1
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Yuan J, Sun G, Xiao B, Hu J, Wang L, Taogetongqimuge, Bao L, Hou Y, Song S, Jiang S, Wu Y, Pan D, Liu Y, Westbury MV, Lai X, Sheng G. Ancient mitogenomes reveal a high maternal genetic diversity of Pleistocene woolly rhinoceros in Northern China. BMC Ecol Evol 2023; 23:56. [PMID: 37752413 PMCID: PMC10521388 DOI: 10.1186/s12862-023-02168-0] [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: 07/23/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Woolly rhinoceros (Coelodonta antiquitatis) is a typical indicator of cold-stage climate that was widely distributed in Northern Hemisphere during the Middle-Late Pleistocene. Although a plethora of fossils have been excavated from Northern China, their phylogenetic status, intraspecific diversity and phylogeographical structure are still vague. RESULTS In the present study, we generated four mitogenomes from Late Pleistocene woolly rhinoceros in Northern China and compared them with published data. Bayesian and network analyses indicate that the analyzed individuals contain at least four maternal haplogroups, and Chinese samples fall in three of them. One of our samples belongs to a previously unidentified early diverging clade (haplogroup D), which separated from other woolly rhinoceros around 0.57 Ma (95% CI: 0.76-0.41 Ma). The timing of this clade's origin coincides with the first occurrence of woolly rhinoceros, which are thought to have evolved in Europe. Our other three samples cluster in haplogroup C, previously only identified from one specimen from Wrangel Island (ND030) and initially considered to be an isolated clade. Herein, our findings suggest that ND030 is likely descended from a northward dispersal of the individuals carrying haplogroup C from Northern China. Additionally, Chinese woolly rhinoceros specimens exhibit higher nucleotide diversity than those from Siberia. CONCLUSION Our findings highlight Northern China as a possible refugium and a key evolution center of the Pleistocene woolly rhinoceros.
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Affiliation(s)
- Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China.
- Bioarchaeology Laboratory, Jilin University, Changchun, 130012, China.
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China.
| | - Guojiang Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Linying Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
- College of Earth and Environmental Science, Lanzhou University, Lanzhou, 730099, China
| | | | - Lei Bao
- Ordos Institute of Cultural Relics and Archaeology, Ordos, 017010, China
| | - Yamei Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Shiwen Song
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China
| | - Shan Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China
| | - Yong Wu
- The Third Geological and Mineral Exploration Institute of Gansu Bureau of Geology and Mineral Resources, Lanzhou, 730050, China
| | - Dong Pan
- Palaeontological Fossil Conservation Center, Qinggang County, Suihua, 151600, China
| | - Yang Liu
- School of Sociology & Anthropology, Sun Yat-sen University, Guangzhou, 510275, China
| | | | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China.
- School of Environmental Studies, China University of Geosciences, Wuhan, 430078, China.
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2
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Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Kalogeropoulos P, Eriksson E, Biryukova I, Sekar V, Ersmark E, Andersson B, Dalén L, Friedländer MR. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Res 2023; 33:1299-1316. [PMID: 37463752 PMCID: PMC10552650 DOI: 10.1101/gr.277663.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, 9006 Tromsø, Norway
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 223 62 Lund, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Panagiotis Kalogeropoulos
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Eli Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Inna Biryukova
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Vaishnovi Sekar
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Institute, 171 77 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden;
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Marc R Friedländer
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
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3
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Biskup E, Schejbel L, de Oliveira DNP, Høgdall E. Test of the FlashFREEZE unit in tissue samples freezing for biobanking purposes. Cell Tissue Bank 2023; 24:435-447. [PMID: 36309911 PMCID: PMC10209260 DOI: 10.1007/s10561-022-10045-1] [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: 06/29/2022] [Accepted: 10/12/2022] [Indexed: 11/28/2022]
Abstract
Availability of molecularly intact biospecimens is essential in genetic diagnostics to obtain credible results. Integrity of nucleic acids (particularly RNA) may be compromised at various steps of tissue handling, and affected by factors such as time to freeze, freezing technique and storing temperature. At the same time, freezing and storing of the biological material should be feasible and safe for the operator. Here, we compared quality of DNA and RNA from biospecimens derived from different organs (breast, colon, adrenal glands, testes, rectum and uterus) frozen either using dry ice-cooled isopentane or with FlashFREEZE unit, in order to verify if the latter is suitable for routine use in biobanking. Implementing FlashFREEZE device would enable us to limit the use of isopentane, which is potentially toxic and environmentally harmful, whilst facilitate standardization of sample freezing time. We considered factors such RNA and DNA yield and purity. Furthermore, RNA integrity and RNA/DNA performance in routine analyses, such as qPCR, next generation sequencing or microarray, were also assessed. Our results indicate that freezing of tissue samples either with FlashFREEZE unit or isopentane ensures biological material with comparable expression profiles and DNA mutation status, indicating that RNA and DNA of similar quality can be extracted from both. Therefore, our findings support the use of the FlashFREEZE device in routine use for biobanking purposes.
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Affiliation(s)
- Edyta Biskup
- Department of Pathology, Copenhagen University Hospital, Herlev, 2730 Denmark
| | - Lone Schejbel
- Department of Pathology, Copenhagen University Hospital, Herlev, 2730 Denmark
| | | | - Estrid Høgdall
- Department of Pathology, Copenhagen University Hospital, Herlev, 2730 Denmark
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4
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Schulze Johann K, Bauer H, Wiegand P, Pfeiffer H, Vennemann M. Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces. Int J Legal Med 2023; 137:33-45. [PMID: 36352329 PMCID: PMC9816238 DOI: 10.1007/s00414-022-02911-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
The aim of this study was to identify artificial single-nucleotide variants (SNVs) in degraded trace DNA samples. In a preliminary study, blood samples were stored for up to 120 days and whole-genome sequencing was performed using the Snakemake workflow dna-seq-gatk-variant-calling to identify positions that vary between the time point 0 sample and the aged samples. In a follow-up study on blood and saliva samples stored under humid and dry conditions, potential marker candidates for the estimation of the age of a blood stain (= time since deposition) were identified. Both studies show that a general decrease in the mean fragment size of the libraries over time was observed, presumably due to the formation of abasic sites during DNA degradation which are more susceptible to strand breaks by mechanical shearing of DNA. Unsurprisingly, an increase in the number of failed genotype calls (no coverage) was detected over time. Both studies indicated the presence of artificial SNVs with the majority of changes happening at guanine and cytosine positions. This confirms previous studies and can be explained by depurination through hydrolytic attacks which more likely deplete guanine while deamination leads to cytosine to thymine variants. Even complete genotype switches from homozygote 0/0 genotypes to the opposite 1/1 genotypes were observed. While positions with such drastic changes might provide suitable candidate markers for estimating short-term time since deposition (TsD), 11 markers were identified which show a slower gradual change of the relative abundance of the artificial variant in both blood and saliva samples, irrespective of storage conditions.
