genetics
razib | February 10, 2010Interesting that I just pointed to Neandertal DNA, a really big story just came out on ancient Greenlander genetics, Whole Genome of Ancient Human Is Decoded:
The genome of a man who lived on the western coast of Greenland some 4,000 years ago has been decoded, thanks to the surprisingly good preservation of DNA in a swatch of his hair so thick it was originally thought to be from a bear.
This is the first time the whole genome of an ancient human has been analyzed, and it joins the list of just eight whole genomes of living people that have been decoded so far. It also sheds new light on the…
milhayser | February 10, 2010
On Neurotopia, Scicurious offers a refresher course on mitosis. This vital process occurs every time a cell divides, as centrosomes pull apart replicated chromosomes with microtubules. Normal cell mechanics limit this "molecular tug of war" to about 50 iterations, meaning we can't keep splitting chromosomes forever. But we can use meiosis make some babies. On Gene Expression, Razib Khan explains that the X chromosome is relatively scarce since males only carry one copy of it, while all other chromosomes travel in pairs. This makes the X chromosome "more susceptible to stochastic…
razib | February 10, 2010Archaeology has a very interesting piece up, Should We Clone Neanderthals?. It begins with the nitty-gritty of ancient DNA extraction & sequencing, moves to the possible avenues of cloning, and of course the bioethical conundrums that we might be placed in. I know that there is an expectation that a neo-Neandertal will be some sort of "ape-man," but we should remember that the ancient Neandertals had greater cranial capacities than modern humans. I suspect thought that the biggest issue for a neo-Neandertal might be disease; "savages" brought back to Europe invariably died from Illnesses…
edyong | February 10, 2010
Meet "Inuk". He is the ninth human to have their entire genome sequenced but unlike the previous eight, he has been dead for some 4,000 years old. Even so, DNA samples from a tuft of his frozen hair have revealed much about his appearance and his ancestry.
Inuk had brown eyes and brown skin. His blood type was A+. His hair was thick and dark but had he lived, he might not have kept it - his genes reveal a high risk of baldness. Inuk may well have died quite young. Like many Asians and Native Americans, his front teeth were "shovel-graded", meaning that their back faces had ridged sides and…
grrlscientist | February 8, 2010tags: evolutionary biology, molecular biology, Thoroughbred race horses, horses, aerobic capacity, muscle development, myostatin, MSTN, myostatin-suppressing C variant, myostatin-suppressing T variant, Horse Genome Project, Equinome, researchblogging.org, peer-reviewed research, peer-reviewed paper
Emerging from the mist is Rachel Alexandra, a champion American Thoroughbred who excels at winning both long and short distance races.
Image: Rob Carr, 2009, Associated Press [larger view]
If you've worked at or been around a racetrack very much, as I have, you'll quickly realize that everyone…
razib | February 8, 2010In my discussion with Eliezer I referred to "recreational genetics." Basically, "for entertainment purposes only" genetics. For example, someone with blue eyes confirming that they have the alleles on OCA2 & HERC2 associated with blue eyes. Or a man with the surname O'Neill discovers that he has the Uà Néill Y chromosomal marker. Yes, people will pay money to find out these facts which are already highly probable.
I think the news that Charles Darwin was likely of the R1b Y chromosomal haplogroup falls into the recreational category, though due to Darwin's fame the media has really been…
razib | February 7, 2010After watching Creation last week I decided to take the plunge and read Origin of Species. As I've mentioned before I did read Origin early in my teen years, but in hindsight with minimal comprehension. Since then I've occasionally started to read Origin, or perused an extract, but I've never made it from front to back as a sentient adult. At this point I'm 3/4 of the way through, and I need to get something off my chest: I now believe that Charles Darwin was a very smart man, a genius. I had heard other people to refer to Darwin in such a fashion, but reading his original works has brought…
razib | February 6, 2010A few days ago I discussed a new paper which explores the patterns of natural selection in the genome of the X chromosome. As you know the X is "carried" disproportionately by females, as males have only one copy, so it offers up an interesting window into evolutionary dynamics (see The Red Queen for a popular treatment). Today Dienekes points me to a new paper in Genome Biology which puts the focus on the X chromosome again, Characterization of X-Linked SNP genotypic variation in globally-distributed human populations:
Background
The transmission pattern of the human X chromosome reduces its…
mikethemadbiologist | February 2, 2010As someone who is Jewish, and thus at an elevated risk for Tay-Sachs disease, a degenerative disease that inevitably kills small children, and does so miserably, I appreciate the need for genetic screening. So, while it's not perfect, I think companies like Counsyl that are selling screening for harmful genetic diseases are providing a useful service (although many conditions will still be missed). Nonetheless, their stated marketing pitch is missing something. Can you figure out what it is?
From The NY Times:
The company, Counsyl, is selling a test that it says can tell couples whether…
razib | February 1, 2010Could be the title of the paper. Anyway, Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex:
...Incidences of specific diseases are elevated in different breeds, indicating that a few genetic risk factors might have accumulated through drift or selective breeding. In this study, a GWA study with 81 affected dogs (cases) and 57 controls from the Nova Scotia duck tolling retriever breed identified five loci associated with a canine systemic lupus erythematosus (SLE)-related disease complex that includes both antinuclear antibody (ANA)-positive…
razib | January 26, 2010Update: Also see p-ter at Gene Expression Classic.
