1
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Advancing FDSTools by integrating STRNaming 1.1. Forensic Sci Int Genet 2022; 61:102768. [PMID: 35994887 DOI: 10.1016/j.fsigen.2022.102768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/25/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022]
Abstract
The introduction of massively parallel sequencing in forensic analysis has been facilitated with typing kits, analysis software and allele naming tools such as the ForenSeq DNA Signature Prep (DSP) kit, FDSTools and STRNaming respectively. Here we describe how FDSTools 2.0 with integrated and refined STRNaming nomenclature was validated for implementation under ISO 17025 accreditation for the ForenSeq DSP kit. Newly-added options result in efficient automatic allele calling for the majority of markers while specific settings are applied for 'novel' sequence variants to avoid the calling of remaining variable noise observed in samples sequenced with the ForenSeq DSP kit that seem to arise in the PCR. Genome-wide built-in reference data allows for greatly simplified configuration of allele naming for human targets.
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2
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Haque I, Dixit S, Kumar A, Kumar A, Verma S, Kumar D, Srivastava A, Kumawat RK, Shrivastava D, Chaubey G, Shrivastava P. An evaluation of inter and intra population structure of Uttar Pradesh, inferred from 24 autosomal STRs. Ann Hum Biol 2021; 49:69-79. [PMID: 34852697 DOI: 10.1080/03014460.2021.1995043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Aim: Present study was designed to explore the STR diversity and genomic history of the inhabitants of the most populous subdivision of the country. A set of 24 hyper variable autosomal STRs was used to estimate the genetic diversity within the studied population. A panel of 15 autosomal STRs, which is most common in the previously reported data sets, was used to estimate the genetic diversity between the studied population and obtained unique relations were reported here.Method: The genetic diversity and polymorphism among 636 individuals of different ethnic groups, residing in Bareilly, Pilibhit, Shahjahanpur, Gorakhpur, Jhansi and Varanasi regions of Uttar Pradesh, India was investigated. This investigation was carried out via 24 autosomal STRs.Result: Studied 24 loci showed the highest value of combined power of discrimination (CPD =1), combined power of exclusion (CPE =0.99999999985), combined paternity index (CPI =6.10x109) and lowest combined matching probability (CPM =7.90x10-31).Conclusion: Studied population showed the genetic closeness with the population of Uttarakhand, Jats of Delhi, Jat Sikh (Punjab) and population of Rajasthan. The locus SE33 and Penta E was found to be most useful in the terms of highest discrimination power, lowest matching probability, highest power of exclusion and highest polymorphism information content for Uttar Pradesh population among the tested loci.
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Affiliation(s)
- Ikramul Haque
- Advanced DNA Laboratory, Central Forensic Science Laboratory, Chandigarh-160036, India
| | - Shivani Dixit
- Advanced DNA Laboratory, Central Forensic Science Laboratory, Chandigarh-160036, India.,Jaipur National University, Jaipur, Rajasthan-302017, India
| | - Akash Kumar
- Dr. A.P.J. Abdul Kalam Institute of Forensic Science & Criminology, Bundelkhand University, Jhansi, U.P-284128, India.,DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, Madhya Pradesh-470001, India
| | - Akshay Kumar
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, Madhya Pradesh-470001, India
| | - Sunita Verma
- Advanced DNA Laboratory, Central Forensic Science Laboratory, Chandigarh-160036, India
| | - Devinder Kumar
- Advanced DNA Laboratory, Central Forensic Science Laboratory, Chandigarh-160036, India
| | - Ankit Srivastava
- Dr. A.P.J. Abdul Kalam Institute of Forensic Science & Criminology, Bundelkhand University, Jhansi, U.P-284128, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Rajasthan, Jaipur -302016, India
| | | | | | - Pankaj Shrivastava
- Dr. A.P.J. Abdul Kalam Institute of Forensic Science & Criminology, Bundelkhand University, Jhansi, U.P-284128, India
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3
