Tuesday, November 26, 2013

FDA orders 23andMe to cease marketing

On November 22nd the FDA issued an order for the genetics company 23andMe to immediately cease marketing for their home DNA screening kits after several warnings about "misleading claims." The FDA argues that the company "has not analytically or clinically validated the personal genome service for its intended uses." The original FDA letter can be found here, and a CNN article can be found here

Thursday, November 21, 2013

Ancient Siberian genome publication out in Nature

The 42,000 year old genome of the Siberian child earlier announced in Science News is now officially published in this week's Nature. When compared with various living human groups, researchers found the individual to be most closely related to Native Americans, but also that a portion of the genome was most closely related to western Europeans. This week's Nature Podcast features an interview with the lead author.

Monday, November 11, 2013

Genetic Adaptation Potluck: Climate

This article published in Plos Genetics focuses on genetic variation due to climate pressures. The researchers used a bioinformatics approach to genotype 873 SNPs in genes involved in energy metabolism across 54 worldwide populations. They found the strongest signals in LEPR R109K, FABP2 A54T, genes that are known to be involved with cold intolerance. Thus, overall this study suggests that climate has been one of many important selective pressures affecting genes implicated in metabolism.

Proceedings of Royal Society B, December 22, 2013

In the most recent issue of Proceedings of Royal Society B, one article was particularly relevant to molecular anthropology.  The paper titled "Chimpanzee fauna isotopes provide new interpretations of fossil ape and hominin ecologies" examined the isotopic composition of oxygen and carbon in the tooth enamel of modern and ancient hominin species including Ardipithicus and  Sivapithicus.  The study found that Sivapithicus, a Miocine ape, likely lived in area with canopy, similar to modern chimpanzees, though fed relatively more on leaves.  In contrast, Ardipithicus was found to feed on arboreal and terrestrial sources in a habitat that was predicted to have more open spaces than that of modern chimpanzees. The author, Sherry V. Nelson, hopes to apply this technique to a wide range of fossil specimens to gain a better understanding of diet and habitat in ancient anthropoid species.

How A Gene For Fair Skin Spread Across India


This article discusses a recent paper examining genes for skin color in India.  Before this study, work on skin color genes had not included large samples from South Asia, but instead had focused on Europe and East Asia.  The team found that the gene that is mostly responsible for light skin color in Indian populations is SLC24A5, the gene that also causes fair coloring in European populations as well.  This is in contrast to a set of genes that are responsible for skin pigmentation in East Asia.  The researchers also found that while normally the distribution of light skin color alleles aries latitudinally in areas, for example in Europe its spread seems to be entirely determined by evolution, in India the pattern is much more closely linked to population movements and history.

Human Adaptation Potluck: Hunter-Gatherer Specific Adaptation

Lachance et al. (2012) sequenced whole genomes of one individual each from three African hunter-gatherer groups: Cameroonian Pygmies, the Hadza, and the Sandawe. Many of the findings of this study were discussed by Dr. Sarah Tishkoff (Penn) in a very interesting lecture given at EEB last week, including the discovery of >3 million novel SNPs (unknown on dbSNP & 1000 Genomes) and evidence for archaic admixture in all three populations.

In terms of adaptation, all three populations showed evidence for local environment-specific selection. Regions of divergence in all three groups were enriched for genes involved in immune system and sensory (smell and taste) function. Particularly interesting, regions showing signatures of selection in the pygmies encompassed genes active in pituitary and reproductive function. This finding suggests that pituitary activity in development may be related to the short-stature pygmy phenotype.

Better Review Article for Recent Human Adaptation

A review article recently published in Nature offers a good overview on the methods, cautions, and recent advancements in studying Recent Human Adaptations. The article touches on methods to account for false-positives in WGS and SNP frequency studies and calls for more attention to intergenic regions of the genome. It also highlights current adaptive genes and pathways, such as those relating to skin pigmentation, altitude, lactase persistence, and type II diabetes.

The original article can be found here: http://www.nature.com/nrg/journal/v14/n10/full/nrg3604.html

Monday, November 4, 2013

Recently in Science!

Hey Y'all!
There have been some pretty cool things in Science recently.  Here they are:

1) RNA Helps Resurrect Ancient DNA
   This News article talks about an exciting new method of getting better ancient DNA results by using RNA probes that bind to human DNA so that bacterial contamination can be washed away.  I don't know about costs, but this also seems like it may be interesting for pesky fecal samples as well!

