Wednesday, March 4, 2015

Pygmy Study a Genomics Reality Check

The hype that connected genes to destiny is eroding. A study on Pygmies and shortness is a case in point.

Pygmy Study a Genomics Reality Check

Today’s column profiles some Penn-led research into the DNA of African Pygmies. To me, the most interesting part of the research project is the way it dispels a prevailing mythology about genetics. Much of that mythology took root when scientists were trying to sell the public and Congress on the $3 billion Human Genome Project. They promised that reading the sequence of code characters in human DNA would lead to cures for cancer, Alzheimer’s disease, cardiovascular disease, mental illness, and autoimmune diseases.

It’s true that the genome has been a useful tool for researchers whose work is improving human health. But where are the cures? In all those promises that went with genome promotion, there was the implication that death was caused by faulty genes. We would live forever if not for little genetic time bombs that would explode and clog our arteries or start tumors. Genome hype also led to myth that our DNA would reveal everything about us. A few were honest about the fact that it wouldn’t be so simple.

One of the early outspoken skeptics was Ken Weiss of Penn State, who was quoted in this story. It reveals the reality that confronts scientists when they try to find the genetic causes behind even seemingly simple traits. Here's the column:

Scientists who study human evolution have long puzzled over why African Pygmies are so short.

It is one of the most visible examples of human diversity, with Pygmy males standing just 4-foot-11 on average, while some of their neighboring ethnic groups are tall. Many biologists have assumed there must be some direct evolutionary advantage to their short stature — perhaps that they better maneuvered through the forest or they survived on less food.

A University of Pennsylvania team went looking for an answer in the Pygmies’ DNA. “This is a trait that has fascinated anthropologists and human geneticists, but it’s only today that we have genetic tools to address it,” said Penn geneticist Sarah Tishkoff.

In a paper published last week, she, Coriell Institute researcher Joseph Jarvis, and colleagues reported that they found many differences between Pygmy DNA and that from neighboring Bantus, but none that would alone account for the Pygmies’ stature, or tie it to an evolutionary benefit, if such a benefit ever existed.

Tishkoff was left wondering if genetic variants that led to shortness spread in the Pygmy populations because they got stuck to mutations that had other benefits. Pygmy shortness may be part evolutionary by-product, part accident. The findings back the views of some biologists who say their colleagues have too readily assumed there are survival advantages behind everything evolution produces.

About 40,000 Pygmies live in Africa, mostly in Cameroon, said Alain Froment, an anthropologist and medical doctor from the Musee de l’Homme in Paris, who collaborated on the study, published last week in the journal PLoS Genetics.

Pygmies lived as hunter-gatherers for centuries, Froment said. Today many still like to hunt and prize wild plants, caterpillars, and honey, he said, but they also eat cultivated foods — bananas and cassava — and use cellphones and other modern conveniences. For the genetic study, he took blood from 67 volunteers living in Pygmy villages, and carefully measured their height. He offered them free medical and dental care in return, as well as a screening for the sickle cell anemia mutation.

As a distinct group, Pygmies are ancient, having branched off from other Africans between 60,000 and 70,000 years ago. At that time, modern humans had yet to leave Africa, Neanderthals and other archaic humans populated Europe and Asia, and America was yet to be populated by any form of humanity.

Tishkoff has been a leader in collecting DNA from Africans because she realized they are underrepresented in genetic studies even though their DNA holds a big part of the story of all humanity. Our species had been spreading and diversifying through Africa for tens of thousands of years before populating the rest of the world. Native Europeans, Australians, American Indians, and others represent small subsets of a diverse population that started in Africa.

“If we want to understand global human diversity, we need to study Africa,” said University of Washington geneticist Josh Akey, who was not part of Tishkoff and Jarvis’ study. “And stature is one of those quintessential human traits we’ve been interested in.”

Read the whole column here.

Journal Reference:

  1. Jarvis JP, Scheinfeldt LB, Soi S, Lambert C, Omberg L, et al. (2012) . PLoS Genet. Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies. PLoS Genet, 2012; 8(4): e1002641 DOI: 10.1371/journal.pgen.1002641




About this blog
Faye Flam - writer
In pursuit of her stories, writer Faye Flam has weathered storms in Greenland, gotten frost nip at the South Pole, and floated weightless aboard NASA’s zero-g plane. She has a degree in geophysics from the California Institute of Technology and started her writing career with the Economist. She later took on the particle physics and cosmology beat at Science Magazine before coming to the Inquirer in 1995. Her previous science column, “Carnal Knowledge,” ran from 2005 to 2008. Her new column and blog, Planet of the Apes, explores the topic of evolution and runs here and in the Inquirer’s health section each Monday. Email Faye at fflam@phillynews.com. Reach Planet of the at fflam@phillynews.com.

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