genetics
razib | February 24, 2010The IGF1 small dog haplotype is derived from Middle Eastern gray wolves:
Background
A selective sweep containing the insulin-like growth factor 1 (IGF1) gene is associated with size variation in domestic dogs. Intron 2 of IGF1 contains a SINE element and single nucleotide polymorphism (SNP) found in all small dog breeds that is almost entirely absent from large breeds. In this study, we surveyed a large sample of grey wolf populations to better understand the ancestral pattern of variation at IGF1 with a particular focus on the distribution of the small dog haplotype and its relationship to…
razib | February 23, 2010Two posts for your consideration.
On the Less Wrong weblog, Babies and Bunnies: A Caution About Evo-Psych. I am not one to make blanket dismissals of "evolutionary psychology." But, there are structural problems with the strong incentives toward generating hypotheses at the equipoise of novelty and intuitive plausibility. In other words, much of the evo-psych which penetrates the broader public mindspace is driven by demand-side forces.
Over at EconLog Bryan Caplan has a post, Born Gay, where the newly famous Ryan Sorba is shown to be pretty close to a total behavior genetics denialist. Until…
milhayser | February 22, 2010
Science is knowledge, and knowledge can inspire certainty. But certainty, as much a fruit of science, can be its enemy. Whatever wonders may meet the eye, there has always been more to the world. On Oscillator, Christina Agapakis explores the frontiers of synthetic biology, where researchers hope to manufacture "altered proteins or entirely different biological polymers" by creating a "parallel genetic code" that uses four-letter codons instead of three. On Starts With A Bang!, Ethan Siegel recounts two centuries of paradigm shifts, and asks what the next "new" law of nature will be.…
edyong | February 21, 2010Whiptail lizards are a fairly ordinary-looking bunch, but some species are among the strangest animals around. You might not be able to work out why at first glance, but looking at their genes soon reveals their secret - they're all female, every single one. A third of whiptails have done away with males completely, a trick that only a small minority of animals have accomplished without going extinct.
Some readers might rejoice at the prospect of a world without males but in general, this isn't good news for a species. Sex has tremendous benefits. Every fling shuffles the genes of the two…
razib | February 20, 2010An interesting exchange in Nature on ways to conceptualize the evolution of virulence. First, Adaptation and the evolution of parasite virulence in a connected world:
Adaptation is conventionally regarded as occurring at the level of the individual organism, where it functions to maximize the individual's inclusive fitness...However, it has recently been argued that empirical studies on the evolution of parasite virulence in spatial populations show otherwise...In particular, it has been claimed that the evolution of lower virulence in response to limited parasite dispersal...provides proof…
milhayser | February 19, 2010
On Not Exactly Rocket Science, Ed Yong reports that two new human genomes have been sequenced: that of South African leader Desmond Tutu, and that of !Gubi, a tribal hunter-gatherer. Along with !Gubi, researchers examined the genes of three other Bushmen, and the diversity they observed was "astounding." Ed writes that there is more genetic variation between any two of these individuals than there is between "a European and an Asian," and trying "to understand human genetics without understanding Africa is like trying to learn a language by only looking at words starting with z." On Gene…
razib | February 17, 2010The language families of Europe fall into a few broad categories. There are the Indo-European languages, which include the Romance, Germanic, Slavic and Celtic subgroups, along with Greek and Albanian. The Iranian languages and most of the languages of India are also Indo-European. Then there are the languages of Finland and Hungary, which are hypothesized to be of a broader Finno-Ugric family. Whatever the validity of this cluster, the relationship of Hungarian and Finnish to languages which are extant deep into Eurasia, beyond the Urals and into Siberia, are not disputed. Turkic and Semitic…
razib | February 17, 2010To the left I've juxtaposed the images of the four Bushmen males whose genomes were analyzed in the recent Nature paper and compared to Desmond Tutu. I've added to the montage a photo of a Swedish and Chinese man. The Nature paper looked at the HapMap data sets which had within them whites from Utah, northwest Europeans, and Chinese from Beijing, and compared these populations to the Bushmen and Desmond Tutu. One important point that this paper emphasized was that the rule-of-thumb that African populations have the most extant genetic diversity of all human groups, and that the Bushmen have…
razib | February 17, 2010There's a new paper out in Nature which details the genomes of several Bushmen, and how they relate to other humans, and one particular Bantu speaking individual, archbishop Desmond Tutu. It's open access, Complete Khoisan and Bantu genomes from southern Africa. I haven't read the whole thing, but it is probably best to check out Ed Yong's very thorough review first. Here's an interesting point Ed brings up:
Most surprising of all, many of their unique SNPs are actually fairly recent developments. The Bushmen are one of the oldest human groups on the planet and you might expect their genes to…
edyong | February 17, 2010
Meet !Gubi, the tribal elder of a group of Bushmen (or Khoisan), one of the oldest known human lineages. He lives the life of a hunter-gatherer in the Namibian part of the Kalahari Desert. But he also has a strange connection to James Watson, the British American scientist who helped to discover the structure of DNA. For a start, they're both around 80 years old. But more importantly, they are two of just 11 humans to have their entire genomes sequenced.
