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Evolutionary genomics
NEWS & COMMENT
Evolutionary genomics
W
ith sequencing of the first complete metazoan DNA sequence just finished, it was highly appropriate that the International Society of Molecular Evolution (ISME) should convene a meeting on Evolutionary Genomics in Costa Rica at the beginning of this year. Furthermore it was fitting that one of the first scientists to study this field, Giorgio Bernardi (Stazione Zoologica Anton Dohrn, Naples, Italy) should open proceedings. Along with his colleagues, he has studied the evolution of large-scale variation in base composition along chromosomes – the ‘isochores’ – since the mid-1970s. However, the field appears to be deadlocked between those who think that variation in composition is driven by selection and those who think it is a consequence of mutation bias (Noboru Suoeka, University of Colorado, Boulder, USA). The publication of several complete genomes from both prokaryotes and eukaryotes, and long contiguous sequences from a number of other species, has allowed us to ask, for the first time, how the genome itself evolves, rather than the genes within it. Duplication and rearrangement both appear to be important factors shaping the genome. As Ken Wolfe (Trinity College, Dublin, Ireland) showed, the genome of the yeast Saccharomyces cerevisiae appears to be the product of a tetraploidization, in which many genes have degenerated. Similar patterns of genome duplication are not evident in either the nematode Caenorhabditis elegans or humans. However, large-scale duplications, of several hundred kilobases, have been important in the evolution of the human major histocompatibility complex (MHC) (Sylvana Gaudieri and Yoshio Tateno, National Institute of Genetics, Mishima, Japan). Gene and genome duplication have been thought to be the major source of new genes. However, in some Drosophila species, a gene known as jingwei, appears to have arisen as a chimera of a gene called yande, and part of a reverse transcribed alcohol dehydrogenase transcript (Manyuan Long, University of Chicago, IL, USA). The function of this hybrid gene is unknown; it has retained the expression pattern of yande, but the protein coding sequence has undergone extensive adaptive evolution since it was formed. Although apparently rare, chimeric genes might have been important in the diversification of the metazoa, given that some metazoan specific genes show evidence that they were formed by exon-shuffling
176
(Laszlo Patthy, Hungarian Academy of Sciences, Budapest, Hungary). Exonshuffling is greatly helped by the presence of introns, which has led to suggestions that they were present when the very first genes were assembled. The fact that many introns, particularly those that fall between codons, also fall between protein domains (Walter Gilbert, Harvard University, Boston, MA, USA; Mitiko Go, Nagoya University, Nagoya, Japan) is consistent with this theory, but it still leaves the big question of why all prokaryotic lineages have lost all spliceosomal introns. Short and long interspersed repetitive DNA elements, otherwise known as SINEs and LINEs, are a major component of the genomes of most higher organisms. The reasons for their presence in a genome remains controversial, with some arguing that they have a function, whilst others regard them as simply parasitic DNA elements. What has been hitherto unappreciated, by either side, is some of the effects they might have on cellular biology. Carl Schmid and colleagues (University of California, Davis, USA) have found that SINEs are transcribed in response to several environmental cues, such as stress, and that this leads to an increase in protein production. This striking pattern tempts one to think that SINEs have a function, but what is required is a demonstration that having SINEs is advantageous. I personally find it difficult to imagine that SINEs and LINEs, which clearly have the capacity to be selfish parasitic DNAs, would be anything other than that. However, SINEs have been beneficial to phylogeneticists. The fact that independent SINE insertions have never been shown to occur at the same place in the genome (yet) means that they are very good, clean phylogenetic markers; what Andrew Shedlock (Tokyo Institute of Technology, Tokyo, Japan) termed ‘noisefree Hernigian synapomorphies’. The problem is finding SINE insertions that differ between species. However, SINE insertions have helped demonstrate that the hippopotamuses’ closest relatives are the whales (Norihori Okada, Tokyo Institute of Technology, Tokyo, Japan). One of the most unexpected discoveries recently has been the transfer of transposable elements across species boundaries. This appears to have been a relatively common occurrence in insects, but now there is evidence that a LINE element was transferred from a snake to the ancestor of the ruminants (Dusan Kordis,
J. Stefan Institute, Ljublijana, Slovenia). The vector for this transmission is unknown; it would be intriguing if it was a snakebite. The genome sequencing community has only recently become interested in genetic variation, but the power available from this sort of data was beautifully illustrated by Hiroshi Akashi (University of Kansas, Lawrence, USA). He showed that using a combination of between- and within-species data, it should be possible to solve one of the oldest problems in molecular evolution, the neutralist– selectionist debate; that is, whether most evolutionary change is driven by selection or genetic drift. Currently, the data from Drosophila simulans suggest that most amino acid substitutions are fixed by positive, adaptive selection, not genetic drift. Unfortunately, the data are currently too limited to draw any firm conclusions. The very first genome to be sequenced was that of the human mitochondrion, sequences of which have now been extensively used in our inferences of human evolution. The power to infer how the world has been colonized can be quite remarkable (Douglas Wallace, Emory University, Atlanta, GA, USA). However, complications might lie ahead. Evidence suggests that there could be recombination between maternally and paternally derived mitochondrial DNA (Adam Eyre-Walker, University of Sussex, Brighton, UK). The next few years look very exciting for the field of evolutionary genomics. With the publication of increasingly large contiguous sequences from higher plants and animals, particularly from closely related species, and new efforts to discover large numbers of single nucleotide polymorphisms (SNPs) in humans, the power to tackle questions old and new will be greatly increased. Adam Eyre-Walker Centre for the Study of Evolution & School of Biological Sciences, University of Sussex, Brighton, UK BN1 9QG ([email protected])
Students! 50% discount on Trends in Ecology & Evolution subscriptions!
0169-5347/99/$ – see front matter © 1999 Elsevier Science. All rights reserved. PII: S0169-5347(99)01614-6
For details see subscription card bound in this issue
TREE vol. 14, no. 5 May 1999
Evolutionary genomics
W
ith sequencing of the first complete metazoan DNA sequence just finished, it was highly appropriate that the International Society of Molecular Evolution (ISME) should convene a meeting on Evolutionary Genomics in Costa Rica at the beginning of this year. Furthermore it was fitting that one of the first scientists to study this field, Giorgio Bernardi (Stazione Zoologica Anton Dohrn, Naples, Italy) should open proceedings. Along with his colleagues, he has studied the evolution of large-scale variation in base composition along chromosomes – the ‘isochores’ – since the mid-1970s. However, the field appears to be deadlocked between those who think that variation in composition is driven by selection and those who think it is a consequence of mutation bias (Noboru Suoeka, University of Colorado, Boulder, USA). The publication of several complete genomes from both prokaryotes and eukaryotes, and long contiguous sequences from a number of other species, has allowed us to ask, for the first time, how the genome itself evolves, rather than the genes within it. Duplication and rearrangement both appear to be important factors shaping the genome. As Ken Wolfe (Trinity College, Dublin, Ireland) showed, the genome of the yeast Saccharomyces cerevisiae appears to be the product of a tetraploidization, in which many genes have degenerated. Similar patterns of genome duplication are not evident in either the nematode Caenorhabditis elegans or humans. However, large-scale duplications, of several hundred kilobases, have been important in the evolution of the human major histocompatibility complex (MHC) (Sylvana Gaudieri and Yoshio Tateno, National Institute of Genetics, Mishima, Japan). Gene and genome duplication have been thought to be the major source of new genes. However, in some Drosophila species, a gene known as jingwei, appears to have arisen as a chimera of a gene called yande, and part of a reverse transcribed alcohol dehydrogenase transcript (Manyuan Long, University of Chicago, IL, USA). The function of this hybrid gene is unknown; it has retained the expression pattern of yande, but the protein coding sequence has undergone extensive adaptive evolution since it was formed. Although apparently rare, chimeric genes might have been important in the diversification of the metazoa, given that some metazoan specific genes show evidence that they were formed by exon-shuffling
176
(Laszlo Patthy, Hungarian Academy of Sciences, Budapest, Hungary). Exonshuffling is greatly helped by the presence of introns, which has led to suggestions that they were present when the very first genes were assembled. The fact that many introns, particularly those that fall between codons, also fall between protein domains (Walter Gilbert, Harvard University, Boston, MA, USA; Mitiko Go, Nagoya University, Nagoya, Japan) is consistent with this theory, but it still leaves the big question of why all prokaryotic lineages have lost all spliceosomal introns. Short and long interspersed repetitive DNA elements, otherwise known as SINEs and LINEs, are a major component of the genomes of most higher organisms. The reasons for their presence in a genome remains controversial, with some arguing that they have a function, whilst others regard them as simply parasitic DNA elements. What has been hitherto unappreciated, by either side, is some of the effects they might have on cellular biology. Carl Schmid and colleagues (University of California, Davis, USA) have found that SINEs are transcribed in response to several environmental cues, such as stress, and that this leads to an increase in protein production. This striking pattern tempts one to think that SINEs have a function, but what is required is a demonstration that having SINEs is advantageous. I personally find it difficult to imagine that SINEs and LINEs, which clearly have the capacity to be selfish parasitic DNAs, would be anything other than that. However, SINEs have been beneficial to phylogeneticists. The fact that independent SINE insertions have never been shown to occur at the same place in the genome (yet) means that they are very good, clean phylogenetic markers; what Andrew Shedlock (Tokyo Institute of Technology, Tokyo, Japan) termed ‘noisefree Hernigian synapomorphies’. The problem is finding SINE insertions that differ between species. However, SINE insertions have helped demonstrate that the hippopotamuses’ closest relatives are the whales (Norihori Okada, Tokyo Institute of Technology, Tokyo, Japan). One of the most unexpected discoveries recently has been the transfer of transposable elements across species boundaries. This appears to have been a relatively common occurrence in insects, but now there is evidence that a LINE element was transferred from a snake to the ancestor of the ruminants (Dusan Kordis,
J. Stefan Institute, Ljublijana, Slovenia). The vector for this transmission is unknown; it would be intriguing if it was a snakebite. The genome sequencing community has only recently become interested in genetic variation, but the power available from this sort of data was beautifully illustrated by Hiroshi Akashi (University of Kansas, Lawrence, USA). He showed that using a combination of between- and within-species data, it should be possible to solve one of the oldest problems in molecular evolution, the neutralist– selectionist debate; that is, whether most evolutionary change is driven by selection or genetic drift. Currently, the data from Drosophila simulans suggest that most amino acid substitutions are fixed by positive, adaptive selection, not genetic drift. Unfortunately, the data are currently too limited to draw any firm conclusions. The very first genome to be sequenced was that of the human mitochondrion, sequences of which have now been extensively used in our inferences of human evolution. The power to infer how the world has been colonized can be quite remarkable (Douglas Wallace, Emory University, Atlanta, GA, USA). However, complications might lie ahead. Evidence suggests that there could be recombination between maternally and paternally derived mitochondrial DNA (Adam Eyre-Walker, University of Sussex, Brighton, UK). The next few years look very exciting for the field of evolutionary genomics. With the publication of increasingly large contiguous sequences from higher plants and animals, particularly from closely related species, and new efforts to discover large numbers of single nucleotide polymorphisms (SNPs) in humans, the power to tackle questions old and new will be greatly increased. Adam Eyre-Walker Centre for the Study of Evolution & School of Biological Sciences, University of Sussex, Brighton, UK BN1 9QG ([email protected])
Students! 50% discount on Trends in Ecology & Evolution subscriptions!
0169-5347/99/$ – see front matter © 1999 Elsevier Science. All rights reserved. PII: S0169-5347(99)01614-6
For details see subscription card bound in this issue
TREE vol. 14, no. 5 May 1999