Archive for February, 2011


When humans are nursing, we all have an enzyme, lactase, that allows us to break down the milk sugar lactose. However, in our early ancestors, the activity of lactase eventually decreased or stopped entirely. Those modern humans that retain this trait are lactose intolerant as adults. However, as we know, some people are able to safely consume milk (and thus lactose) into adulthood. Sarah Tishkoff and her colleagues summarized their recent findings on lactase persistence a couple weeks ago at the American Association for the Advancement of Science meetings in D.C. From one of Tishkoff et al.’s papers on the subject (see reference below):

These individuals have the ‘lactase persistence’ trait. The frequency of lactase persistence is high in northern European populations (>90% in Swedes and Danes), decreases in frequency across southern Europe and the Middle East (~50% in Spanish, French and pastoralist Arab populations) and is low in non-pastoralist Asian and African populations (~1% in Chinese, ~5%–20% in West African agriculturalists). Notably, lactase persistence is common in pastoralist populations from Africa (~90% in Tutsi, ~50% in Fulani)

What do all these populations with high frequencies of the lactase persistence trait have in common? You guessed it….they all have a long history of cattle domestication. What’s cool about this new study is they show that the genetic mutation that gave rise to lactase persistence in modern Europeans is different from that of modern Africans. So, basically, this trait evolved independently at least twice. It also appears as if the evolution and spread of lactase persistence is consistent with a selective sweep (see this post for more info) that began about 7,000 years ago. So, in other words, it’s spread really fast, which means that it conferred a pretty big advantage to those individuals that had it. For more info see this podcast from Scientific American.

Participate in our poll below…are you lactose intolerant? Can you trace your ancestry back to populations that practiced cattle domestication?

References

Tishkoff, S.A., et al. (2006). Convergent adaptation of human lactase persistence in Africa and Europe. Nature Genetics 39: 31-40.

Smithsonian Magazine has a fascinating interview with Daniel Sharfstein about his book, “The Invisible Line: Three American Families and the Secret Journey from Black to White.” His book shows just how fluid the idea of race could be, even in the American South, which was pretty rigid about the concept, particularly during the 17th and 18th centuries. There’s lots of interesting discourse here, so you should check it out, but here are a couple of things worth quoting:

Q: You note that an early 18th-century governor of South Carolina granted the Gibsons, who clearly had African-American ancestry, permission to stay in his colony because “they are not Negroes nor Slaves.” How did the governor reach such a nebulous conclusion?

Sharfstein: It shows how fluid understandings of race can be. The Gibsons were descended from some of the first free people of color in Virginia, and like many people of color in the early 18th century they left Virginia and moved to North Carolina and then to South Carolina, where there was more available land and the conditions of the frontier made it friendlier to people of color. But when they arrived in South Carolina there was a lot of anxiety about the presence of this large mixed-race family. And it seems that the governor determined that they were skilled tradesmen, that they had owned land in North Carolina and in Virginia and—I think most important—that they owned slaves. So wealth and privilege trumped race. What really mattered is that the Gibsons were planters.

Q: One of your subjects, Stephen Wall, crossed from black to white to black to white again, in the early 20th century. How common was that crossing back and forth?

Sharfstein: My sense is that this happened fairly often. There were many stories of people who, for example, were white at work and black at home. There were plenty of examples of people who moved away from their families to become white and for one reason or another decided to come home. Stephen Wall is interesting in part because at work he was always known as African-American, but eventually, at home everyone thought he was Irish.

Q: As you look at the United States now, would you say the color line is disappearing, or even has disappeared?

Sharfstein: I think the idea that race is blood-borne and grounded in science still has a tremendous amount of power about how we think about ourselves. Even as we understand how much racial categories were really just a function of social pressures and political pressures and economic pressures, we still can easily think about race as a function of swabbing our cheek, looking at our DNA and seeing if we have some percentage of African DNA. I think that race has remained a potent dividing line and political tool, even in what we think of as a post-racial era. What my book really works to do is help us realize just how literally we are all related.

Amelia Earhart and her navigator, Fred Noonan, disappeared in 1937 during her attempt to become the first female to fly around the world. Flying near Howland Island in the Pacific, communication with her plane was lost. Finally, after an intense search by the U.S. government, she and Noonan were officially pronounced dead  on January 5, 1939. Since then, there has been speculation about whether they actually died in a crash at sea, or survived for some time on a deserted island.

Amelia Earhart disappeared in 1937. Image from Discover Magazine.