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Affiliation(s)
| | - Hannah Bauer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
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5
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Mullin VE, Stephen W, Arce AN, Nash W, Raine C, Notton DG, Whiffin A, Blagderov V, Gharbi K, Hogan J, Hunter T, Irish N, Jackson S, Judd S, Watkins C, Haerty W, Ollerton J, Brace S, Gill RJ, Barnes I. First large‐scale quantification study of DNA preservation in insects from natural history collections using genome‐wide sequencing. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victoria E. Mullin
- Department of Earth Sciences The Natural History Museum London UK
- Smurfit Institute of Genetics Trinity College Dublin Dublin Ireland
| | - William Stephen
- Department of Earth Sciences The Natural History Museum London UK
| | - Andres N. Arce
- Georgina Mace Centre for The Living Planet Department of Life Sciences, Silwood Park, Imperial College London Berks UK
- School of Engineering, Arts, Science & Technology University of Suffolk Ipswich UK
| | - Will Nash
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Calum Raine
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | | | | | | | - Karim Gharbi
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - James Hogan
- Oxford University Museum of Natural History Oxford UK
| | | | - Naomi Irish
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Simon Jackson
- Tullie House Museum and Art Gallery Trust Carlisle UK
- Ipswich Museum (Colchester and Ipswich Museums) Ipswich UK
| | | | - Chris Watkins
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Wilfried Haerty
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Jeff Ollerton
- Faculty of Arts, Science and Technology University of Northampton Northampton UK
| | - Selina Brace
- Department of Earth Sciences The Natural History Museum London UK
| | - Richard J. Gill
- Georgina Mace Centre for The Living Planet Department of Life Sciences, Silwood Park, Imperial College London Berks UK
| | - Ian Barnes
- Department of Earth Sciences The Natural History Museum London UK
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6
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Davidović S, Marinković S, Kukobat M, Mihajlović M, Tanasić V, Hribšek I, Tanasković M, Stamenković-Radak M. Genetic Diversity Analysis of Mitochondrial Cytb Gene, Phylogeny and Phylogeography of Protected Griffon Vulture (Gyps fulvus) from Serbia. Life (Basel) 2022; 12:life12020164. [PMID: 35207453 PMCID: PMC8880743 DOI: 10.3390/life12020164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Once a widespread and common species across the region of southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia with 290 couples represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region’s reintroduction or recolonization programs. To estimate the level of genetic diversity, the mitochondrial Cytb gene from 58 unrelated birds sampled during the marking in the nests was sequenced and compared to the homologous Griffon vulture sequences available in publicly accessible online databases. Phylogeographic analysis based on Cytb sequences showed that the most frequent haplotype is found in all Griffon vulture populations and that each population possesses private haplotypes. Our data suggest that the Griffon vulture population from Serbia should be used as a source population for restocking and reintroduction programs in the region. The observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds from remote populations should be avoided and that birds from indigenous or neighboring populations, if available, should be used instead.
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Affiliation(s)
- Slobodan Davidović
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (M.T.); (M.S.-R.)
- Correspondence:
| | - Saša Marinković
- Department of Ecology, Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia;
| | - Mila Kukobat
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia;
| | - Milica Mihajlović
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.M.); (V.T.)
| | - Vanja Tanasić
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.M.); (V.T.)
| | - Irena Hribšek
- Birds of Prey Protection Foundation, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia;
| | - Marija Tanasković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (M.T.); (M.S.-R.)
| | - Marina Stamenković-Radak
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (M.T.); (M.S.-R.)
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia;
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7
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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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8
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D'Ercole J, Prosser SWJ, Hebert PDN. A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)-patterns of nucleotide misincorporation. PeerJ 2021; 9:e10420. [PMID: 33520432 PMCID: PMC7811786 DOI: 10.7717/peerj.10420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 11/02/2020] [Indexed: 12/28/2022] Open
Abstract
Natural history collections are a valuable resource for molecular taxonomic studies and for examining patterns of evolutionary diversification, particularly in the case of rare or extinct species. However, the recovery of sequence information is often complicated by DNA degradation. This article describes use of the Sequel platform (Pacific Biosciences) to recover the 658 bp barcode region of the mitochondrial cytochrome c oxidase I (COI) gene from 380 butterflies with an average age of 50 years. Nested multiplex PCR was employed for library preparation to facilitate sequence recovery from extracts with low concentrations of highly degraded DNA. By employing circular consensus sequencing (CCS) of short amplicons (circa 150 bp), full-length barcodes could be assembled without a reference sequence, an important advance from earlier protocols which required reference sequences to guide contig assembly. The Sequel protocol recovered COI sequences (499 bp on average) from 318 of 380 specimens (84%), much higher than for Sanger sequencing (26%). Because each read derives from a single molecule, it was also possible to quantify the incidence of substitutions arising from DNA damage. In agreement with past work on sequence changes induced by DNA degradation, the transition C/G → T/A was the most prevalent category of change, but its rate of occurrence (4.58E−4) was so low that it did not impede the recovery of reliable sequences. Because the current protocol recovers COI sequence from most museum specimens, and because sequence fidelity is unaffected by nucleotide misincorporations, large-scale sequence characterization of museum specimens is feasible.
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Affiliation(s)
- Jacopo D'Ercole
- Centre for Biodiversity Genomics, Guelph, ON, Canada.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, Guelph, ON, Canada.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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9
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Agostini V, Bailo P, Chiti E, Linarello P, Gentile G, Primignani P, Giriodi M, Piccinini A. Ocular swabs on exhumed bodies: An alternative to the collection of “classical” tissue samples in forensic genetics. Forensic Sci Int Genet 2020; 44:102206. [DOI: 10.1016/j.fsigen.2019.102206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 10/16/2019] [Accepted: 11/15/2019] [Indexed: 10/25/2022]
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10
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Billerman SM, Walsh J. Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods, challenges, applications, and future directions. Mol Ecol Resour 2019; 19:1115-1130. [PMID: 31336408 DOI: 10.1111/1755-0998.13066] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 11/30/2022]
Abstract
Museum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high-throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections.
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Affiliation(s)
- Shawn M Billerman
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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11
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Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases. Cells 2019; 8:cells8050433. [PMID: 31075917 PMCID: PMC6562384 DOI: 10.3390/cells8050433] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/17/2019] [Accepted: 05/07/2019] [Indexed: 11/28/2022] Open
Abstract
Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases—and profiling, in certain conditions—especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven’s grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.
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12
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Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol 2018; 120:248-258. [DOI: 10.1016/j.ympev.2017.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
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Di Donato A, Filippone E, Ercolano MR, Frusciante L. Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops. FRONTIERS IN PLANT SCIENCE 2018; 9:441. [PMID: 29719544 PMCID: PMC5914272 DOI: 10.3389/fpls.2018.00441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/21/2018] [Indexed: 05/08/2023]
Abstract
The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture.
