Rapid loss of duplicate gene expression by natural selection

Morphometric traits in the fine-leaved fescues depend on ploidy level: the case of Festuca amethystina L

BACKGROUND

Polyploid specimens are usually characterized by greater exuberance: they reach larger sizes and/or have a larger number of some organs. Festuca amethystina L. belongs to the section Aulaxyper. Based on morphological features, four subspecies of F. amethystina have been already identified. On the other hand, it has two cytotypes: diploid and tetraploid. The main aim of our study was to distinguish morphological differences between the cytotypes of F. amethystina, assuming that its phenotype differs significantly.

METHODS

The nuclear DNA content was measured by flow cytometry in dry leaves from specimens originating from 13 populations of F. amethystina. Several macrometric and micrometric traits of stems, spikelets and leaf blades were taken into account in the comparative analysis of two cytotypes.

RESULTS

In the case of cytotypes, specimens of tetraploids were larger than diploids. The conducted morphometric analysis of leaf cross-sections showed significant differences between the cytotypes.

DISCUSSION

The research has confirmed for the first time that in the case of F. amethystina the principle of greater exuberance of polyploids is true. Differences between the cytotypes are statistically significant, however, they are not enough to make easy the distinction of cytotypes on the basis of the measurements themselves. Our findings favor the rule known in Festuca taxonomy as a whole, i.e. that the ploidy level can be one of the main classification criteria.

Genome evolution of allopolyploids: a process of cytological and genetic diploidization

Allopolyploidy is a prominent mode of speciation in higher plants. Due to the coexistence of closely related genomes, a successful allopolyploid must have the ability to invoke and maintain diploid-like behavior, both cytologically and genetically. Recent studies on natural and synthetic allopolyploids have raised many discrepancies. Most species have displayed non-Mendelian behavior in the allopolyploids, but others have not. Some species have demonstrated rapid genome changes following allopolyploid formation, while others have conserved progenitor genomes. Some have displayed directed, non-random genome changes, whereas others have shown random changes. Some of the genomic changes have appeared in the F1 hybrids, which have been attributed to the union of gametes from different progenitors, while other changes have occurred during or after genome doubling. Although these observations provide significant novel insights into the evolution of allopolyploids, the overall mechanisms of the event are still elusive. It appears that both genetic and epigenetic operations are involved in the diploidization process of allopolyploids. Overall, genetic and epigenetic variations are often associated with the activities of repetitive sequences and transposon elements. Specifically, genomic sequence elimination and chromosome rearrangement are probably the major forces guiding cytological diploidization. Gene non-functionalization, sub-functionalization, neo-functionalization, as well as other kinds of epigenetic modifications, are likely the leading factors promoting genetic diploidization.

The Structure and Early Evolution of Recently Arisen Gene Duplicates in theCaenorhabditis elegansGenome

The significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with ≤10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms.

Genome evolution in polyploids

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

Duplicated genes evolve independently after polyploid formation in cotton

Of the many processes that generate gene duplications, polyploidy is unique in that entire genomes are duplicated. This process has been important in the evolution of many eukaryotic groups, and it occurs with high frequency in plants. Recent evidence suggests that polyploidization may be accompanied by rapid genomic changes, but the evolutionary fate of discrete loci recently doubled by polyploidy (homoeologues) has not been studied. Here we use locus-specific isolation techniques with comparative mapping to characterize the evolution of homoeologous loci in allopolyploid cotton (Gossypium hirsutum) and in species representing its diploid progenitors. We isolated and sequenced 16 loci from both genomes of the allopolyploid, from both progenitor diploid genomes and appropriate outgroups. Phylogenetic analysis of the resulting 73.5 kb of sequence data demonstrated that for all 16 loci (14.7 kb/genome), the topology expected from organismal history was recovered. In contrast to observations involving repetitive DNAs in cotton, there was no evidence of interaction among duplicated genes in the allopolyploid. Polyploidy was not accompanied by an obvious increase in mutations indicative of pseudogene formation. Additionally, differences in rates of divergence among homoeologues in polyploids and orthologues in diploids were indistinguishable across loci, with significant rate deviation restricted to two putative pseudogenes. Our results indicate that most duplicated genes in allopolyploid cotton evolve independently of each other and at the same rate as those of their diploid progenitors. These indications of genic stasis accompanying polyploidization provide a sharp contrast to recent examples of rapid genomic evolution in allopolyploids.