Two years ago, the International Group for Historic Aircraft Recovery found bone fragments on Nikumaroro Island that may be part of Earhart’s finger. However, a dead sea turtle was found nearby, raising the reasonable possibility that the bone fragments also belong to the turtle. Apparently the bone fragments are too small to identify just by looking at them, so researchers want to extract DNA from the bone to compare to Earhart’s. How do we get DNA from her, you may ask? From National Geographic:

The new Earhart DNA project will be headed by Dongya Yang, a genetic archaeologist at Simon Fraser University in Burnaby, Canada. Yang will examine Earhart’s letters and attempt to extract DNA from mouth-lining cells that would have been in the saliva she used to seal the envelopes. Mining a trove of more than 400 correspondences between Earhart and various people, the researchers have chosen four letters to family—deemed the most likely to have been written and sealed by Earhart herself—for analysis.

Yang is aiming to gather two kinds of DNA from the letters: mitochondrial DNA, which children inherit from their mothers only, and nuclear DNA, which contains the bulk of a person’s genetic information and is housed in each human cell’s nucleus. If both DNA types can be obtained, the team says it can create a genetic profile of Earhart that is complete enough to positively identify any potential remains.

If the project proceeds smoothly, Yang said, the team could have a genetic profile for Earhart in “a couple months.”

Let’s see what happens…

We’re starting to go through some of the interesting vignettes in Science’s 10th anniversary celebration of the human genome project. One of these papers takes a realistic view of how genomic research has benefited human health over the past 10 years. A few areas that the authors touch on:

1. Identifying risk:  The predictive power of most genetic variants associated with diseases is not very high. This means that the potential benefits of separating patients even into gross categories such as “high” and “low” risk based on the presence/absence of disease-risk genes are in many cases outweighed by the cost of potentially misclassifying (and thus mistreating) them.

2. The difficulty of changing behavior: When someone is told they are at a genetically higher risk of developing a particular disease, there is really no evidence to indicate that they change their dietary or exercise habits (see also this post on the blog). Altering an individual’s environment (regardless of the presence/absence of disease-risk genes) is probably a better, and more lasting, way of convincing them to be less lazy, or to eat better and not smoke.    

3. False hope: Scientists and the press are both responsible for creating false hopes for genomic research in human health.

The authors do suggest that the following are realistic expectations:

1. The genes responsible for most Mendelian disorders will be identified. This will permit quick diagnoses, particularly for diseases that are caused by a single gene. 

2. Pharmacogenomics (the study of the influence of genetic variation on drug response) will enhance the safety and efficacy of treatments. However, because a lot of variability in drug response is tied to non-genetic factors, we can’t expect genomics to completely solve this issue.    

They make the interesting suggestion that because most mortality in high-income countries results from things like smoking, sedentary behavior, and excessive food and alcohol consumption, the diseases associated with these factors are best (or at least as effectively) researched via the social and behavioral sciences (i.e., how do we change these behaviors?) rather than through genomics (i.e., how do we identify individuals at genetic risk for these diseases?).  

References

Evans, J.P., Meslin, E.M., Marteau, T.M., Caufield, T. (2011). Deflating the genomic bubble. Science 331: 861-862.

UPDATE 2.23.2011. Dr. Hawks blogs about this issue here.

Ok, so we all know what the genome is: the entire sequence of As, Ts, Gs, and Cs (all 6 billion or so of them) that make up the DNA sequence in each of our cells. As you all now know, we’ve had the complete human genome mapped out for ten years now (of course, we’re still trying to figure out what it all does). We also know that whenever there is a change in the DNA molecule (a mutation), that change can become permanent and, in some cases, will be passed down to offspring.  

Well, there are ways that changes can be heritable WITHOUT actually changing the underlying DNA sequence…which is where the epigenome comes into play (“epi” comes from the Greek for “above” or “over”). The epigenome is the host of non-genetic factors that cause genes to change the way that they behave. The classic example is cell differentiation: how is it that a single fertilized egg can differentiate into heart cells, liver cells, skin cells, etc., even though the DNA molecule remains the exact same in all the cells? What happens is that epigenetic factors turn on only the genes that are needed for each cell type to carry out their specific functions. 

Now, most of these epigenetic changes occur only within an individual’s lifetime and are thus only passed from one cell to the next as they divide. However, and this is where it gets really cool, if these changes occur in a sperm or egg cell, then some could be inherited from one generation to the next. This should sound familiar because, in effect, this would be the inheritance of acquired characteristics, which is Jean-Baptiste Larmarck’s oft-ridiculed mechanism for evolution!

