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Population consequences of mutagenesis and antimutagenesis.

Although the progress in basic understanding of mutagenesis and in techniques for precise measurement of mutation rates in test systems has been enormous, there has been very little progress in applying this information to estimates of germline mutation in humans, and even less in translating such estimates into quantitative assessments of the impact on future generations. This doesn't mean that new information about the mutation process, and antimutagens in particular, is not useful. Lowering the human mutation rate would be good, even if we can't say how good. Some simple population kinetics of a change of mutation are discussed, and it is shown that future environmental changes can be ignored if we assume that the impact of a disease on human welfare is changed by the environment in the same proportion as its effect on fitness. Since the human mutation rate appears to be much higher in males than in females, it would be especially important to find ways of reducing the male rate. The role of transposable elements in determining human spontaneous mutation rates is unknown, but unless data from experimental organisms are grossly misleading, this role may be substantial. It is sometimes argued that such responses as error-prone repair systems may be an evolutionary strategy to allow the population to try a larger repertoire of mutations in times of environmental change. They may also be a survival strategy. I suggest that, although such an evolutionary strategy may possibly be adopted in asexual organisms with a very high reproductive rate, it is very unlikely in Mendelian species with limited reproduction such as most higher animals. The amount of existing variability in a large population is so great relative to that which arises in a few generations by mutation that segregation and recombination of existing alleles would appear to be a better way of coping with changing environment. As the human age of reproduction has increased in the recent evolutionary past, it is possible that the compensatory adjustment of mutation rates has not been fast enough to keep up. Perhaps evolution of mutation rates is more determined by selection to reduce somatic mutation than by selection to reduce germinal mutation. Regardless of the answer to the question of the optimum mutation rate for long-time evolution, in my view, the optimum mutation rate from the standpoint of human welfare for the foreseeable future is zero.

Animals↗

Molecular evolution of the human and simian immunodeficiency viruses.

Molecular evolution and phylogeny of different human immunodeficiency virus type 1 (HIV1) strains, of a type 2 (HIV2) strain, and of two simian immunodeficiency viruses (SIVAGM and SIVMAC) have been studied by comparing the nucleotide sequences of the two regions of their pol genes which encode the reverse transcriptase (RT) and endonuclease/integrase (EN). The analyses show that the different HIV 1s form one cluster (HIV1 group) and that the SIVs and HIV2 form another (HIV2 group). When the entire genomes of a HIV1, a HIV2, and the two SIVs were compared, the SIVAGM showed a unique pattern of mutation accumulations; that is, the SIVAGM has accumulated more nonsynonymous changes than synonymous changes in the RT and EN regions after its recent divergence from SIVMAC-142, and, furthermore, it has a deletion of approximately 350 bp in the region between the pol and env genes. The SIVAGM was apparently derived from cell cultures infected with a macaque isolate, SIVMAC-251. The contamination provides an opportunity to measure the maximum rate of evolution in the SIVAGM by comparing its DNA sequence to those of SIVMAC-251 and SIVMAC-142. The analysis shows that the rates are given approximately by (1.95 +/- 1.37) x 10(-3)/site/year for one SIVAGM sequence and (5.18 +/- 2.25) x 10(-3)/site/year for another.

Base Sequence↗

The effect of mono- and divalent salts on the rise and decay kinetics of EPR signal II in Photosystem II preparations from spinach.

The rise and decay kinetics of EPR signal II have been used to probe the organization of the donor side of Photosystem II (PS II) before and after extraction of PS II preparations with high concentrations of salt. 800 mM NaCl or 500-800 mM NaBr substantially depletes the preparations of the 16 and 24 kDa proteins and decreases the steady-state rate of O2-evolution by 70-80% from control rates. These treatments do not largely alter the decay kinetics of Signal II; the rise kinetics remain in the instrument limited time range (2 microseconds or less) during the first 8-12 flashes. Treating PS II preparations with 800 mM CaCl2 removes the 16, 24 and 33 kDa proteins with at least 95% inhibition of the steady-state rates of O2 evolution. The additional removal of the 33 kDa polypeptide decreases the rates of oxidation and rereduction of Z, the species responsible for Signal II. Preparations treated with either mono- or divalent salts show a steady-state light-induced increase in Signal II similar to that seen in Tris-washed samples. Such a steady-state increase indicates that the rate of electron transport from water to Z is greatly decreased or blocked. The data are interpreted within a model in which there is an intermediate electron carrier between the O2 evolving complex and Z.

Calcium Chloride↗

Lineage effects and the index of dispersion of molecular evolution.

Recent efforts to estimate the index of dispersion [R(t)] of molecular evolution-i.e., the ratio of the variance in the number of substitutions on a lineage to the mean number-have suffered from an inability to adjust the data for lineage effects. These effects may include the generation-time dependency of the rate of evolution or improper assumptions about the branching pattern of a phylogenetic tree. In the present paper a method for correcting for lineage effects in the estimation of R(t) is presented for trees made up of three species. The recent data published by Li et al. for 20 loci in three orders of mammals is examined, and the average R(t), corrected for lineage effects, is shown to be 7.75 for replacement substitutions and 3.3 for silent substitutions. Thus the high values reported earlier may not be dismissed as due to generation-time effects or improper assumptions about phylogenies. Computer simulations are presented to give confidence in the estimate for replacement substitutions but also to demonstrate that the estimate for silent substitutions is sensitive to corrections for multiple substitutions and is not as reliable. This work's implications for our understanding of the mechanism of molecular evolution are discussed, and the arguments in favor of the hypothesis that replacement substitutions are mostly selected while silent substitutions are mostly neutral is presented.

Algorithms↗

Genetic variation in HTLV-III/LAV over time in patients with AIDS or at risk for AIDS.

In a study of genetic variation in the AIDS virus, HTLV-III/LAV, sequential virus isolates from persistently infected individuals were examined by Southern blot genomic analysis, molecular cloning, and nucleotide sequencing. Four to six virus isolates were obtained from each of three individuals over a 1-year or 2-year period. Changes were detected throughout the viral genomes and consisted of isolated and clustered nucleotide point mutations as well as short deletions or insertions. Results from genomic restriction mapping and nucleotide sequence comparisons indicated that viruses isolated sequentially had evolved in parallel from a common progenitor virus. The rate of evolution of HTLV-III/LAV was estimated to be at least 10(-3) nucleotide substitutions per site per year for the env gene and 10(-4) for the gag gene, values a millionfold greater than for most DNA genomes. Despite this relatively rapid rate of sequence divergence, virus isolates from any one patient were all much more related to each other than to viruses from other individuals. In view of the substantial heterogeneity among most independent HTLV-III/LAV isolates, the repeated isolation from a given individual of only highly related viruses raises the possibility that some type of interference mechanism may prevent simultaneous infection by more than one major genotypic form of the virus.

Acquired Immunodeficiency Syndrome↗

Evolution of aldehyde reductase: an immunological approach to the relatedness of aldehyde reductase from different species.

Antisera to aldehyde reductase from fruit-fly (Drosophila melanogaster) and chicken were cross-reacted with aldehyde reductase from several species of insects and birds using the technique of microcomplement fixation. Large differences in immunological distances are evident between species of the Class Insecta and of the Class Aves indicating considerable differences in the amino acid sequences of the aldehyde reductase of these species. Immunological distances for aldehyde reductase between pairs of insect species or bird species when plotted against the immunological distances for transferrin, albumin, lysozyme and alpha-glycerophosphate dehydrogenase for the same pairs of species gave a linear relationship in each case. From these relationships the rate of evolution of aldehyde reductase in terms of a unit evolutionary period (UEP) was calculated to be 12 which agreed favorably with the value previously obtained from compositional comparisons. A UEP of 12 is approximately half that of lactate dehydrogenase and shows that aldehyde reductase is evolving at twice the rate of glycolytic enzymes. This may indicate a relatively non-essential metabolism role for the enzyme.

Aldehyde Oxidoreductases↗

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.

Approximate methods for estimating the numbers of synonymous and nonsynonymous substitutions between two DNA sequences involve three steps: counting of synonymous and nonsynonymous sites in the two sequences, counting of synonymous and nonsynonymous differences between the two sequences, and correcting for multiple substitutions at the same site. We examine complexities involved in those steps and propose a new approximate method that takes into account two major features of DNA sequence evolution: transition/transversion rate bias and base/codon frequency bias. We compare the new method with maximum likelihood, as well as several other approximate methods, by examining infinitely long sequences, performing computer simulations, and analyzing a real data set. The results suggest that when there are transition/transversion rate biases and base/codon frequency biases, previously described approximate methods for estimating the nonsynonymous/synonymous rate ratio may involve serious biases, and the bias can be both positive and negative. The new method is, in general, superior to earlier approximate methods and may be useful for analyzing large data sets, although maximum likelihood appears to always be the method of choice.

