An annotated mtDNA database

Röhl, Arne; Brinkmann, B.; Forster, Lucy; Forster, Peter

doi:10.1007/s004140100217

Cited by 61 publications

(42 citation statements)

References 89 publications

(95 reference statements)

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“…The geographic spread of South Tyrolean mtDNA haplotypes was quantified and visualized using the mtRadius database, 8 currently containing data from over 24 000 individuals. A centre-of-gravity (COG) analysis 37 was carried out using a minimal sequence range between positions 16093 and 16362, 15 leaving a total of 19 493 individuals active in the database, of which approximately 12 000 were from Europe and surrounding areas.…”

Section: Molecular Analysismentioning

confidence: 99%

New genetic evidence supports isolation and drift in the Ladin communities of the South Tyrolean Alps but not an ancient origin in the Middle East

et al. 2007

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The Alps are one of the most significant geographical barriers in Europe and several isolated Swiss and Italian valleys retain the distinctive Ladin and Romansch languages, alongside the modern majority of Italian and German languages. Linguistically, Ladin belongs to the Romance languages, but some studies on mitochondrial DNA (mtDNA) variation have suggested a major Middle Eastern component to their genealogical origin. Furthermore, an observed high degree of within-population diversity has been interpreted as reflecting long-standing differentiation from other European populations and the absence of a major bottleneck in Ladin population history. To explore these issues further, we examined Y chromosome and mtDNA variation in two samples of Ladin speakers, two samples of German speakers and one sample of metropolitan Italian speakers. Our results (1) indicate reduced diversity in the Ladinspeaking and isolated German-speaking populations when compared to a sample of metropolitan Italian speakers, (2) fail to identify haplotypes that are rare in other European populations that other researchers have identified, and (3) indicate different Middle Eastern components to Ladin ancestry in different localities. These new results, in combination with Bayesian estimation of demographic parameters of interest (population size, population growth rate, and Palaeolithic/Neolithic admixture proportions) and phylogeographic analysis, suggest that the Ladin groups under study are small genetically isolated populations (subject to strong genetic drift), having a predominantly European ancestry, and in one locality, may have a greater Palaeolithic component to that ancestry than their neighbours.

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Section: Molecular Analysismentioning

confidence: 99%

New genetic evidence supports isolation and drift in the Ladin communities of the South Tyrolean Alps but not an ancient origin in the Middle East

et al. 2007

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“…In many cases, however, there is an overlay of phantom mutations and numerous documentation (or other) errors that is difficult to untwine, as for example, in the data presented in [10][11][12]. With ancient DNA sequencing, one faces a real conundrum of whether unusual mutations were actually induced by (i) sample degradation and resulting post mortem damage [13,14] or (ii) contamination with extrinsic mtDNA [15] or (iii) infidelity of the polymerase at cloning [13] or (iv) phantom mutations in the electrophoresis [1], or (v) documentation errors [16,17]; see [18,19] for discussions of a pertinent case. Therefore, it is necessary to study these factors in isolation that contribute to the error load on sequencing studies.…”

Section: Introductionmentioning

confidence: 98%

Phantom mutation hotspots in human mitochondrial DNA

Brandstätter¹,

Sänger²,

Lutz-Bonengel³

et al. 2005

Electrophoresis

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Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30 000 published hypervariable segment I sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.

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“…HV1 sequences were classified into haplogroups, according to the nomenclature suggested by Richards et al [1,3] and Macaulay et al [34] for West Eurasian mtDNAs. All available data published on HV1-RFLP [3] or HV1 variability alone (summarized by Röhl et al [4]) in West Eurasian populations were used for a comparative analysis. Data on the HV1/HV2 sequence variability in Poles were taken from an earlier study [35].…”

Section: Phylogenetic Classification Of the Hv1 Sequencesmentioning

confidence: 99%

“…However, it is also possible that some detectable heteroplasmic events constitute a fingerprint of artificial "phantom" mutations, i.e., mutations generated in the mtDNA typing process itself. Latest observations of Bandelt et al [22,23] and Röhl et al [4] suggest that phantom mutations are widespread and affect mtDNA data presented in both evolutionary and forensic studies.…”

Section: Introductionmentioning

confidence: 97%

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High levels of mitochondrial DNA heteroplasmy in single hair roots: Reanalysis and revision

et al. 2003

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The present study demonstrates a reinvestigation of the mitochondrial DNA sequence heteroplasmy, which was previously found by the use of nested polymerase chain reaction (PCR) technique in single hairs of 13 individuals. The direct PCR approach was used for the amplification of mitochondrial DNA and a phylogenetic analysis was applied to both data sets for the verification of the authenticity of sequences. The comparative analysis of the sequencing results obtained from the same hair DNA extracts - but using two different techniques - shows that direct mitochondrial DNA amplification results in a considerably lower number of mixed positions. The majority of the confirmed heteroplasmic variants preferentially occurs in mitochondrial DNA hypervariable sites (mutational hotspots). However, the pattern of heteroplasmic mutations observed in four extracts after nested PCR significantly differs from the pattern of natural mutations. Some of these rare polymorphisms should be revised as inconsistent with phylogenetic expectations. The results of the present study contribute to the earlier reports by indicating that phylogenetic analysis is an effective tool in a posteriori quality check of mitochondrial DNA data.

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An annotated mtDNA database

Cited by 61 publications

References 89 publications

New genetic evidence supports isolation and drift in the Ladin communities of the South Tyrolean Alps but not an ancient origin in the Middle East

New genetic evidence supports isolation and drift in the Ladin communities of the South Tyrolean Alps but not an ancient origin in the Middle East

Phantom mutation hotspots in human mitochondrial DNA

High levels of mitochondrial DNA heteroplasmy in single hair roots: Reanalysis and revision

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