Scientists are now on the hunt for a map of the epigenome. For starters, they have been mapping the relatively small epigenomes of the fruit fly and the round worm, and an ongoing study now has a basic epigenomic map for both species. What can this tell us? From an interview with one of the team leaders on the project, Dr. Sarah C.R. Elgin (Washington University, St. Louis), from ScienceDaily:

“We learned many things from the Human Genome Project,” Elgin says, “but of course it didn’t answer every question we had!

“Including one of the oldest: We all start life as a single cell. That cell divides into many cells, each of which carries the same DNA. So why are we poor, bare, forked creatures, as Shakespeare put it, instead of ever-expanding balls of identical cells?

“This work,” says Elgin, “will help us learn the answer to this question and to many others. It will help us to put meat on the bones of the DNA sequences.”

There is actually a conference on human epigenetics, Environmental Epigenetics and Disease Susceptibility, March 27-April 1 in Asheville, NC. Just a smattering of the papers that will be given:

“Epigenetics, Brain Evolution and Behavior”; “Transgenerational Epigenetic Inheritance”; “Epigenetics at the Interface of Genetic and Environmental Risk Factors for Autism Spectrum Disorders”; “The Imprinted Brain Theory: How Genes Set the Balance between Autism and Psychosis”

It was waaaaaaayyy back in Feburary, 2001, when the human genome sequence was first published in the journal Science. This month, Science is running a series of vignettes about the impact of this revolution on genetics, culture, society, policy, and everything else. Take some time and look them over.

Science’s most recent podcasts also deal heavily with human genomics. Check these ones out: Ten years of the human genome sequence; Releasing genomic data; Forensic genetics

Check back for specific posts on these vignettes, because there’s a lot of interesting stuff to discuss here…

No, we’re not talking about brooms here…

When a mutation arises that confers some sort of advantage, those individuals with the mutation have more kids than those without it. Over time, of course, the mutated gene will become more prevalent in a population (this is simply natural selection).  In some cases, other pieces of DNA will hitch-hike along with the advantageous mutant gene because they are linked (i.e., close-by) on the same chromosome and will thus also increase in frequency. A SELECTIVE SWEEP occurs when the positively selected gene and all its neighbors (called a haplotype) become the only variant in a population. So, the result of a selective sweep is a reduction in overall genetic diversity in that region of the genome. 

Selective sweeps have certainly occurred in recent human evolution: for example, the genes (and associated DNA neighbors) for skin pigmentation and lactose tolerance appear to have arisen among modern human populations in a manner consistent with a selective sweep.     

According to a newly published study in Science, selective sweeps were considered to be a relatively common occurrence among humans. However, the new research suggests that this is not so. From a summary in ScienceNews:

Scientists have favored a model of evolution in which beneficial gene mutations quickly and dramatically sweep through a population due to the evolutionary advantages they confer. Such mutations would become nearly universal in a population. But this selective sweep model may not be accurate for humans, a new study indicates. Human evolution likely followed a more subtle and complicated path, say population geneticists Molly Przeworski of the University of Chicago and Guy Sella of Hebrew University of Jerusalem and colleagues.

It may have been difficult for selective sweeps to take hold in humans because of demographics…[p]eople are scattered throughout the globe, so a beneficial mutation would have a long way to spread. Such a mutation would have to have dramatic effects on evolutionary fitness to go global.

References

Hernandez, R.D., et al. (2011). Classic selective sweeps were rare in recent human evolution. Science 331: 920-924.

Laron syndrome (also referred to as Growth Hormone Insensitivity Syndrome, Pituitary Dwarfism II, and Growth Hormone Receptor Deficiency) is an autosomal recessive disorder (i.e., you have to have two copies of the mutated gene–one from mom and one from dad) caused by a mutation on chromosome 5 that results in an individual being non-responsive to growth hormone. Those that are non-responsive fail to produce insulin-like growth factor I, which ultimately leads to short stature.

Jaime Guevara-Aguirre stands with some of the people who took part in his study of Laron syndrome in Ecuador. Photo credit: Valter Longo.

