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REVIEWS Reductive evolution of resident genomes Siv G.E. Andersson and Charles G. Kurland T he genomes of obligate Small, asexual populations are expected to Despite the differences in parasites, endosymbionts accumulate deleterious substitutions and evolutionary dynamics, the and cellular organelles deletions in an irreversible manner, which transmission of both types of evolve under conditions that in the long-term will lead to mutational resident genomes from one are radically different from meltdown and genome decay. Here, we host to the next frequently those of free-living organisms. discuss the influence of such reductive involves bottlenecks and repliOne distinguishing factor is processes on the evolution of genomes that cation in small populations, that they are residents of an replicate within the domain of a host with little opportunity for reenvironment that is conditioned genome. combination between variants. by a host genome. For examFor this reason, the resident ple, it is possible to imagine an S.G.E. Andersson* and C.G. Kurland are in the Dept genomes accumulate deleteriof Molecular Biology, Biomedical Center, Uppsala evolutionary sequence in which ous mutations at a rate that is University, S-751-24 Uppsala, Sweden. a bacterium begins as a faculhigher than that for free-living *tel: ⫹46 18 471 4379, fax: ⫹46 18 55 77 23, tative resident within a cellular organisms. Some of these dee-mail: [email protected] domain. During the course of leterious mutations lead to the adaptation to the intracellular environment, the bac- loss of coding sequences, while others lead to a terium can take one of two alternative evolutionary marked variability of resident genome architectures. routes. On the one hand, the host cell can become de- This tendency of small asexual populations to accupendent on products provided by the activities of the mulate deleterious mutations is referred to as Muller’s bacterial genome. In this case, the fates of the cell and ratchet3,4 (Box 1). the resident are linked through a symbiotic dependence The validity of Muller’s ratchet has been investithat is progressively strengthened by the tendency to gated in RNA viruses, which have extraordinarily lose gene functions from one or other genome as a high mutation rates and are subjected to recurrent consequence of the redundancy of their overlapping bottlenecks5–7. Co-infection provides opportunities genomic functions. In the extreme, the two genomes for genetic exchange through recombination or segcan evolve a relationship as profound as that between mentation in some viral lineages, while others reprothe eukaryote nucleus and the mitochondria. Here, duce in a strictly asexual manner. When populations the symbiosis initiated between the primitive eukary- of asexual and sexual viruses are forced through a seote nucleus and an aerobic bacterium has enabled the ries of bottlenecks, deleterious mutations accumulate eukaryote to evolve an aerobic lifestyle. Gene content by genetic drift, resulting in a loss of fitness in both is markedly reduced in mtDNAs, compared with populations. However, while this loss can be reversed those of their eubacterial ancestors1, and some mito- in sexual viruses by recombination and/or segmentachondrial genomes have undergone so much reduc- tion during intervening periods of mass selection in tive evolution that they seem to be on the verge of dis- large populations, loss of fitness is effectively irreversible in asexual viral populations if the rate of appearing entirely from the eukaryotic cells2. On the other hand, the bacterium may become an compensatory back-mutations is low7. obligate parasite that offers no benefits to the host. Because of their obligate intracellular lifestyles, Thus, the fates of the host cell and the parasite are not there are few or no opportunities for resident genomes reciprocally coupled. Instead, a more or less elaborate of bacteria and organelles to recover from the fitness pattern of pathogenesis and defensive strategies evolves. decline caused by genetic drift during transmission Here, too, losses of neutralized genes will strengthen from one host to the other. Indeed, mitochondrial the dependence of the parasite on the host genome. genomes with low recombination frequencies underThe dependence can proceed so far that the parasite is go higher fixation rates for new mutations than their unable to grow outside its host domain. However, sexually reproducing host genomes8,9. Thus, we may whereas obligate endosymbionts are locked inside their wonder if some lineages of resident genomes, such as hosts for ever, most pathogens must find new hosts those of obligate intracellular parasites, are driven to regularly and, hence, are intrinsically more exposed extinction because of the effects of Muller’s ratchet. to the external environment. Thus, the evolutionary forces driving obligate endosymbionts are probably Mitochondria and their codes dictated by selective factors acting on their hosts to a The most extreme examples of reductively evolved much larger extent than those driving obligate intra- resident genomes are those of the cellular organelles. cellular parasites. Phylogenetic reconstructions suggest that mitochondrial Copyright © 1998 Elsevier Science Ltd. All rights reserved. 0966 842X/98/$19.00 TRENDS IN MICROBIOLOGY 263 PII: S0966-842X(98)01312-2 VOL. 6 NO. 7 JULY 1998 REVIEWS Box 1. Muller’s ratchet Identifying the evolutionary forces that drive the fixation rates for mutations is an important task of evolutionary biology. Nucleotide substitutions consist of synonymous substitutions that do not alter the protein sequence and nonsynonymous substitutions that cause amino acid replacements. It is anticipated that some nonsynonymous substitutions will have a deleterious or slightly deleterious effect on fitness. A gradual accumulation of deleterious mutations can induce an irreversible loss of the most-fit class of organisms from the population5–7,56. This loss can be triggered by high mutation rates, lack of recombination and/or small population sizes. Under these conditions, genetic drift can result in the successive loss of the most-fit class, in a ratchet-like manner. Such a gradual decline in the fitness of a population is referred to as Muller’s ratchet3,4. However, most nonsynonymous mutations are unlikely to be fixed in the population. Indeed, Muller’s ratchet can be opposed by high rates of compensatory mutations, sexual reproduction and/or by large population sizes driven by purifying selection. Because resident genomes are effectively asexual and often subjected to bottlenecks during each transmission from one host to the other, the loss of fitness induced by genetic drift will not be slowed down to the same extent as in large, free-living bacterial populations. Thus, abnormally higher fixation rates for nonsynonymous substitutions, as observed for intracellularly replicating bacteria, are an indicator that Muller’s ratchet is operative in these lineages. U U C A G A C G A Phe Phe Leu Leu Ser Ser Ser Ser Tyr Tyr Term Term Cys Cys Term Trp Leu Leu Leu Leu Pro Pro Pro Pro His His Gln Gln Arg Arg Arg Arg Thr Thr Thr Thr Asn Asn Lys Lys Ser Ser Arg Arg G Ala Ala Ala Ala Asp Asp Glu Glu Gly Gly Gly Gly G Ile Ile Ile Met Val Val Val Val C U G U G A A A C C C U U Fig. 1. Codon assignments. Translation of the universal genetic code requires a minimum of 24 tRNA species; one tRNA species per amino acid for one-, two- and four-codon boxes (16 tRNAs) and two tRNA species per amino acid for the three-codon box encoding isoleucine and the six-codon boxes encoding leucine, serine and arginine (eight tRNAs). In animal mitochondria, the codons AUA and AGA/G have been reassigned to methionine and serine, respectively. Consequently, the two codons for methionine (AUA/G) and the four codons for serine (AGN) can be translated by single tRNA species. Similarly, the two remaining codons for isoleucine (AUU/C) and the four remaining codons for arginine (CGN) can be translated by single tRNA isoacceptor species. Thus, translation of the reassigned code in animal mitochondria requires only 22 tRNA species. TRENDS IN MICROBIOLOGY genomes derive from much larger genomes. In particular, they appear to be most closely related to the ␣-proteobacteria and more specifically to an ancestor of the Rickettsiaceae10–13. Some mitochondrial genomes have retained ⬍1% of the gene repertoire of modern bacteria. This marked reduction in genome size can be partly explained by a massive transfer of genes from the mitochondrial genome to the nuclear genome14, a transfer that may have occurred as long as 1–2 billion years ago when the ancestral bacterium began to establish its symbiotic relationship with the eukaryotes15. Nevertheless, examples of transfer events from mitochondria to nuclear genomes as recently as within the past 200 million years have been detected16,17, suggesting that the process might be continuing. A eukaryotic cell can contain hundreds of mitochondria and thousands of mitochondrial genomes. These genomes are maternally inherited through the cytoplasm of the egg with little or no paternal contribution. This mode of transmission effectively restricts the exchange of genetic material between mitochondrial genomes; in effect, the egg is a bottleneck for mitochondrial genomes. Consequently, mitochondria from multicellular organisms display characteristics that are generally associated with small, asexual populations of resident genomes8,9,18,19. They are the victims of drift and Muller’s ratchet, as well as the neutralizing effect of the host genome on redundant genes. Animal mitochondria have diverged so far from their free-living bacterial ancestors that they have evolved new codes and a correspondingly specialized transfer RNA (tRNA) ensemble. If the universal genetic code were to be translated unambiguously into the canonical 20 amino acids, an absolute minimal set of 24 tRNA species would be required to translate the code. One tRNA species is required for each amino acid that is coded by a single codon or by a two- or four-codon box (16 in total). Two tRNA species are required for each amino acid encoded by the threecodon box for isoleucine and by the six-codon boxes for leucine, serine and arginine. In this minimal set, the tRNA species would have a greater redundancy than is normally seen; for example, each of the four codon readers would be indifferent to the nucleotide in codon position three. In some animal mitochondria, the number of tRNA genes has decreased below the canonical minimum of 24. Thus, there may be as few as 22 tRNA species20. The two missing tRNAs in these systems correspond to an isoleucine–tRNA normally cognate to the codon AUA, and an arginine– tRNA normally cognate to the codons AGA and AGG. In addition, AUA is read by a methionine– tRNA that also translates AUG. The codons AGA and AGG now appear as termination codons or are translated by a serine–tRNA that reads the AGN box. In other words, amino acid reassignments in the genetic code in animal mitochondria are demonstrably associated with changes in codon-recognition patterns for tRNA species that permit all 64 codons to be translated by a smaller number of tRNA species than would be allowed by the universal code21 (Fig. 1). In these systems, the codon reassignments 264 VOL. 6 NO. 7 JULY 1998 REVIEWS Table 1. Mutation and substitution rates in Escherichia coli, Salmonella typhimurium and Buchnera sp.a Estimated mutation rateb (ⴛ 10–9) Synonymous ratec (ⴛ 10–9) Nonsynonymous ratec (ⴛ 10–9) Species Lifestyle Tuf TrpB Tuf TrpB Tuf TrpB Buchnera sp. Intracellular 4–8 6–12 4–8 6–12 0.1–0.2 0.6–1.3 E. coli/ S. typhimurium Free-living 4–5 9–12 0.2–0.3 3–4 <0.02 0.04–0.05 a Data taken from Ref. 26. Number of mutations per position per year. c Number of substitutions per position per year. b seem to be a reflection of the reductive impact of Muller’s ratchet on the mitochondrial genomes18. Dynamics of substitutions A more subtle expression of the working of Muller’s ratchet is the gradual accumulation of sublethal, deleterious mutations that lead to substitutions in the gene sequences. Recently, the rate of sequence evolution has been determined for intracellular bacteria of the genus Buchnera, which live as symbionts of aphids22–25. These bacteria grow inside specialized cells called bacteriocytes that are maternally transmitted via the egg in a manner resembling the transmission of mitochondria from one host generation to the next. The endosymbionts supply the aphid hosts with vital amino acids. Therefore, antibiotic treatment of the aphids results in sterility or death. As yet, it has not been possible to cultivate the endosymbionts outside their aphid hosts, which suggests that the symbiotic relationship is mutual. Phylogenetic reconstructions based on rRNA genes provide strong support for the idea that the endosymbionts and their hosts have diverged from their respective ancestors at the same time and have co-speciated22. Indeed, the aphids and their intracellular bacteria seem to have coexisted in this symbiosis for ⬎100 million years22. There is a fairly good fossil record available for the aphids. By assuming that the