Featured Research

from universities, journals, and other organizations

Subtle shifts, not major sweeps, drove human evolution

Date:
February 28, 2011
Source:
University of Chicago Medical Center
Summary:
The most popular model used by geneticists for the last 35 years to detect the footprints of human evolution may overlook more common subtle changes, a new study finds. A computational analysis reveals that selective sweeps may have been rare, with little influence on the history of our species.

Researchers examined the sequences of nearly 200 human genomes, and discovered new evidence arguing against selective sweeps as the dominant mode of human adaptation.
Credit: iStockphoto/Claude Dagenais

The most popular model used by geneticists for the last 35 years to detect the footprints of human evolution may overlook more common subtle changes, a new international study finds.

Classic selective sweeps, when a beneficial genetic mutation quickly spreads through the human population, are thought to have been the primary driver of human evolution. But a new computational analysis, published in the February 18, 2011 issue of Science, reveals that such events may have been rare, with little influence on the history of our species.

By examining the sequences of nearly 200 human genomes, researchers led by Ryan Hernandez, PhD, assistant professor of Bioengineering and Therapeutic Sciences at the University of California at San Francisco, found new evidence arguing against selective sweeps as the dominant mode of human adaptation.

The reversal suggests that smaller changes in multiple genes may have been the primary driver of changes in human phenotypes, and that new models are needed to retrace the genetic steps of evolution.

"Our findings suggest that recent human adaptation has not taken place through the arrival and spread of single changes of large effect, but through shifts of frequency in many places of the genome," said Molly Przeworski, PhD, professor of Human Genetics and Ecology & Evolution at the University of Chicago and co-senior author of the paper. "It suggests that human adaptation, like most common human diseases, has a complex genetic architecture."

Under the classic selective sweep model, a new, advantageous gene appears and quickly spreads through the population. Because of its rapid rise, the gene becomes fixed in the genome with less variation than a gene that spread more slowly and was subject to the shuffling effects of recombination.

Geneticists have used this model to look for genetic segments surrounded by "troughs" of low variation, the theoretical footprint of a selective sweep. Applying the model has identified more than 2,000 genes -- roughly 10 percent of the human genome -- suggesting that selective sweeps were a frequent occurrence that drove the evolution of humans away from their primate ancestors.

"The selective sweep model was introduced in 1974 and has pretty much been the central model ever since," Przeworski said. "It is fair to say that it is the model behind almost every scan for selection done to date, in humans or in other organisms."

However, areas of low diversity around gene segments might also be produced by other evolutionary mechanisms. To test whether selective sweeps were the predominant cause of these troughs, a group of scientists from the University of Chicago, the University of California at San Francisco, Hebrew University of Jerusalem, and the University of Oxford used data from179 subjects in the 1000 Genomes Project, an international effort to catalogue human variation.

"This is really a groundbreaking dataset that allowed this type of analysis to be done for the very first time," Hernandez said.

The research team looked at genes with human-specific substitutions, where the nucleotide sequence is different from close primate relatives. In some cases, the new sequence switches an amino acid in the protein the gene encodes, a replacement that likely improved the protein's function. In other genes, the sequence change is "synonymous," coding for the same amino acid as before and leaving the protein's function unperturbed. Under the classic selective sweep model, genetic diversity would be lower surrounding the first group of mutations, those that produced beneficial changes in function, because of their quick spread.

But when the two groups were compared, the troughs of low diversity were similar for genes that produce functional changes and genes with synonymous substitutions that do not. The result suggests that classic selective sweeps could not have been the most common cause of these low diversity troughs, leaving the door open for other modes of evolution.

"Phenotypic variation in humans isn't as simple as we thought it would be," Hernandez said. "The idea that human adaptation might proceed by single changes at the amino acid level is quite a nice idea, and it's great that we have a few concrete examples of where that occurred, but it's too simplistic a view."

Further evidence against common selective sweeps was provided by comparing genome variation in different populations. Because Nigerian, European, and Chinese/Japanese populations separated roughly 100,000 years ago and subsequently adapted to different environments, frequent selective sweeps would be expected to fix clear genetic differences between the populations.

However, comparing genomes of different populations from the 1000 Genomes Project detected only subtle differences in allele frequencies, representative of small changes over time rather than rapid sweeps.

"It dovetails quite well with findings coming out of medical mapping studies, which also suggest that many loci of small effect influence disease risk," Przeworski said. "These findings call into question how much more there is to find using the selective sweep approach, and should also make us skeptical of how many of the findings to date will turn out to be validated."

Funding was provided by the National Science Foundation, the National Institutes of Health, and the Howard Hughes Medical Institute.


Story Source:

The above story is based on materials provided by University of Chicago Medical Center. Note: Materials may be edited for content and length.


Journal Reference:

  1. R. D. Hernandez, J. L. Kelley, E. Elyashiv, S. C. Melton, A. Auton, G. McVean, G. Sella, M. Przeworski. Classic Selective Sweeps Were Rare in Recent Human Evolution. Science, 2011; 331 (6019): 920 DOI: 10.1126/science.1198878

Cite This Page:

University of Chicago Medical Center. "Subtle shifts, not major sweeps, drove human evolution." ScienceDaily. ScienceDaily, 28 February 2011. <www.sciencedaily.com/releases/2011/02/110217141307.htm>.
University of Chicago Medical Center. (2011, February 28). Subtle shifts, not major sweeps, drove human evolution. ScienceDaily. Retrieved July 25, 2014 from www.sciencedaily.com/releases/2011/02/110217141307.htm
University of Chicago Medical Center. "Subtle shifts, not major sweeps, drove human evolution." ScienceDaily. www.sciencedaily.com/releases/2011/02/110217141307.htm (accessed July 25, 2014).

Share This




More Plants & Animals News

Friday, July 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

How to Make Single Serving Smoothies: Howdini Hacks

How to Make Single Serving Smoothies: Howdini Hacks

Howdini (July 24, 2014) Smoothies are a great way to get in lots of healthy ingredients, plus they taste great! Howdini has a trick for making the perfect single-size smoothie that will save you time on cleanup too! All you need is a blender and a mason jar. Video provided by Howdini
Powered by NewsLook.com
Boy Attacked by Shark in Florida

Boy Attacked by Shark in Florida

Reuters - US Online Video (July 24, 2014) An 8-year-old boy is bitten in the leg by a shark while vacationing at a Florida beach. Linda So reports. Video provided by Reuters
Powered by NewsLook.com
Goma Cheese Brings Whiff of New Hope to DRC

Goma Cheese Brings Whiff of New Hope to DRC

Reuters - Business Video Online (July 24, 2014) The eastern region of the Democratic Republic of Congo, mainly known for conflict and instability, is an unlikely place for the production of fine cheese. But a farm in the village of Masisi, in North Kivu is slowly transforming perceptions of the area. Known simply as Goma cheese, the Congolese version of Dutch gouda has gained popularity through out the region. Ciara Sutton reports. Video provided by Reuters
Powered by NewsLook.com
Tyrannosaur Pack-Hunting Theory Aided By New Footprints

Tyrannosaur Pack-Hunting Theory Aided By New Footprints

Newsy (July 24, 2014) A new study claims a set of prehistoric T-Rex footprints supports the theory that the giant predators hunted in packs instead of alone. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

    Health News

      Environment News

        Technology News



          Save/Print:
          Share:

          Free Subscriptions


          Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

          Get Social & Mobile


          Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

          Have Feedback?


          Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
          Mobile: iPhone Android Web
          Follow: Facebook Twitter Google+
          Subscribe: RSS Feeds Email Newsletters
          Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins