Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Hundreds of natural-selection studies could be wrong, study demonstrates

Scientists at Penn State and the National Institute of Genetics in Japan have demonstrated that several statistical methods commonly used by biologists to detect natural selection at the molecular level tend to produce incorrect results.

"Our finding means that hundreds of published studies on natural selection may have drawn incorrect conclusions," said Masatoshi Nei, Penn State Evan Pugh Professor of Biology and the team's leader.

The team's results will be published in the Online Early Edition of the journal Proceedings of the National Academy of Sciences during the week ending Friday 3 April 2009 and also in the journal's print edition at a later date.

Nei said that many scientists who examine human evolution have used faulty statistical methods in their studies and, as a result, their conclusions could be wrong. For example, in one published study the scientists used a statistical method to demonstrate pervasive natural selection during human evolution. "This group documented adaptive evolution in many genes expressed in the brain, thyroid, and placenta, which are assumed to be important for human evolution," said Masafumi Nozawa, a postdoctoral fellow at Penn State and one of the paper's authors.

"But if the statistical method that they used is not reliable, then their results also might not be reliable," added Nei. "Of course, we would never say that natural selection is not happening, but we are saying that these statistical methods can lead scientists to make erroneous inferences," he said.

The team examined the branch-site method and several types of site-prediction methods commonly used for statistical analyses of natural selection at the molecular level. The branch-site method enables scientists to determine whether or not natural selection has occurred within a particular gene, and the site-prediction method allows scientists to predict the exact location on a gene in which natural selection has occurred.

"Both of these methods are very popular among biologists because they appear to give valuable results about which genes have undergone natural selection," said Nei. "But neither of the methods seems to give an accurate picture of what's really going on."

Nei said that for many years he has suspected that the statistical methods were faulty. "The methods assume that when natural selection occurs the number of nucleotide substitutions that lead to changes in amino acids is significantly higher than the number of nucleotide substitutions that do not result in amino acid changes," he said. "But this assumption may be wrong. Actually, the majority of amino acid substitutions do not lead to functional changes, and the adaptive change of a protein often occurs by a rare amino acid substitution. For this reason, statistical methods may give erroneous conclusions." Nei also believes that the methods are inaccurate when the number of nucleotide substitutions observed is small.

To demonstrate the faultiness of the statistical methods, Nei's team compiled data collected by their Emory University colleague, Shozo Yokoyama, on the genes that control the abilities of fish to see light at different water depths and on the genes that control color vision in a variety of animals. The team used these data to compare statistically predicted sites of natural selection with experimentally determined sites. They found that the statistical methods rarely predicted the actual sites of natural selection, which had been identified by Yokoyama through experiments. "In some cases, statistical method completely failed to identify the true sites where natural selection occurred," said Nei. "This particular exercise demonstrated the difficulty with which statistical methods are able to detect natural selection."

To demonstrate how small sample sizes can lead to incorrect results, the team used computer simulations to examine the evolution of genes in three primates: humans, chimpanzees, and macaques. The scientists mimicked the procedures used by the authors of a 2007 paper, which applied the branch-site method to 14,000 orthologous genes -- genes that are genealogically identical among different species -- and which found that the method predicted selection in 32 of the genes. Nei and his team also studied selection using Fisher's exact test, but this test did not detect any selection. "The results indicate that the number of nucleotide substitutions that occurred were too small to detect any selection; therefore, all of the 32 cases obtained by the branch-site method must be false positives," said Nozawa.

"These statistical methods have led many scientists to believe that natural selection acted on many more genes in humans than it did in chimpanzees, and they conclude that this is the reason why humans have developed large brains and other morphological differences," said Nei. "But I believe that these scientists are wrong. The number of genes that have undergone selection should be nearly the same in humans and chimps. The differences that make us human are more likely due to mutations that were favorable to us in the particular environment into which we moved, and these mutations then accumulated through time."

Nei said that to obtain a more realistic picture of natural selection, biologists should pair experimental data with their statistical data whenever possible. Scientists usually do not use experimental data because such experiments can be difficult to conduct and because they are very time-consuming.

