Navigation Links
Gene's 'selective signature' aids detection of natural selection in microbial evolution
Date:3/18/2008

Scientists at MIT have come up with a mathematical approach for analyzing a protein simultaneously in a set of ecologically distinct species to identify occurrences of natural selection in an organisms evolution.

The new method determines the selective signature of a gene, that is, the pattern of fast or slow evolution of that gene across a group of species, and uses that signature to infer gene function or to map changes to ecological shifts.

By reversing the usual order of inquirystudying an organism, then trying to identify which genes are involved in a particular functionthe scientists hope to hasten the understanding of microbial evolution by taking advantage of the nearly 2,500 microbes already sequenced.

By comparing across species, we looked for changes in genes that reflect natural selection and then asked, How does this gene relate to the ecology of the species it occurs in? said Eric Alm, the Doherty Assistant Professor of Ocean Utilization in the Department of Civil and Environmental Engineering. The selective signature method also allows us to focus on a single species and better understand the selective pressures on it.

Our hope is that other researchers will take this tool and apply it to sets of related species with fully sequenced genomes to understand the genetic basis of that ecological divergence, said graduate student B. Jesse Shapiro, who co-authored with Alm a paper published in the February issue of PLoS Genetics.

Their work also suggests that evolution occurs on functional modulesgenes that may not sit together on the genome, but that encode proteins that perform similar functions.

When we see similar results across all the genes in a pathway, it suggests the genomic landscape may be organized into functional modules even at the level of natural selection, said Alm. If thats true, it may be easier than expected to understand the complex evolutionary pressures on a cell.

In a single species, a whole set of genes in the same module tend to change together, said Shapiro. Identifying these changes brings us a step closer to understanding the ecological basis of selection in a species and how changes at the genetic level affect the organisms interactions with its environment.

For example, in Idiomarina loihiensis, a marine bacterium that has adapted to life near sulfurous hydrothermal vents in the ocean floor, the genes involved in metabolizing sugar and the amino acid phenylalanine underwent significant changes (over hundreds of millions of years) that may help the bacterium obtain carbon from amino acids rather than from sugars, a necessity for life in that ecological niche. In one of I. loihiensis sister species, Colwellia psychrerythraea, some of those same genes have been lost altogether, an indication that sugar metabolism is no longer important for Colwellia.

Shapiro and Alm focused on 744 protein families among 30 species of gamma-proteobacteria that shared a common ancestor roughly 1 to 2 billion years ago. These bacteria include the laboratory model organism E. coli, as well as intracellular parasites of aphids, pathogens like the bacteria that cause cholera, and soil and plant bacteria. They mapped the evolutionary distance of each species from the ancestor and incorporated information about the gene family (for instance, important proteins evolve more slowly than less vital ones) and the normal rate of evolution in a particular species genome in order to determine a genes selective signature.

These are experiments we could never perform in a lab, said Alm. But Mother Nature has put genes into an environment and run an evolutionary experiment over billions of years. What were doing is mining that data to see if genes that perform a similar function, say motility, evolve at the same rate in different species. To the extent that they differ, it helps us to understand how change in core genes drives functional divergence between species across the tree of life.


'/>"/>

Contact: Denise Brehm
brehm@mit.edu
617-253-8069
Massachusetts Institute of Technology, Department of Civil and Environmental Engineering
Source:Eurekalert

Related biology news :

1. Gene regulation, not just genes, is what sets humans apart
2. Interaction of just 2 genes governs coloration patterns in mice
3. Muscle mass: Scientists identify novel mode of transcriptional regulation during myogenesis
4. Study finds blocking angiogenesis signaling from inside cell may lead to serious health problems
5. Smoking turns on genes -- permanently
6. Genes, Environment and Health Initiative invests in genetic studies, environmental monitoring
7. Hebrew SeniorLife researchers search for aging, osteoporosis genes
8. UT Southwestern researchers identify hundreds of genes controlling female fertility
9. Genes and environment grant funds close look at nature-nurture overlap in common diseases
10. Jumping genes could make for safer gene delivery system
11. Genes from the father facilitate the formation of new species
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/22/2016)... American College of Medical Genetics and Genomics was once again ... of the fastest-growing trade shows during the Fastest 50 Awards ... Las Vegas . Winners are ... of the following categories: net square feet of paid exhibit ... 2015 ACMG Annual Meeting was ranked 23 out of 50 ...
(Date:6/21/2016)... , June 21, 2016 NuData ... the new role of principal product architect and ... the director of customer development. Both will report ... technical officer. The moves reflect NuData,s strategic growth ... response to high customer demand and customer focus ...
(Date:6/15/2016)... ALBANY, New York , June 15, 2016 ... published a new market report titled "Gesture Recognition Market ... Trends and Forecast, 2016 - 2024". According to the ... at USD 11.60 billion in 2015 and is ... and reach USD 48.56 billion by 2024.  ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... -- The Biodesign Challenge (BDC), a university competition that asks ... systems and biotechnology, announced its winning teams at the ... York City . The teams, chosen ... MoMA,s Celeste Bartos Theater during the daylong summit. Keynote ... of architecture and design, and Suzanne Lee , ...
(Date:6/23/2016)... ... June 23, 2016 , ... STACS DNA Inc., the sample tracking software company, ... Crime Laboratory, has joined STACS DNA as a Field Application Specialist. , “I ... President and COO of STACS DNA. “In further expanding our capacity as a scientific ...
(Date:6/23/2016)... , June 23, 2016  Blueprint Bio, a company ... to the medical community, has closed its Series A ... Nunez . "We have received a commitment ... capital we need to meet our current goals," stated ... us the runway to complete validation on the current ...
(Date:6/23/2016)... , ... June 23, 2016 , ... ... exhibiting at the Pennsylvania Convention Center and will showcase its product’s latest features ... will also be presenting a scientific poster on Disrupting Clinical Trials in The ...
Breaking Biology Technology: