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Marshall C, Parson W. Interpreting NUMTs in forensic genetics: Seeing the forest for the trees. Forensic Sci Int Genet 2021; 53:102497. [PMID: 33740708 DOI: 10.1016/j.fsigen.2021.102497] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/29/2023]
Abstract
Nuclear mitochondrial DNA (mtDNA) segments (NUMTs) were discovered shortly after sequencing the first human mitochondrial genome. They have earlier been considered to represent archaic elements of ancient insertion events, but modern sequencing technologies and growing databases of mtDNA and NUMT sequences confirm that they are abundant and some of them phylogenetically young. Here, we build upon mtDNA/NUMT review articles published in the mid 2010 s and focus on the distinction of NUMTs and other artefacts that can be observed in aligned sequence reads, such as mixtures (contamination), point heteroplasmy, sequencing error and cytosine deamination. We show practical examples of the effect of the mtDNA enrichment method on the representation of NUMTs in the mapped sequence data and discuss methods to bioinformatically filter NUMTs from mtDNA reads.
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Affiliation(s)
- Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA; SNA International, Contractor Supporting the AFMES-AFDIL, Alexandria, VA 22314, USA; Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Walther Parson
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA; Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
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Holland CA, McElhoe JA, Gaston-Sanchez S, Holland MM. Damage patterns observed in mtDNA control region MPS data for a range of template concentrations and when using different amplification approaches. Int J Legal Med 2020; 135:91-106. [PMID: 32940843 DOI: 10.1007/s00414-020-02410-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/21/2020] [Indexed: 12/15/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows practitioners the ability to fully resolve heteroplasmic sites. In forensic DNA analysis, identifying heteroplasmy (a naturally occurring mixture of two mtDNA profiles) can provide additional mtDNA profile information which can lead to an increase in the discrimination potential of an mtDNA match between an evidentiary sample and reference source. Forensic samples such as hair and skeletal remains, especially older, more compromised samples, can often exhibit DNA damage. Because both damage and heteroplasmy can manifest as a mixture of two nucleotides, it is important to differentiate between the two conditions when interpreting mtDNA MPS data. In this study, DNA damage was applied under controlled conditions to samples containing a range of template concentrations, including some with identified heteroplasmy. Damage was applied via storage in water at room temperature on samples diluted before or after storage to mimic low template scenarios. Damage was assessed with respect to the following areas: mtDNA quantification and degradation ratios, MPS read depth, MPS profile results, overall damage rates, and the interpretation of heteroplasmy. Datasets were generated to assess and compare two different amplification and library preparation strategies: the Promega PowerSeq™ CRM Nested System kit and a 1.16 kb target amplicon of the entire mtDNA control region followed by a Nextera® XT library preparation. The results of this study provide an evaluation of the Promega 10-plex MPS procedure as an improved process to mitigate the impact of mtDNA damage on low template samples. Some of the negative effects of damage observed in this study were a decrease in mtDNA yield by 20-30% and lower quality MPS sequencing results. These effects were observed more frequently when samples were diluted prior to inducing damage, illustrating that low template samples are more susceptible to damage. The findings of this study will assist forensic laboratories in differentiating between damage and heteroplasmy, which is essential when developing robust mtDNA MPS interpretation guidelines such as setting appropriate reporting thresholds.
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Affiliation(s)
- Charity A Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA
| | - Jennifer A McElhoe
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA
| | - Sidney Gaston-Sanchez
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA.,Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, USA
| | - Mitchell M Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA.
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Koczur LM, Williford D, DeYoung RW, Ballard BM. Bringing back the dead: Genetic data from avian carcasses. WILDLIFE SOC B 2017. [DOI: 10.1002/wsb.823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lianne M. Koczur
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Bart M. Ballard
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
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Masuyama K, Shojo H, Nakanishi H, Inokuchi S, Adachi N. Sex Determination from Fragmented and Degenerated DNA by Amplified Product-Length Polymorphism Bidirectional SNP Analysis of Amelogenin and SRY Genes. PLoS One 2017; 12:e0169348. [PMID: 28052096 PMCID: PMC5214517 DOI: 10.1371/journal.pone.0169348] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 12/15/2016] [Indexed: 11/23/2022] Open
Abstract
Sex determination is important in archeology and anthropology for the study of past societies, cultures, and human activities. Sex determination is also one of the most important components of individual identification in criminal investigations. We developed a new method of sex determination by detecting a single-nucleotide polymorphism in the amelogenin gene using amplified product-length polymorphisms in combination with sex-determining region Y analysis. We particularly focused on the most common types of postmortem DNA damage in ancient and forensic samples: fragmentation and nucleotide modification resulting from deamination. Amplicon size was designed to be less than 60 bp to make the method more useful for analyzing degraded DNA samples. All DNA samples collected from eight Japanese individuals (four male, four female) were evaluated correctly using our method. The detection limit for accurate sex determination was determined to be 20 pg of DNA. We compared our new method with commercial short tandem repeat analysis kits using DNA samples artificially fragmented by ultraviolet irradiation. Our novel method was the most robust for highly fragmented DNA samples. To deal with allelic dropout resulting from deamination, we adopted “bidirectional analysis,” which analyzed samples from both sense and antisense strands. This new method was applied to 14 Jomon individuals (3500-year-old bone samples) whose sex had been identified morphologically. We could correctly identify the sex of 11 out of 14 individuals. These results show that our method is reliable for the sex determination of highly degenerated samples.
