Out of who knows where
In The New York Times, DNA Turning Human Story Into a Tell-All: The tip of a girl’s 40,000-year-old pinky finger found in a cold Siberian cave, paired with faster and cheaper genetic sequencing technology, is helping scientists draw a surprisingly complex new picture of human origins. The new view is fast supplanting the traditional idea […]
Population structure using haplotype data
The Pith: New software which gives you a more fine-grained understanding of relationships between populations and individuals. According to the reader survey >50 percent of you don’t know how to interpret PCA or model-based (e.g., ADMIXTURE) genetic plots, so I am a little hesitant to point to this new paper in PLoS Genetics, Inference of […]
How the Amhara breathe differently
I have blogged about the genetics of altitude adaptation before. There seem to be three populations in the world which have been subject to very strong natural selection, resulting in physiological differences, in response to the human tendency toward hypoxia. Two of them are relatively well known, the Tibetans and the indigenous people of the […]
The quest for an Afrikaner genotype
Update: If interested, please email me at contactgnxp -at- gmail -dot- com. Also, I am getting some feedback via 23andMe that people with white South African matches noticed Africa segments in many of the ancestry paintings. This has definitely increased by probability that the admixture proportion is ~5 percent. There will probably be a few […]
The erectus within?
The Pith: More caveman admixture in modern humans, especially Melanesians! A new paper on archaic adaptive introgression among Melanesians has been discussed elsewhere. But I think it is worth reviewing, because it’s probably a foretaste of what’s to come. Researchers are combing through the human genome, as more and more genomes come on line, in […]
The phylogeography of the trans-Caucasus
Randy McDonald points me to this fascinating post, Genetic clues to the Ossetian past. In the post author outlines phylogeographic inferences one can make from uniparental lineages; maternal and paternal lines of descent. Specifically, they are in interested in the origins and relationships of the Ossete people. I assume that one reason Randy pointed me […]
Genes and Rex Wandalorum et Alanorum
The idea of a “folk wandering” was once a well accepted idea in history, in particular for the phase of the Late Roman Empire, and the subsequent fall of the Western Empire. It’s a rather simple concept: the collapse of the Pax Romana occurred simultaneous with a mass ethnic reordering of Europe, primarily via the […]
The Fulani have an old “Berber” (?) element
After the second Henn et al. paper I did download the data. Unfortunately there are only 62,000 SNPs intersecting with the HGDP. This is somewhat marginal for fine-grained ADMIXTURE analyses, though sufficient for PCA from what I recall. That being said, the intersection with the HapMap data sets runs from ~190,000 SNPs, to the full […]
Mendelism is not magic
Michelle points me to this article in The Lost Angeles Times, The Colors of the Family: I was holding my 1-year-old, ambling about downtown with some friends. White friends. She must have thought my boy belonged to one of them. There’s a simple explanation: I’m black but my son, Ashe, is white. At least he […]
The milkmen
Dienekes and Maju have both commented on a new paper which looked at the likelihood of lactase persistence in Neolithic remains from Spain, but I thought I would comment on it as well. The paper is: Low prevalence of lactase persistence in Neolithic South-West Europe. The location is on the fringes of the modern Basque […]
Reconstructing a generation unsampled
In the near future I will be analyzing the genotype of an individual where all four grandparents have been typed. But this got me thinking about my own situation: is there a way I could “reconstruct” my own grandparents? None of them are living. The easiest way to type them would be to obtain tissue […]
Between the desert and the sea
Zinedine Zidane, a Kabyle There is a new paper in PLoS Genetics out which purports to characterize the ancestry of the populations of northern Africa in greater detail. This is important. The HGDP data set does have a North African population, the Mozabites, but it’s not ideal to represent hundreds of millions of people with […]
“Missing heritability” – interaction edition
The Pith: A great deal of important medical genetic differences between people may be due to the nature of interactions of genetic variants. If you’ve been reading this blog for a while you know that there is a question in genomics right now as to “missing heritability.” The issue is basically that there are traits […]
The sons of Adam: spirit, not blood
Hominin increase in cranial capacity, courtesy of Luke Jostins A few years ago a statistical geneticist at Cambridge’s Sanger Institute, Luke Jostins, posted the chart above using data from fossils on cranial capacity of hominins (the human lineage). As you can see there was a gradual increase in cranial capacity until ~250,000 years before the present, […]
Lactose intolerant when you shouldn’t be
Milk, it does a body good (or not): I’ve discussed this before earlier this year, when we got our results back (my husband, children, in-laws, parents, siblings… etc have all done genomic scans), two results came back that surprised us but proved true. My mother-in-law and husband were likely lactose intolerant. When I pointed that […]
“Descendant of Genghis Khan” sequenced
Chinese Scientists Announce the First Complete Sequencing of Mongolian Genome: In this study, the DNA sample was from a male adult who belongs to the Mongolian “Royal Family” and is the 34th generation descendant of Genghis Khan. “The sample is very valuable for the study with a full record of family pedigree and no background […]
How to reconstruct the Indo-Europeans
As must be obvious, I think now that the spread of Indo-European languages had some demographic impact. It wasn’t analogous to the spread of English to Jamaica, or the existence of French as an official language in Congo-Brazzaville. Because of this, I now believe it is possible in the near future that scientists will reconstruct […]
No studies necessary: do your own replication!
In response to the post below I received the above response on twitter. This is an interesting case. The link goes to a paper in the year 2000, Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits: An analysis of 11 Alu insertion polymorphisms […]
The Basques are genetically distinctive
The Basque people of northern Spain loom large in any attempt to understand the ethnogenesis of European populations. That is because the speak the only indubitably indigenous non-Indo-European language in Western Europe. By this, I mean that other potential non-Indo-European languages such as the Tartessian or Pictish are either doubtful or uncertain in classification and […]
The history and geography of genomes
A new paper in PloS Genetics sheds some light on issues which we were already familiar with through conventional history, Ancestral Components of Admixed Genomes in a Mexican Cohort. What we already know: Mexicans and people of Mexican descent predominantly derive from an admixture event(s) between Europeans and Amerindians, with a minor African component. The […]