Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

For inferring the biological tree of life, simple is better

21.10.2004


UO researchers report ’the old-fashioned way’ is more accurate for comparing DNA sequences



A study published this week in Nature (Nov. 21) shows that the most widely used method for constructing the tree of life from DNA sequences is prone to error. However, a simpler method, largely abandoned in recent years, turns out to be far more accurate.
These surprising findings may change the way evolutionary biologists infer the relationships among species - a cornerstone of modern biology - according to researchers at the University of Oregon.

Joe Thornton, a UO assistant professor of biology, and Bryan Kolaczkowski, a graduate student in computer and information science, used a small supercomputer to simulate the evolution of thousands of gene sequences on a hypothetical evolutionary tree. They examined which methods for inferring historical relationships correctly recovered that tree from the simulated data.



They found that a simple logical method known as maximum parsimony is far more accurate under a wide range of conditions than the state-of-the-art technique known as maximum likelihood, which uses a mathematic model of the evolutionary process. "It turns out that the complicated method performs well when reality is simple, but the simpler method is much more accurate when reality is complex," Thornton said.

During the past decade, maximum likelihood has eclipsed maximum parsimony as a tool for evolutionary biologists, largely because of studies that found it to be a more accurate and powerful tool.

Thornton and Kolaczkowski were not convinced by these studies, which simulated evolution using a simplistic and unrealistic process in which the various parts of a gene evolve at the same rate in all species. So they evaluated, for the first time, the performance of the methods when the evolutionary process changes over time, as it is known to do. "Maximum likelihood often gets the wrong tree because it assumes evolution can be accurately captured in a statistical model, but the assumptions of those models are usually wrong," Thornton said. "Parsimony makes fewer assumptions, so it can cope with a complex reality better."

The results published in Nature suggest that scientists should bring back the maximum parsimony method and interpret with caution results from the maximum likelihood method, many of which have been accepted as established knowledge, Thornton said.

Why is an accurate evolutionary tree important? Inferences scientists make about human biology from model organisms such as mice or zebra fish, are based on an understanding of the evolutionary relationships between species. When scientists compare the embryonic development among species, their conclusions all depend upon accurate knowledge of the evolutionary tree. Thornton and Kolaczkowski performed their experiments on a small supercomputer they assembled in the Thornton laboratory by linking together a cluster of Apple personal computers.

The project was funded in part by a National Science Foundation grant to the UO to train graduate students like Kolaczkowski in interdisciplinary research in evolution, development and genomics. Thornton, who joined the UO faculty in 2002, is an assistant professor of biological sciences in the UO Department of Biology s Center for Ecology and Evolutionary Biology. His laboratory combines computational work on phylogenetic methods with experimental studies to understand how genes evolve new functions. He is particularly interested in the evolution of hormones and the receptor proteins that mediate their effects on the body.

In 2003, Thornton resurrected the ancient gene for the first steroid hormone receptor - which last existed more than 600 million years ago - in the laboratory and expressed it in cultured cells to understand its function, work that was published in the journal Science. He also is an expert in environmental health and policy. He is the author of "Pandora’s Poison: Chlorine, Health, and a New Environmental Strategy" (MIT Press), a landmark book on the effects of toxic chemicals on human health and the environment. He pointed out a parallel between this work and his research on evolutionary tree building.

"Many dangerous chemicals are licensed today by calculating how much of each one we can safely be exposed to, using an assumption-laden, statistical method called quantitative risk assessment," he said. "The problem is that the assumptions of risk assessment models are routinely violated, and safe levels often turn out to be hazardous. In many cases, we could prevent damage from these chemicals altogether by using safer alternatives, but these are often overlooked because of government’s reliance on risk assessment. Here again, simpler would lead to a better outcome."

Melody Ward Leslie | EurekAlert!
Further information:
http://uoregon.edu

More articles from Life Sciences:

nachricht Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory

nachricht How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Argon is not the 'dope' for metallic hydrogen

24.03.2017 | Materials Sciences

Astronomers find unexpected, dust-obscured star formation in distant galaxy

24.03.2017 | Physics and Astronomy

Gravitational wave kicks monster black hole out of galactic core

24.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>