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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Sea Peoples behind Philistines were Aegeans, including R1b-M269 lineages

New open access paper Ancient DNA sheds light on the genetic origins of early Iron Age Philistines, by Feldman et al. Science Advances (2019) 5(7):eaax0061.

Interesting excerpts (modified for clarity, emphasis mine):

Here, we report genome-wide data from human remains excavated at the ancient seaport of Ashkelon, forming a genetic time series encompassing the Bronze to Iron Age transition. We find that all three Ashkelon populations derive most of their ancestry from the local Levantine gene pool. The early Iron Age population was distinct in its high genetic affinity to European-derived populations and in the high variation of that

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A Song of Sheep and Horses, revised edition, now available as printed books

cover-song-sheep-and-horses

As I said 6 months ago, 2019 is a tough year to write a blog, because this was going to be a complex regional election year and therefore a time of political promises, hence tenure offers too. Now the preliminary offers have been made, elections have passed, but the timing has slightly shifted toward 2020. So I may have the time, but not really any benefit of dedicating too much effort to the blog, and a lot of potential benefit of dedicating any time to evaluable scientific work.

On the other hand, I saw some potential benefit for … Read the rest “A Song of Sheep and Horses, revised edition, now available as printed books”

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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A Game of Thrones in Indo-European: proto-languages in Westeros and Essos, and population genomics

game-of-thrones-westeros-essos-map

I think proto-languages can be applied to basically any appropriate prehistoric setting, and especially to science fiction and fantasy settings. I often viewed the lack of interest for them as based on the idea that they are not fantastic enough, that they would render a fantastic world too realistic to allow for an adequate immersion of the reader (or viewer) into a new world.

With time, I have become more and more convinced that most authors don’t use proto-languages (or tweaked versions of them) simply because they can’t, and resort to the easier way: inventing some rules … Read the rest “A Game of Thrones in Indo-European: proto-languages in Westeros and Essos, and population genomics”

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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Happy new year 2019…and enjoy our new books!

song-sheep-horses-header

Sorry for the last weeks of silence, I have been rather busy lately. I am having more projects going on, and (because of that) I also wanted to finish a project I have been working on for many months already.

I have therefore decided to publish a provisional version of the text, in the hope that it will be useful in the following months, when I won’t be able to update it as often as I would like to:

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