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Evolving beyond point mutations
110
News & Comment
TRENDS in Ecology & Evolution Vol.17 No.3 March 2002
Which oceans are we really talking about? Substantial effort has been expended in recent decades to show that the changes occurring in marine ecosystems are the consequences of anthropogenic effects, including pollution, lower water quality and climate change. This has resulted in a large body of research on the status of the oceans and their capacity to recover that focuses on analyses of pollutants and temperature increases. Based on a detailed study of paleontological, archeological and historical information on various ecosystems, particularly kelp forests, coral reefs and estuaries, Jackson et al. [1] propose a new approach that calls into question many of the contributions of recent ecological studies. According to the authors, there have been three partially overlapping periods of human impact on the oceans: aboriginal, colonial and global. A close study of the first two periods led Jackson et al. to suggest that overfishing of all marine ecosystems began in the 16th century and changed the ecological balance of the
oceans so much that they became more susceptible to the more recent changes brought about by pollution, for example. The large-scale removal of large predators led to their being replaced in marine food chains by humans. As a result, there is a noticeable tendency for some large predators, such as fish, to be replaced by other organisms, such as medusae or other fish species. This replacement leads to a new equilibrium state that makes it unlikely that marine food chains will ever return to their original states. This new paper forces us to reconsider seriously different aspects that are becoming more meaningful to the study of marine ecosystems. In designing an appropriate strategy for the recovery of the oceans, studies based on paleontological or historical, along with ecological information, must be undertaken to seek the original causes of the deterioration of marine ecosystems. Unless we take steps to improve our understanding of large predators, there will be little that we can
contribute to an understanding of the evolution of ecosystems, as present studies deal excessively with tiny marine organisms (phytoplankton, zooplankton and microorganisms). Current approaches to marine biodiversity focus on the discovery and description of pristine ecosystems, where there is no recent record of pollution and exploitation. Yet those very same ecosystems might have a history of overexploitation of which we are largely unaware and so might be unsuitable for such research. Could it be that we are studying unnatural oceans? And could it be that an overemphasis on a strict ecological approach is causing us to bypass a developmental and historical overview of the oceans? 1 Jackson, J.B.C. et al. (2001) Historical overfishing and the recent collapse of coastal ecosystems. Science 239, 629–638
Josep-Maria Gili [email protected]
Evolving beyond point mutations Genomic structure and content are remarkably labile over evolutionary time. Yet we know little about the relative importance of genomic changes versus point mutations in adaptive evolution. Using microarray technology, a new paper [1] suggests that large-scale duplications and deletions might play a more common role in adaptation than was previously thought. Using microarrays to obtain a genomic rather than an expression profile, Riehle et al. examined genomic changes in six lines of Escherichia coli adapted to high temperature (41.5°C). In competition with ancestral lines, the evolved lines displayed a 33.5% increase in fitness, on average, over 2000 generations of adaptation. Riehle et al. extracted genomic DNA (rather than mRNA), from which they generated radioactively labeled DNA fragments, and hybridized these to a microarray containing all 4290 genes of E. coli. Differences between two lines in the pattern of radiation intensity across the microarray potentially indicate differences in gene copy number, but they raise the http://tree.trends.com
sticky statistical problem of identifying which differences are significant. When looking for large-scale deletion and duplication events, however, the solution is relatively easy, because similar patterns are expected at all genes within the affected region. Thus, the authors used a sliding window approach with a permutation test to identify significant changes in gene copy number. What they found was remarkable: three of the six lines contained duplications within the same genomic region. These duplications differed in size but shared 23 open reading frames, including four candidate genes known to play a role in response to stress. Two additional genomic alterations were found in one strain: another duplication and a deletion. Knowing which genomic alterations arose during the course of adaptation, the authors could then pinpoint when they spread, isolate cells immediately before and after this event, and measure the fitness effect of the genomic alteration. The three genomic changes examined in this way increased fitness by 12%, 7% and 25%, respectively.
Thus, these genomic alterations alone account for 22% of the total adaptation to high temperature observed in the six lines. This study demonstrates that genomic alterations provide important raw material for adaptation to novel environments, even within short-term evolution experiments and even within compact bacterial genomes. An ongoing study in yeast [2] has also found that large-scale genomic alterations attend adaptation to a glucose-limiting environment (M, Dunham, H. Badrane, D. Botstein and F. Rosenzweig, pers. commun.). Such studies promise to provide us with a clearer and more precise picture of the genetic basis of adaptation. 1 Riehle, M.M. et al. (2001) Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 98, 525–530 2 Ferea, T.L. et al. (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. U. S. A. 96, 9721–9726
Sarah Otto [email protected]
0169-5347/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved.
