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Canale LC, McElhoe JA, Dimick G, DeHeer KM, Beckert J, Holland MM. Routine Mitogenome MPS Analysis from 1 and 5 mm of Rootless Human Hair. Genes (Basel) 2022; 13:2144. [PMID: 36421819 PMCID: PMC9690917 DOI: 10.3390/genes13112144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 08/16/2023] Open
Abstract
While hair shafts are a common evidence type in forensic cases, they are often excluded from DNA analysis due to their limited DNA quantity and quality. Mitochondrial (mt) DNA sequencing is the method of choice when working with rootless hair shaft fragments due to the elevated copy number of mtDNA and the highly degraded nature of nuclear (n) DNA. Using massively parallel sequencing (MPS) of the mitochondrial (mito) genome, we studied the impact of hair age (time since collection) and physical characteristics (hair diameter, medullary structure, and length of hair tested) on mtDNA recovery and MPS data quality. Hair shaft cuttings of 1 and 5 mm from hairs less than five years to 46 years of age from 60 donors were characterized microscopically. Mitogenome sequences were generated using the Promega PowerSeqTM Whole Mito System prototype kit and the Illumina MiSeq instrument. Reportable mitogenome sequences were obtained from all hairs up to 27 years of age (37 donors), with at least 98% of the mitogenome reported for more than 94% of the 74 hair samples analyzed; the minimum reported sequence was 88%. Furthermore, data from the 1 and 5 mm replicates gave concordant haplotypes. As expected, mtDNA yield decreased, mtDNA degradation increased, and mitogenome MPS data quality declined as the age of the hair increased. Hair diameter and medullary structure had minimal impact on yield and data quality. Our findings support that MPS is a robust and reliable method for routinely generating mitogenome sequences from 1 and 5 mm hair shaft samples up to 27 years of age, which is of interest to the forensic community, biological anthropologists, and medical geneticists.
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Affiliation(s)
- Lauren C. Canale
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Jennifer A. McElhoe
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Gloria Dimick
- Mitotyping Technologies, 2565 Park Center Blvd., Suite 200, State College, PA 16801, USA
| | | | - Jason Beckert
- Microtrace 790 Fletcher Drive, Suite 106, Elgin, IL 60123, USA
| | - Mitchell M. Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA
- Mitotyping Technologies, 2565 Park Center Blvd., Suite 200, State College, PA 16801, USA
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Medieval mummies of Zeleny Yar burial ground in the Arctic Zone of Western Siberia. PLoS One 2019; 14:e0210718. [PMID: 30682121 PMCID: PMC6347368 DOI: 10.1371/journal.pone.0210718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 01/01/2019] [Indexed: 11/19/2022] Open
Abstract
Notwithstanding the pioneering achievements of studies on arctic mummies in Siberia, there are insufficient data for any comprehensive understanding of the bio-cultural details of medieval people living in the region. In the Western Siberian arctic, permafrost mummies have been found in 12th to 13th century graves located in the Zeleny Yar (Z-Y) burial ground (66°19'4.54"С; 67°21'13.54"В). In 2013-2016, we were fortunate to be able to excavate that cemetery, locating a total of 47 burials, including cases of mummification. Some of these mummies had been wrapped in a multi-layered birch-bark cocoon. After removal of the cocoon, we conducted interdisciplinary studies using various scientific techniques. Gross anatomical examination and CT radiography showed that the internal organs were still well preserved inside the body cavities. Under light and electron microscopy, the histological findings were very similar to those for naturally mummified specimens discovered in other countries. Ancient DNA analysis showed that the Z-Y mummies' mtDNA haplotypes belong to five different haplogroups, namely U5a (#34), H3ao (#53), D (#67-1), U4b1b1 (#67-2), and D4j8 (#68), which distinguish them for their unique combination of Western- and Eastern Siberia-specific mtDNA haplogroups. Our interdisciplinary study obtained fundamental information that will form the foundation of successful future investigations on medieval mummies found in the Western Siberian arctic.
