Visualizing phylogenetic trees of ancient DNA in a map

haplogroup-r1b-v88-v2219-phylogenetic

Yesterday the Eaton Lab at Columbia University announced on Twitter a nifty little tool by Carlos Alonso Maya-Lastra called TreeToM, which accepts Newick trees and CSV latitude/longitude data to explore phylogeny and geography interactively, with no coding required.

I thought it could complement nicely my All Ancient DNA Dataset, particularly for those newly described SNPs (FTDNA private variants, etc.) that have not been incorporated yet into SNP Tracker.

Here are two examples with snippets to copy&paste to the appropriate boxes in TreeToM. Feel free to add others in the comments:… Read the rest “Visualizing phylogenetic trees of ancient DNA in a map”

Villabruna cluster in Late Epigravettian Sicily supports South Italian corridor for R1b-V88

epipalaeolithic-whg-expansion

New preprint Late Upper Palaeolithic hunter-gatherers in the Central Mediterranean: new archaeological and genetic data from the Late Epigravettian burial Oriente C (Favignana, Sicily), by Catalano et al. bioRxiv (2019).

Interesting excerpts (emphasis mine):

Grotta d’Oriente is a small coastal cave located on the island of Favignana, the largest (~20 km2) of a group of small islands forming the Egadi Archipelago, ~5 km from the NW coast of Sicily.

The Oriente C funeral pit opens in the lower portion of layer 7, specifically sublayer 7D. Two radiocarbon dates on charcoal from the sublayers 7D (12149±65 uncal. BP) and 7E,

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Fulani from Cameroon show ancestry similar to Afroasiatic speakers from East Africa

sahel-region-fulani

Open access African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations, by Fan et al. Genome Biology (2019) 20:82.

Interesting excerpts (emphasis mine):

Introduction

To extend our knowledge of patterns of genomic diversity in Africa, we generated high coverage (30×) genome sequencing data from 43 geographically diverse Africans originating from 22 ethnic groups, representing a broad array of ethnic, linguistic, cultural, and geographic diversity (Additional file 1: Table S1). These include a number of populations of anthropological interest that have never previously been characterized for high-coverage genome sequence diversity such as Afroasiatic-speaking El

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Ancient Sardinia hints at Mesolithic spread of R1b-V88, and Western EEF-related expansion of Vasconic

nuragic-sardinia-neolithic

New preprint Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective, by Marcus et al. bioRxiv (2019)

Interesting excerpts (emphasis mine, edited for clarity):

On the high frequency of R1b-V88

Our genome-wide data allowed us to assign Y haplogroups for 25 ancient Sardinian individuals. More than half of them consist of R1b-V88 (n=10) or I2-M223 (n=7).

Francalacci et al. (2013) identified three major Sardinia-specific founder clades based on present-day variation within the haplogroups I2-M26, G2-L91 and R1b-V88, and here we found each of those broader haplogroups in at least one

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ASoSaH Reread (II): Y-DNA haplogroups among Uralians (apart from R1a-M417)

corded-ware-yamna-ancestry

This is mainly a reread of from Book Two: A Game of Clans of the series A Song of Sheep and Horses: chapters iii.5. Early Indo-Europeans and Uralians, iv.3. Early Uralians, v.6. Late Uralians and vi.3. Disintegrating Uralians.

“Sredni Stog”

While the true source of R1a-M417 – the main haplogroup eventually associated with Corded Ware, and thus Uralic speakers – is still not known with precision, due to the lack of R1a-M198 in ancient samples, we already know that the Pontic-Caspian steppes were probably not it.

We have many samples from the north Pontic area since Read the rest “ASoSaH Reread (II): Y-DNA haplogroups among Uralians (apart from R1a-M417)”

“Steppe ancestry” step by step: Khvalynsk, Sredni Stog, Repin, Yamna, Corded Ware

dzudzuana_pca-large

Wang et al. (2018) is obviously a game changer in many aspects. I have already written about the upcoming Yamna Hungary samples, about the new Steppe_Eneolithic and Caucasus Eneolithic keystones, and about the upcoming Greece Neolithic samples with steppe ancestry.

An interesting aspect of the paper, hidden among so many relevant details, is a clearer picture of how the so-called Yamnaya or steppe ancestry evolved from Samara hunter-gatherers to Yamna nomadic pastoralists, and how this ancestry appeared among Proto-Corded Ware populations.

Please note: arrows of “ancestry movement” in the following PCAs do not necessarily represent physical Read the rest ““Steppe ancestry” step by step: Khvalynsk, Sredni Stog, Repin, Yamna, Corded Ware”

On the origin of haplogroup R1b-L51 in late Repin / early Yamna settlers

steppe-eneolithic-migrations

A recent comment on the hypothetical Central European origin of PIE helped me remember that, when news appeared that R1b-L51 had been found in Khvalynsk ca. 4250-4000 BC, I began to think about alternative scenarios for the expansion of this haplogroup, with one of them including Central Europe.

Because, if YFull‘s (and Iain McDonald‘s) estimation of the split of R1b-L23 in L51 and Z2103 (ca. 4100 BC, TMRCA ca. 3700 BC) was wrong, by as much as the R1a-Z645 estimates proved wrong, and both subclades were older than expected, then maybe R1b-L51 was not part of … Read the rest “On the origin of haplogroup R1b-L51 in late Repin / early Yamna settlers”

Sahara’s rather pale-green and discontinuous Sahelo-Sudanian steppe corridor, and the R1b – Afroasiatic connection

palaeolakes-world

Interesting new paper (behind paywall) Megalakes in the Sahara? A Review, by Quade et al. (2018).

Abstract (emphasis mine):

The Sahara was wetter and greener during multiple interglacial periods of the Quaternary, when some have suggested it featured very large (mega) lakes, ranging in surface area from 30,000 to 350,000 km2. In this paper, we review the physical and biological evidence for these large lakes, especially during the African Humid Period (AHP) 11–5 ka. Megalake systems from around the world provide a checklist of diagnostic features, such as multiple well-defined shoreline benches, wave-rounded beach gravels where coarse material is

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R1b-V88 migration through Southern Italy into Green Sahara corridor, and the Afroasiatic connection

palaeolithic

Open access article The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages, by D’Atanasio, Trombetta, Bonito, et al., Genome Biology (2018) 19:20.

Abstract:

Background
Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment.

Results
In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of

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