genetics
razib | December 11, 2008Interesting bit of interdisciplinary work on the spread of lactase persistance:
Thomas found that the gene variant coincided well with the rise of animal domestication, indicating that humans became dairy farmers almost as soon as they began to keep animals.
To track the gene's spread across Europe, Thomas designed a computer model that took into account both archaeological and genetic data. He then ran multiple simulations, randomly changing other variables and looking for patterns that matched what is known today.
The closest matches pegged the rise of milk-drinking Europeans to about 7,400…
pharyngula | December 10, 2008
The Institute for Creation Research has a charming little magazine called "Acts & Facts" that prints examples of their "research" — which usually means misreading some scientific paper and distorting it to make a fallacious case for a literal interpretation of the bible. Here's a classic example: Chimps and People Show 'Architectural' Genetic Design, by Brian Thomas, M.S. (Note: this is not the peer-reviewed research paper implied by the logo to the left — that comes later.) The paper is a weird gloss on recent work on CNVs, or copy number variants. Mr Thomas makes a standard creationist…
razib | December 8, 2008Today Ed Yong has a post up, Social status shapes racial identity:
To Penner and Saperstein, the study contradicts the idea that races, and the differences between them, are dominated by biological differences between groups of people. They see race not as a fixed entity that is purely determined from birth, but a flexible one, settled by a tug-of-war between different possible classifications.
Biological traits like skin colour obviously have a strong pull, but they aren't alone - changes in social position can also affect how people see themselves and are seen by others. The researchers…
gregladen | December 8, 2008The copying of DNA's master instructions into messenger molecules of RNA, a process known as DNA transcription, has always been thought to be a unidirectional process whereby a copying machine starts and moves in one direction. But in work that represents a fundamental shift in scientists' understanding of the phenomenon, MIT researchers have found evidence that two DNA copying machines frequently start from the same site and move in different directions.
Press release here
razib | December 8, 2008Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans:
ariation in gene expression is a fundamental aspect of human phenotypic variation, and understanding how this variation is apportioned among human populations is an important aim. Previous studies have compared gene expression levels between distinct populations, but it is unclear whether the differences that were observed have a genetic or nongenetic basis. Admixed populations, such as African Americans, offer a solution to this problem because individuals vary in their proportion of European ancestry while…
razib | December 7, 2008From the comments:
When I first saw this, the first thing that popped in my head was "big [vulgarity expurgated] surprise."
Has someone done a PC analysis on people from all over the United States? That would probably be pretty interesting, given that it almost certainly wouldn't reflect geography as strongly. I wonder what kind of clustering you would get...
A substantial number of Americans are derived from the settler population; those Europeans who arrived during the colonial period. In New England most of the population in 1776 was descended from a large wave of Puritans who arrived…
razib | December 6, 2008Analysis of East Asia Genetic Substructure Using Genome-Wide SNP Arrays:
In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst…
edyong | December 6, 2008
Since the time when humans and chimps evolved from our common ancestor, our species appears to have come on by leaps and bounds. We walk on two legs, we have spoken language and while there is no doubt that chimps are intelligent, there is even less doubt that our brainpower outclasses theirs.
But are our advanced abilities reflected in our genetics? After all, traits like intelligence and language give us great adaptive advantages - surely they should be mirrored by similarly large changes in our genome, compared to the chimp one?
Not so. Researchers at the University of Michigan sifted…
razib | December 5, 2008Adaptive Complexity takes issue at a post over at Information Processing over race & genetics. On that specific topic, let me just quote Luigi Luca Cavalli-Sforza:
[my question] Question #3 hinted at the powerful social impact your work has had in reshaping how we view the natural history of our species. One of the most contentious issues of the 20th, and no doubt of the unfolding 21st century, is that of race. In 1972 Richard Lewontin offered his famous observation that 85% of the variation across human populations was within populations and 15% was between them. Regardless of whether…
gregladen | December 5, 2008Allen's Rule. One of those things you learn in graduate school along with Bergmann's Rule and Cope's Rule. It is all about body size. Cope's Rule ... which is a rule of thumb and not an absolute ... says that over time the species in a given lineage tend to be larger and larger. Bergmann's Rule says that mammals get larger in colder environments. Allen's Rule has mammals getting rounder in colder climates, by decreasing length of appendages such as limbs, tails and ears.