symbionts are co-specific, the dated nodes in the aphid subtree can be transferred to the bacterial subtree. These dated nodes can then provide estimates of times of divergence, which can, in turn, be used to calculate rates of evolution for the endosymbionts. For example, analysis of the gene coding for elongation factor Tu has been carried out for five species of Buchnera26, suggesting that this gene evolves at a rate of 1.3–2.5 ⫻ 10⫺10 substitutions per position and per year at sites that result in amino acid replacements (nonsynonymous substitutions). It has also been found that there are 3.9–8.0 ⫻ 10⫺9 substitutions per position and per year at sites that have no effects on amino acid composition (synonymous substitutions)26. Comparative analysis of codon-usage patterns in a variety of genes from Buchnera provides no evidence for selective constraints on synonymous third-codon positions (S.G.E. Andersson, unpublished). Indeed, synonymous substitution rates appear to be roughly TRENDS IN MICROBIOLOGY similar among genes with different expression levels, in support of their neutrality26,27. Similar results have been obtained from the obligate intracellular parasite Rickettsia prowazekii, where selection does not appear to influence base composition patterns at synonymous third-codon positions28. Also, synonymous substitution rates appear to be similar among genes in this species. This suggests that the genomes of Buchnera and Rickettsia are under a randomizing mutational pressure from Muller’s ratchet, which overwhelms the weak selection pressure for preferred synonymous codons. Thus, for both of these species, synonymous rates should reflect the neutral, intrinsic mutation rate. By contrast, measurable selective pressures for subsets of synonymous codons characterize free-living organisms, such as Escherichia coli and Salmonella typhimurium, and these are correlated to the abundance of the corresponding isoacceptor tRNAs29,30. In these species, highly expressed genes have stronger codon-usage biases and lower synonymous substitution rates than less-expressed genes. However, the mutational divergence between E. coli and S. typhimurium has been calculated31, and the resulting estimates are remarkably similar to the observed synonymous substitution rate in Buchnera26. This suggests that the intrinsic mutation rate may be very similar in Buchnera, E. coli and S. typhimurium. By contrast, the substitution rates at nonsynonymous sites differ by more than a factor of ten in these species26,27. Consequently, amino acid replacements occur much faster in Buchnera than in E. coli and S. typhimurium (Table 1). These findings suggest that resident genomes, such as those of organelles, endosymbionts and obligate intracellular parasites, endure an enhanced rate of deleterious substitutions8,9,18,19,26,27. This is a verification of the influence of drift and Muller’s ratchet on their evolution. Small, scrambled genomes Obligate intracellular parasites, such as Rickettsia, Chlamydia and Coxiella, have genome sizes in the 1-Mbp range19. The free-living bacteria from which these parasites have evolved probably had genomes that were 4–5 times larger13,19,32. Such genomic shrinkage is not a random process, in the sense that any and all genes may be deleted from the genome: it is potentially less damaging to a parasite to lose a gene that is 265 VOL. 6 NO. 7 JULY 1998 REVIEWS on the orientations of the repeated sites36 (Fig. 2). Populations of freeA B A C C B living bacteria seem to accumulate freakish genomic variants only at D A very low frequencies37. In contrast, because of their special circumstances, genomes that replicate exclusively D C D B as residents within the intracellular or extracellular domain of another (b) genome evolve idiosyncratic gene B C C arrangements that disrupt the conB C D served gene-order structures seen in A D D A their free-living relatives. A B The most highly conserved geneorder structures in microbial genomes are those that encode components of the transcription and translation systems. One such exFig. 