NPR reports on a study in Ecuador that shows that this mutation, while causing Laron syndrome,  seems to prevent diseases such as diabetes and cancer (diseases typically, though not exclusively, associated with ageing). What is super interesting is that a mutation similar to Laron syndrome is known to extend lifespans in other organisms like yeast and worms. From the interview with researcher Valter Longo:

The mutation seems to prevent diabetes by allowing people to get by on very low levels of insulin, Longo says. It wards off cancer by reducing DNA damage in cells, and helping to eliminate abnormal cells. You might expect all this protection would allow the small people in Ecuador to live longer than their taller relatives, Longo says. But that’s not what he found. “The majority of them die of strange causes,” he says, including alcohol abuse and accidents. These are things that are preventable and not caused by a disease, Longo says. Subtract these deaths, he says, and it looks like people with Laron syndrome really would live longer than their relatives. Longo says his study suggests that a whole group of people might be able to lower their risk of cancer and diabetes if they could lower their levels of growth hormone, or change the body’s response to it. The benefit would probably be greatest in people who have unusually high levels of the hormone, he says.

Connecting to a previous post on the blog, scientists also suggest that people with pituitary tumors (a similar situation to these growth hormone abnormalities) may also be at greater risk for cancer (see Irish giants and DNA)

Based on archaeology, linguistics, and, most recently, genetics, it is traditionally thought that Polynesia was inhabited by mariners originating in Taiwan or south China beginning about 3,500 years ago (in fact, our departmental reading, Relethford’s “Reflections of Our Past,” has an interesting chapter on this issue).

Polynesia is made up of hundreds of islands. Figure from acmecompany.com

A recently published study modifies this story somewhat. This study looked at the largest mtDNA (which is only passed through the maternal line) sample to date in order to determine which populations were most similar to modern Polynesians. From an interview with Martin Richards, one of the members of the research team, in the ScienceDaily summary:

“Most previous studies looked at a small piece of mtDNA, but for this research we studied 157 complete mitochondrial genomes in addition to smaller samples from over 4,750 people from across Southeast Asia and Polynesia. We also reworked our dating techniques to significantly reduce the margin of error. This means we can be confident that the Polynesian population — at least on the female side — came from people who arrived in the Bismarck Archipelago of Papua New Guinea thousands of years before the supposed migration from Taiwan took place.”

 What is especially interesting here is that the linguistic and archaeological evidence still strongly suggest some sort of connection with Taiwan. For one, modern Polynesian languages are thought to belong to the Austronesian language family, which is a group of languages spoken from Madagascar to Easter Island, but differ from the native languages of Australia and New Guinea. Archaeologists maintain that the earliest Polynesian pottery (called the “Lapita Culture”) shares many similarities to earlier pottery found on Taiwan and in south China. So, how do we reconcile these findings with the genetics? Again, Dr. Richards:

“Although our results throw out the likelihood of any maternal ancestry in Taiwan for the Polynesians, they don’t preclude the possibility of a Taiwanese linguistic or cultural influence on the Bismarck Archipelago at that time,” explains Professor Richards. “In fact, some minor mitochondrial lineages back up this idea. It seems likely there was a ‘voyaging corridor’ between the islands of Southeast Asia and the Bismarck Archipelago carrying maritime traders who brought their language and artefacts and perhaps helped to create the impetus for the migration into the Pacific.

“Our study of the mtDNA evidence shows the interactions between the islands of Southeast Asia and the Pacific was far more complex than previous accounts tended to suggest and it paves the way for new theories of the spread of Austronesian languages.”

This implies that later populations were moving through the area with their language and culture, but they were not necessarily bringing their genes (i.e., interbreeding), at least on the female side.

References

Soares, P., et al. Ancient Voyaging and Polynesian Origins. American Journal of Human Genetics 88: 239-247.

We’ve talked about SNPs (single nucleotide polymorphisms) before on the blog. These are mutations in single bases along the DNA molecule. Because it has been found that some SNPs are associated with particular diseases, geneticists scan genomes to identify SNPs that may either explain a disease or at least identify individuals that may be at risk for a disease. As described in a recent report in Reuters, one unintended consequence of these genome scans has been the identification of incest. As many of you know, the development of abnormalities in offspring is more common in incestuous (i.e., mating with a close relative–how “close” is “close” varies by culture)  matings. Because closely related individuals share a greater proportion of their genes, the chances are greater that deleterious recessive genes (genes that are only expressed when an individual has two copies, one from either parent) will pair up in their offspring and cause problems.

Although this new information of course has important legal implications, in most cases the physicians were already aware of the incestuous relationship.

References

Schaaf, C.P., Scott, D.A., Wiszniewska, J., Beaudet, A.L. (2011). Identification of incestuous parental relationships by SNP-based DNA microarrays. Lancet 377: 555-556.