Follow up on yesterday's post on the new Dickson et al. paper from David Goldstein's lab, A New Way to Look for Diseases' Genetic Roots:
The Icelandic gene-hunting firm deCODE genetics, which emerged last week from bankruptcy, has long led in detecting SNPs associated with common disease. Dr. Kari Stefansson, the company's founder and research director, agreed that whole genome sequencing would "give us a lot of extremely exciting data." But he disputed Dr. Goldstein's view that rare variants carried most of the missing heritability. Both…
razib | January 26, 2010One of the more substantive consequences of the powerful new genomic techniques has been in the area of ancient DNA extraction and analysis. The Neandertal genome story is arguably the sexiest, but closer to the present day there've been plenty of results which have changed the way we look at the past. The input of genetics has basically demanded a revision of the contemporary consensus of the origins of the Etruscans which emerged from archaeology. Though certainly ancestry and genetic relationship are informative, ancient DNA has also given us windows into the change of function and a…
grrlscientist | January 26, 2010tags: evolutionary biology, behavioral ecology, biochemistry, biophysics, magnetoreception, photoreceptor, cryptochromes, geomagnetic fields, butterflies, Monarch Butterfly, Danaus plexippus, birds, migration, signal transduction, researchblogging.org,peer-reviewed research, peer-reviewed paper
Every autumn, millions of monarch butterflies, Danaus plexippus, each weighing less than one gram (one US penny weighs 2.5 grams), migrate nearly 4000 kilometers (3000 miles) between their summer breeding grounds in the United States and their wintering areas either in southern California or in the…
razib | January 25, 2010David Goldstein, a geneticist at Duke, has critiqued the current focus on large-scale genomwide associations before. Now he is taking to the next step, as his group has a paper out which suggests that the reason that association studies have been relatively unfruitful in terms of bang-for-buck is due to the fact that they're picking up "synthetic associations." Rare Variants Create Synthetic Genome-Wide Associations:
It has long been assumed that common genetic variants of modest effect make an important contribution to common human diseases, such as most forms of cardiovascular disease,…
razib | January 25, 2010In Bats and Whales, Convergence in Echolocation Ability Runs Deep:
..."However, it is generally assumed that most of these so-called convergent traits have arisen by different genes or different mutations. Our study shows that a complex trait -- echolocation -- has in fact evolved by identical genetic changes in bats and dolphins."
A hearing gene known as prestin in both bats and dolphins (a toothed whale) has picked up many of the same mutations over time, the studies show. As a result, if you draw a phylogenetic tree of bats, whales, and a few other mammals based on similarities in the…
razib | January 24, 2010Changes in human diet driven by cultural evolution seem to be at the root of many relatively recently emerged patterns of genetic variation. In particular, lactase persistence and varied production of amylase are two well known cases. Both of these new evolutionary genetic developments are responses to the shift toward carbohydrates over the last 10,000 years as mainstays of caloric intake. Rice and wheat serve as the foundations of much of human civilization. It is notable that both China and India are divided into rice and wheat (or millet) belts, so essential are modes of agriculture in…
razib | January 23, 2010In the wake of my post on selection and variation in dog skull shape, I thought it would be useful to point to this short paper, A canine chromosome 7 locus confers compulsive disorder susceptibility. Here's the conclusion:
The highly significant association of CCD with the CDH2 region on chromosome 7 is the first genetic locus identified for any animal compulsive disorder, and raises the intriguing possibility that CDH2 and other neuronal adhesion proteins are involved in human compulsive behaviors. A genetic association of cadherins with autism spectrum disorder, which often includes…
razib | January 21, 2010A western Eurasian male is found in 2000-year-old elite Xiongnu cemetery in Northeast Mongolia:
We analyzed mitochondrial DNA (mtDNA), Y-chromosome single nucleotide polymorphisms (Y-SNP), and autosomal short tandem repeats (STR) of three skeletons found in a 2,000-year-old Xiongnu elite cemetery in Duurlig Nars of Northeast Mongolia. This study is one of the first reports of the detailed genetic analysis of ancient human remains using the three types of genetic markers. The DNA analyses revealed that one subject was an ancient male skeleton with maternal U2e1 and paternal R1a1 haplogroups.…
grrlscientist | January 21, 2010tags: synthetic biology, molecular biology, genetics,Bacteria make Mexican Waves, A synchronized quorum of genetic clocks, bacteria, fluorescence,biological clock, NPG, peer-reviewed research, NATURE, 10.1038/nature08753, streaming video
By synchronizing our clocks, we can coordinate our activities with people around the world. Now, scientists have genetically engineered bacteria to synchronize their molecular timekeepers, creating the stunning fluorescent waves that you see in this video (this video shows new research published today in NATURE).
Read the original research here: http://dx.…
razib | January 20, 2010Sometimes scientists report on research which clarifies what we already know. 'Survival of the Cutest' Proves Darwin Right:
The study, published in The American Naturalist on January 20, 2010, compared the skull shapes of domestic dogs with those of different species across the order Carnivora, to which dogs belong along with cats, bears, weasels, civets and even seals and walruses.
It found that the skull shapes of domestic dogs varied as much as those of the whole order. It also showed that the extremes of diversity were farther apart in domestic dogs than in the rest of the order. This…