Animals↗

The molecular evolution of the vertebrate trypsinogens.

We expand the already large number of known trypsinogen nucleotide and amino acid sequences by presenting additional trypsinogen sequences from the tunicate (Boltenia villosa), the lamprey (Petromyzon marinus), the pufferfish (Fugu rubripes), and the frog (Xenopus laevis). The current array of known trypsinogen sequences now spans the entire vertebrate phylogeny. Phylogenetic analysis is made difficult by the presence of multiple isozymes within species and rates of evolution that vary highly between both species and isozymes. We nevertheless present a Fitch-Margoliash phylogeny constructed from pairwise distances. We employ this phylogeny as a vehicle for speculation on the evolution of the trypsinogen gene family as well as the general modes of evolution of multigene families. Unique attributes of the lamprey and tunicate trypsinogens are noted.

Amino Acid Sequence↗

Can fast early rates reconcile molecular dates with the Cambrian explosion?

Molecular dates consistently place the divergence of major metazoan lineages in the Precambrian, leading to the suggestion that the 'Cambrian explosion' is an artefact of preservation which left earlier forms unrecorded in the fossil record. While criticisms of molecular analyses for failing to deal with variation in the rate of molecular evolution adequately have been countered by analyses which allow both site-to-site and lineage-specific rate variation, no analysis to date has allowed the rates to vary temporally. If the rates of molecular evolution were much higher early in the metazoan radiation, molecular dates could consistently overestimate the divergence times of lineages. Here, we use a new method which uses multiple calibration dates and an empirically determined range of possible substitution rates to place bounds on the basal date of divergence of lineages in order to ask whether faster rates of molecular evolution early in the metazoan radiation could possibly account for the discrepancy between molecular and palaeontological date estimates. We find that allowing basal (interphylum) lineages the fastest observed substitution rate brings the minimum possible divergence date (586 million years ago) to the Vendian period, just before the first multicellular animal fossils, but excludes divergence of the major metazoan lineages in a Cambrian explosion.

Animals↗

Structural evolution of the Drosophila 5S ribosomal genes.

We compare the 5S gene structure from nine Drosophila species. New sequence data (5S genes of D. melanogaster, D. mauritiana, D. sechellia, D. yakuba, D. erecta, D. orena, and D. takahashii) and already-published data (5S genes of D. melanogaster, D. simulans, and D. teissieri) are used in these comparisons. We show that four regions within the Drosophila 5S genes display distinct rates of evolution: the coding region (120 bp), the 5'-flanking region (54-55 bp), the 3'-flanking region (21-22 bp), and the internal spacer (149-206 bp). Intra- and interspecific heterogeneity is due mainly to insertions and deletions of 6-17-bp oligomers. These small rearrangements could be generated by fork slippages during replication and could produce rapid sequence divergence in a limited number of steps.

Animals↗

Genomic organization and evolution of alternative exons in a Drosophila calcium channel gene.

The genomic organization of a gene coding for an alpha 1 subunit of a voltage-gated calcium channel of Drosophila melanogaster (Dmca IA) was determined. Thirty-four exons, distributed over 45 kb of genomic sequence, have been identified and mapped, including exons in three regions involved in alternative splicing and new sites potentially involved in RNA editing. The comparison of the intron/exon boundaries of this channel with a mammalian counterpart shows that the genomic structure of these two genes has remained fairly similar during evolution, with more than half of the Drosophila intron positions being perfectly conserved compared to the human channel. Phylogenetic analysis of the mutually exclusive alternative exons revealed that they have diverged considerably. It is suggested that this divergence, rather than reflecting evolutionary age, is the likely result of accelerated rates of evolution following duplication.

Amino Acid Sequence↗

Evolution of circulating wild poliovirus and of vaccine-derived poliovirus in an immunodeficient patient: a unifying model.