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Aguilar-Velázquez JA, Stephenson-Ojea MM, García-King MD, Rangel-Villalobos H. Genetic diversity, structure, and admixture in Mayans from Guatemala and Mexico based on 15 short tandem repeats. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:238-250. [PMID: 33522608 DOI: 10.1002/ajpa.24203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 11/14/2020] [Accepted: 11/30/2020] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To analyze the genetic origin, relationships, structure, and admixture in Mayan Native American groups from Guatemala and Mexico based on 15 autosomal short tandem repeats (STRs) loci commonly used in human identification (HID). METHODS We genotyped 513 unrelated Mayan samples from Guatemala based on 15 STR loci (AmpFlSTR® Identifiler kit). Moreover, we included 4408 genotypes previously reported, as following: Mayas from Guatemala and Mexico (n = 1666) and from Latin American, European, and African (n = 2742) populations. Forensic parameters, genetic distances, admixture, and population structure were assessed. RESULTS Forensic parameters of the 15 STRs in different Mayan groups from Guatemala were reported. Low (Fst = 0.78%; p = 0.000) and non-significant differentiation (Fst = 1.8%; p = 0.108) were observed in Mayas from Guatemala and Mexico, respectively. The relative homogeneity observed among Mayan groups supported theories of extensive pre-Columbian gene flow and trade throughout the Mayan Empire. The distribution of the three Native American ancestries among these Mayan groups did not support the presumable Guatemalan origin of Tojolabal and Lacandon people (South, Mexico). The nonsignificant differentiation between Ladinos and Mayas suggests a relative panmixia in Guatemala. Mestizos from southeastern Mexico and Guatemala constitute a core of Native American ancestry in Latin America related to the Mayan Empire in Central America. CONCLUSIONS The higher European admixture and homogeneity in Mexican Mayas of the Yucatan Peninsula suggest more intensive post-Columbian gene flow in this region than in Guatemalan Mayas.
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Affiliation(s)
- José Alonso Aguilar-Velázquez
- Instituto de Investigación en Genética Molecular, Departamento de Ciencias Médicas y de la Vida, Universidad de Guadalajara, Av. Universidad #1115, Col, Lindavista, Ocotlán, Jalisco, 47810, Mexico.,Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud (CUCS-UdeG), Universidad de Guadalajara, Sierra Mojada #950, Guadalajara, Jalisco, Mexico
| | - Mishel Marie Stephenson-Ojea
- Laboratorio de Genética Forense, Fundación de Antropología Forense de Guatemala (FAFG), 1a Calle 1-53, Guatemala, Zona 2, Guatemala
| | - Marco David García-King
- Laboratorio de Genética Forense, Fundación de Antropología Forense de Guatemala (FAFG), 1a Calle 1-53, Guatemala, Zona 2, Guatemala
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Departamento de Ciencias Médicas y de la Vida, Universidad de Guadalajara, Av. Universidad #1115, Col, Lindavista, Ocotlán, Jalisco, 47810, Mexico
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4
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STRNaming: Generating simple, informative names for sequenced STR alleles in a standardised and automated manner. Forensic Sci Int Genet 2021; 52:102473. [PMID: 33607395 DOI: 10.1016/j.fsigen.2021.102473] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 11/20/2022]
Abstract
The introduction of Massively Parallel Sequencing in the forensic domain has exposed the need for comprehensive nomenclature of sequenced Short Tandem Repeat (STR) alleles. In general, three strategies are at hand: 1) the full sequence mapped to the human genome reference sequence, which ensures exact data exchange; 2) shortened, human-readable formats for forensic reporting and data presentation and 3) very short codes that enable compact figures and tables but do not convey any sequence information. Here, we describe an algorithm of the second type: STRNaming, which generates human-readable names for sequenced STR alleles. STRNaming is guided by a reference sequence at each locus and then functions independently to automatically assign a unique, sequence-descriptive name that also includes the capillary electrophoresis allele number. STRNaming settings were established based on preferences that were surveyed internationally in the forensic community. These settings ensure that a small change in the sequence corresponds to a small change in the allele name, which is helpful for recognising for instance stutter products. Sequence variants outside of the repeat units are indicated as simple variant calls. Since the STR name is sequence-descriptive, the sequence can be traced back from the allele name. Because STRNaming is fully guided by an assignable reference sequence, no central coordination or configuration is required and the method will work for any STR locus, be it autosomal, Y-, X-chromosomal in current or future use. The algorithm is publicly available online and offline.
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5
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Zhang H, Ji T, Pagel M, Mace R. Dated phylogeny suggests early Neolithic origin of Sino-Tibetan languages. Sci Rep 2020; 10:20792. [PMID: 33247154 PMCID: PMC7695722 DOI: 10.1038/s41598-020-77404-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/09/2020] [Indexed: 11/21/2022] Open
Abstract
An accurate reconstruction of Sino-Tibetan language evolution would greatly advance our understanding of East Asian population history. Two recent phylogenetic studies attempted to do so but several of their conclusions are different from each other. Here we reconstruct the phylogeny of the Sino-Tibetan language family, using Bayesian computational methods applied to a larger and linguistically more diverse sample. Our results confirm previous work in finding that the ancestral Sino-Tibetans first split into Sinitic and Tibeto-Burman clades, and support the existence of key internal relationships. But we find that the initial divergence of this group occurred earlier than previously suggested, at approximately 8000 years before the present, coinciding with the onset of millet-based agriculture and significant environmental changes in the Yellow River region. Our findings illustrate that key aspects of phylogenetic history can be replicated in this complex language family, and calls for a more nuanced understanding of the first Sino-Tibetan speakers in relation to the "early farming dispersal" theory of language evolution.
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Affiliation(s)
- Hanzhi Zhang
- Department of Anthropology, University College London, London, WC1H 0BW, UK.
| | - Ting Ji
- Key Laboratory of Animal Ecology and Conservation Biology, Centre for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mark Pagel
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Ruth Mace
- Department of Anthropology, University College London, London, WC1H 0BW, UK.
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6
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Arciero E, Kraaijenbrink T, Asan, Haber M, Mezzavilla M, Ayub Q, Wang W, Pingcuo Z, Yang H, Wang J, Jobling MA, van Driem G, Xue Y, de Knijff P, Tyler-Smith C. Demographic History and Genetic Adaptation in the Himalayan Region Inferred from Genome-Wide SNP Genotypes of 49 Populations. Mol Biol Evol 2018; 35:1916-1933. [PMID: 29796643 PMCID: PMC6063301 DOI: 10.1093/molbev/msy094] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We genotyped 738 individuals belonging to 49 populations from Nepal, Bhutan, North India, or Tibet at over 500,000 SNPs, and analyzed the genotypes in the context of available worldwide population data in order to investigate the demographic history of the region and the genetic adaptations to the harsh environment. The Himalayan populations resembled other South and East Asians, but in addition displayed their own specific ancestral component and showed strong population structure and genetic drift. We also found evidence for multiple admixture events involving Himalayan populations and South/East Asians between 200 and 2,000 years ago. In comparisons with available ancient genomes, the Himalayans, like other East and South Asian populations, showed similar genetic affinity to Eurasian hunter-gatherers (a 24,000-year-old Upper Palaeolithic Siberian), and the related Bronze Age Yamnaya. The high-altitude Himalayan populations all shared a specific ancestral component, suggesting that genetic adaptation to life at high altitude originated only once in this region and subsequently spread. Combining four approaches to identifying specific positively selected loci, we confirmed that the strongest signals of high-altitude adaptation were located near the Endothelial PAS domain-containing protein 1 and Egl-9 Family Hypoxia Inducible Factor 1 loci, and discovered eight additional robust signals of high-altitude adaptation, five of which have strong biological functional links to such adaptation. In conclusion, the demographic history of Himalayan populations is complex, with strong local differentiation, reflecting both genetic and cultural factors; these populations also display evidence of multiple genetic adaptations to high-altitude environments.
