Horizontal gene transfer--the exchange of genes across mating barriers--is recognized as a major force in bacterial evolution. However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes. Although the human genome was initially reported to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted. Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements. Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.

New genes with novel functions arise by duplication and divergence, but the process poses a problem. After duplication, an extra gene copy must rise to sufficiently high frequency in the population and remain free of common inactivating lesions long enough to acquire the rare mutations that provide a new selectable function. Maintaining a duplicated gene by selection for the original function would restrict the freedom to diverge. (We refer to this problem as Ohno's dilemma). A model is described by which selection continuously favors both maintenance of the duplicate copy and divergence of that copy from the parent gene. Before duplication, the original gene has a trace side activity (the innovation) in addition to its original function. When an altered ecological niche makes the minor innovation valuable, selection favors increases in its level (the amplification), which is most frequently conferred by increased dosage of the parent gene. Selection for the amplified minor function maintains the extra copies and raises the frequency of the amplification in the population. The same selection favors mutational improvement of any of the extra copies, which are not constrained to maintain their original function (the divergence). The rate of mutations (per genome) that improve the new function is increased by the multiplicity of target copies within a genome. Improvement of some copies relaxes selection on others and allows their loss by mutation (becoming pseudogenes). Ultimately one of the extra copies is able to provide all of the new activity.

When a particular lac mutant of Escherichia coli starves in the presence of lactose, nongrowing cells appear to direct mutations preferentially to sites that allow growth (adaptive mutation). This observation suggested that growth limitation stimulates mutability. Evidence is provided here that this behavior is actually caused by a standard Darwinian process in which natural selection acts in three sequential steps. First, growth limitation favors growth of a subpopulation with an amplification of the mutant lac gene; next, it favors cells with a lac ؉ revertant allele within the amplified array. Finally, it favors loss of mutant copies until a stable haploid lac ؉ revertant arises and overgrows the colony. By increasing the lac copy number, selection enhances the likelihood of reversion within each developing clone. This sequence of events appears to direct mutations to useful sites. General mutagenesis is a side-effect of growth with an amplification (SOS induction). The F plasmid, which carries lac, contributes by stimulating gene duplication and amplification. Selective stress has no direct effect on mutation rate or target specificity, but acts to favor a succession of cell types with progressively improved growth on lactose. The sequence of events-amplification, mutation, segregation-may help to explain both the origins of some cancers and the evolution of new genes under selection. A selection system developed by John Cairns (1, 2) provided evidence that bacteria might sense growth-limiting stress and direct mutations to sites that enhance growth (adaptive mutation). The behavior of Cairns' system does not contradict classical demonstrations that some mutations arise independent of selection (3, 4). However, the behavior raises the possibility that another fraction of mutations might be induced or even directed by growth limitation. Stress-induced mutations (general or directed) would contradict the neo-Darwinian view that agents of selection play no role in causing mutations, but affect only the relative reproductive success of organisms with different genotypes.Experiments supporting directed mutation used an Escherichia coli strain with a lac deletion on the chromosome and a revertible lacZ (ϩ1) frameshift mutation on an FЈ 128 plasmid (2). During growth, the lac point mutation reverts at a rate of 10 Ϫ8 per cell per division. When 10 8 of these Lac Ϫ cells are starved in the presence of lactose, about 100 revertant colonies accumulate over a period of 6 days, during which the plated population does not grow and does not accumulate unselected mutations (5). This behavior suggested that selection directs mutations to growth-promoting sites (2, 6).Subsequent studies showed that lac ϩ revertants have a 10-to 100-fold higher probability of carrying an unselected mutation than do unselected cells or starved nonrevertant cells (7). Thus, the revertants (but not the starved population as a whole) were generally mutagenized in the process of reversion. Once isolated, the revertants show a normal mutation rate....

Several plants are known to have acquired a single mitochondrial gene by horizontal gene transfer (HGT), but whether these or any other plants have acquired many foreign genes is entirely unclear. To address this question, we focused on Amborella trichopoda, because it was already known to possess one horizontally acquired gene and because it was found in preliminary analyses to contain several more. We comprehensively sequenced the mitochondrial protein gene set of Amborella, sequenced a variable number of mitochondrial genes from 28 other diverse land plants, and conducted phylogenetic analyses of these sequences plus those already available, including the five sequenced mitochondrial genomes of angiosperms. Results indicate that Amborella has acquired one or more copies of 20 of its 31 known mitochondrial protein genes from other land plants, for a total of 26 foreign genes, whereas no evidence for HGT was found in the five sequenced genomes. Most of the Amborella transfers are from other angiosperms (especially eudicots), whereas others are from nonangiosperms, including six striking cases of transfer from (at least three different) moss donors. Most of the transferred genes are intact, consistent with functionality and͞or recency of transfer. Amborella mtDNA has sustained proportionately more HGT than any other eukaryotic, or perhaps even prokaryotic, genome yet examined. Genome sequencing has revealed that horizontal gene transfer (HGT), the transfer of genes between nonmating species, is remarkably common and important in bacterial evolution (1). The current picture of HGT in eukaryotes is decidedly mixed. Other than the special case of mobile genetic elements (and plant mitochondrial genomes, see below), HGT is largely unknown in multicellular eukaryotes but is more or less common in diverse groups of unicellular protists, which contain several to many genes derived by HGT from both prokaryotes and other protists (2).Recent studies indicate that plant mtDNAs are unusually active in HGT relative to all other organellar genomes and nuclear genomes of multicellular eukaryotes. Four papers (3-6) have reported a total of nine cases of mitochondrial HGT within seed plants. Three transfers involve parasitic angiosperms as putative donors or recipients and implicate direct, plant-to-plant transfer of DNA as one mechanism of HGT (5, 6). Each of the nine transfers involves a different set of recipient plants. For this reason, and because only a few mitochondrial genes have been scrutinized for potential HGT in these or any other plants, it is unclear whether these cases are singular exceptions in each genome or whether they are harbingers of perhaps massive mitochondrial HGT in certain plants.To address this uncertainty, we have assessed the origin and history of the mitochondrial protein gene set of Amborella trichopoda and the five angiosperms whose mtDNAs have been sequenced. Amborella was chosen because it was already known to contain one foreign gene (3) and because preliminary studies suggested it might be u...