Evolutionary preservation of redundant duplicated genes

Gene duplication events produce both perfect and imperfect copies of genes. Perfect copies are said to be functionally redundant when knockout of one gene produces no 'scoreable', phenotypic effects. Preserving identical, duplicate copies of genes is problematic as all copies are prone to accumulate neutral mutations as pseudogenes, or more rarely, evolve into new genes with novel functions. We summarise theoretical treatments for the invasion and subsequent evolutionary modification of functionally redundant genes. We then consider the preservation of functionally identical copies of a gene over evolutionary time. We present several models for conserving redundancy: asymmetric mutation, asymmetric efficacy, pleiotropy, developmental buffering, allelic competition and regulatory asymmetries. In all cases, some form of symmetry breaking is required to maintain functional redundancy indefinitely.

The population genetics of synthetic lethals

Synthetic lethals are variants at different loci that have little or no effect on viability singly but cause lethality in combination. The importance of synthetic lethals and, more generally, of synthetic deleterious loci (SDL) has been controversial. Here, we derive the expected frequencies for SDL under a mutation-selection balance for the complete haploid model and selected cases of the diploid model. We have also obtained simple approximations that demonstrate good fit to exact solutions based on numerical iterations. In the haploid case, equilibrium frequencies of carrier haplotypes (individuals with only a single mutation) are comparable to analogous single-locus results, after allowing for the effects of linkage. Frequencies in the diploid case, however, are much higher and more comparable to the square root of the single-locus results. In particular, when selection operates only on the double-mutant homozygote and linkage is not too tight, the expected frequency of the carriers is approximately the quartic root of the ratio between the mutation rate and the selection coefficient of the synthetics. For a reasonably wide set of models, the frequencies of carriers can be on the order of a few percent. The equilibrium frequencies of these deleterious alleles can be relatively high because, with SDL, both dominance and epistasis act to shield carriers from exposure to selection. We also discuss the possible role of SDL in maintaining genetic variation and in hybrid breakdown.

Models of the evolution of some genetic systems

This paper reviews models of two aspects of genome evolution. The first is the problem of the conditions for establishment of chromosome rearrangements, as a result of their suppression of recombination between polymorphic genes that interact in their effects on fitness. The second is the spread of genomic elements either by their differential contributions to gametes, or by their ability to replicate and transpose themselves to new sites within the genome.

Dynamics of unconditionally deleterious mutations: Gaussian approximation and soft selection

This paper studies the influence of two opposite forces, unidirectional unconditionally deleterious mutations and directional selection against them, on an amphimictic population. Mutant alleles are assumed to be equally deleterious and rare, so that homozygous mutations can be ignored. Thus, a genotype is completely described by its value with respect to a quantitative trait chi, the number of mutations it carries, while a population is described by its distribution p(chi) with mean M[p] and variance V[p] = sigma(2)[p]. When mutations are only slightly deleterious, so that M > 1, before selection p(chi) is close to Gaussian with any mode of selection. I assume that selection is soft in the sense that the fitness of a genotype depends on the difference between its value of chi and M, in units of sigma. This leads to a simple system of equations connecting the values of M and V in successive generations. This system has a unique and stable equilibrium, M = U/delta)2(2--rho) and V = (U/delta)2, where U is the genomic deleterious mutation rate, delta is the selection differential for chi in units of sigma, and rho is the ratio of variances of p(chi) after and before selection. Both delta and rho are parameters of the mode of soft selection, and do not depend on M or V. In an equilibrium population, the selection coefficient against a mutant allele is s = delta2[U(2--rho)]-1. The mutation load can be tolerable only if the genome degradation rate v = U/sigma is below 2. Other features of mutation-selection equilibrium are also discussed.

Developmental rate and viability of rainbow trout with a null allele at a lactate dehydrogenase locus

We show that a previously described isozyme polymorphism in rainbow trout (Salmo gairdneri) is the result of an enzymatically inactive (i.e., null) allele (n). Ldh3 null homozygotes (n/n) and heterozygotes (100/n) have reductions of about 20 and 12% in total lactate dehydrogenase (LDH) activity at hatching, respectively. As juveniles, (100/n) fish have reductions in LDH activity of 15, 37, and 21% in brain, heart, and white muscle, respectively. Embryos with different Ldh3 phenotypes from 11 families do not differ significantly in either survival or hatching time. However, a second measure of developmental rate, the amount of malate dehydrogenase (MDH) and phosphoglucomutase (PGM) activity in 33-day-old embryos, suggests that (100/n) embryos develop more slowly than (100/100) embryos. In three of four families examined, (100/n) embryos have significantly lower amounts of total MDH activity (8-10%). In one of these, (100/n) embryos also have significantly lower total PGM activity (15%). These data suggest that the reduction in total LDH activity is associated with small but detectable delays in developmental rate but nondetectable differences in survival to hatching.