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Matsumura H, Shinoda KI, Shimanjuntak T, Oktaviana AA, Noerwidi S, Octavianus Sofian H, Prastiningtyas D, Nguyen LC, Kakuda T, Kanzawa-Kiriyama H, Adachi N, Hung HC, Fan X, Wu X, Willis A, Oxenham MF. Cranio-morphometric and aDNA corroboration of the Austronesian dispersal model in ancient Island Southeast Asia: Support from Gua Harimau, Indonesia. PLoS One 2018; 13:e0198689. [PMID: 29933384 PMCID: PMC6014653 DOI: 10.1371/journal.pone.0198689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/23/2018] [Indexed: 12/23/2022] Open
Abstract
The Austronesian language is spread from Madagascar in the west, Island Southeast Asia (ISEA) in the east (e.g. the Philippines and Indonesian archipelagoes) and throughout the Pacific, as far east as Easter Island. While it seems clear that the remote ancestors of Austronesian speakers originated in Southern China, and migrated to Taiwan with the development of rice farming by c. 5500 BP and onto the northern Philippines by c. 4000 BP (the Austronesian Dispersal Hypothesis or ADH), we know very little about the origins and emergence of Austronesian speakers in the Indonesian Archipelago. Using a combination of cranial morphometric and ancient mtDNA analyses on a new dataset from Gua Hairmau, that spans the pre-Neolithic through to Metal Period (5712—5591cal BP to 1864—1719 cal BP), we rigorously test the validity of the ADH in ISEA. A morphometric analysis of 23 adult male crania, using 16 of Martin’s standard measurements, was carried out with results compared to an East and Southeast Asian dataset of 30 sample populations spanning the Late Pleistocene through to Metal Period, in addition to 39 modern samples from East and Southeast Asia, near Oceania and Australia. Further, 20 samples were analyzed for ancient mtDNA and assigned to identified haplogroups. We demonstrate that the archaeological human remains from Gua Harimau cave, Sumatra, Indonesia provide clear evidence for at least two (cranio-morphometrically defined) and perhaps even three (in the context of the ancient mtDNA results) distinct populations from two separate time periods. The results of these analyses provide substantive support for the ADH model in explaining the origins and population history of ISEA peoples.
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Affiliation(s)
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tokyo, Japan
| | | | | | - Sofwan Noerwidi
- The National Research Centre of Archaeology, Jakarta, Indonesia
| | | | | | - Lan Cuong Nguyen
- Institute of Archaeology, Vietnam Academy of Social Science, Hanoi, Vietnam
| | - Tsuneo Kakuda
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | | | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | - Hsiao-Chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, Australia
| | | | - Xiujie Wu
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Anna Willis
- College of Arts, Society and Education, James Cook University, Townsville, Australia
| | - Marc F Oxenham
- School of Archeology and Anthropology, Australian National University, Canberra, Australia
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Norhalifah HK, Syaza FH, Chambers GK, Edinur HA. The genetic history of Peninsular Malaysia. Gene 2016; 586:129-35. [DOI: 10.1016/j.gene.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 03/17/2016] [Accepted: 04/05/2016] [Indexed: 12/27/2022]
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Hatin WI, Nur-Shafawati AR, Etemad A, Jin W, Qin P, Xu S, Jin L, Tan SG, Limprasert P, Feisal MA, Rizman-Idid M, Zilfalil BA. A genome wide pattern of population structure and admixture in peninsular Malaysia Malays. THE HUGO JOURNAL 2014; 8:5. [PMID: 27090253 PMCID: PMC7735395 DOI: 10.1186/s11568-014-0005-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 05/19/2014] [Indexed: 12/23/2022]
Abstract
Background The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit; the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian SNP Initiative (PASNPI) Consortium and International HapMap project database. Results We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98% of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced back to have shared a common ancestor with the Proto-Malays and Chinese. Conclusions These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided valuable information on the enigmatic demographical history as well as shed some insights into the origins of the Malays in the Malay Peninsula.
