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 Closing the carbon loop
08.12.2016 | University of Pittsburgh

nachricht Newly discovered bacteria-binding protein in the intestine
08.12.2016 | University of Gothenburg

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Significantly more productivity in USP lasers

In recent years, lasers with ultrashort pulses (USP) down to the femtosecond range have become established on an industrial scale. They could advance some applications with the much-lauded “cold ablation” – if that meant they would then achieve more throughput. A new generation of process engineering that will address this issue in particular will be discussed at the “4th UKP Workshop – Ultrafast Laser Technology” in April 2017.

Even back in the 1990s, scientists were comparing materials processing with nanosecond, picosecond and femtosesecond pulses. The result was surprising:...

Im Focus: Shape matters when light meets atom

Mapping the interaction of a single atom with a single photon may inform design of quantum devices

Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

Closing the carbon loop

08.12.2016 | Life Sciences

Applicability of dynamic facilitation theory to binary hard disk systems

08.12.2016 | Physics and Astronomy

Scientists track chemical and structural evolution of catalytic nanoparticles in 3-D

08.12.2016 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>