SUMMARY Gene and genome duplications are the primary source of new genes and novel functions and have played a pivotal role in the evolution of genomic and organismal complexity [1, 2]. The spontaneous rate of gene duplication is a critical parameter for understanding the evolutionary dynamics of gene duplicates; yet few direct empirical estimates exist and differ widely. The presence of a large population of recently derived gene duplicates in sequenced genomes suggests a high rate of spontaneous origin, also evidenced by population-genomic studies reporting rampant copy-number polymorphism at the intraspecific level [3–6]. An analysis of long-term mutation-accumulation lines of Caenorhabditis elegans for gene copy-number changes using array Comparative Genomic Hybridization yields the first direct estimate of the genome-wide rate of gene duplication in a multicellular eukaryote. The gene duplication rate in C. elegans is quite high, on the order of 10−7 duplications/gene/generation. This rate is two orders of magnitude greater than the spontaneous rate of point mutation per nucleotide site in this species and also greatly exceeds an earlier estimate derived from the frequency distribution of extant gene duplicates in the sequenced C. elegans genome.

Gene copy-number differences due to gene duplications and deletions are rampant in natural populations and play a crucial role in the evolution of genome complexity. Per-locus analyses of gene duplication rates in the pre-genomic era revealed that gene duplication rates are much higher than the per nucleotide substitution rate. Analyses of gene duplication and deletion rates in mutation accumulation lines of model organisms have revealed that these high rates of copy-number mutations occur at a genome-wide scale. Furthermore, comparisons of the spontaneous duplication and deletion rates to copy-number polymorphism data and bioinformatic-based estimates of duplication rates from sequenced genomes suggest that the vast majority of gene duplications are detrimental and removed by natural selection. The rate at which new gene copies appear in populations greatly influences their evolutionary dynamics and standing gene copy-number variation in populations. The opportunity for mutations that result in the maintenance of duplicate copies, either through neofunctionalization or subfunctionalization, also depends on the equilibrium frequency of additional gene copies in the population, and hence on the spontaneous gene duplication (and loss) rate. The duplication rate may therefore have profound effects on the role of adaptation in the evolution of duplicated genes as well as important consequences for the evolutionary potential of organisms. We further discuss the broad ramifications of this standing gene copy-number variation on fitness and adaptive potential from a population-genetic and genome-wide perspective.

Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mutations for four decades. In the pregenomic era, phenotypic measurements of fitness-related traits in MA lines were used to indirectly estimate key mutational parameters, such as the genomic mutation rate, new mutational variance per generation, and the average fitness effect of mutations. Rapidly emerging next-generating sequencing technology has supplanted this phenotype-dependent approach, enabling direct empirical estimates of the mutation rate and a more nuanced understanding of the relative contributions of different classes of mutations to the standing genetic variation. Whole-genome sequencing of MA lines bears immense potential to provide a unified account of the evolutionary process at multiple levels—the genetic basis of variation, and the evolutionary dynamics of mutations under the forces of selection and drift. In this review, we have attempted to synthesize key insights into the spontaneous mutation process that are rapidly emerging from the partnering of classical MA experiments with high-throughput sequencing, with particular emphasis on the spontaneous rates and molecular properties of different mutational classes in nuclear and mitochondrial genomes of diverse taxa, the contribution of mutations to the evolution of gene expression, and the rate and stability of transgenerational epigenetic modifications. Future advances in sequencing technologies will enable greater species representation to further refine our understanding of mutational parameters and their functional consequences.

Large-scale variation in chromosome size was analyzed in 35 natural isolates of Escherichia coli by physical mapping with a restriction enzyme whose sites are restricted to rDNA operons. Although the genetic maps and chromosome lengths of the laboratory strains E. coli K12 and Salmonella enterica sv. Typhimurium LT2 are highly congruent, chromosome lengths among natural strains of E. coli can differ by as much as 1 Mb, ranging from 4.5 to 5.5 Mb in length. This variation has been generated by multiple changes dispersed throughout the genome, and these alterations are correlated; i.e., additions to one portion of the chromosome are often accompanied by additions to other chromosomal regions. This pattern of variation is most probably the result of selection acting to maintain equal distances between the replication origin and terminus on each side of the circular chromosome. There is a large phylogenetic component to the observed size variation: natural isolates from certain subgroups of E. coli have consistently larger chromosome, suggesting that much of the additional DNA in larger chromosomes is shared through common ancestry. There is no significant correlation between genome sizes and growth rates, which counters the view that the streamlining of bacterial genomes is a response to selection for faster growth rates in natural populations.