The Genetic History of the Middle East: into Arabia
A new massive preprint on the Middle East is out. I’ve edited the first figure to give people a general sense of the broad results and populations sampled. First, you […]
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 […]
The Human Genome Diversity Project at high-coverage!
After a few years of presentations and preprints, the new high-quality whole-genome analysis of the HGDP dataset is finally published in Science, Insights into human genetic variation and population history from 929 diverse genomes. The HGDP dates back 30 years, so this is the culmination of a long line of research. The authors in this […]
The genomics of the Viking Age
A huge new preprint on Vikings (as well as the Bronze Age, Iron Age, and comparisons to moderns), Population genomics of the Viking world: …we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early modern period (c. 1600 CE), with particular […]
The vines around the tree trunks
A lot of the understanding of scientific theories and models in the public domain is communicated by evocative metaphors and turns of phrase. For example, Charles Darwin famously wrote: It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, […]
It’s raining selective sweeps
A week ago a very cool new preprint came out, Identifying loci under positive selection in complex population histories. It’s something that you can’t even imagine just ten years ago. The authors basically figure out ways to identify deviations of markers from expected allele frequency given a null neutral evolutionary model. The method is put […]
The population genetic structure of China (through noninvasive prenatal testing)
This week a big whole genome analysis of China was published in Cell, Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. The abstract: We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population […]
Tracing the paths of Noah’s sons
The above admixture graph is from a new preprint, Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry. To be honest, if you read the supplementary text there’s almost no point in reading the main preprint, as it is far more in depth when it comes to the methodology as well as […]
The great human migrations (coming in waves)
The figure above is from a new paper, Estimating mobility using sparse data: Application to human genetic variation, which uses genomic data from late Pleistocene to the Iron Age in western Eurasia, and then infers migration rate considering both spatial distribution and the variable of time (remember that samples apart in time should also be […]
Beyond “Out of Africa” within Africa
It looks as if the vast majority (95% or more depending on the population) of the ancestry of non-African humans derives from a population expansion which began around ~60,000 years ago. Before this period some researchers argue there was a non-trivial period of isolation. The “long bottleneck” (David Reich alludes to this in Who We […]
Beyond “Out of Africa” within Africa
It looks as if the vast majority (95% or more depending on the population) of the ancestry of non-African humans derives from a population expansion which began around ~60,000 years ago. Before this period some researchers argue there was a non-trivial period of isolation. The “long bottleneck” (David Reich alludes to this in Who We […]
Rainforest hunter-gatherers are not primitive or primal
Recently I had a discussion with a friend that I suspect the “tropical pygmy” phenotype you see Central Africa and Southeast Asia is a pretty recent development. So this sort of assertion, “The Sentinelese tribe have remained on their North Sentinel Island, almost completely uncontacted for nearly 60,000 years…” is probably wrong. First, the Sentinelese […]
The genome of “Cheddar Man” is about to be published
If you are American you have probably heard about “Cheddar Man” in Bryan Sykes’ Seven Daughters of Eve. If you don’t know, Cheddar Man is a Mesolithic individual from prehistoric Britain, dating to 9,150 years before the present. Sykes’ DNA analysis concluded that he was mtDNA haplogroup U5, which is found in ~10% of modern […]
Runs of homozygosity are not good for your functioning
A must read review in Nature Reviews Genetics, Runs of homozygosity: windows into population history and trait architecture. Because it’s a paper on runs of homozygosity, James F. Wilson is on the apper. If you are the product of a first cousin marriage, you have lots of runs of homozygosity. That’s because some of you […]
Natural selection in humans (OK, 375,000 British people)
The above figure is from Evidence of directional and stabilizing selection in contemporary humans. I’ll be entirely honest with you: I don’t read every UK Biobank paper, but I do read those where Peter Visscher is a co-author. It’s in PNAS, and a draft which is not open access. But it’s a pretty interesting […]
Visualizing intra-European phylogenetic distances
In L. L. Cavalli-Sforza’s The History and Geography of Human Genes he used between population group genetic distances, as measured in FST values, to generate a series of visualizations, which then allowed him to infer historical processes. Basically the way it works is that you look at genetic variation, and see how much of […]
Visualizing intra-European phylogenetic distances
In L. L. Cavalli-Sforza’s The History and Geography of Human Genes he used between population group genetic distances, as measured in FST values, to generate a series of visualizations, which then allowed him to infer historical processes. Basically the way it works is that you look at genetic variation, and see how much of […]
Understanding prehistory through genetic inference and ancient DNA
Before David Reich’s book, Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, I highly recommend a new preprint from Pontus Skoglund and Iain Mathieson*, Ancient genomics: a new view into human prehistory and evolution. It’s basically at the sweet spot for a lot of readers: […]
Soft selection for gentleness in Puerto Rican African Honeybees
When I was a kid “killer bees” were a major pop culture thing. There were movies about the bees, and we would get updates about their march northward in the news. They were a cautionary tale of our species’ hubris. Today we have a little bit more perspective. These bees were actually just African […]
Africa, the churning continent
Martin Meredith’s The Fortunes of Africa glosses very quickly over one of the major reasons that the “great scramble” for the continent occurred in the late 19th century, the discovery of the usefulness of quinine as an anti-malarial agent. Perhaps because I’ve read Plagues and Peoples and The Retreat of the Elephants: An Environmental History […]