A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from Its Root

Behar, Doron M.; Oven, Mannis van; Metspalu, Mait; Loogväli, Eva-Liis; Silva, Nuno; Kivisild, Toomas; Torroni, Antonio; Villems, Richard

doi:10.1016/j.ajhg.2012.04.007

Cited by 76 publications

(98 citation statements)

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“…37 T2e1b is supported by 11 complete mtDNA sequences, including the Braganc¸a Jews. Except for two samples from mtDNA Community database, 67 without information concerning their ethnicity, all the remaining nine individuals are Jews, Sephardim or Ashkenazim.…”

Section: Echoes From Sepharad I Nogueiro Et Almentioning

confidence: 99%

Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants

et al. 2014

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The majority of genetic studies on Jewish populations have been focused on Ashkenazim, and genetic data from the Sephardic original source, the Iberian Peninsula, are particularly scarce. Regarding the mitochondrial genome, the available information is limited to a single Portuguese village, Belmonte, where just two different lineages (a single one corresponding to 93.3%) were found in 30 individuals. Aiming at disclosing the ancestral maternal background of the Portuguese Jewry, we enlarged the sampling to other crypto-Jewish descendants in the Braganc¸a district (NE Portugal). Fifty-seven complete mtDNA genomes were newly sequenced and -in contrast with Belmonte -a high level of diversity was found, with five haplogroups (HV0b, N1, T2b11, T2e and U2e) being putatively identified as Sephardic founding lineages. Therefore -in sharp contrast with Belmonte -these communities have managed to escape the expected inbreeding effects caused by centuries of religious repression and have kept a significant proportion of the Sephardic founder gene pool. This deeper analysis of the surviving Sephardic maternal lineages allowed a much more comprehensive and detailed perspective on the origins and survival of the Sephardic genetic heritage. In line with previously published results on Sephardic paternal lineages, our findings also show a surprising resistance to the erosion of genetic diversity in the maternal lineages.

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Section: Echoes From Sepharad I Nogueiro Et Almentioning

confidence: 99%

Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants

et al. 2014

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“…We then only analysed sequences that matched the expected 7mer barcodes, allowing up to two mismatches. Using bwa 0.6.1-r104 [32] we performed alignments twice: (i) to the human reference genome (hg19) which contains the rCRS mitochondrial genome, and to (ii) the reconstructed sapiens reference sequence mitochondrial sequence [33]. We computed target coverage with BEDTOOLS v. 2.16.2 [34] and used MAPDAMAGE v. 2.0 [35] to compute damage rates and fragmentation patterns.…”

Section: ( J) Target Capturementioning

confidence: 99%

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

Rohland

Harney

Mallick

et al. 2015

Phil. Trans. R. Soc. B

422

441

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The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 ancient human samples.

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“…For convenience, the nomenclature for haplogroups A-G were updated from our previous study based on CR (Liu et al, 2006), and in part because they were already used frequently. The nomenclature conformed to the rules for the human mtDNA phylogeny (van Oven and Kayser, 2009;Behar et al, 2012) for the newly defined haplogroups (that is, H, I and W-Z), subhaplogroups (for example, C1, C2 and C3) and macro-haplogroups (for example, ABZY and CD). An example of the nested hierarchy was as follows: C1-C-CD.…”

Section: Phylogeny Of Chickens Based On Mtdna Genomesmentioning

confidence: 99%

Chicken domestication: an updated perspective based on mitochondrial genomes

et al. 2012

Heredity

222

359

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Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A-I and W-Z. Common haplogroups A-G were shared by domestic chickens and red junglefowl. Rare haplogroups H-I and W-Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.

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A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from Its Root

Cited by 76 publications

References 0 publications

Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants

Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

Chicken domestication: an updated perspective based on mitochondrial genomes

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