All three rules seem to be exemplified in human evolution. Modern humans tend to be larger and rounder in cooler…
razib | December 3, 2008The Etruscan timeline: a recent Anatolian connection:
The origin of the Etruscans (the present day Tuscany, Italy), one of the most enigmatic non-Indo-European civilizations, is under intense controversy. We found novel genetic evidences on the mitochondrial DNA (mtDNA) establishing a genetic link between Anatolia and the ancient Etruria. By way of complete mtDNA genome sequencing of a novel autochthonous Tuscan branch of haplogroup U7 (namely U7a2a), we have estimated an historical time frame for the arrival of Anatolian lineages to Tuscany ranging from 1.1 +/- 0.1 to 2.3 +/- 0.1 0.4 kya B.P…
razib | December 3, 2008Though Barbara Oakley's Evil Genes: Why Rome Fell, Hitler Rose, Enron Failed, and My Sister Stole My Mother's Boyfriend is ostensibly about Machiavellian behavior, it is also a testament to her intellectual ambition. The subheading is a clear pointer to this. Oakley attempts to synthesize a wide range of fields, behavior genetics, cognitive neuroscience, clinical psychology, diplomatic history, evolutionary psychology, economic history, along with heavy dollops of political and personal biography, to produce a portrait of how Machiavellian intelligence emerges from its biological substrate…
edyong | December 1, 2008You are not alone. Even if you're currently reading this in complete isolation, you are still far from a singular individual. You're more of a colony - one human, together with microbes in their trillions. For every one of your own genes, your body is also host to thousands of bacterial ones. Some of the most important of these tenants - the microbiota - live in our gut. Their genes, collectively known as our microbiome, provide us with the ability to break down sources of food, like complex carbohydrates, that we would otherwise find completely indigestible.
Peter Turnbaugh from the…
razib | November 30, 2008A few years ago I blogged about prosopagnosia, "face blindness." Nature Neuroscience now has a new paper finding some correlates with brain architecture, Reduced structural connectivity in ventral visual cortex in congenital prosopagnosia:
Using diffusion tensor imaging and tractography, we found that a disruption in structural connectivity in ventral occipito-temporal cortex may be the neurobiological basis for the lifelong impairment in face recognition that is experienced by individuals who suffer from congenital prosopagnosia. Our findings suggest that white-matter fibers in ventral…
razib | November 30, 2008I was waiting for Dan MacArthur to comment on the "ACTN3 sports gene" story because I knew he had done research on this very locus. As usual, he's rather diplomatic, with a post titled The ACTN3 sports gene test: what can it really tell you?. He says:
Kevin Fischer has already noted that from a pure cost-benefit point of view the ATLAS test doesn't compete with the offerings of personal genomics companies. ATLAS will charge you $150 for testing ACTN3; for just $250 more, you get genetic information pertaining to more than 90 different conditions and traits from 23andMe. Neither test is…
gregladen | November 29, 2008Markita Landry, a half-Bolivian, half-French Canadian physics Ph.D. student at the University of Illinois, Urbana-Champaign, ... used a tango to convey her thesis, "Single Molecule Measurements of Protelomerase TelK-DNA Complexes." She is trying to understand how a protein called TelK bends DNA into hairpin loops. The mechanism makes for beautiful dance, with Landry bending like pliable DNA in her partner's arms.
aaas Science
mikethemadbiologist | November 25, 2008I suppose I'll have to start at the beginning. One of the things we do in the microbiome project is analyze microbial communities by assessing the diversity of 16S DNA sequences*. In other words, we want to know what species or 'operational taxonomic units'--OTUs--are present and how many of that OTU are there.
Operationally, we are taking a bunch of DNA sequences and placing them in categories. This, of course, is more difficult than it sounds.
One of the issues with 16S is that many (nine to be exact) regions of the gene are hypervariable--they evolve so quickly that these regions can't…
evolgen | November 24, 2008
The 26th edition of Mendel's Garden will be hosted by A Free Man on December 7. If you have written a blog post about any topics in Genetics in the past month or so, send a link to Chris (chris[at]afreeman[dot]org) to be included in the carnival.
We're also looking for hosts for upcoming editions. If you would like to host the original genetics blog carnival, send me an email (evolgen-at-yahoo-dot-com). Every month from February onward is available.
razib | November 21, 2008Another paper on European phyogeography, Investigation of the fine structure of European populations with applications to disease association studies:
An investigation into fine-scale European population structure was carried out using high-density genetic variation on nearly 6000 individuals originating from across Europe. The individuals were collected as control samples and were genotyped with more than 300 000 SNPs in genome-wide association studies using the Illumina Infinium platform. A major East-West gradient from Russian (Moscow) samples to Spanish samples was identified as the first…
razib | November 20, 2008Regenerating a Mammoth for $10 Million:
If the genome of an extinct species can be reconstructed, biologists can work out the exact DNA differences with the genome of its nearest living relative. There are talks on how to modify the DNA in an elephant's egg so that after each round of changes it would progressively resemble the DNA in a mammoth egg. The final-stage egg could then be brought to term in an elephant mother, and mammoths might once again roam the Siberian steppes.
The same would be technically possible with Neanderthals, whose full genome is expected to be recovered shortly, but…