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Affiliation(s)
- Kotoka Masuyama
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Hideki Shojo
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
- * E-mail: (NA); (HS)
| | - Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Shota Inokuchi
- Department of Forensic Medicine, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
- * E-mail: (NA); (HS)
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[Real-time quantification to analyze historical Colombian samples detecting a short fragment of hypervariable region II of mitochondrial DNA]. BIOMEDICA 2016; 36:475-482. [PMID: 27869396 DOI: 10.7705/biomedica.v36i3.3098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 03/17/2016] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples. Materials and methods: The proposed method is based on the use of mini-primers for the specific amplification of short fragments of mitochondrial DNA. The subsequent purification of these amplified fragments allows a standard curve to be constructed with concentrations in accordance to the state of degradation of the samples. Results: The proposed method successfully detected DNA from ancient samples including bone remains and mummified tissue. DNA inhibitory substances were also detected. Conclusion: The proposed method represents a simpler and cost-effective way to detect low amounts of aDNA, and a tool to differentiate DNA-free samples from samples with inhibitory substances.
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Pauli JN, Moss WE, Manlick PJ, Fountain ED, Kirby R, Sultaire SM, Perrig PL, Mendoza JE, Pokallus JW, Heaton TH. Examining the uncertain origin and management role of martens on Prince of Wales Island, Alaska. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1257-1267. [PMID: 25855043 DOI: 10.1111/cobi.12491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/14/2015] [Indexed: 06/04/2023]
Abstract
Conservation biologists are generally united in efforts to curtail the spread of non-native species globally. However, the colonization history of a species is not always certain, and whether a species is considered non-native or native depends on the conservation benchmark. Such ambiguities have led to inconsistent management. Within the Tongass National Forest of Alaska, the status of American marten (Martes americana) on the largest, most biologically diverse and deforested island, Prince of Wales (POW), is unclear. Ten martens were released to POW in the early 1930s, and it was generally believed to be the founding event, although this has been questioned. The uncertainty surrounding when and how martens colonized POW complicates management, especially because martens were selected as a design species for the Tongass. To explore the history of martens of POW we reviewed other plausible routes of colonization; genetically and isotopically analyzed putative marten fossils deposited in the late Pleistocene and early Holocene to verify marten occupancy of POW; and used contemporary genetic data from martens on POW and the mainland in coalescent simulations to identify the probable source of the present-day marten population on POW. We found evidence for multiple routes of colonization by forest-associated mammals beginning in the Holocene, which were likely used by American martens to naturally colonize POW. Although we cannot rule out human-assisted movement of martens by Alaskan Natives or fur trappers, we suggest that martens be managed for persistence on POW. More generally, our findings illustrate the difficulty of labeling species as non-native or native, even when genetic and paleo-ecological data are available, and support the notion that community resilience or species invasiveness should be prioritized when making management decisions rather than more subjective and less certain conservation benchmarks.
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Affiliation(s)
- Jonathan N Pauli
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Wynne E Moss
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Philip J Manlick
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Emily D Fountain
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Rebecca Kirby
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Sean M Sultaire
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Paula L Perrig
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Jorge E Mendoza
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - John W Pokallus
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Timothy H Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, SD, 57069, U.S.A
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Dovgerd AP, Zharkov DO. Application of repair enzymes to improve the quality of degraded DNA templates for PCR amplification. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814030053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lacan M, Keyser C, Crubézy E, Ludes B. Ancestry of modern Europeans: contributions of ancient DNA. Cell Mol Life Sci 2013; 70:2473-87. [PMID: 23052219 PMCID: PMC11113793 DOI: 10.1007/s00018-012-1180-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 09/21/2012] [Accepted: 09/24/2012] [Indexed: 12/25/2022]
Abstract
Understanding the peopling history of Europe is crucial to comprehend the origins of modern populations. Of course, the analysis of current genetic data offers several explanations about human migration patterns which occurred on this continent, but it fails to explain precisely the impact of each demographic event. In this context, direct access to the DNA of ancient specimens allows the overcoming of recent demographic phenomena, which probably highly modified the constitution of the current European gene pool. In recent years, several DNA studies have been successfully conducted from ancient human remains thanks to the improvement of molecular techniques. They have brought new fundamental information on the peopling of Europe and allowed us to refine our understanding of European prehistory. In this review, we will detail all the ancient DNA studies performed to date on ancient European DNA from the Middle Paleolithic to the beginning of the protohistoric period.
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Affiliation(s)
- Marie Lacan
- Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde,Toulouse cedex 3, France.
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Melchior L, Lynnerup N, Siegismund HR, Kivisild T, Dissing J. Genetic diversity among ancient Nordic populations. PLoS One 2010; 5:e11898. [PMID: 20689597 PMCID: PMC2912848 DOI: 10.1371/journal.pone.0011898] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 07/09/2010] [Indexed: 11/19/2022] Open
Abstract
Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (∼2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.
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Affiliation(s)
- Linea Melchior
- Research Laboratory, Faculty of Health Sciences, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (LM); (JD)
| | - Niels Lynnerup
- Anthropological Laboratory, Faculty of Health Sciences, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hans R. Siegismund
- Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Toomas Kivisild
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Jørgen Dissing
- Research Laboratory, Faculty of Health Sciences, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (LM); (JD)
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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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