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Affiliation(s)
- Elena Arciero
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Thirsa Kraaijenbrink
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Asan
- BGI-Shenzhen, Shenzhen, China
| | - Marc Haber
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Massimo Mezzavilla
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia Genomics Facility, Selangor Darul Ehsan, Malaysia
- School of Science, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
| | | | - Zhaxi Pingcuo
- The Third People’s Hospital of the Tibet Autonomous Region, Lhasa, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | - Yali Xue
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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7
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Cole AM, Cox S, Jeong C, Petousi N, Aryal DR, Droma Y, Hanaoka M, Ota M, Kobayashi N, Gasparini P, Montgomery H, Robbins P, Di Rienzo A, Cavalleri GL. Genetic structure in the Sherpa and neighboring Nepalese populations. BMC Genomics 2017; 18:102. [PMID: 28103797 PMCID: PMC5248489 DOI: 10.1186/s12864-016-3469-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 12/23/2016] [Indexed: 12/31/2022] Open
Abstract
Background We set out to describe the fine-scale population structure across the Eastern region of Nepal. To date there is relatively little known about the genetic structure of the Sherpa residing in Nepal and their genetic relationship with the Nepalese. We assembled dense genotype data from a total of 1245 individuals representing Nepal and a variety of different populations resident across the greater Himalayan region including Tibet, China, India, Pakistan, Kazakhstan, Uzbekistan, Tajikistan and Kirghizstan. We performed analysis of principal components, admixture and homozygosity. Results We identified clear substructure across populations resident in the Himalayan arc, with genetic structure broadly mirroring geographical features of the region. Ethnic subgroups within Nepal show distinct genetic structure, on both admixture and principal component analysis. We detected differential proportions of ancestry from northern Himalayan populations across Nepalese subgroups, with the Nepalese Rai, Magar and Tamang carrying the greatest proportions of Tibetan ancestry. Conclusions We show that populations dwelling on the Himalayan plateau have had a clear impact on the Northern Indian gene pool. We illustrate how the Sherpa are a remarkably isolated population, with little gene flow from surrounding Nepalese populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3469-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amy M Cole
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sean Cox
- Centre for Human Health and Performance, and Institute for Sport, Exercise and Health, University College London, London, UK
| | - Choongwon Jeong
- Department of Human Genetics, University of Chicago, Chicago, USA
| | - Nayia Petousi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Dhana R Aryal
- Paropakar Maternity and Women's Hospital, Thapathali, Kathmandu, Nepal
| | - Yunden Droma
- First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Masayuki Hanaoka
- First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Masao Ota
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Nobumitsu Kobayashi
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Paolo Gasparini
- University of Triests, Trieste, Italy.,Division of Experimental Genetics, Sidra, Doha, Qatar
| | - Hugh Montgomery
- Centre for Human Health and Performance, and Institute for Sport, Exercise and Health, University College London, London, UK
| | - Peter Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, USA
| | - Gianpiero L Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland.
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8
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Massively parallel sequencing of short tandem repeats—Population data and mixture analysis results for the PowerSeq™ system. Forensic Sci Int Genet 2016; 24:86-96. [DOI: 10.1016/j.fsigen.2016.05.016] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/25/2016] [Accepted: 05/29/2016] [Indexed: 11/17/2022]
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9
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Preet K, Malhotra S, Shrivastava P, Jain T, Rawat S, Varte LR, Singh S, Singh I, Sarkar S. Genetic Diversity in Gorkhas: an Autosomal STR Study. Sci Rep 2016; 6:32494. [PMID: 27580933 PMCID: PMC5007509 DOI: 10.1038/srep32494] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/08/2016] [Indexed: 12/02/2022] Open
Abstract
Genotyping of highly polymorphic autosomal short tandem repeat (STR) markers is a potent tool for elucidating genetic diversity. In the present study, fifteen autosomal STR markers were analyzed in unrelated healthy male Gorkha individuals (n = 98) serving in the Indian Army by using AmpFlSTR Identifiler Plus PCR Amplification Kit. In total, 138 alleles were observed with corresponding allele frequencies ranging from 0.005 to 0.469. The studied loci were in Hardy-Weinberg Equilibrium (HWE). Heterozygosity ranged from 0.602 to 0.867. The most polymorphic locus was Fibrinogen Alpha (FGA) chain which was also the most discriminating locus as expected. Neighbor Joining (NJ) tree and principal component analysis (PCA) plot clustered the Gorkhas with those of Nepal and other Tibeto-Burman population while lowlander Indian population formed separate cluster substantiating the closeness of the Gorkhas with the Tibeto-Burman linguistic phyla. Furthermore, the dataset of STR markers obtained in the study presents a valuable information source of STR DNA profiles from personnel for usage in disaster victim identification in military exigencies and adds to the Indian database of military soldiers and military hospital repository.
