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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Tales of Human Migration, Admixture, and Selection in Africa

african-migrations

Comprehensive review (behind paywall) Tales of Human Migration, Admixture, and Selection in Africa, by Carina M. Schlebusch & Mattias Jakobsson, Annual Review of Genomics and Human Genetics (2018), Vol. 9.

Abstract (emphasis mine):

In the last three decades, genetic studies have played an increasingly important role in exploring human history. They have helped to conclusively establish that anatomically modern humans first appeared in Africa roughly 250,000–350,000 years before present and subsequently migrated to other parts of the world. The history of humans in Africa is complex and includes demographic events that influenced patterns of genetic variation across the continent.

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A history of male migration in and out of the Green Sahara

Open access research highlight A history of male migration in and out of the Green Sahara, by Yali Xue, Genome Biology (2018) 19:30, on the recent paper by D’Atanasio et al.

Insights from the Green Saharan Y-chromosomal findings (emphasis mine):

It is widely accepted that sub-Saharan Y chromosomes are dominated by E-M2 lineages carried by Bantu-speaking farmers as they expanded from West Africa starting < 5 kya, reaching South Africa within recent centuries [4]. The E-M2-Bantu lineages lie phylogenetically within the E-M2-Green Sahara lineage and show at least three explosive lineage expansions beginning 4.9–5.3 kya [5] (Fig. 1a). These events of

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