Featured Research

from universities, journals, and other organizations

Techniques used to infer pathways of protein evolution found unreliable

Date:
October 11, 2012
Source:
American Institute of Biological Sciences
Summary:
Biologists have published thousands of papers that used statistical techniques to infer the likely evolutionary paths that led to the present-day forms of proteins. But careful experimental studies of the properties of reconstructed ancestral forms of visual pigments and variants created by mutation suggest that core simplifying assumptions used in the statistical approaches are unreliable and make the approaches unable to identify the actual paths.

A key assumption that biologists have relied on widely over the past quarter-century in studying the evolution of protein molecules is "highly questionable," according to an article published in the November issue of BioScience.

The article, by Shozo Yokoyama, a vision researcher at Emory University, summarizes experimental work that involved creating and measuring the properties of dozens of reconstructed ancestral versions of visual pigments found in the eyes of vertebrates, including humans, as well as deliberately altered variants. Yokoyama concludes that the studies he assessed "cast serious doubt" on the "fundamental principle of molecular adaptation," the bedrock of thousands of published papers based on reconstructions of evolutionary changes in a wide range of proteins. The statistical tools used by such studies are "not reliable," he writes.

In attempting to understand how proteins and their properties might have changed over time, biologists have typically made simplifying assumptions. One is that a known change at a particular spot in a protein would affect the properties of ancestral and modern forms of proteins in similar ways. That simplification makes it relatively easy for computers to infer the likely evolutionary paths that led to the forms of the proteins found in modern organisms -- for example, the visual pigments found in deep-sea fishes (which live with no ultraviolet light) and the different pigments found in shallow-water fishes.

Yokoyama tested the assumptions by making the hypothesized ancestral pigments and variants of them that might have been produced by mutation, then accurately measuring their properties. The results were disturbing: the properties of related versions of proteins would often change in very different ways when the same mutation was introduced into each. Consequently, standard computational and statistical methods would rarely have identified the experimentally supported evolutionary pathway. Yokoyama expresses the hope that other researchers will start to make and test the properties of reconstructed ancestral proteins to evaluate hypotheses about their evolution, rather than relying on computational approaches.


Story Source:

The above story is based on materials provided by American Institute of Biological Sciences. Note: Materials may be edited for content and length.


Cite This Page:

American Institute of Biological Sciences. "Techniques used to infer pathways of protein evolution found unreliable." ScienceDaily. ScienceDaily, 11 October 2012. <www.sciencedaily.com/releases/2012/10/121011090645.htm>.
American Institute of Biological Sciences. (2012, October 11). Techniques used to infer pathways of protein evolution found unreliable. ScienceDaily. Retrieved July 28, 2014 from www.sciencedaily.com/releases/2012/10/121011090645.htm
American Institute of Biological Sciences. "Techniques used to infer pathways of protein evolution found unreliable." ScienceDaily. www.sciencedaily.com/releases/2012/10/121011090645.htm (accessed July 28, 2014).

Share This




More Matter & Energy News

Monday, July 28, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

The Carbon Trap: US Exports Global Warming

The Carbon Trap: US Exports Global Warming

AP (July 28, 2014) AP Investigation: As the Obama administration weans the country off dirty fuels, energy companies are ramping-up overseas coal exports at a heavy price. (July 28) Video provided by AP
Powered by NewsLook.com
Shipping Crates Get New 'lease' On Life

Shipping Crates Get New 'lease' On Life

Reuters - Business Video Online (July 25, 2014) Shipping containers have been piling up as America imports more than it exports. Some university students in Washington D.C. are set to get a first-hand lesson in recycling. Their housing is being built using refashioned shipping containers. Lily Jamali reports. Video provided by Reuters
Powered by NewsLook.com
Europe's Highest Train Turns 80 in French Pyrenees

Europe's Highest Train Turns 80 in French Pyrenees

AFP (July 25, 2014) Europe's highest train, the little train of Artouste in the French Pyrenees, celebrates its 80th birthday. Duration: 01:05 Video provided by AFP
Powered by NewsLook.com
TSA Administrator on Politics and Flight Bans

TSA Administrator on Politics and Flight Bans

AP (July 24, 2014) TSA administrator, John Pistole's took part in the Aspen Security Forum 2014, where he answered questions on lifting of the ban on flights into Israel's Tel Aviv airport and whether politics played a role in lifting the ban. (July 24) Video provided by AP
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