2. Intragenomic recombination events at repeated sequences, demonstrating how the orientation of the repeats will affect the outcome of the recombination event. (a) Pairing of repeat ample is the so-called super-ribomotifs in inverse orientation will generate an inversion of the segment (red) located between the somal protein gene operon, which repeat units. (b) Pairing of repeat motifs in direct orientation will generate an excision of the comprises a total of ~40 genes: in segment (red) located between the repeat units. E. coli these are organized in seven operons (secE–nusG, L11, L10, also present in the host genome. Therefore, it is perhaps str, S10, spc and ␣) (Fig. 3). The genes within these not surprising that many genes coding for proteins in- operons are located in close proximity to each other volved in amino acid biosynthesis have been discarded in many bacterial and archaeal genomes38,39. Because from the genomes of R. prowazekii and Mycoplasma there is a very small probability that 30–40 genes genitalium33,34. Not unexpectedly, these bacterial have become linked independently of each other, it is genomes also have a very limited set of regulatory generally believed that these shared structures repregenes33,34. The finding that a gene coding for S-adeno- sent ancient conserved genomic motifs38. Indeed, sylmethionine synthetase is in different stages of mu- remnants of the super-ribosomal protein gene operon tational meltdown in a number of Rickettsia species have been observed in plastid genomes, as well as in suggests that elimination of biosynthetic genes is an the mitochondrial genome of the fresh-water protoongoing process in Rickettsia (J.O. Andersson and zoan Reclinomonas americana40, suggesting that these S.G.E. Andersson, unpublished). A consequence of genes were clustered in an ancestral bacterial genome these reductions in the metabolic repertoire of intra- prior to the divergence of mitochondria and chlorocellular and cell-surface parasites is that a relatively plasts from their bacterial ancestors. larger fraction of the genome is devoted to basic Despite the unusually high degree of gene-order genetic functions, such as replication, transcription conservation in the ribosomal protein gene operons, and translation. we have identified both inversion and deletion events Why should the depredations of Muller’s ratchet in this area of the R. prowazekii genome19,41. We suggenerate smaller genomes? The principle mechanism gest that an intrachromosomal recombination event for excision and insertion of genomic sequences in between the two ancestral tuf genes resulted in a bacteria seems to involve intrachromosomal recom- major inversion of the genome, after which one of the bination at repeated sequences35. Duplications can two copies was deleted19,41. Deviations from the analways be reversed by an intrachromosomal recombi- cestral organization of these genes have also been nation event, but once a string of nucleotides is deleted, detected in the tiny genome of M. genitalium. For this the information cannot be recovered by an intrachro- species, numerous rearrangement events have to be mosomal recombination event. Furthermore, the intra- inferred to explain the distribution of this set of genes cellular habitat efficiently prevents the acquisition of into the six different gene blocks observed39. lost genetic material via horizontal transfer from other Additional examples of scrambled gene-order strucbacterial species. This means that deletions in the ab- tures in small parasitic genomes are provided by the sence of effective counterselection will accumulate rRNA genes. Most of the deviations from the convenwith time. Many such deletions are probably weakly tional gene-order structure (16S–23S–5S) are associated deleterious; these will spread to fixation relatively with bacterial genomes in the 1-Mbp range, having only frequently in small asexual populations. Such reduc- one or two copies of each of the rRNA genes19,42,43. A tive processes will occur at enhanced rates if there is a general survey of gene order conservation in the selective advantage of a small genome size, owing R. prowazekii genome is consistent with the idea that either to selection for genomes that replicate fast or to this genome is a highly derived, rearranged minimal selection for small cell volumes19. genome44. Thus, small sizes and scrambled gene organiIntrachromosomal recombination events result zation patterns seem to be a characteristic feature of either in sequence deletions or inversions, depending the genomes of resident bacteria. (a) TRENDS IN MICROBIOLOGY 266 VOL. 6 NO. 7 JULY 1998 REVIEWS (a) nusG L11 rif L10 str spc S10 α (c) (b) nusG L11 L10 rif str S10 spc α Tu nusG L11 L10 rif 90 ori 4 ori str S10 spc α 74 Escherichia coli Bacillus subtilis (e) (d) L10 29 str L11 rif 46 L11 str L10 nusG rif S10 spc α S10 spc α Haemophilus influenzae Mycoplasma genitalium Tu (f) nusG S10 spc α str nusG L11 L10 rif Rickettsia prowazekii Fig. 3. Genomic rearrangements. (a) It is believed that an ancestor of Bacteria and Archaea had a set of transcriptional and translational genes located in close proximity to each other in the following order: nusG, L11 (rpsLA), L10 (rpsKJ), rif (rpoBC), str (rpsLG–tuf–fus), S10 (rpsJ–rplCDWB–rpsS–rplV–rpsC–rplP–rpmC–rpsQ), spc (rplNXE–rpsNH–rplFR–rpsE–rpmD–rplO–prlA–rpmJ) and ␣ (rpsMKD–rpoA–rplQ). These segments are conservatively arranged in the genomes of (b) Bacillus subtilis and (c) Escherichia coli, but are scattered around the genomes of (d) Haemophilus influenzae, (e) Mycoplasma genitalium and (f) Rickettsia prowazekii. The organization of these genes in the R. prowazekii genome is consistent with an intrachromosomal recombination event at the tuf genes41. The circumferences of the circles are directly proportional to the genome sizes. Data taken from Ref. 39. Genomic extinction Transitions to new environmental niches can induce the loss of metabolic functions previously supplied by a long-term endosymbiont. For example, photosynthesis has been secondarily lost in some plants, algae and protists that live as parasites of other plants. Not suprisingly, the chloroplast genomes of these species are markedly reduced and the photosynthetic genes have either been eliminated or are present as pseudogenes45–47. The presence of a residual plastid genome is indicative of a role for chloroplast gene products in metabolic processes other than photosynthesis. The TRENDS IN MICROBIOLOGY most extreme examples of such reductive processes are the complete loss of mitochondrial genomes in eukaryotes that have adapted to anaerobic or obligate intracellular lifestyles, their past being evident only from the presence of the mitochondrial heat-shock proteins Hsp10, Hsp60 and Hsp70 (Refs 48–50). Another interesting case of extreme reductive evolution is the incorporation of a green algae by a group of marine protists called chlorarchinophytes, in which the remnants of the invading nuclear genome, the nucleomorph, have been reduced to ⬍1 Mbp (Refs 51,52). In some other groups of algae, unusual membrane 267 VOL. 6 NO. 7 JULY 1998 REVIEWS Questions for future research • How small must sexual populations be to behave as asexual populations (i.e. populations where there is little or no recombination between individuals)? • Are bottle-necked subpopulations, which start growth cycles from a limited number of individuals, a valuable source of mutational variation for large, sexual populations? • Does the successful incorporation of resident genomes also serve as a bottleneck for their hosts, by eliminating a large number of infected hosts, in the case of pathogens, or by boosting the population with infected offspring, in the case of symbionts? structures provide support for a similar kind of secondary endosymbiotic event, although in these species the nucleomorph has become extinct53,54. Similarly, the presence of four membranes enclosing the plastids of apicomplexan parasites suggests that their origin can be traced back to a secondary invasion event55. Transitions to intracellular environments are important evolutionary processes that enable biological diversity and novel life forms to be created over relatively short time periods. However, the genetic isolation of the invading genome could ultimately lead to its extinction. Conclusions Duplication events can, in principle, be reversed by compensatory deletion events. By contrast, deleted sequences cannot be restored by compensatory duplication events. Because of their asexual or nearly asexual population structure, deletions in resident genomes will have a higher probability of becoming fixed than in the populations of free-living bacteria. The accumulation of small deletion events and the gradual disruptions or loss of genes in the resident genomes are, therefore, expected. The elevated fixation rates for deleterious substitution and deletion will adversely influence the fitness of the parasite5–7,56. Eventually, it might not be able to survive the defensive stratagems of the host or competition from younger, less-attenuated parasites. Accordingly, the rich and protective cytoplasmic environment, which initially is so supportive for a newly established intracellular pathogen, might ultimately contribute to its decline and extinction. For endosymbionts and cellular organelles, host dependence might limit the accumulation of deleterious mutations. However, a replacement of one resident with another could also happen in mutualistic endosymbionts; indeed, the host could be selected to facilitate such changes if a more ancient symbiont is not as efficient as a more recent one. In effect, the evolution of intracellular parasitism and symbiosis might be characterized by waves of obligate intracellular bacteria that replace each other at rates determined by Muller’s ratchet. Acknowledgements The support of the National Science Research Council of Sweden is gratefully acknowledged. References 1 Palmer, J.D. (1997) Nature 387, 454–455 2 Palmer, J.D. (1997) Science 275, 790–791 3 Muller, H.J. (1964) Mutat. Res. 1, 2–9 TRENDS IN MICROBIOLOGY Felsenstein, J. (1974) Genetics 52, 737–756 Chao, L. (1990) Nature 348, 454–455 Chao, L. et al. (1992) Evolution 46, 289–299 Chao, L. (1997) Gene 205, 301–308 Lynch, M. (1996) Mol. Biol. Evol. 13, 209–220 Lynch, M. (1997) Mol. Biol. Evol. 14, 914–925 Yang, D. et al. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 4443–4447 Gray. M.W. et al. (1989) Proc. Natl. Acad. Sci. U. S. A. 86, 2267–2271 Viale, A. and Arakaki, A.K. (1994) FEBS Lett. 341, 146–151 Olsen, G.J., Woese, C.R. and Overbeek, R. (1994) J. Bacteriol. 176, 1–6 Brennicke, A. et al. (1993) FEBS Lett. 325, 140–145 Knoll, A. (1992) Science 256, 622–627 Covello, P.S. and Gray, M. (1992) EMBO J. 11, 3815–3820 Nugent, J.M. and Palmer, J.D. (1991) Cell 66, 473–481 Kurland, C.G. (1992) Bioessays 14, 709–714 Andersson, S.G.E. and Kurland, C.G. (1995) Biochem. Cell Biol. 73, 775–787 20 Andersson, S. et al. (1981) Nature 290, 457–465 21 Andersson, S.G.E. and Kurland, C.G. (1991) Mol. Biol. Evol. 8, 530–544 22 Moran, N.A. et al. (1993) Proc. R. Soc. London Ser. B 253, 167–171 23 Baumann, P. et al. (1995) Ann. Rev. Microbiol. 49, 55–94 24 Baumann, P. et al. (1997) BioScience 47, 12–20 25 Baumann, P. et al. (1998) ASM News 64, 203–209 26 Brynnel, E.U. et al. (1998) Mol. Biol. Evol. 15, 574–582 27 Moran, N.A. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 2873–2878 28Andersson, S.G.E. and Sharp, P.M. (1996) J. Mol. Evol. 42, 525–536 29 Ikemura, T. (1981) J. Mol. Biol. 146, 1–21 30 Dong, H., Nilsson, L. and Kurland, C.G. (1996) J. Mol. Biol. 260, 649–663 31 Berg, O.G. and Martelius, M. (1995) J. Mol. Evol. 41, 449–456 32 Weisburg, W.G. et al. (1989) J. Bacteriol. 171, 6455–6457 33 Fraser, C.M. et al. (1995) Science 270, 397–403 34 Andersson, S.G.E. et al. (1996) Microb. Comp. Genomics 1, 293–315 35 Krawiec, S. and Riley, M. (1990) Microbiol. Rev. 54, 502–598 36 Segall, A., Mahan, M. and Roth, J.R. (1988) Science 241, 1314–1318 37 Orston, L.N., Neidle, E.L. and Houghton, J.E. (1990) in The Bacterial Chromosome (Drlica, K. and Riley, M., eds), pp. 325–334, ASM Press 38 Keeling, P.J., Charlebois, R.L. and Doolittle, W.F. (1994) Curr. Opin. Genet. Dev. 4, 816–822 39 Sicheritz-Pontén, T. and Andersson, S.G.E. (1997) Microb. Comp. Genomics 2, 123–139 40 Lang, B.F. et al. (1997) Nature 387, 493–496 41 Syvänen, A.C. et al. (1996) J. Bacteriol. 178, 6192–6199 42 Andersson, S.G.E. et al. (1995) J. Bacteriol. 177, 4171–4175 43 Munson, M.A. et al. (1993) Gene 137, 171–178 44 Andersson, J.O. and Andersson, S.G.E. (1997) Microbiology 143, 2783–2795 45 Wolfe, K.H. et al. (1992) Proc. Natl. Acad. U. S. A. 89, 10648–10652 46 Gockel, G. et al. (1994) Curr. Genet. 26, 256–262 47 Wilson, R.J.M. et al. (1996) J. Mol. Biol. 261, 155–172 48 Bui, E.T.N. et al. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 9651–9656 49 Horner, D.S. et al. (1996) Proc. R. Soc. London Ser. B 263, 1053–1059 50 Roger, A.J. et al. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 14618–14622 51 Gilson, P.R. and McFadden, G.I. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 7737–7742 52 Gilson, P.R. and McFadden, G.I. (1997) Bioessays 19, 167–173 53 McFadden, G. and Gilson, P. (1995) Trends Ecol. Evol. 10, 12–17 54 Palmer, J.D. and Delwiche, C.F. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 7432–7435 55 Köhler, S. et al. (1997) Science 275, 1485–1489 56 Andersson, D.I. and Hughes, D. (1995) Proc. Natl. Acad. Sci. U. S. A. 93, 906–907 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 268 VOL. 6 NO. 7 JULY 1998