Mitochondrial Genetic Diversity and Its Determinants in Island Melanesia Jonathan S
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Y-Chromosome and Surname Analyses for Reconstructing Past Population Structures: the Sardinian Population As a Test Case
International Journal of Molecular Sciences Article Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case Viola Grugni 1, Alessandro Raveane 1, Giulia Colombo 1, Carmen Nici 1, Francesca Crobu 1,2, Linda Ongaro 1,3,4, Vincenza Battaglia 1, Daria Sanna 1,5, Nadia Al-Zahery 1, Ornella Fiorani 6, Antonella Lisa 6, Luca Ferretti 1 , Alessandro Achilli 1, Anna Olivieri 1, Paolo Francalacci 7, Alberto Piazza 8, Antonio Torroni 1 and Ornella Semino 1,* 1 Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; [email protected] (V.G.); [email protected] (A.R.); [email protected] (G.C.); [email protected] (C.N.); [email protected] (F.C.); [email protected] (L.O.); [email protected] (V.B.); [email protected] (D.S.); [email protected] (N.A.-Z.); [email protected] (L.F.); [email protected] (A.A.); [email protected] (A.O.); [email protected] (A.T.) 2 Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Italy 3 Estonian Biocentre, Institute of Genomics, Riia 23, 51010 Tartu, Estonia 4 Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, 51010 Tartu, Estonia 5 Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy 6 Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; fi[email protected] -
Mitochondrial Haplogroup Background May Influence
Genetics Mitochondrial Haplogroup Background May Influence Southeast Asian G11778A Leber Hereditary Optic Neuropathy Supannee Kaewsutthi,1,2 Nopasak Phasukkijwatana,2,3 Yutthana Joyjinda,1 Wanicha Chuenkongkaew,3,4 Bussaraporn Kunhapan,1 Aung Win Tun,1 Bhoom Suktitipat,1 and Patcharee Lertrit1,4 PURPOSE. To investigate the role of mitochondrial DNA markedly incomplete penetrance. The three most common (mt DNA) background on the expression of Leber hereditary primary LHON mutations, G3460A in ND1, G11778A in ND4, optic neuropathy (LHON) in Southeast Asian carriers of the and T14484C in ND6, account for more than 90% of LHON G11778A mutation. cases worldwide2 with G11778A being the most common. In 3 4–6 METHODS. Complete mtDNA sequences were analyzed from 53 Thailand and other Asian countries, G11778A is responsi- unrelated Southeast Asian G11778A LHON pedigrees in Thai- ble for approximately 90% of LHON families. land and 105 normal Thai controls, and mtDNA haplogroups The sex bias and the marked incomplete penetrance of were determined. Clinical phenotypes were tested for associ- LHON indicate that there must be other factors that modify disease expression. Mitochondrial background,7–8 nuclear ation with mtDNA haplogroup, with adjustment for potential 9–11 12 confounders such as sex and age at onset. background, and environmental factors have been impli- cated in disease expression, although the precise mechanisms RESULTS. mtDNA subhaplogroup B was significantly associated of pathogenesis are largely undefined. with LHON. Follow-up analysis -
The Study of Human Y Chromosome Variation Through Ancient DNA
Hum Genet DOI 10.1007/s00439-017-1773-z REVIEW The study of human Y chromosome variation through ancient DNA Toomas Kivisild1,2 Received: 12 January 2017 / Accepted: 24 February 2017 © The Author(s) 2017. This article is published with open access at Springerlink.com Abstract High throughput sequencing methods have com- accumulate and get fixed over time. This review considers pletely transformed the study of human Y chromosome genome-scale evidence on ancient Y chromosome diver- variation by offering a genome-scale view on genetic vari- sity that has recently started to accumulate in geographic ation retrieved from ancient human remains in context of areas favourable to DNA preservation. More specifically a growing number of high coverage whole Y chromosome the review focuses on examples of regional continuity and sequence data from living populations from across the change of the Y chromosome haplogroups in North Eurasia world. The ancient Y chromosome sequences are providing and in the New World. us the first exciting glimpses into the past variation of male- specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from Background patterns of genetic variation in living populations. Analy- ses of the ancient Y chromosome sequences are challenging Until recently, ancient DNA studies of human remain not only because of issues generally related to ancient DNA focused primarily on variation embedded in mitochon- work, such as DNA damage-induced mutations and low drial DNA (mtDNA). For decades, mtDNA had been a content of endogenous DNA in most human remains, but target of choice in population genetic studies because of also because of specific properties of the Y chromosome, its high mutation rate and high density of polymorphic such as its highly repetitive nature and high homology with markers (Wilson et al. -
Y-Chromosomal and Mitochondrial SNP Haplogroup Distribution In
Open Access Austin Journal of Forensic Science and Criminology Review Article Y-Chromosomal and Mitochondrial SNP Haplogroup Distribution in Indian Populations and its Significance in Disaster Victim Identification (DVI) - A Review Based Molecular Approach Sinha M1*, Rao IA1 and Mitra M2 1Department of Forensic Science, Guru Ghasidas Abstract University, India Disaster Victim Identification is an important aspect in mass disaster cases. 2School of Studies in Anthropology, Pt. Ravishankar In India, the scenario of disaster victim identification is very challenging unlike Shukla University, India any other developing countries due to lack of any organized government firm who *Corresponding author: Sinha M, Department of can make these challenging aspects an easier way to deal with. The objective Forensic Science, Guru Ghasidas University, India of this article is to bring spotlight on the potential and utility of uniparental DNA haplogroup databases in Disaster Victim Identification. Therefore, in this article Received: December 08, 2016; Accepted: January 19, we reviewed and presented the molecular studies on mitochondrial and Y- 2017; Published: January 24, 2017 chromosomal DNA haplogroup distribution in various ethnic populations from all over India that can be useful in framing a uniparental DNA haplogroup database on Indian population for Disaster Victim Identification (DVI). Keywords: Disaster Victim identification; Uniparental DNA; Haplogroup database; India Introduction with the necessity mentioned above which can reveal the fact that the human genome variation is not uniform. This inconsequential Disaster Victim Identification (DVI) is the recognized practice assertion put forward characteristics of a number of markers ranging whereby numerous individuals who have died as a result of a particular from its distribution in the genome, their power of discrimination event have their identity established through the use of scientifically and population restriction, to the sturdiness nature of markers to established procedures and methods [1]. -
Y-Chromosome Marker S28 / U152 Haplogroup R-U152 Resource Page
Y-Chromosome Marker S28 / U152 Haplogroup R-U152 Resource Page David K. Faux To use this page as a resource tool, click on the blue highlighted words, which will take the reader to a relevant link. How was this marker discovered? In 2005 Hinds et al. published a paper outlining the discovery of almost 1.6 million SNPs in 71 Americans by Perlegen.com, and which were deposited in the online dbSNP database. Gareth Henson noticed three SNPs that appeared to be associated with M269, what was then known as haplogroup R1b1c. Dr. James F. Wilson of EthnoAncestry developed primers for these Single Nucleotide Polymorphism (SNP) markers on the Y-chromosome, one of which was given the name of S28 (part of the S-series of SNPs developed by Dr. Wilson). Who were the first to be identified with this SNP? In testing the DNA of a number of R- M269 males (customers or officers of EthnoAncestry), two were found to be positive for S28 (U152). These were Charles Kerchner (of German descent) and David K. Faux, co- founder of EthnoAncestry (of English descent). How is this marker classified? In 2006 the International Society of Genetic Genealogists (ISOGG) developed a phylogenetic tree since the academic grouping (the Y Chromosome Consortium – YCC) set up to do this task had lapsed in 2002. They determined, with the assistance of Dr. Wilson, that the proper placement would be R1b1c10, in other words downstream of M269 the defining marker for R1b1c. Karafet et al. (2008) (including Dr. Michael Hammer of the original YCC group) published a new phylogenetic tree in the journal Genome Research. -
Y-Chromosome Analysis Reveals Genetic Divergence and New Founding Native Lineages in Athapaskan- and Eskimoan-Speaking Populations
Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations Matthew C. Dulika, Amanda C. Owingsa, Jill B. Gaieskia, Miguel G. Vilara, Alestine Andreb, Crystal Lenniec, Mary Adele Mackenzied, Ingrid Kritschb, Sharon Snowshoeb, Ruth Wrightb, James Martind, Nancy Gibsond, Thomas D. Andrewse, Theodore G. Schurra,1, and The Genographic Consortium2 aDepartment of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398; bGwich’in Social and Cultural Institute, Tsiigehtchic, NT, Canada X0E 0B0; cInuvialuit Regional Corporation, Inuvik, NT, Canada X0E 0T0; dTłįchǫ Community Services Agency, Behchoko, NT, Canada X0E 0Y0; and ePrince of Wales Northern Heritage Centre, Yellowknife, NT, Canada X1A 2L9 Edited* by Francisco Mauro Salzano, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil, and approved April 10, 2012 (received for review November 21, 2011) For decades, the peopling of the Americas has been explored mtDNA data (5). Even the dental traits used to justify a three- through the analysis of uniparentally inherited genetic systems in migration hypothesis did not group all Na-Dene speakers into Native American populations and the comparison of these genetic a single category separate from the other two (Amerind and data with current linguistic groupings. In northern North America, Eskimo-Aleut) groups and furthermore, suggested the inclusion two language families predominate: Eskimo-Aleut and Na-Dene. of Aleuts with Athapaskan speakers from northwestern America Although the genetic evidence from nuclear and mtDNA loci (3). Thus, although it is generally accepted that the two language suggest that speakers of these language families share a distinct families differ from each other, it is not clear whether they have biological origin, this model has not been examined using data from different genetic origins or instead, are the result of separate paternally inherited Y chromosomes. -
Ancient Mitochondrial DNA from Pre-Historic
Grand Valley State University ScholarWorks@GVSU Masters Theses Graduate Research and Creative Practice 4-30-2011 Ancient Mitochondrial DNA From Pre-historic Southeastern Europe: The rP esence of East Eurasian Haplogroups Provides Evidence of Interactions with South Siberians Across the Central Asian Steppe Belt Jeremy R. Newton Grand Valley State University Follow this and additional works at: http://scholarworks.gvsu.edu/theses Part of the Cell Biology Commons, and the Molecular Biology Commons Recommended Citation Newton, Jeremy R., "Ancient Mitochondrial DNA From Pre-historic Southeastern Europe: The rP esence of East Eurasian Haplogroups Provides Evidence of Interactions with South Siberians Across the Central Asian Steppe Belt" (2011). Masters Theses. 5. http://scholarworks.gvsu.edu/theses/5 This Thesis is brought to you for free and open access by the Graduate Research and Creative Practice at ScholarWorks@GVSU. It has been accepted for inclusion in Masters Theses by an authorized administrator of ScholarWorks@GVSU. For more information, please contact [email protected]. ANCIENT MITOCHONDRIAL DNA FROM PRE-HISTORIC SOUTH- EASTERN EUROPE: THE PRESENCE OF EAST EURASIAN HAPLOGROUPS PROVIDES EVIDENCE OF INTERACTIONS WITH SOUTH SIBERIANS ACROSS THE CENTRAL ASIAN STEPPE BELT A thesis submittal in partial fulfillment of the requirements for the degree of Master of Science By Jeremy R. Newton To Cell and Molecular Biology Department Grand Valley State University Allendale, MI April, 2011 “Not all those who wander are lost.” J.R.R. Tolkien iii ACKNOWLEDGEMENTS I would like to extend my sincerest thanks to every person who has motivated, directed, and encouraged me throughout this thesis project. I especially thank my graduate advisor, Dr. -
A Prehistory of Indian Y Chromosomes: Evaluating Demic Diffusion Scenarios
A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios Sanghamitra Sahoo†, Anamika Singh†, G. Himabindu†, Jheelam Banerjee†, T. Sitalaximi†, Sonali Gaikwad†, R. Trivedi†, Phillip Endicott‡, Toomas Kivisild§, Mait Metspalu§, Richard Villems§, and V. K. Kashyap†¶ʈ †National DNA Analysis Centre, Central Forensic Science Laboratory, Kolkata 700014, India; ‡Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; §Estonian Biocentre, 51010 Tartu, Estonia; and ¶National Institute of Biologicals, Noida 201307, India Edited by Colin Renfrew, University of Cambridge, Cambridge, United Kingdom, and approved November 23, 2005 (received for review September 5, 2005) Understanding the genetic origins and demographic history of mode of subsistence or social system. Even so, the trend of Indian populations is important both for questions concerning the finding farming (castes) and IE languages grouped together has early settlement of Eurasia and more recent events, including the led some to suggest a major demic diffusion, associated with the appearance of Indo-Aryan languages and settled agriculture in the spread of agriculture, from West Asia and͞or Central Asia to subcontinent. Although there is general agreement that Indian India, (16). The situation in Northeast India is less intensely caste and tribal populations share a common late Pleistocene studied, but the proximity to related language families in East maternal ancestry in India, some studies of the Y-chromosome and Southeast Asia suggests possible origins for the Tibeto- markers have suggested a recent, substantial incursion from Cen- Burman (TB) clade of the Sino-Tibetan family outside India. tral or West Eurasia. To investigate the origin of paternal lineages The Mundari group of Austro-Asiatic (AA) languages is cur- of Indian populations, 936 Y chromosomes, representing 32 tribal rently found almost exclusively in East India. -
Meta-Analysis of Mitochondrial DNA Reveals Several Population
Table S1. Haplogroup distributions represented in Figure 1. N: number of sequences; J: banteng, Bali cattle (Bos javanicus ); G: yak (Bos grunniens ). Other haplogroup codes are as defined previously [1,2], but T combines T, T1’2’3’ and T5 [2] while the T1 count does not include T1a1c1 haplotypes. T1 corresponds to T1a defined by [2] (16050T, 16133C), but 16050C–16133C sequences in populations with a high T1 and a low T frequency were scored as T1 with a 16050C back mutation. Frequencies of I are only given if I1 and I2 have not been differentiated. Average haplogroup percentages were based on balanced representations of breeds. Country, Region Percentages per Haplogroup N Reference Breed(s) T T1 T1c1a1 T2 T3 T4 I1 I2 I J G Europe Russia 58 3.4 96.6 [3] Yaroslavl Istoben Kholmogory Pechora type Red Gorbatov Suksun Yurino Ukrain 18 16.7 72.2 11.1 [3] Ukrainian Whiteheaded Ukrainian Grey Estonia, Byelorussia 12 100 [3] Estonian native Byelorussia Red Finland 31 3.2 96.8 [3] Eastern Finncattle Northern Finncattle Western Finncattle Sweden 38 100.0 [3] Bohus Poll Fjall cattle Ringamala Cattle Swedish Mountain Cattle Swedish Red Polled Swedish Red-and-White Vane Cattle Norway 44 2.3 0.0 0.0 0.0 97.7 [1,4] Blacksided Trondheim Norwegian Telemark Westland Fjord Westland Red Polled Table S1. Cont. Country, Region Percentages per Haplogroup N Reference Breed(s) T T1 T1c1a1 T2 T3 T4 I1 I2 I J G Iceland 12 100.0 [1] Icelandic Denmark 32 100.0 [3] Danish Red (old type) Jutland breed Britain 108 4.2 1.2 94.6 [1,5,6] Angus Galloway Highland Kerry Hereford Jersey White Park Lowland Black-Pied 25 12.0 88.0 [1,4] Holstein-Friesian German Black-Pied C Europe 141 3.5 4.3 92.2 [1,4,7] Simmental Evolene Raetian Grey Swiss Brown Valdostana Pezzata Rossa Tarina Bruna Grey Alpine France 98 1.4 6.6 92.0 [1,4,8] Charolais Limousin Blonde d’Aquitaine Gascon 82.57 Northern Spain 25 4 13.4 [8,9] 1 Albera Alistana Asturia Montana Monchina Pirenaica Pallaresa Rubia Gallega Southern Spain 638 0.1 10.9 3.1 1.9 84.0 [5,8–11] Avileña Berrenda colorado Berrenda negro Cardena Andaluzia Table S1. -
Mitochondrial DNA Diversity of Present-Day Aboriginal Australians and Implications for Human Evolution in Oceania
Journal of Human Genetics (2016), 1–11 & 2016 The Japan Society of Human Genetics All rights reserved 1434-5161/16 www.nature.com/jhg ORIGINAL ARTICLE Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania Nano Nagle1, Kaye N Ballantyne2,3, Mannis van Oven3, Chris Tyler-Smith4, Yali Xue4, Stephen Wilcox5, Leah Wilcox1, Rust Turkalov5, Roland AH van Oorschot2, Sheila van Holst Pellekaan6,7, Theodore G Schurr8, Peter McAllister9, Lesley Williams10, Manfred Kayser3, R John Mitchell1 and The Genographic Consortium27 Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors’ arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages 440 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. -
The Enigmatic Origin of Bovine Mtdna Haplogroup R: Sporadic Interbreeding Or an Independent Event of Bos Primigenius Domestication in Italy?
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central The Enigmatic Origin of Bovine mtDNA Haplogroup R: Sporadic Interbreeding or an Independent Event of Bos primigenius Domestication in Italy? Silvia Bonfiglio1, Alessandro Achilli1,2, Anna Olivieri1, Riccardo Negrini3, Licia Colli3, Luigi Liotta4, Paolo Ajmone-Marsan3, Antonio Torroni1, Luca Ferretti1* 1 Dipartimento di Genetica e Microbiologia, Universita` di Pavia, Pavia, Italy, 2 Dipartimento di Biologia Cellulare e Ambientale, Universita` di Perugia, Perugia, Italy, 3 Istituto di Zootecnica, Universita` Cattolica del Sacro Cuore, Piacenza, Italy, 4 Dipartimento di Morfologia, Biochimica, Fisiologia e Produzioni Animali, Universita` di Messina, Messina, Italy Abstract Background: When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. Methodology: The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. -
Cattle Mitogenome Variation Reveals a Post-Glacial Expansion Of
www.nature.com/scientificreports OPEN Cattle mitogenome variation reveals a post‑glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds Hideyuki Mannen1,4*, Takahiro Yonezawa2,4, Kako Murata1, Aoi Noda1, Fuki Kawaguchi1, Shinji Sasazaki1, Anna Olivieri3, Alessandro Achilli3 & Antonio Torroni3 Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post‑glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub‑haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence. All modern cattle derive from wild ancestral aurochs (Bos primigenius), which were distributed throughout large parts of Eurasia and Northern Africa during the Pleistocene and the early Holocene1,2.