Blondes of the ‘black islands’
Recently I was looking for images of the alpine biomes of the New Guinea highlands* and stumbled onto some intriguing, though not entirely surprising, set of photographs of individuals from Papua New Guinea. They were noteworthy because they manifested the conventional Melanesian physical type, but their hair had a blonde cast to it. For example, […]
Native American ancestry in African Americans
That is, in the African American sample in the HapMap3 population set. I was just browsing the Admixture manual, and stumbled onto this plot:
CEU = Utah Whites, and YRI = Yoruba. They should be familiar from the previous versions of the HapMap. MEX = Mexican Americans from Los Angeles. K = 3, three ancestral populations. […]
Hybridization is like sex
One of the major issues which has loomed at the heart of biology since The Origin of Species is why species exist, as well as how species come about. Why isn’t there a perfect replicator which performs all the conversion of energy and matter into biomass on this planet? If there is a God the tree […]
PCA, Razib around the world (a little)
I have put up a few posts warning readers to be careful of confusing PCA plots with real genetic variation. PCA plots are just ways to capture variation in large data sets and extract out the independent dimensions. Its great at detecting population substructure because the largest components of variation often track between population differences, […]
Koreans, not quite the purest race?
PLoS One has a paper out on Korean (South) population genetics and phylogeography, Gene Flow between the Korean Peninsula and Its Neighboring Countries:
SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry […]
Diseases of the Silk Road
Nature has two papers out about something called “Behçet’s disease.” It has apparently also been termed the “Silk Road Disease”, because of its associations with populations connected to the Central Eurasian trade networks.Though described by Hippocrates 2,500 years ago, apparently it was “discovered” only in the 20th century by a Turkish physician. The reason that […]
Personal genomics & the state
Dr. Daniel MacAthur & Dan Vorhaus offer their takes on the recent hearings in Congress on the direct-to-consumer genomics industry, A sad day for personal genomics & “From Gulf Oil to Snake Oil”: Congress Takes Aim at DTC Genetic Testing. I guess I lean toward light regulation. I don’t think that DTC personal genomics will […]
One principal component to rule them all?
Despite the reality that I’ve cautioned against taking PCA plots too literally as Truth, unvarnished and without any interpretive juice needed, papers which rely on them are almost magnetically attractive to me. They transform complex patterns of variation which you are not privy to via your gestalt psychology into a two or at most three […]
Disease as a byproduct of adaptation
How we perceive nature and describe its shape are a matter of values and preferences. Nature does not take notice of our distinctions; they exist only as instruments which aid in our comprehension. I’ve brought this up in relation to issues such as categorization of recessive vs. dominant traits. The offspring of people of […]
Genome-wide association for newbies
It looks like Genomes Unzipped has their own Mortimer Adler, with an excellent posting, How to read a genome-wide association study. For those outside the biz I suspect that #4, replication, is going to be the easiest. In the early 2000s a biologist who’d been in the business for a while cautioned about reading too […]
More Jews, fewer markers
At around the same time that the two big Jewish genetics papers came out, there was another one in BMC Genetics which I had overlooked. It’s open access so you can read the whole thing, but seems like they used 32 STR’s as markers. Their primary finding about Jewish populations was that there was a […]
Really fine grained genetic maps of Europe
A few years ago you started seeing the crest of studies which basically took several hundred individuals (or thousands) from a range of locations, and then extracted out the two largest components of genetic variation from the hundreds of thousands of variants. The clusters which fell out of the genetic data, with each point being […]
Genomic liftoff
The firm GenomeQuest has a blog, and on that blog they have a post, Implications of exponential growth of global whole genome sequencing capacity. In that post there are some bullet points with numbers. Here they are:
* 2001-2009: A Human Genome
* 2010: 1,000 Genomes – Learning the Ropes
* 2011: 50,000 Genomes – Clinical Flirtation
* 2012: […]
“Unzipped,” not the film about Isaac Mizrahi
Just got notice of a new weblog, Unzipped, which I have added to my RSS feed. One of the primary contributors is Dr. Daniel MacArthur of Genetic Future (no, he’s not leaving ScienceBlogs!). Another is the always impressive Luke Jostins. Here’s their raison d’etre:
Welcome to Genomes Unzipped, a new group blog bringing together experts in […]
Why Tibetans breathe so easy up high
I said yesterday I would say a bit more about the new paper on rapid recent high altitude adaptation among the Tibetans when I’d read the paper. Well, I’ve read it now. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude:
Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced […]
More markers, or more populations?
Here’s a letter to The American Journal of Human Genetics worth reading, Genetic Landscape of Eurasia and “Admixture” in Uyghurs:
…In the papers…by Xu and Jin, the genetic structure of Uyghurs was described by 8150 ancestry-informative markers (AIMs). These markers estimated the admixture rate of the Uyghur population to be around 50% East Asian ancestry by […]
Amerindians of Brazil more numerous than you think
A few months ago I was thinking a fair amount about the Neandertals. One issue which became more stark to me due to that particular finding, that a few percent of the human genome seems to have derived from Neandertal populations, is the reality that genetic distinctiveness can persist long after cultural coherency is no […]
The “how” of cystic fibrosis through the “why”
It’s just a fact that contemporary human evolutionary genetics has relied upon its potential insights into disease to generate funding, support and interest. I don’t think that this is much of a silver lining when set next to the suffering caused by disease, but it’s a silver lining nevertheless. Therefore findings which would be of […]
“What has bioinformatics done for us”
So asks Anthony Goldbloom: A British bioinformatician asks what bioinformatics has ever done for us? Or put differently, what is the single greatest biological discovery made possible by bioinformatics? He is offering $USD100 to the person who puts forward the most compelling answer (the prize is small but the idea is to stoke discussion). Kaggle […]
The State May Have Your Genome Sooner Than You Think
Slate has an interesting article, O Brother, Where Art Thou? It’s time for legislators to look more closely at familial searches of DNA databases. The principle is simple. States and national governments are already collecting genetic material from persons who have had brushes with the criminal justice system and assembling databases. These individuals naturally have […]