We determined nucleotide sequences of the VP1 and 2AB genes and portions of the 2C and 3D genes of two evolving poliovirus lineages: circulating wild viruses of T geotype and Sabin vaccine-derived isolates from an immunodeficient patient. Different regions of the viral RNA were found to evolve nonsynchronously, and the rate of evolution of the 2AB region in the vaccine-derived population was not constant throughout its history. Synonymous replacements occurred not completely randomly, suggesting the need for conservation of certain rare codons (possibly to control translation elongation) and the existence of unidentified constraints in the viral RNA structure. Nevertheless the major contribution to the evolution of the two lineages came from linear accumulation of synonymous substitutions. Therefore, in agreement with current theories of viral evolution, we suggest that the majority of the mutations in both lineages were fixed as a result of successive sampling, from the heterogeneous populations, of random portions containing predominantly neutral and possibly adverse mutations. As a result of such a mode of evolution, the virus fitness may be maintained at a more or less constant level or may decrease unless more-fit variants are stochastically generated. The proposed unifying model of natural poliovirus evolution has important implications for the epidemiology of poliomyelitis.

Adolescent↗

Protein tolerance to random amino acid change.

Mutagenesis of protein-encoding sequences occurs ubiquitously; it enables evolution, accumulates during aging, and is associated with disease. Many biotechnological methods exploit random mutations to evolve novel proteins. To quantitate protein tolerance to random change, it is vital to understand the probability that a random amino acid replacement will lead to a protein's functional inactivation. We define this probability as the "x factor." Here, we develop a broadly applicable approach to calculate x factors and demonstrate this method using the human DNA repair enzyme 3-methyladenine DNA glycosylase (AAG). Three gene-wide mutagenesis libraries were created, each with 10(5) diversity and averaging 2.2, 4.6, and 6.2 random amino acid changes per mutant. After determining the percentage of functional mutants in each library using high-stringency selection (>19,000-fold), the x factor was found to be 34% +/- 6%. Remarkably, reanalysis of data from studies of diverse proteins reveals similar inactivation probabilities. To delineate the nature of tolerated amino acid substitutions, we sequenced 244 surviving AAG mutants. The 920 tolerated substitutions were characterized by substitutability index and mapped onto the AAG primary, secondary, and known tertiary structures. Evolutionarily conserved residues show low substitutability indices. In AAG, beta strands are on average less substitutable than alpha helices; and surface loops that are not involved in DNA binding are the most substitutable. Our results are relevant to such diverse topics as applied molecular evolution, the rate of introduction of deleterious alleles into genomes in evolutionary history, and organisms' tolerance of mutational burden.

Amino Acid Substitution↗

No BLUE among phylogenetic estimators.

Multivariate analysis is a branch of statistics that successfully exploits the powerful tools of linear algebra to obtain a fairly comprehensive theory of estimation. The purpose of this paper is to explore to what extent a linear theory of estimation can be developed in the context of coalescent models used in the analysis of DNA polymorphism. We consider a large class of coalescent models, of which the neutral infinite sites model is one example. In the process, we discover several limitations of linear estimators that are quite distinct from those in the classical theory. In particular, we prove that there does not exist a uniformly BLUE (best linear unbiased estimator) for the scaled mutation parameter, under the assumptions of the neutral model of evolution. In fact, we show that no linear estimator performs uniformly better than the Watterson (1975) method based on the total number of segregating sites. For certain coalescent models, the segregating-sites estimator is actually optimal.The general conclusion is the following. If genealogical information is useful for estimating the rate of evolution, then there is no optimal linear method. If there is an optimal linear method, then no information other than the total number of segregating sites is needed.

Base Sequence↗

Mitochondrial DNA evolution in the obscura species subgroup of Drosophila.

Mitochondrial DNA (mtDNA) restriction site maps for nine species of the Drosophila obscura subgroup and for Drosophila melanogaster were established. Taking into account all restriction enzymes (12) and strains (45) analyzed, a total of 105 different sites were detected, which corresponds to a sample of 3.49% of the mtDNA genome. Based on nucleotide divergences, two phylogenetic trees were constructed assuming either constant or variable rates of evolution. Both methods led to the same relationships. Five differentiated clusters were found for the obscura subgroup species, one Nearctic, represented by Drosophila pseudoobscura, and four Palearctic, two grouping the related triads of species Drosophila subobscura, Drosophila madeirensis, Drosophila obscura, Drosophila subsilvestris, and two more represented by one species each, Drosophila bifasciata, and Drosophila tristis. The different Palearctic clusters are as distant between themselves as with the Nearctic one. For the related species D. subobscura, D. madeirensis, and D. guanche, the pair D. subobscura-D. madeirensis is the closest one. The relationships found by nucleotide divergence were confirmed by differences in mitochondrial genome size, with related species sharing similar genome lengths and differing from the distant ones. The total mtDNA size range for the obscura subgroup species was from 15.5 kb for D. pseudoobscura to 17.1 for D. tristis.