Along with Archbishop Desmond Tutu, !Gubi is one of two southern Africans, whose full genomes have been sequenced by Stephan Schuster and…
razib | February 16, 2010Lactase persistence results in the ability to break down the lactose sugar in milk as an adult, lactase being the enzyme which breaks down lactose. If one can not digest that sugar, and still consumes milk, then one exhibits the symptoms of lactose intolerance. Originally diagnosed as a disease it has come to light that 2/3 of the world's population is lactose intolerant, and, that this is probably the ancestral "wild type" (I would be interested if readers could name a mammal which exhibited lactase persistence aside from humans). Lactase persistence is a relatively new trait which emerged…
edyong | February 16, 2010All of our cells are staffed by armies of executioners. They are usually restrained but when unleashed, they can set off a fatal chain reaction that kills the cell. This suicide squad does away with billions of cells every day. It helps to balance the production of new cells with the loss of old ones, to sculpt growing tissues and to destroy potential cancer cells.
But a new study suggests that the executioners aren't always lethal. In fact, they're essential for life. Through the unorthodox method of damaging our DNA, they can actually activate important genes. This technique for switching…
razib | February 15, 2010Dr. Daniel MacArthur reports on shenanigans in his homeland, Australian insurance company offers discounted genome scans to customers; read the fine print!:
A reader pointed me to this article in the Australian news: it appears that a major Australian insurance company, NIB, is planning to offer half-price genome scans from personal genomics company Navigenics to 5,000 of its customers.
The catch is in the fine print: those who take up the offer "may have to give the information to life insurance or superannuation providers", according to the article. In a letter to customers, the chief…
razib | February 14, 2010Dr. Daniel MacArthur returns from hiatus, and observes that deCODE is now in the advanced stages of corporate death. Pointers to a Newsweek article and other bloggers at Dr. MacArthur's post. Over at Gene Expression Classic p-ter points out that Small genetic effects do not preclude drug development (one of the rationales given for why deCODE couldn't translate associations in $$$).
Also, for historical perspective, check out this 2002 article about deCODE.
razib | February 14, 2010One of the interesting aspects ensuing from the rise of molecular phylogenetics is that the trees are generally concordant in broad strokes with older research which was based on morphology. This is not too surprising, as nature does tend to show some intelligible patterns which can be cross-checked with different methods (e.g., the fact of evolutionary change in the tree of life is evident in both the paleontological record and analysis of molecular genetic variation). Additionally, the cladistic revolution has produced a general uniformity of underlying logic when it comes to systematic…
edyong | February 14, 2010
Millions of people in Latin America have been invade by a parasite - a trypanosome called Trypanosome cruzi. They are passed on through the bite of the blood-sucking assassin bug and they cause Chagas disease, a potentially fatal illness that affects the heart and digestive system. The infections are long-lasting; it can take decades for symptoms to show and a third of infected people eventually die from the disease. But T.cruzi does much more than invade our flesh and blood; it also infiltrates our genomes.
T.cruzi is unusual in that a massive proportion of its DNA, around 15-30%, lies…
clock | February 12, 2010A new forum at World Science is up. As always, listen to the podcast first, then ask questions in the forum:
This week, India rejected what would have been the country's first a genetically modified food crop, a transgenic eggplant.
The company that developed it, an Indian subsidiary of Monsanto, claims the crop would reduce pesticide use and boost yields. But the Indian government has decided to do independent assessments of the crop's potential impacts on consumer health and the environment.
What does this mean for the future of GM crops in India and elsewhere? And does this technology have…
razib | February 11, 2010Genome-Wide Association Study in Asian Populations Identifies Variants in ETS1 and WDFY4 Associated with Systemic Lupus Erythematosus:
In this study, we first conducted a genome-wide association study in a Hong Kong Chinese population, followed by replication in three other cohorts from Mainland China and a cohort from Thailand, which totaled 3,300 Asian patients and 4,200 ethnically and geographically matched controls. We identified novel variants in ETS1 and WDFY4 associated with SLE with genome-wide significance and confirmed the association of HLA locus, STAT4, BLK, IRF5, BANK1, TNFSF,…
razib | February 11, 2010Breeding Ancient Cattle Back from Extinction:
The only place to see an aurochs in nature these days? A cave painting. The enormous wild cattle that once roamed the European plains have been extinct since 1627, when the last survivor died in a Polish nature reserve. But this could soon change thanks to the work of European preservationists who are hoping they can make the great beast walk again. If they succeed -- through a combination of modern genetic expertise and old-fashioned breeding -- it would be the first time an animal has been brought back from extinction and released into the wild…