Barbara K. Kennedy | EurekAlert!
Further information:

More articles from Studies and Analyses:

nachricht Rutgers-led innovation could spur faster, cheaper, nano-based manufacturing
14.02.2018 | Rutgers University

nachricht New study from the University of Halle: How climate change alters plant growth
12.01.2018 | Martin-Luther-Universität Halle-Wittenberg

All articles from Studies and Analyses >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Space observation with radar to secure Germany's space infrastructure

Satellites in near-Earth orbit are at risk due to the steady increase in space debris. But their mission in the areas of telecommunications, navigation or weather forecasts is essential for society. Fraunhofer FHR therefore develops radar-based systems which allow the detection, tracking and cataloging of even the smallest particles of debris. Satellite operators who have access to our data are in a better position to plan evasive maneuvers and prevent destructive collisions. From April, 25-29 2018, Fraunhofer FHR and its partners will exhibit the complementary radar systems TIRA and GESTRA as well as the latest radar techniques for space observation across three stands at the ILA Berlin.

The "traffic situation" in space is very tense: the Earth is currently being orbited not only by countless satellites but also by a large volume of space...

Im Focus: Researchers Discover New Anti-Cancer Protein

An international team of researchers has discovered a new anti-cancer protein. The protein, called LHPP, prevents the uncontrolled proliferation of cancer cells in the liver. The researchers led by Prof. Michael N. Hall from the Biozentrum, University of Basel, report in “Nature” that LHPP can also serve as a biomarker for the diagnosis and prognosis of liver cancer.

The incidence of liver cancer, also known as hepatocellular carcinoma, is steadily increasing. In the last twenty years, the number of cases has almost doubled...

Im Focus: Researchers at Fraunhofer monitor re-entry of Chinese space station Tiangong-1

In just a few weeks from now, the Chinese space station Tiangong-1 will re-enter the Earth's atmosphere where it will to a large extent burn up. It is possible that some debris will reach the Earth's surface. Tiangong-1 is orbiting the Earth uncontrolled at a speed of approx. 29,000 km/h.Currently the prognosis relating to the time of impact currently lies within a window of several days. The scientists at Fraunhofer FHR have already been monitoring Tiangong-1 for a number of weeks with their TIRA system, one of the most powerful space observation radars in the world, with a view to supporting the German Space Situational Awareness Center and the ESA with their re-entry forecasts.

Following the loss of radio contact with Tiangong-1 in 2016 and due to the low orbital height, it is now inevitable that the Chinese space station will...

Im Focus: Alliance „OLED Licht Forum“ – Key partner for OLED lighting solutions

Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology FEP, provider of research and development services for OLED lighting solutions, announces the founding of the “OLED Licht Forum” and presents latest OLED design and lighting solutions during light+building, from March 18th – 23rd, 2018 in Frankfurt a.M./Germany, at booth no. F91 in Hall 4.0.

They are united in their passion for OLED (organic light emitting diodes) lighting with all of its unique facets and application possibilities. Thus experts in...

Im Focus: Mars' oceans formed early, possibly aided by massive volcanic eruptions

Oceans formed before Tharsis and evolved together, shaping climate history of Mars

A new scenario seeking to explain how Mars' putative oceans came and went over the last 4 billion years implies that the oceans formed several hundred million...

All Focus news of the innovation-report >>>



Industry & Economy
Event News

New solar solutions for sustainable buildings and cities

23.03.2018 | Event News

Virtual reality conference comes to Reutlingen

19.03.2018 | Event News

Ultrafast Wireless and Chip Design at the DATE Conference in Dresden

16.03.2018 | Event News

Latest News

For graphite pellets, just add elbow grease

23.03.2018 | Materials Sciences

Unique communication strategy discovered in stem cell pathway controlling plant growth

23.03.2018 | Agricultural and Forestry Science

Sharpening the X-ray view of the nanocosm

23.03.2018 | Physics and Astronomy

Science & Research
Overview of more VideoLinks >>>