News & Comment
TRENDS in Ecology & Evolution Vol.17 No.3 March 2002
Which oceans are we really talking about? Substantial effort has been expended in recent decades to show that the changes occurring in marine ecosystems are the consequences of anthropogenic effects, including pollution, lower water quality and climate change. This has resulted in a large body of research on the status of the oceans and their capacity to recover that focuses on analyses of pollutants and temperature increases. Based on a detailed study of paleontological, archeological and historical information on various ecosystems, particularly kelp forests, coral reefs and estuaries, Jackson et al. [1] propose a new approach that calls into question many of the contributions of recent ecological studies. According to the authors, there have been three partially overlapping periods of human impact on the oceans: aboriginal, colonial and global. A close study of the first two periods led Jackson et al. to suggest that overfishing of all marine ecosystems began in the 16th century and changed the ecological balance of the
oceans so much that they became more susceptible to the more recent changes brought about by pollution, for example. The large-scale removal of large predators led to their being replaced in marine food chains by humans. As a result, there is a noticeable tendency for some large predators, such as fish, to be replaced by other organisms, such as medusae or other fish species. This replacement leads to a new equilibrium state that makes it unlikely that marine food chains will ever return to their original states. This new paper forces us to reconsider seriously different aspects that are becoming more meaningful to the study of marine ecosystems. In designing an appropriate strategy for the recovery of the oceans, studies based on paleontological or historical, along with ecological information, must be undertaken to seek the original causes of the deterioration of marine ecosystems. Unless we take steps to improve our understanding of large predators, there will be little that we can
contribute to an understanding of the evolution of ecosystems, as present studies deal excessively with tiny marine organisms (phytoplankton, zooplankton and microorganisms). Current approaches to marine biodiversity focus on the discovery and description of pristine ecosystems, where there is no recent record of pollution and exploitation. Yet those very same ecosystems might have a history of overexploitation of which we are largely unaware and so might be unsuitable for such research. Could it be that we are studying unnatural oceans? And could it be that an overemphasis on a strict ecological approach is causing us to bypass a developmental and historical overview of the oceans? 1 Jackson, J.B.C. et al. (2001) Historical overfishing and the recent collapse of coastal ecosystems. Science 239, 629–638
Josep-Maria Gili [email protected]
Evolving beyond point mutations Genomic structure and content are remarkably labile over evolutionary time. Yet we know little about the relative importance of genomic changes versus point mutations in adaptive evolution. Using microarray technology, a new paper [1] suggests that large-scale duplications and deletions might play a more common role in adaptation than was previously thought. Using microarrays to obtain a genomic rather than an expression profile, Riehle et al. examined genomic changes in six lines of Escherichia coli adapted to high temperature (41.5°C). In competition with ancestral lines, the evolved lines displayed a 33.5% increase in fitness, on average, over 2000 generations of adaptation. Riehle et al. extracted genomic DNA (rather than mRNA), from which they generated radioactively labeled DNA fragments, and hybridized these to a microarray containing all 4290 genes of E. coli. Differences between two lines in the pattern of radiation intensity across the microarray potentially indicate differences in gene copy number, but they raise the http://tree.trends.com
sticky statistical problem of identifying which differences are significant. When looking for large-scale deletion and duplication events, however, the solution is relatively easy, because similar patterns are expected at all genes within the affected region. Thus, the authors used a sliding window approach with a permutation test to identify significant changes in gene copy number. What they found was remarkable: three of the six lines contained duplications within the same genomic region. These duplications differed in size but shared 23 open reading frames, including four candidate genes known to play a role in response to stress. Two additional genomic alterations were found in one strain: another duplication and a deletion. Knowing which genomic alterations arose during the course of adaptation, the authors could then pinpoint when they spread, isolate cells immediately before and after this event, and measure the fitness effect of the genomic alteration. The three genomic changes examined in this way increased fitness by 12%, 7% and 25%, respectively.
Thus, these genomic alterations alone account for 22% of the total adaptation to high temperature observed in the six lines. This study demonstrates that genomic alterations provide important raw material for adaptation to novel environments, even within short-term evolution experiments and even within compact bacterial genomes. An ongoing study in yeast [2] has also found that large-scale genomic alterations attend adaptation to a glucose-limiting environment (M, Dunham, H. Badrane, D. Botstein and F. Rosenzweig, pers. commun.). Such studies promise to provide us with a clearer and more precise picture of the genetic basis of adaptation. 1 Riehle, M.M. et al. (2001) Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 98, 525–530 2 Ferea, T.L. et al. (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. U. S. A. 96, 9721–9726
Sarah Otto [email protected]
0169-5347/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved.