Gene's 'selective signature' aids detection of natural selection in microbial evolutionMarch 19, 2008CAMBRIDGE, Mass. -- 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 organism's 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 inquiry-studying an organism, then trying to identify which genes are involved in a particular function-the 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 Departments of Civil and Environmental Engineering and Biological 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 modules-genes 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 that's 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 gene's 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 we're 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." This work is part of the Virtual Institute for Microbial Stress and Survival. The research was also supported by additional grants from the U.S. Department of Energy Genomics: GTL Program, the National Institutes of Health, and a scholarship from the Natural Sciences and Engineering Research Council of Canada. Massachusetts Institute of Technology | |||||||||||||||||||||
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Related Natural Selection Current Events and Natural Selection News Articles MU Anthropologist Develops New Approach to Explain Religious Behavior Without a way to measure religious beliefs, anthropologists have had difficulty studying religion. Now, two anthropologists from the University of Missouri and Arizona State University have developed a new approach to study religion by focusing on verbal communication, an identifiable behavior, instead of speculating about alleged beliefs in the supernatural that cannot actually be identified. Old before their time? Aging in flies under natural vs. laboratory conditions Evolutionary studies of aging typically utilize small, short-lived animals (insects, worms, mice) under benign conditions - constant temperature and humidity, no parasites, superabundant food - in the laboratory. Oddly enough, very little is known about aging in such animals in their harsh, stressful natural environments. Could it be that these laboratory "guinea pigs" actually age much more slowly in captive luxury than do their wild cousins? How 'secondary' sex characters can drive the origin of species The ostentatious, sometimes bizarre qualities that improve a creature's chances of finding a mate may also drive the reproductive separation of populations and the evolution of new species, say two Indiana University Bloomington biologists. Duke-NIEHS team shows how DNA repairs may reshape the genome Researchers at Duke University Medical Center and at the National Institute of Environmental Health Sciences (NIEHS) have shown how broken sections of chromosomes can recombine to change genomes and spawn new species. New research reveals why chili peppers are hot Despite the popularity of spicy cuisine among Homo sapiens, the hotness in chili peppers has always been something of an evolutionary mystery. World's smallest snake found in Barbados The world's smallest species of snake, with adults averaging just under four inches in length, has been identified on the Caribbean island of Barbados. The species -- which is as thin as a spaghetti noodle and small enough to rest comfortably on a U.S. quarter --was discovered by Blair Hedges, an evolutionary biologist at Penn State. New study of gene evolution could lead to better understanding of neurodegenerative disease Genetic evolution is strongly shaped by genes' efforts to prevent or tolerate errors in the production of proteins, scientists at The University of Texas at Austin and Harvard University have found. Viral recombination another way HIV fools the immune system When individuals infected with HIV become infected with a second strain of the virus, the two viral strains can exchange genetic information, creating a third, recombinant strain of the virus. It is known that the presence of multiple viral strains, called superinfection, frequently leads to a loss of immune control of viral levels. Life on the edge: To disperse, or become extinct? The hardiest plants and those most likely to survive the climatic shifts brought about by global warming are now easier to identify, thanks to new research findings by a team from Queen's University. New research on mutation in yeast can enhance understanding of human diseases Yeast, a model organism heavily relied upon for studying basic biological processes as they relate to human health, mutates in a distinctly different pattern than other model organisms, a finding that brings researchers closer to understanding the role of evolutionary genetics in human diseases and cancer. More Natural Selection Current Events and Natural Selection News Articles |
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