The last glacial maximum bottlenecks and human phylogeny
I’ve mentioned The genomic origins of the world’s first farmers a few times. It’s an intense model-based paper that revises some expectations and models of the origins of diverse human […]
New David Reich talk
Eurogenes points me to a new talk by David Reich, that has a nice new long abstract online. I’ll just insert my comments within the blockquote… We present an integrative […]
Eurasia, the Stone Age and revenge of the Danes!
In the last week, I put up a big two-part series of posts on Substack, The wolf at history’s door and Casting out the wolf in our midst, about the […]
Population Pairwise Fst on 250,000 SNPs
People routinely ask me about a place to find pairwise Fst values. I have a dataset with 250,000 SNPs and 200 populations, and a script using plink that generates pairwise […]
The humans of Wallacea
A new open-access paper, Genome of a middle Holocene hunter-gatherer from Wallacea: Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record […]
Funnel Beaker, Corded Ware, Únětice, oh my!
Since David hasn’t mentioned it, I’m going to post some notes on Dynamic changes in genomic and social structures in third millennium BCE central Europe. This is a big deal […]
Complex history of archaic ancestry
On the Apportionment of Archaic Human Diversity: The apportionment of human genetic diversity within and between populations has been measured to understand human relatedness and demographic history. Likewise, the distribution […]
Natural selection caught in the act
Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes: Pathogens and associated outbreaks of infectious disease exert selective pressure on human […]
All the Yamnaya horizon zone people looked the same
The above figure is from The Beaker Phenomenon and the Genomic Transformation of Northwest Europe. At the time I noted it because the Bell Beaker people who arrived ~2500 BC […]
Lewontin’s Paradox in the 21st century
Why do species get a thin slice of π? Revisiting Lewontin’s Paradox of Variation: Under neutral theory, the level of polymorphism in an equilibrium population is expected to increase with […]
Natural selection continues (in the Viking world)
Nature has published a new Viking genomics paper. This morning I didn’t even bother to check it out, as I had other things going on, and there’s been so much ancient DNA from Scandinavia that my thought was “what else could we learn?” Well, it turns out I should have checked it out. The sample […]
It’s raining founder events
There’s a new preprint on bioRxiv that is very interesting, Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals: …To learn about the frequency and evolutionary history of founder events, we introduce ASCEND (Allele Sharing Correlation for the Estimation of Non-equilibrium Demography), a flexible two-locus method to infer the age […]
Who do the English think they are?
For centuries, debate has raged about whether England’s population is largely descended from German immigrants. Now, we have answers
Who do the English think they are?
In the early 5th century the Roman legions abandoned Britain, and the sceptered isle fell off the pages of history. When it reemerges two centuries later Celtic Britain had become the seedbed for the nation-state of England. The Christian religion, newly-established on the island at the time, had given way once again to paganism. Brythonic […]
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Who do the English think they are?
For centuries, debate has raged about whether England’s population is largely descended from German immigrants. Now, we have answers
Selection for pigmentation loci…but not pigmentation?
About a year and a half ago at ASHG, I had a discussion with Dan Ju and Iain Mathieson about their work on ancient pigmentation. Or, more precisely, ancient pigmentation related genes. Now it’s out in a preprint, The evolution of skin pigmentation associated variation in West Eurasia: …It is unclear whether selection has operated […]
Assessing the utility of models in ancient DNA admixture analyses
Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture: qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest […]
The Knanaya of Kerala do seem a bit more Near Eastern than other St. Thomas Christians
Last year I was approached by someone from the Knanaya community of South India as to their genetics. The Knanaya believe themselves to be descendants of later Near Eastern migrants than the other Nasrani St. Thomas Christians (both communities seem to believe in some connection to Near Eastern Jews). The history of these communities is […]
The details of Eurasian back-migration into Africa
Carl Zimmer has an interesting write-up on the new method to detect Neanderthal ancestry in Africa, Neanderthal Genes Hint at Much Earlier Human Migration From Africa. There are two quotes from researchers that are of note. First, from David Reich: Despite his hesitation over the analysis of African DNA, Dr. Reich said the new findings […]
If you meed a model, kill it!
If you are awake in the year 2019 you have heard of “machine learning.” And, if you listened to my podcast The Insight you know that Andy Kern’s lab at University of Oregon is leveraging machine learning (and “deep learning” and “neural networks”) for population genetics. Now, obviously in population genetics, you know that models […]