Tuesday, March 29, 2011

Maternal diet and aging alter the epigenetic control of a promoter–enhancer interaction at the Hnf4a gene in rat pancreatic islets

"...we show that the transcription factor Hnf4a, which has been implicated in the etiology of type 2 diabetes (T2D), is epigenetically regulated by maternal diet and aging in rat islets." Epigenetics is very cool.

Hunter-gatherer genomic diversity suggests a southern African origin for modern humans

"We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations." Based on data for more than 580,000 SNPs.

Monday, March 21, 2011

Book review: How to get ahead

Gee review of Lieberman's new book The Evolution of the Human Head

Old Female Elephants Make the Best Leaders

cool video

article HERE

Less is more...

particularly re penis spines.
New study from David Kingsley's group on the loss of cis-regulatory elements on the human lineage.
Most notable:
"One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage"

Monday, March 14, 2011

Genomic signatures of diet-related shifts during human origins

nice review from Greg Wray group...

Co-Residence Patterns in Hunter-Gatherer Societies Show Unique Human Social Structure

..and a commentary by Bernard Chapais HERE

Comparative Data Reveal Similar Mortality Patterns Across Primates

"Contrary to assumptions of human uniqueness, human senescence falls within the primate continuum of aging"

Friday, March 11, 2011

Countershading is related to positional behavior in primates!

Kamilar, J. M. and Bradley, B. J. (2011), Countershading is related to positional behavior in primates. Journal of Zoology, 283: 227–233. doi: 10.1111/j.1469-7998.2010.00765.x

Monday, March 7, 2011

Dividing chimp species / populations

Interesting Katy Gonder PNAS paper on microsats and clustering of chimp populations using e.g. STRUCTURE: pretty clear verus vs everyone else split.

But HERE (Hahn and Worobey -- probably done in connection with Ochman's microbiome stuff) is a recent view of the same issue focused on mtDNA genomes and finds verus + vellerosus vs everyone else split.

Generation of Melanocytes from Neural Crest Cells

PC&M paper: "summarize the current view of how melanocytes are specified from the neural crest "

Save the behavioral ecologists

recent Caro & Sherman review in TREE: Endangered species and a threatened discipline: behavioural ecology

"Behavioural ecologists often see little connection between the current conservation crisis and the future of their discipline. This view is myopic because our abilities to investigate and interpret the adaptive significance and evolutionary histories of behaviours are increasingly being compromised in human-dominated landscapes because of species extinctions, habitat destruction, invasive species, pollution, and climate change."

"Classic Selective Sweeps Were Rare in Recent Human Evolution"

From Molly Przeworski's group:

"Data from the pilot for the 1000 Genomes Project suggest that classic selective sweeps were not the primary mode of evolution of the human genome. Instead, it seems that the majority of human genetic diversity is best explained by purifying selection against deleterious mutations."

Forensic DNA phenotyping

"The Dutch parliament adopted a law in 2003 regulating forensic DNA phenotyping, the use of DNA samples to predict a suspect's ancestry or physical characteristics. But the Netherlands is still the only country to have done so.?

Manfred Kayser: "DNA sleuth"

cool profile of Manfred and forensic DNA profiling in Science

Friends and genotype networks

Maybe I posted this already?

"Framingham Heart Study verifies that DRD2 exhibits significant homophily and that CYP2A6 exhibits significant heterophily."

Pronghorn Genomics and Sexual Selection

Science news tidbit on potentially cool project!:

Byers et al "have over the years collected tissue samples from 835 pronghorns across the generations, and they now plan to genetically profile each animal to determine whether female pronghorns do indeed pick genetic studs."

Microbiome insertion sequencing

Insertion sequencing... involves using mobile DNA elements called transposons to introduce mutations into tens of thousands of bacteria. Before adding the transposons to the bacteria, the researchers tag each transposon with an identifiable DNA “bar code” that allows each mutant bacterium to be tracked—and for the gene disrupted by the transposon to be characterized. With the new sequencing technology, researchers can follow mixed populations of these mutant strains on various growth mediums or in different environments.

Anthropologists Trace Human Origins Back To One Large Goat

'Wait, That Can't Be Right,' Scientists Say

Predicting human cone distribution using pics of Botswana

"only 6% of our cone cells detect blue, and they are mostly located around the edge of our retina. Of the remaining cones, the ratio of red to green cones varies wildly between individuals.

To find out why this is, Tkačik, along with neurobiologist Vijay Balasubramanian of Penn and colleagues, created a database of more than 5000 high-resolution photographs taken at various locations in Botswana, a place near where humans likely evolved and other primates still live. The same scenes were shot at different times of day, with different exposure lengths, apertures, and distances from the camera. Using an algorithm they developed from previous studies of how human cones detect light, the researchers calculated how many photons of different wavelengths the camera had captured and what cone arrangement would pick up the largest number of them."

... and it matched the arrangement of human eyes.

Wine genomics

PNAS paper (by Sean Myles et al) on grape domestication!

New directed gene therapy -- CCR5 disruption in humans

"A gene-therapy method that specifically disrupts a single gene may have had its first success in the clinic, potentially boosting immune-cell counts in a small number of patients with HIV."

Twin studies - new role

Nice review paper on twin studies of epigenetics in recent TIG:

"We describe how large-scale epigenetic studies of twins can improve our understand- ing of how genetic, environmental and stochastic factors impact upon epigenetics, and how such studies can provide a comprehensive understanding of how epige- netic variation affects complex traits."