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14
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Pérez-Martínez C, Pérez-Cárceles MD, Legaz I, Prieto-Bonete G, Luna A. Quantification of nitrogenous bases, DNA and Collagen type I for the estimation of the postmortem interval in bone remains. Forensic Sci Int 2017; 281:106-112. [PMID: 29125988 DOI: 10.1016/j.forsciint.2017.10.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 10/02/2017] [Accepted: 10/29/2017] [Indexed: 11/28/2022]
Abstract
Estimating the postmortem interval (PMI) is an important goal in forensic medicine and continues to be one of the most difficult tasks of the forensic investigator. Few accurate methods exist to determine the time since death of skeletonized human remains due to the great number of intrinsic and external factors that may alter the normal course of postmortem change. The purpose of this research was to assess the usefulness of various biochemical parameters, such as nitrogenous bases (adenine, guanine, purines, cytosine, thymine, pyrimidines, hypoxanthine and xanthine), DNA and Collagen Type I peptides to estimate PMI. These parameters were analysed in cortical bone for the establishment of data in a total of 80 long bones of 80 corpses (50 males, 30 females) with a mean age of 68.31 years (S.D.=18.021, range=20-97). The bones were removed from the cement niches of a cemetery in Murcia (south-eastern Spain), where they had lain for between 5 and 47 years (mean time 23.83 years, S.D.=10.85). Our results show a significant decrease in adenine (p=0.0004), guanine (p=0.0001), purines (p=0.0001), cytosine (p=0.0001), thymine (p=0.0226), pyrimidines (p=0.0002) and the number of peptides of Collagen type I (p=0.0053) in those with a PMI≥20 years. In a curvilinear regression analysis the results show that 30.6% of the variable PMI could be explained by guanine concentration, in bones with a PMI<20 years, while in cases of a PMI≥20 years, the variable that best explained membership of this group was adenine (38.0%). In the discriminant analysis applied to the all the variables as a function of PMI when two groups were established, 86.7% of the cases were correctly classified. These results show that the quantification of Collagen type I proteins and nitrogenous bases could be used as a complementary tool, together with other analyses, in the estimation of PMI.
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Affiliation(s)
| | | | - Isabel Legaz
- Department of Legal and Forensic Medicine, University of Murcia, Spain
| | | | - Aurelio Luna
- Department of Legal and Forensic Medicine, University of Murcia, Spain
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15
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Liu YH, Wang L, Xu T, Guo X, Li Y, Yin TT, Yang HC, Hu Y, Adeola AC, Sanke OJ, Otecko NO, Wang M, Ma Y, Charles OS, Sinding MHS, Gopalakrishnan S, Alfredo Samaniego J, Hansen AJ, Fernandes C, Gaubert P, Budd J, Dawuda PM, Knispel Rueness E, Jiang L, Zhai W, Gilbert MTP, Peng MS, Qi X, Wang GD, Zhang YP. Whole-Genome Sequencing of African Dogs Provides Insights into Adaptations against Tropical Parasites. Mol Biol Evol 2017; 35:287-298. [DOI: 10.1093/molbev/msx258] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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16
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Zaucha J, Heddle JG. Resurrecting the Dead (Molecules). Comput Struct Biotechnol J 2017; 15:351-358. [PMID: 28652896 PMCID: PMC5472138 DOI: 10.1016/j.csbj.2017.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/11/2017] [Accepted: 05/21/2017] [Indexed: 12/15/2022] Open
Abstract
Biological molecules, like organisms themselves, are subject to genetic drift and may even become "extinct". Molecules that are no longer extant in living systems are of high interest for several reasons including insight into how existing life forms evolved and the possibility that they may have new and useful properties no longer available in currently functioning molecules. Predicting the sequence/structure of such molecules and synthesizing them so that their properties can be tested is the basis of "molecular resurrection" and may lead not only to a deeper understanding of evolution, but also to the production of artificial proteins with novel properties and even to insight into how life itself began.
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Affiliation(s)
- Jan Zaucha
- Departament of Computer Science, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Jonathan G. Heddle
- Bionanoscience and Biochemistry Laboratory, Jagiellonian University, Malopolska Centre of Biotechnology, Gronstajowa 7A, 30-387 Kraków, Poland
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17
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Pérez-Zamorano B, Vallebueno-Estrada M, Martínez González J, García Cook A, Montiel R, Vielle-Calzada JP, Delaye L. Organellar Genomes from a ∼5,000-Year-Old Archaeological Maize Sample Are Closely Related to NB Genotype. Genome Biol Evol 2017; 9:904-915. [PMID: 28338960 PMCID: PMC5387994 DOI: 10.1093/gbe/evx048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
The story of how preColumbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here, we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, México. Accelerator mass spectrometry dated the maize sample to be 5,040–5,300 years before present (95% probability). Phylogenetic analysis of the mitochondrial genome shows that the archaeological sample branches basal to the other Zea mays genomes, as expected. However, this analysis also indicates that fertile genotype NB is closely related to the archaeological maize sample and evolved before cytoplasmic male sterility genotypes (CMS-S, CMS-T, and CMS-C), thus contradicting previous phylogenetic analysis of mitochondrial genomes from maize. We show that maximum-likelihood infers a tree where CMS genotypes branch at the base of the tree when including sites that have a relative fast rate of evolution thus suggesting long-branch attraction. We also show that Bayesian analysis infer a topology where NB and the archaeological maize sample are at the base of the tree even when including faster sites. We therefore suggest that previous trees suffered from long-branch attraction. We also show that the phylogenetic analysis of the ancient chloroplast is congruent with genotype NB to be more closely related to the archaeological maize sample. As shown here, the inclusion of ancient genomes on phylogenetic trees greatly improves our understanding of the domestication process of maize, one of the most important crops worldwide.
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Affiliation(s)
| | - Miguel Vallebueno-Estrada
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Guanajuato, México
| | | | - Angel García Cook
- Instituto Nacional de Antropología e Historia, Ciudad de México, CDMX, México
| | - Rafael Montiel
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Guanajuato, México
| | - Jean-Philippe Vielle-Calzada
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Guanajuato, México
| | - Luis Delaye
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Guanajuato, México
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18
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Anco C, Kolokotronis SO, Henschel P, Cunningham SW, Amato G, Hekkala E. Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:455-473. [PMID: 28423965 DOI: 10.1080/24701394.2017.1307973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Once found throughout Africa and Eurasia, the leopard (Panthera pardus) was recently uplisted from Near Threatened to Vulnerable by the International Union for the Conservation of Nature (IUCN). Historically, more than 50% of the leopard's global range occurred in continental Africa, yet sampling from this part of the species' distribution is only sparsely represented in prior studies examining patterns of genetic variation at the continental or global level. Broad sampling to determine baseline patterns of genetic variation throughout the leopard's historical distribution is important, as these measures are currently used by the IUCN to direct conservation priorities and management plans. By including data from 182 historical museum specimens, faecal samples from ongoing field surveys, and published sequences representing sub-Saharan Africa, we identify previously unrecognized genetic diversity in African leopards. Our mtDNA data indicates high levels of divergence among regional populations and strongly differentiated lineages in West Africa on par with recent studies of other large vertebrates. We provide a reference benchmark of genetic diversity in African leopards against which future monitoring can be compared. These findings emphasize the utility of historical museum collections in understanding the processes that shape present biodiversity. Additionally, we suggest future research to clarify African leopard taxonomy and to differentiate between delineated units requiring monitoring or conservation action.
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Affiliation(s)
- Corey Anco
- a Department of Biological Sciences , Fordham University , Bronx , USA.,b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
| | - Sergios-Orestis Kolokotronis
- b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA.,c Department of Epidemiology and Biostatistics, School of Public Health , SUNY Downstate Medical Center , Brooklyn , USA
| | | | - Seth W Cunningham
- a Department of Biological Sciences , Fordham University , Bronx , USA
| | - George Amato
- b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
| | - Evon Hekkala
- a Department of Biological Sciences , Fordham University , Bronx , USA.,b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
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19
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GUARINO FM, BUCCELLI C, GRAZIANO V, LA PORTA P, MEZZASALMA M, ODIERNA G, PATERNOSTER M, PETRONE P. Recovery and amplification of ancient DNA from Herculaneum victims killed by the 79 AD Vesuvius hot surges. Turk J Biol 2017. [DOI: 10.3906/biy-1702-48] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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20
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Simón M, Montiel R, Smerling A, Solórzano E, Díaz N, Álvarez-Sandoval BA, Jiménez-Marín AR, Malgosa A. Molecular analysis of ancient caries. Proc Biol Sci 2015; 281:rspb.2014.0586. [PMID: 25056622 DOI: 10.1098/rspb.2014.0586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. Modern samples show four polymorphic sites that have not been found in the ancient samples studied so far. The nucleotide and haplotype diversity of this region have increased over time, which could be reflecting the footprint of a population expansion. While this segment has apparently evolved according to neutral evolution, we have been able to detect one site that is under positive selection pressure both in present and past populations. This study is a first step to study the evolution of this microorganism, analysed using direct evidence obtained from ancient remains.
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Affiliation(s)
- Marc Simón
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Rafael Montiel
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato - León, Irapuato, Guanajuato, Mexico
| | - Andrea Smerling
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Eduvigis Solórzano
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Nancy Díaz
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Brenda A Álvarez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato - León, Irapuato, Guanajuato, Mexico
| | - Andrea R Jiménez-Marín
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato - León, Irapuato, Guanajuato, Mexico
| | - Assumpció Malgosa
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
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21
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Mikić AM. The First Attested Extraction of Ancient DNA in Legumes (Fabaceae). FRONTIERS IN PLANT SCIENCE 2015; 6:1006. [PMID: 26635833 PMCID: PMC4646974 DOI: 10.3389/fpls.2015.01006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/30/2015] [Indexed: 06/05/2023]
Abstract
Ancient DNA (aDNA) is any DNA extracted from ancient specimens, important for diverse evolutionary researches. The major obstacles in aDNA studies are mutations, contamination and fragmentation. Its studies may be crucial for crop history if integrated with human aDNA research and historical linguistics, both general and relating to agriculture. Legumes (Fabaceae) are one of the richest end economically most important plant families, not only from Neolithic onwards, since they were used as food by Neanderthals and Paleolithic modern man. The idea of extracting and analyzing legume aDNA was considered beneficial for both basic science and applied research, with an emphasis on genetic resources and plant breeding. The first reported successful and attested extraction of the legume aDNA was done from the sample of charred seeds of pea (Pisum sativum) and bitter vetch (Vicia ervilia) from Hissar, southeast Serbia, dated to 1,350-1,000 Before Christ. A modified version of cetyltrimethylammonium bromide (CTAB) method and the commercial kit for DNA extraction QIAGEN DNAesy yielded several ng μl(-1) of aDNA of both species and, after the whole genome amplification and with a fragment of nuclear ribosomal DNA gene 26S rDNA, resulted in the detection of the aDNA among the PCR products. A comparative analysis of four informative chloroplast DNA regions (trnSG, trnK, matK, and rbcL) among the modern wild and cultivated pea taxa demonstrated not only that the extracted aDNA was genuine, on the basis of mutation rate, but also that the ancient Hissar pea was most likely an early domesticated crop, related to the modern wild pea of a neighboring region. It is anticipated that this premier extraction of legume aDNA may provide taxonomists with the answers to diverse questions, such as leaf development in legumes, as well as with novel data on the single steps in domesticating legume crops worldwide.
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22
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Parducci L, Väliranta M, Salonen JS, Ronkainen T, Matetovici I, Fontana SL, Eskola T, Sarala P, Suyama Y. Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130382. [PMID: 25487333 DOI: 10.1098/rstb.2013.0382] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, ØsterVoldgade 5-7, 1350 Copenhagen, Denmark
| | - Minna Väliranta
- Department of Environmental Sciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - J Sakari Salonen
- Department of Geosciences and Geography, University of Helsinki, PO Box 64, 00014 Helsinki, Finland
| | - Tiina Ronkainen
- Department of Environmental Sciences, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - Irina Matetovici
- Molecular Biology Centre, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babes-Bolyai-University ClujNapoca, 42 TreboniuLaurian Street, 400271 Cluj-Napoca, Romania
| | - Sonia L Fontana
- School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, Belfast BT7 1NN, UK
| | - Tiina Eskola
- Department of Geosciences, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Pertti Sarala
- Geological Survey of Finland, PO Box 77, 96101 Rovaniemi, Finland
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
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23
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Samaniego Castruita JA, Zepeda Mendoza ML, Barnett R, Wales N, Gilbert MTP. Odintifier--A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing. BMC Bioinformatics 2015. [PMID: 26216337 PMCID: PMC4517485 DOI: 10.1186/s12859-015-0682-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny. The extent of the occurrence of these organellar-derived inserted sequences (odins) is still unknown, but if not accounted for in genomic and phylogenetic studies, they can be a source of error. However, if correctly identified, these inserted sequences can be used for evolutionary and comparative genomic studies. Although such insertions can be detected using various laboratory and bioinformatic strategies, there is currently no straightforward way to apply them as a standard organellar genome assembly on next-generation sequencing data. Furthermore, most current methods for identification of such insertions are unsuitable for use on non-model organisms or ancient DNA datasets. Results We present a bioinformatic method that uses phasing algorithms to reconstruct both source and inserted organelle sequences. The method was tested in different shotgun and organellar-enriched DNA high-throughput sequencing (HTS) datasets from ancient and modern samples. Specifically, we used datasets from lions (Panthera leo ssp. and Panthera leo leo) to characterize insertions from mitochondrial origin, and from common grapevine (Vitis vinifera) and bugle (Ajuga reptans) to characterize insertions derived from plastid genomes. Comparison of the results against other available organelle genome assembly methods demonstrated that our new method provides an improvement in the sequence assembly. Conclusion Using datasets from a wide range of species and different levels of complexity we showed that our novel bioinformatic method based on phasing algorithms can be used to achieve the next two goals: i) reference-guided assembly of chloroplast/mitochondrial genomes from HTS data and ii) identification and simultaneous assembly of odins. This method represents the first application of haplotype phasing for automatic detection of odins and reference-based organellar genome assembly. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0682-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jose Alfredo Samaniego Castruita
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
| | - Marie Lisandra Zepeda Mendoza
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
| | - Ross Barnett
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
| | - Nathan Wales
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
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24
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Harkins KM, Buikstra JE, Campbell T, Bos KI, Johnson ED, Krause J, Stone AC. Screening ancient tuberculosis with qPCR: challenges and opportunities. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130622. [PMID: 25487341 PMCID: PMC4275897 DOI: 10.1098/rstb.2013.0622] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the Mycobacterium tuberculosis complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies.