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Affiliation(s)
- Kiran Preet
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Ministry of Defence, Government of India, Lucknow Road, Delhi, 110054, India
| | - Seema Malhotra
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Ministry of Defence, Government of India, Lucknow Road, Delhi, 110054, India
| | - Pankaj Shrivastava
- State Forensic Science Laboratory, Civil Lines, Sagar, Madhya Pradesh, 470001, India
| | - Toshi Jain
- State Forensic Science Laboratory, Civil Lines, Sagar, Madhya Pradesh, 470001, India
| | - Shweta Rawat
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Ministry of Defence, Government of India, Lucknow Road, Delhi, 110054, India
| | - L. Robert Varte
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Ministry of Defence, Government of India, Lucknow Road, Delhi, 110054, India
| | - Sayar Singh
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Ministry of Defence, Government of India, Lucknow Road, Delhi, 110054, India
| | - Inderjeet Singh
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Ministry of Defence, Government of India, Lucknow Road, Delhi, 110054, India
| | - Soma Sarkar
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Ministry of Defence, Government of India, Lucknow Road, Delhi, 110054, India
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10
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Rangel-Villalobos H, Martínez-Sevilla VM, Martínez-Cortés G, Aguilar-Velázquez JA, Sosa-Macías M, Rubi-Castellanos R, González-Martín A. Importance of the geographic barriers to promote gene drift and avoid pre- and post-Columbian gene flow in Mexican native groups: Evidence from forensic STR Loci. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:298-316. [PMID: 26946467 DOI: 10.1002/ajpa.22969] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 01/21/2016] [Accepted: 02/06/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To analyze the origin, structure, relationships, and recent admixture in Mexican Native groups based on 15 STRs commonly used in human identification. METHODS We analyzed 39 Mexican Native population samples using STR databases based on the AmpFlSTR® Identifiler kit (n = 3,135), including Mexican-Mestizos (admixed), European and African populations, as reference. RESULTS Based upon effective population size (Ne) differences, Native groups were clustered into three regions: i) Center-Southeast groups, characterized by larger Ne, migration rate (Nm), genetic diversity (He), and relative homogeneity principally in the Yucatan Peninsula; ii) Isolated southern groups from Chiapas and Oaxaca, characterized by lower Ne, Nm, and He (i.e. higher isolation and genetic differentiation); iii) North-Northwest groups, which are similar to the previous group but are characterized by generating the widest gene flow barrier in the Pre-Hispanic Mexican territory, and currently by elevated admixture in some northern Native groups. Despite the relative congruence between genetic relationships with cultural, linguistic, geographic criteria, these factors do not explain the present-day population structure of Native groups, excepting in those linguistically related to the Mayan that show higher homogeneity. The Isolation by distance model was demonstrated at long distances (>1,500 km), whereas geographic isolation stands as a determining factor to avoid both non-indigenous admixture and bottleneck processes. CONCLUSIONS Different dynamics of gene flow and drift were observed among Mexican Native groups, highlighting the geographic barriers (mountains, canyons and jungle regions) as the main factor differentiating Pre-Hispanic populations, and eventually helping to avoid Post-European contact admixture and population bottleneck. Am J Phys Anthropol 160:298-316, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Héctor Rangel-Villalobos
- Instituto De Investigación En Genética Molecular, Centro Universitario De La Ciénega (CUCI-UdeG), Ocotlán, Jalisco, México
| | - Víctor Manuel Martínez-Sevilla
- Instituto De Investigación En Genética Molecular, Centro Universitario De La Ciénega (CUCI-UdeG), Ocotlán, Jalisco, México
| | - Gabriela Martínez-Cortés
- Instituto De Investigación En Genética Molecular, Centro Universitario De La Ciénega (CUCI-UdeG), Ocotlán, Jalisco, México
| | - José Alonso Aguilar-Velázquez
- Instituto De Investigación En Genética Molecular, Centro Universitario De La Ciénega (CUCI-UdeG), Ocotlán, Jalisco, México
