Ancient phylogeography: spread of haplogroups R1b, R1a and N

haplogroups-r1a-r1b-q

The previous post showed the potential use of TreeToM to visualize ancient DNA samples in maps together with their Y-DNA phylogenetic trees. I have written Newick trees for Y-chromosome haplogroups R1b-L388 (encompassing R-V1636 and R-P297, which in turn split into R-M73 and R-M269), R1a, and N.

I have reviewed some of the BAM files from my previous bulk analyses with YLeaf v.2, to add information that I had not previously included in the All Ancient DNA Dataset, and which might be relevant to the proper depiction of phylogenetic trees; in particular, positive and negative SNPs potentially distinguishing archaicRead the rest “Ancient phylogeography: spread of haplogroups R1b, R1a and N”

The expansion of Indo-Europeans in Y-chromosome haplogroups

yamnaya-corded-ware-y-dna-haplogroups

I have compiled for two years now the reported Y-DNA and mtDNA haplogroups of ancient DNA samples published, including also SNPs from analysis of the BAM files by hobbyists.

Y-DNA timeline

Here is a video with a timeline of the evolution of Indo-European speakers, according to what is known today about reconstructed languages, prehistoric cultures and ancient DNA:

NOTE. The video is best viewed in HD 1080p (1920×1080) with a display that allows for this or greater video quality, and a screen big enough to see haplogroup symbols, i.e. tablet or greater. The YouTube link is here. The Read the rest “The expansion of Indo-Europeans in Y-chromosome haplogroups”

Biparental inheritance of mitochondrial DNA in humans

mtdna-inheritance-paternal

New paper Biparental Inheritance of Mitochondrial DNA in Humans, by Luo et al. PNAS (2018).

Interesting excerpts (emphasis mine):

Abstract

Although there has been considerable debate about whether paternal mitochondrial DNA (mtDNA) transmission may coexist with maternal transmission of mtDNA, it is generally believed that mitochondria and mtDNA are exclusively maternally inherited in humans. Here, we identified three unrelated multigeneration families with a high level of mtDNA heteroplasmy (ranging from 24 to 76%) in a total of 17 individuals. Heteroplasmy of mtDNA was independently examined by high-depth whole mtDNA sequencing analysis in our research laboratory and in two Clinical

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Y-chromosome mixture in the modern Corsican population shows different migration layers

mesolithic-europe

Open access Prehistoric migrations through the Mediterranean basin shaped Corsican Y-chromosome diversity, by Di Cristofaro et al. PLOS One (2018).

Interesting excerpts:

This study included 321 samples from men throughout Corsica; samples from Provence and Tuscany were added to the cohort. All samples were typed for 92 Y-SNPs, and Y-STRs were also analyzed.

Haplogroup R represented approximately half of the lineages in both Corsican and Tuscan samples (respectively 51.8% and 45.3%) whereas it reached 90% in Provence. Sub-clade R1b1a1a2a1a2b-U152 predominated in North Corsica whereas R1b1a1a2a1a1-U106 was present in South Corsica. Both SNPs display clinal distributions of frequency variation in

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Yleaf: software for human Y-chromosomal haplogroup inference from next generation sequencing data

portugal-bronze-age-admixture

Brief communication (behind paywall) Yleaf: software for human Y-chromosomal haplogroup inference from next generation sequencing data, by Arwin Ralf, Diego Montiel González, Kaiyin Zhong, and Manfred Kayser, Mol Biol Evol (2018), msy032.

Abstract

Next generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data it now contains many thousands. The complexity of both, Y tree and NGS data

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Potential Afroasiatic Urheimat near Lake Megachad

palaeolithic-migrations

The publication of new ancient DNA samples from Africa is near, according to people at the SMBE meeting. As reported by Anthropology.net, a group by Pontus Skoglund has analysed new samples (complementing the study made by Carina Schlebusch), so we will have ancient samples of Africans from 300 to 6,000 years ago. They have been compared to the data of modern African populations, and among their likely conclusions (to be published):

  • Several thousand years ago, likely Tanzanian herders migrated far and wide, reaching Southern Africa centuries before the first farmers.
  • West Africans were likely early contributors to the
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