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Affiliation(s)
- Kelly M Harkins
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Jane E Buikstra
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Tessa Campbell
- Department of Archaeology, University of Cape Town, Cape Town, South Africa
| | - Kirsten I Bos
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Eric D Johnson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
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25
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Besnard G, Christin PA, Malé PJG, Lhuillier E, Lauzeral C, Coissac E, Vorontsova MS. From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6711-21. [PMID: 25258360 DOI: 10.1093/jxb/eru395] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Collections of specimens held by natural history museums are invaluable material for biodiversity inventory and evolutionary studies, with specimens accumulated over 300 years readily available for sampling. Unfortunately, most museum specimens yield low-quality DNA. Recent advances in sequencing technologies, so called next-generation sequencing, are revolutionizing phylogenetic investigations at a deep level. Here, the Illumina technology (HiSeq) was used on herbarium specimens of Sartidia (subfamily Aristidoideae, Poaceae), a small African-Malagasy grass lineage (six species) characteristic of wooded savannas, which is the C3 sister group of Stipagrostis, an important C4 genus from Africa and SW Asia. Complete chloroplast and nuclear ribosomal sequences were assembled for two Sartidia species, one of which (S. perrieri) is only known from a single specimen collected in Madagascar 100 years ago. Partial sequences of a few single-copy genes encoding phosphoenolpyruvate carboxylases (ppc) and malic enzymes (nadpme) were also assembled. Based on these data, the phylogenetic position of Malagasy Sartidia in the subfamily Aristidoideae was investigated and the biogeographical history of this genus was analysed with full species sampling. The evolutionary history of two genes for C4 photosynthesis (ppc-aL1b and nadpme-IV) in the group was also investigated. The gene encoding the C4 phosphoenolpyruvate caroxylase of Stipagrostis is absent from S. dewinteri suggesting that it is not essential in C3 members of the group, which might have favoured its recruitment into a new metabolic pathway. Altogether, the inclusion of historical museum specimens in phylogenomic analyses of biodiversity opens new avenues for evolutionary studies.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France
| | | | - Pierre-Jean G Malé
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Emeline Lhuillier
- GeT-PlaGe, Campus INRA-Auzeville, F-31326 Castanet-Tolosan, France; INRA, UAR 1209 Département de Génétique Animale, INRA Auzeville, F-31326 Castanet-Tolosan, France
| | - Christine Lauzeral
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France
| | - Eric Coissac
- Laboratoire d'écologie Alpine (LECA), UMR5553, CNRS/Université Joseph Fourier-Grenoble I, Université de Savoie, F-38041 Grenoble, France
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26
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Zouganelis GD, Ogden R, Nahar N, Runfola V, Bonab M, Ardalan A, Radford D, Barnett R, Larson G, Hildred A, Jones M, Scarlett G. An old dog and new tricks: Genetic analysis of a Tudor dog recovered from the Mary Rose wreck. Forensic Sci Int 2014; 245:51-7. [DOI: 10.1016/j.forsciint.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/23/2014] [Accepted: 10/04/2014] [Indexed: 11/25/2022]
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Heintzman PD, Elias SA, Moore K, Paszkiewicz K, Barnes I. Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera). Mol Ecol Resour 2013; 14:606-15. [PMID: 24266987 DOI: 10.1111/1755-0998.12205] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 01/08/2023]
Abstract
DNA preserved in degraded beetle (Coleoptera) specimens, including those derived from dry-stored museum and ancient permafrost-preserved environments, could provide a valuable resource for researchers interested in species and population histories over timescales from decades to millenia. However, the potential of these samples as genetic resources is currently unassessed. Here, using Sanger and Illumina shotgun sequence data, we explored DNA preservation in specimens of the ground beetle Amara alpina, from both museum and ancient environments. Nearly all museum specimens had amplifiable DNA, with the maximum amplifiable fragment length decreasing with age. Amplification of DNA was only possible in 45% of ancient specimens. Preserved mitochondrial DNA fragments were significantly longer than those of nuclear DNA in both museum and ancient specimens. Metagenomic characterization of extracted DNA demonstrated that parasite-derived sequences, including Wolbachia and Spiroplasma, are recoverable from museum beetle specimens. Ancient DNA extracts contained beetle DNA in amounts comparable to museum specimens. Overall, our data demonstrate that there is great potential for both museum and ancient specimens of beetles in future genetic studies, and we see no reason why this would not be the case for other orders of insect.
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Affiliation(s)
- Peter D Heintzman
- School of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
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28
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Staats M, Erkens RHJ, van de Vossenberg B, Wieringa JJ, Kraaijeveld K, Stielow B, Geml J, Richardson JE, Bakker FT. Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens. PLoS One 2013; 8:e69189. [PMID: 23922691 PMCID: PMC3726723 DOI: 10.1371/journal.pone.0069189] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 06/03/2013] [Indexed: 12/03/2022] Open
Abstract
Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well.
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Affiliation(s)
- Martijn Staats
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands
| | - Roy H. J. Erkens
- Maastricht Science Program, Maastricht University, Maastricht, The Netherlands
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Bart van de Vossenberg
- Dutch National Plant Protection Organization, National Reference Centre, Wageningen, The Netherlands
| | - Jan J. Wieringa
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands
- Netherlands Centre for Biodiversity Naturalis (section NHN), Herbarium Vadense (WAG), Wageningen University, Wageningen, The Netherlands
| | - Ken Kraaijeveld
- Department of Human Genetics/Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Stielow
- Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre (CBS-KNAW), Utrecht, The Netherlands
| | - József Geml
- Naturalis Biodiversity Center, Section National Herbarium of the Netherlands, Leiden, The Netherlands
| | - James E. Richardson
- Royal Botanic Garden Edinburgh, Inverleith Row, Edinburgh, United Kingdom
- Laboratorio de Botánica y Sistemática, Universidad de Los Andes, Apartado Aéreo 4976, Bogotá, Colombia
| | - Freek T. Bakker
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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Abstract
Under favorable conditions DNA can survive for thousands of years in the remains of dead organisms. The DNA extracted from such remains is invariably degraded to a small average size by processes that at least partly involve depurination. It also contains large amounts of deaminated cytosine residues that are accumulated toward the ends of the molecules, as well as several other lesions that are less well characterized.
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Affiliation(s)
- Jesse Dabney
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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30
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Parducci L, Matetovici I, Fontana SL, Bennett KD, Suyama Y, Haile J, Kjaer KH, Larsen NK, Drouzas AD, Willerslev E. Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. Mol Ecol 2013; 22:3511-24. [PMID: 23587049 DOI: 10.1111/mec.12298] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/18/2013] [Accepted: 01/29/2013] [Indexed: 11/26/2022]
Abstract
Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
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31
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McCallum J, Hall S, Lissone I, Anderson J, Huynen L, Lambert DM. Highly informative ancient DNA 'snippets' for New Zealand moa. PLoS One 2013; 8:e50732. [PMID: 23341875 PMCID: PMC3547012 DOI: 10.1371/journal.pone.0050732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/24/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Analysis of ancient DNA has provided invaluable information on past ecologies, ancient populations, and extinct species. We used a short snippet of highly variable mitochondrial control region sequence from New Zealand's moa to characterise a large number of bones previously intractable to DNA analysis as well as bone fragments from swamps to gain information about the haplotype diversity and phylogeography that existed in five moa species. METHODOLOGY/PRINCIPAL FINDINGS By targeting such 'snippets', we show that moa populations differed substantially in geographic structure that is likely to be related to population mobility and history. We show that populations of Pachyornis geranoides, Dinornis novaezealandiae, and Dinornis robustus were highly structured and some appear to have occupied the same geographic location for hundreds of thousands of years. In contrast, populations of the moa Anomalopteryx didiformis and Euryapteryx curtus were widespread, with specific populations of the latter occupying both the North and South Islands of New Zealand. We further show that for a specific area, in this case a North Island swamp, complete haplotype diversity and even sex can be recovered from collections of small, often discarded, bone fragments. CONCLUSIONS/SIGNIFICANCE Short highly variable mitochondrial 'snippets' allow successful typing of environmentally damaged and fragmented skeletal material, and can provide useful information about ancient population diversity and structure without the need to sample valuable, whole bones often held by museums.
