mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences

Lee, Hwan Young; Song, In-Jee; Ha, Eunho; Cho, Sung Bae; Yang, Woo Ick; Shin, Kyoung Jin

doi:10.1186/1471-2105-9-483

Cited by 82 publications

(64 citation statements)

References 63 publications

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“…This specific U5b haplotype, characterized by the specific mutation in np 16271, has never before been described in France (Rousselet and Mangin, 1998;Dubut et al, 2004;Richard et al, 2007), or in the databases of modern populations (Richards et al, 2000; GenBank database; mtDNA manager database, Lee et al, 2008;Genographic dataset, Behar et al, 2007). Subhaplogroup U5b has also been encountered in German Neolithic remains from the Corded Ware Culture (Haak et al, 2008) and in the hunter-gatherers studied by Bramanti et al (2009), although in both instances, the branches concerned were distinct from the U5b in the Prissé sample.…”

Section: Resultsmentioning

confidence: 92%

News from the west: Ancient DNA from a French megalithic burial chamber

Deguilloux

Soler²,

Pémonge

et al. 2010

American J Phys Anthropol

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Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices.

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Section: Resultsmentioning

confidence: 92%

News from the west: Ancient DNA from a French megalithic burial chamber

Deguilloux

Soler²,

Pémonge

et al. 2010

American J Phys Anthropol

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“…For mtDnA, the majority of haplogroups (95%) were of sub-saharan origin with exception of X and X2d that were of West eurasian origin and D4k and n9b that were of east Asian origin [8].…”

Section: Resultsmentioning

confidence: 99%

“…sequences were obtained with ABI PRIsm Big Dye Terminator and dRhodamine Terminator Cycle Sequencing Ready Reaction Kits, with amplitaq DNA polymerase FS, and were detected in an ABI 3100 Avant sequencer. Haplogroups were classified based on the different polymorphic positions of these two hypervariable regions using the software mtDNA manager-forensic mtDNA database [8].…”

Section: Methodsmentioning

confidence: 99%

Paternal and maternal lineages in Cabo Verde archipelago population

Côrte-Real¹,

Gusmão²,

Anjos³

et al. 2010

Acta Medicinae Legalis Et Socialis

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A navegação consulta e descarregamento dos títulos inseridos nas Bibliotecas Digitais UC Digitalis, UC Pombalina e UC Impactum, pressupõem a aceitação plena e sem reservas dos Termos e Condições de Uso destas Bibliotecas Digitais, disponíveis em https://digitalis.uc.pt/pt-pt/termos.Conforme exposto nos referidos Termos e Condições de Uso, o descarregamento de títulos de acesso restrito requer uma licença válida de autorização devendo o utilizador aceder ao(s) documento(s) a partir de um endereço de IP da instituição detentora da supramencionada licença.Ao utilizador é apenas permitido o descarregamento para uso pessoal, pelo que o emprego do(s) título(s) descarregado(s) para outro fim, designadamente comercial, carece de autorização do respetivo autor ou editor da obra.Na medida em que todas as obras da UC Digitalis se encontram protegidas pelo Código do Direito de Autor e Direitos Conexos e demais legislação aplicável, toda a cópia, parcial ou total, deste documento, nos casos em que é legalmente admitida, deverá conter ou fazer-se acompanhar por este aviso. Paternal and maternal lineages in

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“…To ensure data quality by a redundant approach to data generation and analysis [13], duplicate amplifications were sequenced in both the forward and reverse directions, and the resultant consensus sequences were analyzed using mtDNAmanager (available from http://mtmanager.yonsei. ac.kr/) to estimate the most probable mtDNA haplogroup based on the patterns of shared haplogroup-specific or haplogroup-associated polymorphisms in the control region [14]. Sequences have been submitted and will be searchable via the EMPOP database (http://www.empop.org) under accession numbers EMP00287-EMP00288.…”

Section: Dna Samplesmentioning

confidence: 99%

Forensic and genetic characterization of mtDNA from Pathans of Pakistan

et al. 2010

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Complete mitochondrial control region data were generated for 230 unrelated Pathans from North West Frontier Province and Federally Administered Tribal Areas of Pakistan. To confirm data quality and to explore the genetic structure of Pathans, mitochondrial DNA haplogroup affiliation was determined by shared haplogroup-specific polymorphisms in the control region and by the analysis of diagnostic coding region single-nucleotide polymorphisms using a multiplex system for the assignment of eight haplogroups: M, N1'5, W, R, R0, T, J, and U. Sequence comparison revealed that 193 haplotypes were defined by 215 variable sites when major insertions were ignored at nucleotide positions 16193, 309, and 573. From a phylogenetic perspective, Pathans have a heterogeneous origin, displaying a high percentage of West Eurasian haplogroups followed by haplogroups native to South Asia and a small fraction from East Asian lineages. In population comparisons, this ethnic group differed significantly from several other ethnic groups from Pakistan and surrounding countries. These results suggest that frequency estimates for mtDNA haplotypes should be determined for endogamous ethnic groups individually instead of pooling data for these subpopulations into a single dataset for the Pakistani population. Data presented here may contribute to the accuracy of forensic mtDNA comparisons in the Pathans of Pakistan.

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mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences

Cited by 82 publications

References 63 publications

News from the west: Ancient DNA from a French megalithic burial chamber

News from the west: Ancient DNA from a French megalithic burial chamber

Paternal and maternal lineages in Cabo Verde archipelago population

Forensic and genetic characterization of mtDNA from Pathans of Pakistan

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