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”
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,
… Read the rest “Villabruna cluster in Late Epigravettian Sicily supports South Italian corridor for R1b-V88”
Recent open access paper The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean, by Hernández, Dugoujon, Novelletto, Rodríguez, Cuesta and Calderón, BMC Genetics (2017).
Abstract (emphasis mine):
The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These
… Read the rest “Distribution of Southern Iberian haplogroup H indicates exchanges in the western Mediterranean”
Josif Lazaridis tweets about an interesting preprint at BioRxiv (eclipsed by today’s Nature papers), Ancestral heterogeneity of ancient Eurasians, by Daniel Shriner.
Supervised clustering or projection analysis is a staple technique in population genetic analysis. The utility of this technique depends critically on the reference panel. The most commonly used reference panel in the analysis of ancient DNA to date is based on the Human Origins array. We previously described a larger reference panel that captures more ancestries on the global level. Here, I reanalyzed DNA data from 279 ancient Eurasians using our reference panel, finding substantially
… Read the rest “Ancestral heterogeneity of ancient Eurasians”
Article behind paywall, Whole-sequence analysis indicates that the Y chromosome C2*-Star Cluster traces back to ordinary Mongols, rather than Genghis Khan, by Wei, Yan, Lu, et al. Eur J Hum Genet (2018); 26:230–237
The Y-chromosome haplogroup C3*-Star Cluster (revised to C2*-ST in this study) was proposed to be the Y-profile of Genghis Khan. Here, we re-examined the origin of C2*-ST and its associations with Genghis Khan and Mongol populations. We analyzed 34 Y-chromosome sequences of haplogroup C2*-ST and its most closely related lineage. We redefined this paternal lineage as C2b1a3a1-F3796 and generated a highly revised phylogenetic tree of
… Read the rest “Y chromosome C2*-star cluster traces back to ordinary Mongols, rather than Genghis Khan”
Adam Rutherford writes You’re Descended from Royalty and So Is Everybody Else – Anybody you can name from ancient history is in your family tree, which I discovered via John Hawks’ new post The surprising connectedness of human genealogies over centuries.
One way to think of it is to accept that everyone of European descent should have billions of ancestors at a time in the 10th century, but there weren’t billions of people around then, so try to cram them into the number of people that actually were. The math that falls out of that apparent impasse
… Read the rest “We are all special, which also means that none of us is”
New open access article published in Scientific Reports, Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ, by Solé-Morata et al. (2017).
Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where
… Read the rest “Analysis of R1b-DF27 haplogroups in modern populations adds new information that contrasts with ‘steppe admixture’ results”
A preprint paper has been published in BioRxiv, Relationships between clans and genetic kin explain cultural similarities over vast distances: the case of Yakutia, by Zvenigorosky et al (2017).
Archaeological studies sample ancient human populations one site at a time, often limited to a fraction of the regions and periods occupied by a given group. While this bias is known and discussed in the literature, few model populations span areas as large and unforgiving as the Yakuts of Eastern Siberia. We systematically surveyed 31,000 square kilometres in the Sakha Republic (Yakutia) and completed the archaeological study of 174
… Read the rest “How to do modern phylogeography: Relationships between clans and genetic kin explain cultural similarities over vast distances”