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Affiliation(s)
- Jonathan McCallum
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - Samantha Hall
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - Iman Lissone
- Institute of Natural Resources, Massey University, North Shore City, New Zealand
| | - Jennifer Anderson
- Institute of Natural Resources, Massey University, North Shore City, New Zealand
| | - Leon Huynen
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - David M. Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
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32
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Corthals A, Koller A, Martin DW, Rieger R, Chen EI, Bernaski M, Recagno G, Dávalos LM. Detecting the immune system response of a 500 year-old Inca mummy. PLoS One 2012; 7:e41244. [PMID: 22848450 PMCID: PMC3405130 DOI: 10.1371/journal.pone.0041244] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 06/22/2012] [Indexed: 11/19/2022] Open
Abstract
Disease detection in historical samples currently relies on DNA extraction and amplification, or immunoassays. These techniques only establish pathogen presence rather than active disease. We report the first use of shotgun proteomics to detect the protein expression profile of buccal swabs and cloth samples from two 500-year-old Andean mummies. The profile of one of the mummies is consistent with immune system response to severe pulmonary bacterial infection at the time of death. Presence of a probably pathogenic Mycobacterium sp. in one buccal swab was confirmed by DNA amplification, sequencing, and phylogenetic analyses. Our study provides positive evidence of active pathogenic infection in an ancient sample for the first time. The protocol introduced here is less susceptible to contamination than DNA-based or immunoassay-based studies. In scarce forensic samples, shotgun proteomics narrows the range of pathogens to detect using DNA assays, reducing cost. This analytical technique can be broadly applied for detecting infection in ancient samples to answer questions on the historical ecology of specific pathogens, as well as in medico-legal cases when active pathogenic infection is suspected.
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Affiliation(s)
- Angelique Corthals
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, New York, New York, United States of America.
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33
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Ho SYW. Phylogenetic analysis of ancient DNA using BEAST. Methods Mol Biol 2012; 840:229-41. [PMID: 22237538 DOI: 10.1007/978-1-61779-516-9_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Under exceptional circumstances, it is possible to obtain DNA sequences from samples that are up to hundreds of thousands of years old. These data provide an opportunity to look directly at past genetic diversity, to trace the evolutionary process through time, and to infer demographic and phylogeographic trends. Ancient DNA (aDNA) data sets have some degree of intrinsic temporal structure because the sequences have been obtained from samples of different ages. When analyzing these data sets, it is usually necessary to take the sampling times into account. A number of phylogenetic methods have been designed with this purpose in mind. Here I describe the steps involved in Bayesian phylogenetic analysis of aDNA data. I outline a procedure that can be used to co-estimate the genealogical relationships, mutation rate, evolutionary timescale, and demographic history of the study species in a single analytical framework. A number of modifications to the methodology can be made in order to deal with complicating factors such as postmortem damage, sequences from undated samples, and data sets with low information content.
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Affiliation(s)
- Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, 2006, NSW, Australia.
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34
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O'Rourke D, Enk J. Genetics, Geography, and Human Variation. Hum Biol 2012. [DOI: 10.1002/9781118108062.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Parducci L, Jorgensen T, Tollefsrud MM, Elverland E, Alm T, Fontana SL, Bennett KD, Haile J, Matetovici I, Suyama Y, Edwards ME, Andersen K, Rasmussen M, Boessenkool S, Coissac E, Brochmann C, Taberlet P, Houmark-Nielsen M, Larsen NK, Orlando L, Gilbert MTP, Kjaer KH, Alsos IG, Willerslev E. Glacial Survival of Boreal Trees in Northern Scandinavia. Science 2012; 335:1083-6. [DOI: 10.1126/science.1216043] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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36
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Kirsanow K, Burger J. Ancient human DNA. Ann Anat 2012; 194:121-32. [PMID: 22169595 DOI: 10.1016/j.aanat.2011.11.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 12/11/2022]
Abstract
The contribution of palaeogenetic data to the study of various aspects of hominin biology and evolution has been significant, and has the potential to increase substantially with the widespread implementation of next generation sequencing techniques. Here we discuss the present state-of-the-art of ancient human DNA analysis and the characteristics of hominin aDNA that make sequence validation particularly complex. A brief overview of the development of anthropological palaeogenetic analysis is given to illustrate the technical challenges motivating recent technological advancements.
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Affiliation(s)
- Karola Kirsanow
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Germany
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37
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Capillary electrophoresis of human mtDNA control region sequences from highly degraded samples using short mtDNA amplicons. Methods Mol Biol 2012; 830:283-99. [PMID: 22139668 DOI: 10.1007/978-1-61779-461-2_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The forensic applications of mtDNA sequencing center primarily on samples that are either highly degraded or contain little or no nuclear DNA, since the testing of these sample types is often unsuccessful with more widely used nuclear STR profiling assays. In these cases, sequence data from the noncoding mtDNA control region are targeted due to its high variability. However, the ease of authentic DNA recovery and the strategy used for recovery depend strictly on the quality of the sample. In this chapter, we will cover mitochondrial DNA sequencing procedures for short mtDNA amplicons which range in size from 100 to 350 bp. Generally speaking, amplicons of this size are required only for the most degraded specimens, and the protocols described here have been specifically developed for recalcitrant human skeletal remains encountered during the course of a large-scale missing persons' identification effort. DNA templates from these types of specimens tend to exhibit various forms of intrastrand damage that, in turn, manifest as artifacts in the sequence data. Because these artifacts are not generally observed among sequence data from pristine templates, we address the particular data idiosyncrasies that warrant additional scrutiny. Although this chapter will primarily highlight this particular application, the basic experimental parameters and data considerations should easily extend to other applications and/or sample types. The protocols described here have been deliberately designed to produce raw sequence electropherograms and final mtDNA profiles that adhere to the strictest forensic guidelines in terms of overall data quality.
