genetics
razib | January 28, 2009Read Genetic Future on Navigenics crappy new product. Better yet, link to the post yourself to crank up the google ranking, you're doing potential consumers a service.
razib | January 28, 2009Monoamine oxidase A gene (MAOA) predicts behavioral aggression following provocation:
Monoamine oxidase A gene (MAOA) has earned the nickname "warrior gene" because it has been linked to aggression in observational and survey-based studies. However, no controlled experimental studies have tested whether the warrior gene actually drives behavioral manifestations of these tendencies. We report an experiment, synthesizing work in psychology and behavioral economics, which demonstrates that aggression occurs with greater intensity and frequency as provocation is experimentally manipulated upwards…
razib | January 22, 2009Carl Zimmer pointed me to a new paper, A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans. The title is so informative that pasting the abstract is almost unnecessary, but here is the conclusion which gets to the point:
In conclusion, we show that, at least in the context of the studied sample, it is possible to predict full Ashkenazi Jewish ancestry with 100% sensitivity and 100% specificity, although it should be noted that the exact dividing line between a Jewish and non-…
razib | January 21, 2009About every single post on human population clusters tend to shift into a discussion as to whether human variation is clinal, or where one can make assertions of discrete groups. I think it is fair to note that most of the populations sampled have been skewed to one locale. For example, "French" might mean a few hundred patients from hospitals in the Paris area. "Belgian" might be a few hundred patients in hospitals in Brussels. The "gap" between the French and Belgian cluster may simply have to do with the fact that the populations are not representative of their nationalities. Surely as…
edyong | January 19, 2009People seem inordinately keen to pit nature and nurture as imagined adversaries, but this naive view glosses over the far more interesting interactions between the two. These interactions between genes and environment lie at the heart of a new study by Rose McDermott from Brown University, which elegantly fuses two of my favourite topics - genetic influences on behaviour and the psychology of punishment.
three previous pieces on punishment. Each was based on a study that used clever psychological games to investigate how people behave when they are given a choice to cooperate with, cheat, or…
razib | January 19, 2009The post yesterday about the deletion which results in heart disease later in life had some interesting ancestry related material. This makes sense, the genetic maps which I post on now and then ultimately have a medical rationale behind them; eliminate population structure so that you don't have spurious correlations confusing you when you try and get a fix on the genetic underpinnings of a disease. By example, consider a study with cases & controls, and individuals with the trait or disease have five times the likelihood of carrying a particular allele at a particular gene. But you…
razib | January 18, 2009In some of the popular press pieces on the genetic variant which is implicated in heart disease among South Asians there are references to the fact that only 1% of the world's population carries it. Actually, that's obscuring an important piece of information: that 1% is almost exclusively South Asian, so that the 1% is simply 5% X 20% (20% being the proportion of the world's population that is South Asian). I've placed the table from the supplementary data which shows the populations in the HGDP data set which do, and don't, have the deletion on MYBPC3.
Notice the trend? Except for 2…
razib | January 18, 2009
A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia:
Heart failure is a leading cause of mortality in South Asians. However, its genetic etiology remains largely unknown1. Cardiomyopathies due to sarcomeric mutations are a major monogenic cause for heart failure...Here, we describe a deletion of 25 bp in the gene encoding cardiac myosin binding protein C (MYBPC3) that is associated with heritable cardiomyopathies and an increased risk of heart failure in Indian populations (initial study OR = 5.3...replication study OR = 8.59...combined…
razib | January 16, 2009There's a new paper, The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers:
Methodology and Results
We analyzed mitochondrial DNA...sequence variation in the hypervariable segments I and II...and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations...In addition, published mtDNA haplogroup data...mtDNA HVS-I sequences...Y chromosome haplogroup data...and Y chromosome STR da...were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into…
razib | January 16, 2009Farewell to evolgen. I guess the Facebook account must occupy all his time....
razib | January 16, 2009Pervasive Hitchhiking at Coding and Regulatory Sites in Humans. Here's the author summary:
There is much reported evidence for positive selection at specific loci in the human genome. Additional papers based on comparisons between the genomes of humans and chimpanzees have also suggested that adaptive evolution may be quite common. At the same time, it has been surprisingly hard to find unambiguous evidence that either positive or negative (background) selection is affecting genome-wide patterns of variation at neutral sites. Here, we evaluate the prevalence of positive or background…
razib | January 15, 2009A neat new paper on Icelandic genetics, then and now, Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool:
A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA) control region sequences from 68 early medieval Icelandic skeletal…
razib | January 14, 2009About 3 years ago a paper was published on pigmentation which heralded the breaking of the dam when it comes to skin color genetics, SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans. The zebrafish, a model organism familiar to evo-devoists the world over, played an important role in the paper. The new issue of Zebrafish is totally devoted to pigmentation. The press release was kind of weird, Zebrafish Journal Publishes Skin Pigmentation Studies That Shed Light on the Evolution of Race:
"With the election of the first African-American president of the United…
razib | January 12, 2009More ancient DNA, Hair Of Tasmanian Tiger Yields Genes Of Extinct Species:
All the genes that the exotic Tasmanian Tiger inherited only from its mother will be revealed by an international team of scientists in a research paper to be published on 13 January 2009 in the online edition of Genome Research. The research marks the first successful sequencing of genes from this carnivorous marsupial, which looked like a large tiger-striped dog and became extinct in 1936.
...
... "I want to learn as much as I can about why large mammals become extinct because all my friends are large mammals,"…
pharyngula | January 12, 2009Genome sequencing is getting cheaper and faster, and more and more people are having it done. A new addition to the ranks is Steve Pinker, who contemplates the details of his personal genome in an interesting essay. It's got to be fascinating, in a terribly self-centered way — I'd love to have a copy of mine someday. It's an opportunity to see a manifestation of one's own lineage, your biological history all laid out for you. There's the ability to compare with others, and see hints of statistical correlations and associations with specific traits and even, unpleasantly, diseases. Pinker also…
razib | January 12, 2009While The Cat's Away: How Removing An Invasive Species Devastated A World Heritage Island:
Removing an invasive species from sub-Antarctic Macquarie Island, a World Heritage Site, has caused environmental devastation that will cost more than A$24 million to remedy, ecologists have revealed. Writing in the new issue of the British Ecological Society's Journal of Applied Ecology, they warn that conservation agencies worldwide must learn important lessons from what happened on Macquarie Island.
Shorter:"invasive" and "introduced" organisms for a long enough period results in an ecosystem…
razib | January 12, 2009Genetic Future (and again), John Hawks and FuturePundit have all touched upon a new Steven Pinker piece in The New York Times Magazine, My Genome, My Self. If you read all the weblogs which talk about personal genomics, I suspect we'll look back at this era like those who read PC Magazine in the early 1980s must feel right now. The future is often bigger and stranger than we perceive from the present, and the near future is often more banal than the more exaggerated propagandist might assert. Pinker's strength as a scientific intellectual is the ability to distill these sorts of truths…
edyong | January 8, 2009
Living things, from bacteria to humans, depend on a workforce of proteins to carry out essential tasks within their cells. Proteins are chains of amino acids that are strung together according to instructions encoded within that most important of molecules - DNA.
The string of "letters" that make up DNA correspond to chains of amino acids, and they are read in threes, with every combination representing one of many amino acids. Until now, scientists believed that this relationship is unambiguous - within any single genome, every three-letter combination maps to one and only one amino acid.…