PhyloTree Build 17: Growing the human mitochondrial DNA tree

Oven, Mannis van

doi:10.1016/j.fsigss.2015.09.155

Cited by 175 publications

(163 citation statements)

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“…We assigned haplogroups using HaploGrep [36], in accordance with the nomenclature in PhyloTree (Build 17, February 2016) [37]. …”

Section: Methodsmentioning

confidence: 99%

“…We reconstructed the mitogenome phylogenetic tree manually, based on a preliminary reduced-median network analysis [38] with Network v.4.611, checked considering the frequency of each mutation [30] and the nomenclature of PhyloTree (Build 17) [37]. We estimated coalescence ages within haplogroups M and N using both the ρ statistic [39] and maximum likelihood (ML).…”

Section: Methodsmentioning

confidence: 99%

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A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

et al. 2017

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BackgroundIndia is a patchwork of tribal and non-tribal populations that speak many different languages from various language families. Indo-European, spoken across northern and central India, and also in Pakistan and Bangladesh, has been frequently connected to the so-called “Indo-Aryan invasions” from Central Asia ~3.5 ka and the establishment of the caste system, but the extent of immigration at this time remains extremely controversial. South India, on the other hand, is dominated by Dravidian languages. India displays a high level of endogamy due to its strict social boundaries, and high genetic drift as a result of long-term isolation which, together with a very complex history, makes the genetic study of Indian populations challenging.ResultsWe have combined a detailed, high-resolution mitogenome analysis with summaries of autosomal data and Y-chromosome lineages to establish a settlement chronology for the Indian Subcontinent. Maternal lineages document the earliest settlement ~55–65 ka (thousand years ago), and major population shifts in the later Pleistocene that explain previous dating discrepancies and neutrality violation. Whilst current genome-wide analyses conflate all dispersals from Southwest and Central Asia, we were able to tease out from the mitogenome data distinct dispersal episodes dating from between the Last Glacial Maximum to the Bronze Age. Moreover, we found an extremely marked sex bias by comparing the different genetic systems.ConclusionsMaternal lineages primarily reflect earlier, pre-Holocene processes, and paternal lineages predominantly episodes within the last 10 ka. In particular, genetic influx from Central Asia in the Bronze Age was strongly male-driven, consistent with the patriarchal, patrilocal and patrilineal social structure attributed to the inferred pastoralist early Indo-European society. This was part of a much wider process of Indo-European expansion, with an ultimate source in the Pontic-Caspian region, which carried closely related Y-chromosome lineages, a smaller fraction of autosomal genome-wide variation and an even smaller fraction of mitogenomes across a vast swathe of Eurasia between 5 and 3.5 ka.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0936-9) contains supplementary material, which is available to authorized users.

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“…We assigned haplogroups using HaploGrep [36], in accordance with the nomenclature in PhyloTree (Build 17, February 2016) [37]. …”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

et al. 2017

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“…The mtDNA haplogroup was determined using SAMtools pileup tool calling the positions defined in the Phylotree database (42). We used a genome browser ( IGV .v2.4.14) to study the genomic context of each possible SNP (43).…”

Section: Methodsmentioning

confidence: 99%

Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793)

de-Dios

Dorp

Charlier

et al. 2019

Preprint

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Significance 26The advent of second-generation sequencing technologies allows for the retrieval of ancient 27 genomes from long-dead people and, using non-human sequencing reads, of the pathogens that 28 infected them. In this work we combined both approaches to gain insights into the ancestry and 29 health of the controversial French revolutionary leader and physicist Jean-Paul Marat (1743-30 1793). Specifically, we investigate the pathogens, which may have been the cause of the 31 debilitating skin condition that was affecting him, by analysing DNA obtained from a paper 32 stained with his blood at the time of his death. This allowed us to confidently rule out several 33 conditions that have been put forward. To our knowledge, this represents the oldest successful 34 retrieval of genetic material from cellulose paper. Abstract 38The French revolutionary Jean-Paul Marat was assassinated in 1793 in his bathtub, where he 39 was trying to find relief from the debilitating skin disease he was suffering from. At the time of 40 his death, Marat was annotating newspapers, which got stained with his blood and were 41 subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain 42 and also from another section of the newspaper, which we used for comparison. Analysis of 43 human DNA sequences supported the heterogeneous ancestry of Marat, with his mother being 44 of French origin and his father born in Sardinia, although bearing more affinities to mainland 45 Italy or Spain. Metagenomic analyses of the non-human reads uncovered the presence of fungal, 46 bacterial and low levels of viral DNA. Relying on the presence/absence of microbial species in 47 the samples, we could confidently rule out several putative infectious agents that had been 48 previously hypothesised as the cause of his condition. Conversely, some of the detected species 49 are uncommon as environmental contaminants and may represent plausible infective agents.50

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“…Haploid variants were called using the endoCaller program implemented in Schmutzi ( 69 ) and only variants with a posterior probability exceeding 50 on the PHRED scale (probability of error: 1/100000) were retained. We then used Haplogrep 2.2 ( 70 ) to determine the mtDNA haplogroups, specifying PhyloTree (build 17) as the reference phylogeny ( 71 ) .…”

Section: Methodsmentioning

confidence: 99%

Stone Age "chewing gum" yields 5,700 year-old human genome and oral microbiome

Jensen

Niemann

Iversen

et al. 2018

Preprint

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We present a complete ancient human genome and oral microbiome sequenced from a piece of resinous "chewing gum" recovered from a Stone Age site on the island of Lolland, Denmark, and directly dated to 5,8585,661 cal. BP (GrM13305; 5,007±11). We sequenced the genome to an average depthofcoverage of 2.3× and find that the individual who chewed the resin was female and genetically more closely related to western huntergatherers from mainland Europe, than huntergatherers from central Scandinavia. We use imputed genotypes to predict physical characteristics and find that she had dark skin and hair, and blue eyes. Lastly, we also recovered microbial DNA that is characteristic of an oral microbiome and faunal reads that likely associate with diet. The results highlight the potential for this type of sample material as a new source of ancient human and microbial DNA.

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PhyloTree Build 17: Growing the human mitochondrial DNA tree

Cited by 175 publications

References 6 publications

A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793)

Stone Age "chewing gum" yields 5,700 year-old human genome and oral microbiome

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