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38
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Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Romero IG, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 2011; 334:94-8. [PMID: 21940856 PMCID: PMC3991479 DOI: 10.1126/science.1211177] [Citation(s) in RCA: 350] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
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Affiliation(s)
- Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
| | - Xiaosen Guo
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Wang
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kirk E. Lohmueller
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Line Skotte
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Stinus Lindgreen
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mait Metspalu
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
| | - Thibaut Jombart
- MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Toomas Kivisild
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Weiwei Zhai
- Beijing Institute of Genomics, Chinese Academy of Sciences, No. 7 Beitucheng West Road, Chaoyang District, Beijing 100029, China
| | - Anders Eriksson
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Silvana Tridico
- Ancient DNA Lab, School of Biological Sciences and Biotechnology, Murdoch University, Western Australia 6150, Australia
| | - Ene Metspalu
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
| | - Kasper Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - María C. Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - J. Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Undergraduate Program on Genomic Sciences, National Autonomous University of Mexico, Avenida Universidad s/n Chamilpa 62210, Cuernavaca, Morelos, Mexico
| | - Craig Muller
- Goldfields Land and Sea Council Aboriginal Corporation, 14 Throssell Street, Kalgoorlie, Western Australia 6430, Australia
| | - Joe Dortch
- Archaeology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Agata Wesolowska
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Monika Karmin
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
| | - Lucy A. Weinert
- MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Bo Wang
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Li
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Shuaishuai Tai
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Fei Xiao
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0374, Japan
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, 3000 Bern 9, Switzerland
| | - Aashish R. Jha
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - François-Xavier Ricaut
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Université de Toulouse (Paul Sabatier)–CNRS UMR 5288, 31073 Toulouse Cedex 3, France
| | - Peter de Knijff
- Department of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Andrea B Migliano
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
- Department of Anthropology, University College London, London WC1E 6BT, UK
| | | | - Karsten Kristiansen
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - David M. Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland 4111, Australia
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Peter Forster
- Murray Edwards College, University of Cambridge, Cambridge CB3 0DF, UK
- Institute for Forensic Genetics, D-48161 Münster, Germany
| | | | - Olaf Nehlich
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Bunce
- Ancient DNA Lab, School of Biological Sciences and Biotechnology, Murdoch University, Western Australia 6150, Australia
| | - Michael Richards
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ramneek Gupta
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anders Krogh
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Marta M. Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Francois Balloux
- MRC Centre for Outbreak, Analysis and Modeling, Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, London W2 1PG, UK
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Richard Villems
- Department of Evolutionary Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
- Estonian Academy of Sciences, 6 Kohtu Street, 10130 Tallinn, Estonia
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jun Wang
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, and Department of Biology, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen, Denmark
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JØRGENSEN TINA, HAILE JAMES, MÖLLER PER, ANDREEV ANDREI, BOESSENKOOL SANNE, RASMUSSEN MORTEN, KIENAST FRANK, COISSAC ERIC, TABERLET PIERRE, BROCHMANN CHRISTIAN, BIGELOW NANCYH, ANDERSEN KENNETH, ORLANDO LUDOVIC, GILBERT MTHOMASP, WILLERSLEV ESKE. A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability. Mol Ecol 2011; 21:1989-2003. [DOI: 10.1111/j.1365-294x.2011.05287.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I, Shapiro B, Hofreiter M, Al-Rasheid KAS, Gilbert MTP, Willerslev E. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res 2011; 21:1705-19. [PMID: 21803858 DOI: 10.1101/gr.122747.111] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing libraries of ancient DNA molecules, as required for second-generation sequencing, introduce biases into the data that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. We demonstrate that simple modifications to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by threefold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates, indicating the presence of 3'-sequence overhangs. Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third-generation sequencing approaches.
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Affiliation(s)
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, Copenhagen DK-1350, Denmark.
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Rowe KC, Singhal S, Macmanes MD, Ayroles JF, Morelli TL, Rubidge EM, Bi K, Moritz CC. Museum genomics: low-cost and high-accuracy genetic data from historical specimens. Mol Ecol Resour 2011; 11:1082-92. [PMID: 21791033 DOI: 10.1111/j.1755-0998.2011.03052.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome.
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Affiliation(s)
- Kevin C Rowe
- Sciences Department, Museum Victoria, GPO Box 666, Melbourne, Vic. 3001, Australia.
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Winters M, Barta JL, Monroe C, Kemp BM. To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples. PLoS One 2011; 6:e21247. [PMID: 21738625 PMCID: PMC3124491 DOI: 10.1371/journal.pone.0021247] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/24/2011] [Indexed: 01/06/2023] Open
Abstract
The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from "modern" DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be "gold standards" in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones.To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous.
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Affiliation(s)
- Misa Winters
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Jodi Lynn Barta
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
| | - Cara Monroe
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, University of California-Santa Barbara, Santa Barbara, California, United States of America
| | - Brian M. Kemp
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
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Ancient DNA from marine mammals: studying long-lived species over ecological and evolutionary timescales. Ann Anat 2011; 194:112-20. [PMID: 21652193 DOI: 10.1016/j.aanat.2011.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 04/14/2011] [Accepted: 04/15/2011] [Indexed: 11/21/2022]
Abstract
Marine mammals have long generation times and broad, difficult to sample distributions, which makes inferring evolutionary and demographic changes using field studies of extant populations challenging. However, molecular analyses from sub-fossil or historical materials of marine mammals such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) approaches provide an opportunity for investigating such changes over evolutionary and ecological timescales. Here, we review the application of aDNA techniques to the study of marine mammals. Most of the studies have focused on detecting changes in genetic diversity following periods of exploitation and environmental change. To date, these studies have shown that even small sample sizes can provide useful information on historical genetic diversity. Ancient DNA has also been used in investigations of changes in distribution and range of marine mammal species; we review these studies and discuss the limitations of such 'presence only' studies. Combining aDNA data with stable isotopes can provide further insights into changes in ecology and we review past studies and suggest future potential applications. We also discuss studies reconstructing inter- and intra-specific phylogenies from aDNA sequences and discuss how aDNA sequences could be used to estimate mutation rates. Finally, we highlight some of the problems of aDNA studies on marine mammals, such as obtaining sufficient sample sizes and calibrating for the marine reservoir effect when radiocarbon-dating such wide-ranging species.
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Fulton TL, Wagner SM, Fisher C, Shapiro B. Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons. Ann Anat 2011; 194:52-7. [PMID: 21482085 DOI: 10.1016/j.aanat.2011.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 02/16/2011] [Accepted: 02/22/2011] [Indexed: 11/18/2022]
Abstract
Passenger Pigeons (Ectopistes migratorius) were once the most abundant bird in North America, with flock sizes estimated in the billions. However, by the turn of the 20th century, this previously abundant species had been driven to extinction. Morphological analyses linked the Passenger Pigeon with the New World mourning doves of the genus Zenaida. However, mitochondrial analyses strongly support its placement within the group of typical pigeons and doves (New and Old World pigeons, cuckoo-doves, turtledoves). Here, the first nuclear DNA sequence obtained for this extinct species confirms the placement of the Passenger Pigeon as sister to the New World pigeons, Patagioenas. These findings have implications for the colonization of North America by pigeons and doves.
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Affiliation(s)
- Tara L Fulton
- Department of Biology, Pennsylvania State University, University Park, 16801, United States.
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Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG, Rambaut A. A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol 2010; 28:879-87. [PMID: 20889726 DOI: 10.1093/molbev/msq262] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Heterochronous data sets comprise molecular sequences sampled at different points in time. If the temporal range of the sampled sequences is large relative to the rate of mutation, the sampling times can directly calibrate evolutionary rates to calendar time. Here, we extend this calibration process to provide a full probabilistic method that utilizes temporal information in heterochronous data sets to estimate sampling times (leaf-ages) for sequenced for which this information unavailable. Our method is similar to relaxing the constraints of the molecular clock on specific lineages within a phylogenetic tree. Using a combination of synthetic and empirical data sets, we demonstrate that the method estimates leaf-ages reliably and accurately. Potential applications of our approach include incorporating samples of uncertain or radiocarbon-infinite age into ancient DNA analyses, evaluating the temporal signal in a particular sequence or data set, and exploring the reliability of sequence ages that are somehow contentious.
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Affiliation(s)
- Beth Shapiro
- Department of Biology, The Pennsylvania State University, PA, USA.