Animals↗

Regional differences in rates of plant speciation and molecular evolution: a comparison between eastern Asia and eastern North America.

The eastern Asian (EAS)-eastern North American (ENA) floristic disjunction is one of the best-known biogeographic patterns in the Northern Hemisphere. Recent paleontological and molecular analyses have illuminated the origins of the biogeographic pattern, but subsequent diversification and evolution of the disjunct floras in each of the two continents after isolation remains poorly understood. Although similar in climate and floristic composition, EAS has twice as many species as ENA in genera occurring in both regions. Explaining such differences in species diversity between regions with similar environmental conditions (diversity anomalies) is an important goal of the study of the global patterns of biodiversity. We used a phylogenetic approach to compare rates of net speciation and molecular evolution between the two regions. We first identified EAS-ENA disjunct sister clades from ten genera (Asarum, Buckleya, Carpinus, Carya, Cornus, Hamamelis, Illicium, Panax, Stewartia, and Styrax) that represent diverse angiosperm lineages using phylogenetic analyses of ITS (internal transcribed spacer of nuclear ribosomal DNA) sequence data. Species richness and substitution rate of ITS between sister clades were compared. The results revealed a pattern of greater species diversity in the EAS counterparts. A positive relationship between species diversity and ITS substitution rate was also documented. These results suggest greater net speciation and accelerated molecular evolution in EAS. The data support the idea that a regional difference in net speciation rate related to topographic heterogeneity contributes to the diversity anomaly between EAS and ENA. The close relationship between rates of ITS evolution and species richness further suggests that species production may be directly linked to rate of nucleotide substitution.

Biodiversity↗

Climatic adaptation and the evolution of basal and maximum rates of metabolism in rodents.

Metabolic rate is a key aspect of organismal biology and the identification of selective factors that have led to species differences is a major goal of evolutionary physiology. We tested whether environmental characteristics and/or diet were significant predictors of interspecific variation in rodent metabolic rates. Mass-specific basal metabolic rates (BMR) and maximum metabolic rates (MMR, measured during cold exposure in a He-O2 atmosphere) were compiled from the literature. Maximum (Tmax) and minimum (Tmin) annual mean temperatures, latitude, altitude, and precipitation were obtained from field stations close to the capture sites reported for each population (N = 57). Diet and all continuous-valued traits showed statistically significant phylogenetic signal, with the exception of mass-corrected MMR and altitude. Therefore, results of phylogenetic analyses are emphasized. Body mass was not correlated with absolute latitude, but was positively correlated with precipitation in analyses with phylogenetically independent contrasts. Conventional multiple regressions that included body mass indicated that Tmax (best), Tmin, latitude, and diet were significant additional predictors of BMR. However, phylogenetic analyses indicated that latitude was the only significant predictor of mass-adjusted BMR (positive partial regression coefficient, one-tailed P = 0.0465). Conventional analyses indicated that Tmax, Tmin (best), and altitude explained significant amounts of the variation in mass-adjusted MMR. With body mass and Tmin in the model, no additional variables were significant predictors. Phylogenetic contrasts yielded similar results. Both conventional and phylogenetic analyses indicated a highly significant positive correlation between residual BMR and MMR (as has also been reported for birds), which is consistent with a key assumption of the aerobic capacity model for the evolution of vertebrate energetics (assuming that MMR and exercise-induced maximal oxygen consumption are positively functionally related). Our results support the hypothesis that variation in environmental factors leads to variation in the selective regime for metabolic rates of rodents. However, the causes of a positive association between BMR and latitude remain obscure. Moreover, an important area for future research will be experiments in all taxa are raised under common conditions to allow definitive tests of climatic adaptation in endotherm metabolic rates and to elucidate the extent of adaptive phenotypic plasticity.

Animals↗

Ribosomal DNA: molecular evolution and phylogenetic inference.

Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.

Animals↗