Albumin evolution in polyploid species of the genus Xenopus

Electrophoresis of serum from 21 Xenopus species and subspecies reveals variable numbers of albumin bands. The diploid X. tropicalis has one albumin, while the tetraploid species (laevis, borealis, muelleri, clivii, fraseri, epitropicalis) have two. The octoploid species (amieti, boumbaensis, wittei, vestitus, andrei) have two to three bands, and the dodecaploid X. ruwenzoriensis has three. The molecular weight of the Xenopus albumins varies from 68 kd (in the tropicalis group) to 74 kd. The subspecies of X. laevis possess two albumins of different molecular weights (70 and 74 kd), whereas most species have only 70-kd albumins. Peptide maps have been obtained from albumin electromorphs by limited proteolysis in sodium dodecyl sulfate (SDS) gels, using S. aureus V8 protease. The peptide patterns produced by electromorphs from the same tetraploid Xenopus species generally differ from each other, suggesting that the two albumin genes contain a substantial amount of structural differences. In addition, the peptide maps are diagnostic for most tetraploid species and for some subspecies of X. laevis as well. Proteolysis of albumins from most octoploid and dodecaploid species results in patterns which are very similar to the ones produced by the electromorphs from X. fraseri. The albumins of X. vestitus differ from those of the other octoploid species. X. andrei possesses two fraseri-type and one vestitus-type albumin, which indicates that it probably originated by allopolyploidy.

The expression of creatine kinase isozymes in Xenopus tropicalis, Xenopus laevis laevis, and their viable hybrid

Starch gel electrophoresis of creatine kinase (CK) isozymes of Xenopus tropicalis shows that at least two different genes code for CK in this diploid (2n = 20) species. These genes seen to be orthologous to the CK-A and CK-C genes of extant crossopterygian fish. Additional isozymes may be interpreted either as products of duplicate genes or, more probably, as epigenetically modified forms of the homodimers AtAt and CtCt, respectively. The originally tetraploid species X. laevis laevis (2n = 36), which may have arisen by hybridization of diploid ancestors some 30-40 million years ago, has retained expression of all duplicate CK-A and CK-C genes. Differential expression during ontogenesis (CK-A genes) and in different adult tissues (CK-C genes) indicates that divergence occurred not only with respect to the primary sequence of these duplicate genes, but also with respect to the regulation of their expression. In the interspecific hybrid X. l. laevis x X. tropicalis, all parental CK genes appear to be expressed simultaneously in the heart. However, several subunit combinations cannot be detected on the zymograms.

Towards an understanding of the molecular mechanisms regulating gene expression during diploidization in phylogenetically polyploid lower vertebrates

Polyploidization and regional gene duplication have occurred frequently during vertebrate evolution, providing the genetic material necessary for creating evolutionary novelties. Mammals, including man, can be regarded as diploid species with a polyploid history of evolution. Polyploidization steps during the phylogeny of mammals probably took place in the genomes of amphibian- or fish-like mammalian ancestors. The polyploid status has subsequently been shaped by the process of diploidization, leading to genomes that are polyploid with respect to the amount of genetic material and the number of gene copies, and diploid with respect to the level of gene expression and chromosomal characteristics. Phylogenetically tetraploid amphibian and teleost species together with their diploid close relatives can be used as a model system to study the effect of polyploidization and the mechanisms of diploidization of a parallel event during early mammalian evolution. Experimental evidence permits the assumption that the diploidization of gene expression in tetraploid cyprinid fish may be functionally correlated with structural modifications of the ribosomal components, RNA and protein. These findings are discussed in the light of reduced protein synthesis in diploidized tetraploid species and a mechanism to explain diploidization during mammalian evolution.

Loss of duplicate gene expression in salmonids: evidence for a null allele polymorphism at the duplicate aspartate aminotransferase loci in brook trout (Salvelinus fontinalis)

Unusual phenotypic distributions at the muscle-specific, duplicate aspartate aminotransferase (AAT) loci were found in wild populations of brook trout (Salvelinus fontinalis), a species of the tetraploid-derivative Salmonidae. Analysis of these phenotypic distributions ruled out disparate gene frequencies, nonrandom association between the two loci, and inbreeding as possible explanations; however, models incorporating a null allele fit the data. Inheritance data from hatchery populations of brook trout also indicated a null allele polymorphism. This proposed AAT null allele, along with other null allele polymorphisms in salmonids, is evidence that loss of duplicate gene expression is still occurring. In contrast, there is no such evidence of ongoing loss of duplicate gene expression in the Catostomidae, another tetraploid-derivative lineage. We interpret this and other differences between salmonids an catostomids as reflecting an autotetraploid origin for salmonids and an allotetraploid origin for catostomids. The significance of these findings is also considered with respect to current models of the rate of loss of duplicate gene expression in tetraploid-derivative organisms.