genetics
razib | March 16, 2010There's an article in The New York Times on the recent paper which extracted genetic material from remains in Xinjiang dated to 4,000 years ago. Remember that these remains exhibited male lineages which were west Eurasian, specifically R1a1, while the female lineages (mtDNA) were more heterogeneous, both eastern and western. This particular twist in history is of very strong interest. I think there are three reasons for this. First, it is counter-intuitive, as we don't have a good grasp of how mobile ancient nomadic populations were. Most of their history is unaccessible because they were…
grrlscientist | March 12, 2010tags: evolution, evolutionary biology, gynandromorph, bilateral gynandromorph bird, half-sider, mixed-sex chimaera, sex determination, molecular biology, genetics, developmental biology, endocrinology, birds, chicken, Gallus gallus, ornithology, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club
Half-sider.
Almost exactly one year ago, hundreds of American birders
were thrilled by sightings and photographs of this remarkable
Northern Cardinal, or Redbird, Cardinalis cardinalis,
photographed in Warrenton, VA.
Image: DW Maiden, 2 March 2009.
I'll never forget the…
edyong | March 11, 2010Not Exactly Pocket Science is a set of shorter write-ups on new stories with links to more detailed takes by the world's best journalists and bloggers. It is meant to complement the usual fare of detailed pieces that are typical for this blog.
Geneticist sequences own genome, finds genetic cause of his disease
If you've got an inherited disease and you want to find the genetic faults responsible, it certainly helps if you're a prominent geneticist. James Lupski (right) from the Baylor College of Medicine suffers from an incurable condition called Charcot-Marie-Tooth (CMT) disease, which…
razib | March 10, 2010Reviewed by other ScienceBloggers:
Prehistoric DNA reveals the story of a Pleistocene survivor, the muskox
Ancient DNA Isolated from Fossil Eggshells May Provide Clues to Eggstinction of Giant Birds
laelaps | March 10, 2010A muskox (Ovibos moschatus), photographed in Alaska. From Flickr user drurydrama.
Of all the mass extinctions that have occurred during earth's history, among the most hotly debated is the one which wiped out mammoths, saber-toothed cats, giant ground sloths, and the other peculiar members of the Pleistocene megafauna around 12,000 years ago. It was not the most severe mass extinction, not by a long shot, but unlike the end-Cretaceous catastrophe 65 million years ago there is no single "smoking gun" that can account for the pattern of extinction. Instead the Pleistocene mass extinction…
grrlscientist | March 10, 2010tags: evolution, evolutionary biology, ancient DNA, aDNA, molecular biology, molecular ecology, archaeology, paleontology, fossil eggshell, extinct birds, giant moa, Dinornis robustus, elephant birds, Aepyornis maximus, Mullerornis, Thunderbirds, Genyornis, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club
Elephant bird, Aepyornis maximus, egg
compared to a human hand with a hummingbird egg balanced on a fingertip.
To conduct my avian research, I've isolated and sequenced DNA from a variety of specimens, such as blood, muscle, skin and a variety of internal…
edyong | March 10, 2010The animal on the right is no ordinary chicken. Its right half looks like a hen but its left half (with a larger wattle, bigger breast, whiter colour and leg spur) is that of a cockerel. The bird is a 'gynandromorph', a rare sexual chimera. Thanks to three of these oddities, Debiao Zhao and Derek McBride from the University of Edinburgh have discovered a truly amazing secret about these most familiar of birds - every single cell in a chicken's body is either male or female. Each one has its own sexual identity. It seems that becoming male or female is a very different process for birds than…
edyong | March 9, 2010Even extinction and the passing of millennia are no barriers to clever geneticists. In the past few years, scientists have managed to sequence the complete genome of a prehistoric human and produced "first drafts" of the mammoth and Neanderthal genomes. More controversially, some groups have even recovered DNA from dinosaurs. Now, a variety of extinct birds join the ancient DNA club including the largest that ever lived - Aepyornis, the elephant bird.
In a first for palaeontology, Charlotte Oskam from Murdoch University, Perth, extracted DNA from 18 fossil eggshells, either directly…
razib | March 7, 2010The odds of knowing your cousins: 23andme Part 1:
Bizarrely, Jonathan Zittrain turns out to be my cousin -- which is odd because I have known him for some time and he is also very active in the online civil rights world. How we came to learn this will be the first of my postings on the future of DNA sequencing and the company 23andMe.
Just read the whole thing. This is really a matter of the humanities, not science. Specifically, the almost mystical significance people seem to put into the finding that they share genetic ancestry with people, even people who they knew and were friendly with…
clock | March 5, 2010From the American Scientist:
Our American Scientist pizza lunch talk falls later than usual this month to accommodate our magazine's May-June issue deadline. Keep open the noon hour on March 30 and come hear Geoff Ginsburg, director of the Center for Genomic Medicine at Duke University, discuss genomic and personalized medicine.
To keep you on your toes, we'll convene at a different spot: the easy-to-get-to headquarters of the NC Biotechnology Center here in RTP. Actually, as many of you know, there would be no pizza lunch this year without the support of the Biotech Center. In addition to…
razib | March 4, 2010Over the history of this weblog I have blogged about pigmentation a fair amount. The major reason is that that's where the money is; unlike height, let alone intelligence, the genetic architecture and evolutionary history of pigmentation has been elucidated with relative clarity. That is, we know roughly the number and nature of the genes which control much of the between population variation in pigmentation. And, we also have some sense of whether the variation is due to natural selection, as well the historical trajectory of the between population differences.
For example, consider the…
razib | March 4, 2010A new paper in PLoS, Rapid Assessment of Genetic Ancestry in Populations of Unknown Origin by Genome-Wide Genotyping of Pooled Samples:
Many association studies have been published looking for genetic variants contributing to a variety of human traits such as obesity, diabetes, and height. Because the frequency of genetic variants can differ across populations, it is important to have estimates of genetic ancestry in the individuals being studied. In this study, we were able to measure genetic ancestry in populations of mixed ancestry by genotyping pooled, rather than individual, DNA samples…
razib | March 3, 2010I'm hearing about rumblings at 23andMe, and not in a good way. The company made a big splash a few years ago, and came highly recommended by friends (e.g., "They know their science, and have a bottomless pool of money"). This story at BNET got my attention though, and confirmed what many have been hinting at, or just telling me straight-up. Let's start the from the beginning. Back in late 2008 23andMe seemed absolutely untouchable. Here's Andrew Yates of Think Gene from then:
People, 23andMe isn't going anywhere. They are the Bill & Melinda Gates Sergey & Anne Brin Foundation,…
edyong | March 3, 2010You are outnumbered by a factor of 10 to one, by forces you cannot see. Your body has around ten trillion cells, but it's also home to a hundred trillion bacteria. For every gene in your genome, there are 100 bacterial ones. Most of these are found the dark, dank environment of your bowel but their incredible diversity is being brought to the surface. Say hello to the gut metagenome.
Together with a team of international scientists, Junjie Qin and Ruiqiang Li from BGI-Shenzen had the unenviable task of studying the bacteria from the faeces of 124 Europeans. They used a formidable and…
neurophilosophy | March 3, 2010THE perception and recognition of faces is crucial for the social situations we encounter every day. From the moment we are born, we prefer looking at faces than at inanimate objects, because the brain is geared to perceive them, and has specialized mechanisms for doing so. Such is the importance of the face to everyday life, that we see faces everywhere, even when they are not there.
We know that the ability to recognize faces varies among individuals. Some people are born with prosopagnosia, the inability to recognize faces, and others acquire the condition as a result of brain damage. At…
razib | March 2, 2010As you know lactase persistence (LP), which confers the ability to digest lactose sugar as an adult, is an evolutionarily recent development. On the order of 1/3 of the human population exhibits LP, due to a variety of genetic mutations which seem to arise in the cultural background of the domestication of cattle. Some have asked about the possible associations between LP & height & weight before. A new paper in Human Molecular Genetics looks at just that, European lactase persistence genotype shows evidence of association with increase in body mass index:
The global prevalence of…
razib | March 1, 2010I have pointed to the fact that mtDNA genetics has suggested that the polar bear is actually a derived lineage of brown bears. And, more specifically, that some extant lineages of brown bears share a more recent common ancestor with polar bears than other brown bears. In other words, brown bears are paraphyletic. Apparently there has been dispute of when the polar bear morph emerged from the brown bears. Luckily polar bears have been resident in a region where the likelihood of preservation of ancient DNA is relatively high. PNAS has a new paper which reports on the extraction of genetic…
razib | March 1, 2010A few days ago I pointed to a paper which suggests the possible utility of looking at selection on standing genetic variation on quantitative traits to get a sense of the role of adaptation in the human genome. We humans like to think we're a complex species, so I see no a priori reason why our evolutionary history should be easily reducible to spare compact dynamics. Granted, we can start with the assumption that on the order of 50,000 years before the present there was a rapid demographic expansion of anatomically modern humans out of the continent of Africa. This story is simple, and is…
razib | February 27, 2010Check out Dr. Dan MacArthur's assessment of the Pacific Biosciences presentation at the Advances in Genome Biology and Technology conference. Also check out Genetic Inferences take on AGBT (yes, they're really original with catchy blog names at the Sanger Institute!). In any case, a friend of mine was raving about Pacific Biosciences a few months ago, so I assumed it would blow up soon.
razib | February 27, 2010The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation:
There has long been interest in understanding the genetic basis of human adaptation. To what extent are phenotypic differences among human populations driven by natural selection? With the recent arrival of large genome-wide data sets on human variation, there is now unprecedented opportunity for progress on this type of question. Several lines of evidence argue for an important role of positive selection in shaping human variation and differences among populations. These include studies of comparative…