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Affiliation(s)
- Wan Isa Hatin
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia
| | - Ab Rajab Nur-Shafawati
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia
| | - Ali Etemad
- Department of Pediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia
| | - Wenfei Jin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Pengfei Qin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Shuhua Xu
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Li Jin
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Soon-Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Selangor, Malaysia
| | - Pornprot Limprasert
- Human Genetics Unit, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Merican Amir Feisal
- Institute of Biological Sciences, 50603, Kuala Lumpur, Malaysia.,Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL),Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Bin Alwi Zilfalil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia. .,Department of Pediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kelantan, Malaysia.
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Jinam TA, Hong LC, Phipps ME, Stoneking M, Ameen M, Edo J, Saitou N. Evolutionary History of Continental Southeast Asians: “Early Train” Hypothesis Based on Genetic Analysis of Mitochondrial and Autosomal DNA Data. Mol Biol Evol 2012; 29:3513-27. [DOI: 10.1093/molbev/mss169] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Timothy A. Jinam
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Lih-Chun Hong
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University (Sunway Campus), Selangor, Malaysia
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mahmood Ameen
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Juli Edo
- Department of Anthropology, Faculty of Arts and Social Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Naruya Saitou
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
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Bengtsson CF, Olsen ME, Brandt LØ, Bertelsen MF, Willerslev E, Tobin DJ, Wilson AS, Gilbert MTP. DNA from keratinous tissue. Part I: hair and nail. Ann Anat 2011; 194:17-25. [PMID: 21530205 DOI: 10.1016/j.aanat.2011.03.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/05/2011] [Accepted: 03/22/2011] [Indexed: 11/26/2022]
Abstract
Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle - although little systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear and mitochondrial DNA appear to be present in almost all hair and nail samples, the quality of DNA, both in quantity and length of amplifiable DNA fragments, vary considerably not just by species, but by individual, and even within individual between hair types.
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Affiliation(s)
- Camilla Friis Bengtsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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Peng MS, Quang HH, Dang KP, Trieu AV, Wang HW, Yao YG, Kong QP, Zhang YP. Tracing the Austronesian footprint in Mainland Southeast Asia: a perspective from mitochondrial DNA. Mol Biol Evol 2010; 27:2417-30. [PMID: 20513740 DOI: 10.1093/molbev/msq131] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cham people remain a welter of controversies. Among the points of dissension is the muddled issue of whether the Cham people arose from demic or cultural diffusion from the Austronesians. Addressing this issue also helps elucidate the dispersal mode of the Austronesian language. In the present study, we have analyzed mitochondrial DNA (mtDNA) control-region and coding-region sequence variations in 168 Cham and 139 Kinh individuals from Vietnam. Around 77% and 95% matrilineal components in the Chams and the Kinhs, respectively, could be assigned into the defined mtDNA haplogroups. Additionally, three common East Eurasian haplogroups B, R9, and M7 account for the majority (>60%) of maternal components in both populations. Entire sequencing of 20 representative mtDNAs selected from the thus far unclassified lineages, together with four new mtDNA genome sequences from Thailand, led to the identification of one new haplogroup M77 and helped to re-evaluate several haplogroups determined previously. Comparing the Chams with other Southeast Asian populations reveals that the Chams had a closer affinity with the Mon-Khmer populations in MSEA than with the Austronesian populations from Island Southeast Asia (ISEA). Further analyses failed to detect the potential homelands of the Chams in ISEA. Therefore, our results suggested that the origin of the Cham was likely a process of assimilation of massive local Mon-Khmer populations accompanied with language shift, thus indicating that the Austronesian diffusion in MSEA was mainly mediated by cultural diffusion, at least from the matrilineal genetic perspective, an observation in agreement with the hypothesis of the Nusantao Maritime Trading and Communication Networks.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P.R. China
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