2) Ancient DNA links Native Americans to Europe
  This News article talks about how a new genome from an ancient boy in Siberia shows that Native Americans share large parts of their genome with western Eurasia.

3) A Science News article and Research Article on that lovely skull that made the NYT front page.  The morphology of this skull suggests that there were not multiple Homo lineages existing at the same time.  Instead variation is due to sexual dimorphism and individual variation.

4) Did Denisovans Cross Wallace's Line?
   This perspective looks at the geographic distribution of Denisovans, an ancient hominin contemporary with the Neanderthal.

5) Mitochondrial DNA study looks at processes of variation in Central Europe

(I've learned that Science doesn't really like monkeys, but really likes ancient humans)

Evolutionary Medicine: Skin Depigmentation

The MC1R gene is expressed in follicles and skin. In this study, the researchers found that the MC1R gene is more diverse in Eurasian populations compared to African populations. This news article states that selection for the MC1R locus is strong in southern Europeans, but weak in Northern Europeans. Specifically, the researchers found an allele termed V60L that is mostly present in Europe and the Near East. From the results of the study, the researchers posit that fair skin depigmentation can potentially be a beneficial adaptation for humans living in this new environment.

New Implications for Phage Therapy

A new study published in September holds new implications for using Bacteriophages to treat pathogenic bacteria. Bacteriophages are viruses that infect and replicate inside of bacteria, and have previously been explored for the use of treating human pathogenic bacteria. Unfortunately, bacteriophage (or phage) treatment suffers from the same drawback as antibacterial treatments -- rapid emergence of resistant bacterial strains. In this study, researchers explore the use of a "Phage Cocktail" in the use of treating pathogenic bacteria in shrimp, as it is ill advised to use antibiotics in the food industry. Preliminary results showed that a cocktail consisting of three different phages targeting one bacteria was effective at killing bacteria and experienced significantly slowed rates of resistance. While this finding has only been demonstrated in a controlled environment, it could potentially have great use in the medical treatment of human pathogens in light of the antibiotic arms race we are currently engaged in. 

Proceedings of Royal Society B, Dec. 8, 2013

In this past issue of Proceedings of Royal Society B, several articles dealt with anthropological topics.  The first was a study of the rates of extra-pair paternity in a population in Flanders, Belgium. The team looked compared the Y-chromosome of different individuals with their genealogies and surnames which are also passed patrilineally. The study found that the rate of extra pair paternity was about 1-2% per generation and remained fairly constant over the last 400 years.  The results are surprising as in the past, rates of extra-pair paternity were estimated at around 8-30% per generation.

Another study looked at potential sexual conflict in the genome over reproductive life history events. The researchers looked at a pedigreed population from pre-industrial Finland for their study.  Certain events like age at first and last reproduction, reproductive rate, and reproductive lifespan appeared to be in conflict between the sexes.  However, upon further examinations, the team found that although it seemed like there was a phenotypic conflict between the sexes, it was not playing out at a genetic level.  They claim that this shows the importance of studying the genetics behind life history events in humans.

Long-lived mammals may hold clues about aging


This article talks about research being conducted by Vadim Gladyshev, a genetics researcher at Brigham and Women's Hopsital in Boston.  He is studying longevity in mammals to learn more about aging and lifespan in humans. While this type of research is not new, he wants to approach the idea differently by instead of looking at long-lived individuals in a particular species, looking at longer or shorter- lived clades of species.  He in particular is comparing numerous species of bats to one another, sequencing their genomes, and examining genes that participate in aging.  He hopes  that this method will give a better understanding than past research on what factors can increase lifespan.  He is also hoping to perform similar techniques on whales and elephants.

Sunday, November 3, 2013

Ev Med Potluck: Ancient Microbial Antibiotic-Resistance Genes Found in Late Pleistocene Permafrost

In this study, researchers extracted aDNA from ~30kya Alaskan Permafrost sediments and detected genes conveying resistance to penicillin, tetracycline, and vancomycin. This finding demonstrates that the acquisition of antibiotic resistance in modern microbes is likely usually via horizontal genes transfer of genes already in existence and accounts for the rapidity with which antibiotic resistance can develop.