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Olivieri C, Ermini L, Rizzi E, Corti G, Bonnal R, Luciani S, Marota I, De Bellis G, Rollo F. Characterization of nucleotide misincorporation patterns in the iceman's mitochondrial DNA. PLoS One 2010; 5:e8629. [PMID: 20072618 PMCID: PMC2799664 DOI: 10.1371/journal.pone.0008629] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 12/15/2009] [Indexed: 12/03/2022] Open
Abstract
Background The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation (“miscoding lesions”) has been the object of extensive investigations. Methodology/Principal Findings To improve our knowledge regarding the nature and incidence of ancient DNA nucleotide misincorporations, we have utilized 6,859 (629,975 bp) mitochondrial (mt) DNA sequences obtained from the 5,350–5,100-years-old, freeze-desiccated human mummy popularly known as the Tyrolean Iceman or Ötzi. To generate the sequences, we have applied a mixed PCR/pyrosequencing procedure allowing one to obtain a particularly high sequence coverage. As a control, we have produced further 8,982 (805,155 bp) mtDNA sequences from a contemporary specimen using the same system and starting from the same template copy number of the ancient sample. From the analysis of the nucleotide misincorporation rate in ancient, modern, and putative contaminant sequences, we observed that the rate of misincorporation is significantly lower in modern and putative contaminant sequence datasets than in ancient sequences. In contrast, type 2 transitions represent the vast majority (85%) of the observed nucleotide misincorporations in ancient sequences. Conclusions/Significance This study provides a further contribution to the knowledge of nucleotide misincorporation patterns in DNA sequences obtained from freeze-preserved archeological specimens. In the Iceman system, ancient sequences can be clearly distinguished from contaminants on the basis of nucleotide misincorporation rates. This observation confirms a previous identification of the ancient mummy sequences made on a purely phylogenetical basis. The present investigation provides further indication that the majority of ancient DNA damage is reflected by type 2 (cytosine→thymine/guanine→adenine) transitions and that type 1 transitions are essentially PCR artifacts.
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Affiliation(s)
- Cristina Olivieri
- Laboratorio di Archeo-Antropologia molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Camerino, Italy
| | - Luca Ermini
- Institute of Cellular Medicine, University of Newcastle, Newcastle, United Kingdom
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Giorgio Corti
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Raoul Bonnal
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Stefania Luciani
- Laboratorio di Archeo-Antropologia molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Camerino, Italy
| | - Isolina Marota
- Laboratorio di Archeo-Antropologia molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Camerino, Italy
| | - Gianluca De Bellis
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Franco Rollo
- Laboratorio di Archeo-Antropologia molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Camerino, Italy
- * E-mail:
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Brotherton P, Sanchez JJ, Cooper A, Endicott P. Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX. Nucleic Acids Res 2009; 38:e7. [PMID: 19864251 PMCID: PMC2811011 DOI: 10.1093/nar/gkp897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples, the pervasive presence of highly PCR-amplifiable human DNA contaminants in the vast majority of samples can lead to the creation of recombinant hybrids and other non-authentic artefacts. The resulting PCR-generated sequences can then be difficult, if not impossible, to authenticate. In contrast, single primer extension (SPEX)-based approaches can genotype single nucleotide polymorphisms from ancient fragments of DNA as accurately as modern DNA. A single SPEX-type assay can amplify just one of the duplex DNA strands at target loci and generate a multi-fold depth-of-coverage, with non-authentic recombinant hybrids reduced to undetectable levels. Crucially, SPEX-type approaches can preferentially access genetic information from damaged and degraded endogenous ancient DNA templates over modern human DNA contaminants. The development of SPEX-type assays offers the potential for highly accurate, quantitative genotyping from ancient hominin samples.
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Affiliation(s)
- Paul Brotherton
- Australian Centre for Ancient DNA, Darling Building, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, Adelaide, South Australia 5005, Australia
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Grigorenko AP, Borinskaya SA, Yankovsky NK, Rogaev EI. Achievements and peculiarities in studies of ancient DNA and DNA from complicated forensic specimens. Acta Naturae 2009; 1:58-69. [PMID: 22649615 PMCID: PMC3347533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Studies of ancient DNA specimens started 25 years ago. At that time short mitochondrial DNA (mtDNA) fragments were the main targets in ancient DNA studies. The last three years were especially productive in the development of new methods of DNA purification and analysis. Complete mtDNA molecules and relatively large fragments of nuclear DNA are the targets of ancient DNA studies today. Ancient DNA studies allowed us to study organisms that went extinct more than ten thousand years ago, to reconstruct their phenotypic traits and evolution. Ancient DNA analyses can help understand the development of ancient human populations and how they migrated. A new evolutionary hypothesis and reconstruction of the biota history have been re-created from recent ancient DNA data. Some peculiarities and problems specific to the study of ancient DNA were revealed, such as very limited amounts of DNA available for study, the short length of the DNA fragments, breaks and chemical modifications in DNA molecules that result in "postmortem" mutations or complete blockage of DNA replication in vitro. The same specific features of DNA analysis were revealed for specimens from complicated forensic cases that result in the lack of experimental data or interpretation problems.. Here, we list the specific features of ancient DNA methodology and describe some achievements in fundamental and applied research of ancient DNA, including our own work in the field.
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Affiliation(s)
- A P Grigorenko
- Vavliov Institute of General Genetics, Russian Academy of Sciences
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Pinhasi R, von Cramon-Taubadel N. Craniometric data supports demic diffusion model for the spread of agriculture into Europe. PLoS One 2009; 4:e6747. [PMID: 19707595 PMCID: PMC2727056 DOI: 10.1371/journal.pone.0006747] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 07/20/2009] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The spread of agriculture into Europe and the ancestry of the first European farmers have been subjects of debate and controversy among geneticists, archaeologists, linguists and anthropologists. Debates have centred on the extent to which the transition was associated with the active migration of people as opposed to the diffusion of cultural practices. Recent studies have shown that patterns of human cranial shape variation can be employed as a reliable proxy for the neutral genetic relationships of human populations. METHODOLOGY/PRINCIPAL FINDINGS Here, we employ measurements of Mesolithic (hunter-gatherers) and Neolithic (farmers) crania from Southwest Asia and Europe to test several alternative population dispersal and hunter-farmer gene-flow models. We base our alternative hypothetical models on a null evolutionary model of isolation-by-geographic and temporal distance. Partial Mantel tests were used to assess the congruence between craniometric distance and each of the geographic model matrices, while controlling for temporal distance. Our results demonstrate that the craniometric data fit a model of continuous dispersal of people (and their genes) from Southwest Asia to Europe significantly better than a null model of cultural diffusion. CONCLUSIONS/SIGNIFICANCE Therefore, this study does not support the assertion that farming in Europe solely involved the adoption of technologies and ideas from Southwest Asia by indigenous Mesolithic hunter-gatherers. Moreover, the results highlight the utility of craniometric data for assessing patterns of past population dispersal and gene flow.
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Affiliation(s)
- Ron Pinhasi
- Department of Archaeology, University College Cork, Cork, Ireland.
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50
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Palmer SA, Moore JD, Clapham AJ, Rose P, Allaby RG. Archaeogenetic evidence of ancient nubian barley evolution from six to two-row indicates local adaptation. PLoS One 2009; 4:e6301. [PMID: 19623249 PMCID: PMC2707625 DOI: 10.1371/journal.pone.0006301] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 05/31/2009] [Indexed: 12/02/2022] Open
Abstract
Background Archaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years. Methodology and Findings We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure. Conclusions The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures.
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Affiliation(s)
- Sarah A. Palmer
- Warwick HRI, The University of Warwick, Wellesbourne, United Kingdom
| | - Jonathan D. Moore
- Warwick HRI, The University of Warwick, Wellesbourne, United Kingdom
| | - Alan J. Clapham
- Worcestershire Historic Environment & Archaeology Service, Woodbury, University of Worcester, Worcester, United Kingdom
| | - Pamela Rose
- The McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Robin G. Allaby
- Warwick HRI, The University of Warwick, Wellesbourne, United Kingdom
- * E-mail:
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