45:34-43. [PMID: 29216758 DOI: 10.1080/03014460.2017.1414876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed. AIMS To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis. SUBJECTS AND METHODS In a first set of 10 individuals from Novilara, we performed deep sequencing of the HVS-I region of the mtDNA, combined with the genotyping of 22 SNPs in the coding region and the analysis of several autosomal markers. RESULTS The results show a low nucleotide diversity for the inhabitants of Novilara and highlight a genetic affinity of this ancient population with the current inhabitants of central Italy. No family relationship was observed between the individuals analysed here. CONCLUSIONS This study provides a preliminary characterisation of the mtDNA variability of the Piceni of Novilara, as well as a kinship assessment of two peculiar burials.
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Affiliation(s)
- Patrizia Serventi
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy.,b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Panicucci
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Roberta Bodega
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Sara De Fanti
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Stefania Sarno
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Manuel Fondevila Alvarez
- c Instituto de Ciencias Forenses 'Luis Concheiro' , University of Santiago de Compostela, Santiago de Compostela , Galicia , Spain
| | - Francesca Brisighelli
- d Sezione di Medicina Legale-Istituto di Sanità Pubblica , Università Cattolica del Sacro Cuore , Roma , Italy
| | - Beniamino Trombetta
- e Department of Biology and Biotechnology 'Charles Darwin' , Sapienza University , Rome , Italy
| | - Paolo Anagnostou
- f Department of Environmental Biology , University of Rome 'La Sapienza' , Rome , Italy.,g ISItA, Istituto Italiano di Antropologia , Rome , Italy
| | - Gianmarco Ferri
- h Department of Diagnostic and Clinical Medicine and Public Health , University of Modena and Reggio Emilia , Modena , Italy
| | - Antonino Vazzana
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Delpino
- i Superintendence of Archaeological Heritage of Marche Region , Ancona , Italy
| | - Giorgio Gruppioni
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Donata Luiselli
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Elisabetta Cilli
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
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Taron UH, Lell M, Barlow A, Paijmans JLA. Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool. Genes (Basel) 2018. [PMID: 29533977 PMCID: PMC5867878 DOI: 10.3390/genes9030157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present 'TAPAS', (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.
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Affiliation(s)
- Ulrike H Taron
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Moritz Lell
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
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Díez-del-Molino D, Sánchez-Barreiro F, Barnes I, Gilbert MTP, Dalén L. Quantifying Temporal Genomic Erosion in Endangered Species. Trends Ecol Evol 2018; 33:176-185. [DOI: 10.1016/j.tree.2017.12.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022]
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Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nat Ecol Evol 2018; 2:520-528. [PMID: 29335577 DOI: 10.1038/s41559-017-0446-6] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/07/2017] [Indexed: 11/08/2022]
Abstract
Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Through the introduction of a new metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked, based on historical and archaeological evidence, to the 1545-1550 CE epidemic that affected large parts of Mexico. Locally, this epidemic was known as 'cocoliztli', the pathogenic cause of which has been debated for more than a century. Here, we present genome-wide data from ten individuals for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.
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A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica. Nat Commun 2017; 8:15951. [PMID: 28654082 PMCID: PMC5490259 DOI: 10.1038/ncomms15951] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/12/2017] [Indexed: 11/09/2022] Open
Abstract
The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of ∼66 Ma (95% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.
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Didier G, Fau M, Laurin M. Likelihood of Tree Topologies with Fossils and Diversification Rate Estimation. Syst Biol 2017; 66:964-987. [DOI: 10.1093/sysbio/syx045] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 04/05/2017] [Indexed: 11/15/2022] Open
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Tissue Microarray Analysis Applied to Bone Diagenesis. Sci Rep 2017; 7:39987. [PMID: 28051148 PMCID: PMC5209720 DOI: 10.1038/srep39987] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 11/29/2016] [Indexed: 11/08/2022] Open
Abstract
Taphonomic processes affecting bone post mortem are important in forensic, archaeological and palaeontological investigations. In this study, the application of tissue microarray (TMA) analysis to a sample of femoral bone specimens from 20 exhumed individuals of known period of burial and age at death is described. TMA allows multiplexing of subsamples, permitting standardized comparative analysis of adjacent sections in 3-D and of representative cross-sections of a large number of specimens. Standard hematoxylin and eosin, periodic acid-Schiff and silver methenamine, and picrosirius red staining, and CD31 and CD34 immunohistochemistry were applied to TMA sections. Osteocyte and osteocyte lacuna counts, percent bone matrix loss, and fungal spheroid element counts could be measured and collagen fibre bundles observed in all specimens. Decalcification with 7% nitric acid proceeded more rapidly than with 0.5 M EDTA and may offer better preservation of histological and cellular structure. No endothelial cells could be detected using CD31 and CD34 immunohistochemistry. Correlation between osteocytes per lacuna and age at death may reflect reported age-related responses to microdamage. Methodological limitations and caveats, and results of the TMA analysis of post mortem diagenesis in bone are discussed, and implications for DNA survival and recovery considered.
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Affiliation(s)
- Douglas J. Richmond
- Section for Evolutionary Genomics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
| | - Mikkel‐Holger S. Sinding
- Section for Evolutionary Genomics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
- Natural History Museum University of Oslo P.O. Box 1172 Blindern NO‐0318 Oslo Norway
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics 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 Perth WA 6102 Australia
- NTNU University Museum NO‐7491 Trondheim Norway
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Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies. FEMS Microbiol Ecol 2016; 92:fiw182. [PMID: 27559027 DOI: 10.1093/femsec/fiw182] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2016] [Indexed: 11/15/2022] Open
Abstract
Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification.
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Affiliation(s)
- Tasha M Santiago-Rodriguez
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Gino Fornaciari
- Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa 56126, Italy Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy
| | - Stefania Luciani
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Scot E Dowd
- Molecular Research LP (MR DNA), Shallowater, Texas 79363, USA
| | - Gary A Toranzos
- Department of Biology, University of Puerto Rico, Julio Garcia Diaz Building, San Juan 00931, Puerto Rico
| | - Isolina Marota
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Raul J Cano
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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Abstract
ABSTRACT
This chapter aims to provide some key points for researchers interested in the study of ancient gastrointestinal parasites. These few pages are dedicated to my colleague and friend, Prof. Adauto Araújo (1951-2015), who participated in the writing of this chapter. His huge efforts in paleoparasitology contributed to the development and promotion of the discipline during more than 30 years.
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Shapiro B. Pathways to de‐extinction: how close can we get to resurrection of an extinct species? Funct Ecol 2016. [DOI: 10.1111/1365-2435.12705] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Beth Shapiro
- Department of Ecology and Evolutionary Biology and UCSC Genomics Institute University of California Santa Cruz 1156 High Street Santa Cruz CA95064 USA
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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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vonHoldt BM, Cahill JA, Fan Z, Gronau I, Robinson J, Pollinger JP, Shapiro B, Wall J, Wayne RK. Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. SCIENCE ADVANCES 2016; 2:e1501714. [PMID: 29713682 PMCID: PMC5919777 DOI: 10.1126/sciadv.1501714] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/28/2016] [Indexed: 05/22/2023]
Abstract
Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - James A. Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center, Herzliya 46150, Israel
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095–1606, USA
| | - John P. Pollinger
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095–1606, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jeff Wall
- Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095–1606, USA
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