| | - Martha Sosa-Macías
- Unidad Durango (CIIDIR-IPN), Centro Interdisciplinario De Investigación Para El Desarrollo Integral Regional Del Instituto Politécnico Nacional, Durango, México
| | - Rodrigo Rubi-Castellanos
- Laboratorio De Genética, Centro De Investigaciones Regionales Hideyo Noguchi, Universidad Autónoma De Yucatán (UADY), Mérida, Yucatán
| | - Antonio González-Martín
- Departamento De Zoología Y Antropología Física, Facultad De Biología, Universidad Complutense De Madrid, Madrid, Spain
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11
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Hackinger S, Kraaijenbrink T, Xue Y, Mezzavilla M, van Driem G, Jobling MA, de Knijff P, Tyler-Smith C, Ayub Q. Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas. Hum Genet 2016; 135:393-402. [PMID: 26883865 PMCID: PMC4796332 DOI: 10.1007/s00439-016-1641-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/23/2016] [Indexed: 12/19/2022]
Abstract
High-altitude adaptation in Tibetans is influenced by introgression of a 32.7-kb haplotype from the Denisovans, an extinct branch of archaic humans, lying within the endothelial PAS domain protein 1 (EPAS1), and has also been reported in Sherpa. We genotyped 19 variants in this genomic region in 1507 Eurasian individuals, including 1188 from Bhutan and Nepal residing at altitudes between 86 and 4550 m above sea level. Derived alleles for five SNPs characterizing the core Denisovan haplotype (AGGAA) were present at high frequency not only in Tibetans and Sherpa, but also among many populations from the Himalayas, showing a significant correlation with altitude (Spearman’s correlation coefficient = 0.75, p value 3.9 × 10−11). Seven East- and South-Asian 1000 Genomes Project individuals shared the Denisovan haplotype extending beyond the 32-kb region, enabling us to refine the haplotype structure and identify a candidate regulatory variant (rs370299814) that might be interacting in an additive manner with the derived G allele of rs150877473, the variant previously associated with high-altitude adaptation in Tibetans. Denisovan-derived alleles were also observed at frequencies of 3–14 % in the 1000 Genomes Project African samples. The closest African haplotype is, however, separated from the Asian high-altitude haplotype by 22 mutations whereas only three mutations, including rs150877473, separate the Asians from the Denisovan, consistent with distant shared ancestry for African and Asian haplotypes and Denisovan adaptive introgression.
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Affiliation(s)
- Sophie Hackinger
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Thirsa Kraaijenbrink
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Massimo Mezzavilla
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - George van Driem
- Institute of Linguistics, University of Bern, Bern, CH 3012, Switzerland
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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Zeng YW, Du J, Pu XY, Yang JZ, Yang T, Yang SM, Yang XM. Coevolution between Human's Anticancer Activities and Functional Foods from Crop Origin Center in the World. Asian Pac J Cancer Prev 2015; 16:2119-28. [DOI: 10.7314/apjcp.2015.16.6.2119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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SOLÉ-LLUSSÀ A, GOROSTIZA A, RUBÍ-CASTELLANOS R, ACUNHA-ALONZO V, GENÉ M, RANGEL-VILLALOBOS H, GONZÁLEZ-MARTÍN A. Exploring the African genetic influence in the first settlement founded by African slaves in America. ANTHROPOL SCI 2015. [DOI: 10.1537/ase.150422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- A. SOLÉ-LLUSSÀ
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid
| | - A. GOROSTIZA
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid
- Laboratorio de Identificación Genética GENOMICA SAU, Grupo Zeltia, Madrid
| | - R. RUBÍ-CASTELLANOS
- Laboratorio de Genética, Centro de Investigaciones Regionales, Universidad Autónoma de Yucatán, Mérida
| | - V. ACUNHA-ALONZO
- Laboratorio de Genética Molecular, Escuela Nacional de Antropología e Historia, México
| | - M. GENÉ
- Departamento de Medicina Legal y Forense, Facultad de Medicina, Universitat de Barcelona, Barcelona
| | - H. RANGEL-VILLALOBOS
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénaga, Universidad de Guadalajara, Ocotlán
| | - A. GONZÁLEZ-MARTÍN
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid
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