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PubMed2005

Parallel evolution of chimeric fusion genes.

To understand how novel functions arise, we must identify common patterns and mechanisms shaping the evolution of new genes. Here, we take advantage of data from three Drosophila genes, jingwei, Adh-Finnegan, and Adh-Twain, to find evolutionary patterns and mechanisms governing the evolution of new genes. All three of these genes are independently derived from Adh, which enabled us to use the extensive literature on Adh in Drosophila to guide our analyses. We discovered a fundamental similarity in the temporal, spatial, and types of amino acid changes that occurred. All three genes underwent rapid adaptive amino acid evolution shortly after they were formed, followed by later quiescence and functional constraint. These genes also show striking parallels in which amino acids change in the Adh region. We showed that these early changes tend to occur at amino acid residues that seldom, if ever, evolve in Drosophila Adh. Changes at these slowly evolving sites are usually associated with loss of function or hypomorphic mutations in Drosophila melanogaster. Our data indicate that shifting away from ancestral functions may be a critical step early in the evolution of chimeric fusion genes. We suggest that the patterns we observed are both general and predictive.

Adaptation, Biological↗

PubMed2005

Spontaneous evolution of modularity and network motifs.

Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns termed network motifs. Little is known about the evolutionary origin of these properties. Current models of biological evolution typically produce networks that are highly nonmodular and lack understandable motifs. Here, we suggest a possible explanation for the origin of modularity and network motifs in biology. We use standard evolutionary algorithms to evolve networks. A key feature in this study is evolution under an environment (evolutionary goal) that changes in a modular fashion. That is, we repeatedly switch between several goals, each made of a different combination of subgoals. We find that such "modularly varying goals" lead to the spontaneous evolution of modular network structure and network motifs. The resulting networks rapidly evolve to satisfy each of the different goals. Such switching between related goals may represent biological evolution in a changing environment that requires different combinations of a set of basic biological functions. The present study may shed light on the evolutionary forces that promote structural simplicity in biological networks and offers ways to improve the evolutionary design of engineered systems.

Algorithms↗

PubMed2006

Evolution of hepatitis C viral quasispecies and hepatic injury in perinatally infected children followed prospectively.

Perinatal infection with hepatitis C virus (HCV) is characterized by a wide range of alanine aminotransferase (ALT) levels. The mechanisms responsible for this variability are unknown. We examined whether the evolution of the HCV quasispecies was associated with different ALT profiles in perinatally infected children. Sequences within HCV envelope 1 and 2 genes, inclusive of the hypervariable region 1, the viral load, and the nascent humoral immunity were analyzed in serial serum samples from 12 perinatally infected children prospectively followed for a median of 53 months. These patients were selected to represent two different ALT patterns during the first year of life: 6 had high levels (maximum values ranging from 4.2 to 30 times the normal upper limit), and 6 had normal or slightly elevated levels (< 2 times the normal upper limit). Two patterns of viral evolution were identified according to the ALT profiles. Biochemical evidence of hepatic injury was invariably associated with a mono- or oligoclonal viral population, whereas mild or no liver damage correlated with the early emergence of a heterogeneous viral quasispecies. Consistent with selective immune pressure, amino acid changes occurred almost exclusively within the hypervariable region 1 and were temporally associated with antibody seroconversion; at this time, the difference in genetic diversity between the two groups was highly significant (P = 0.002). The two patterns of viral evolution persisted over time and did not correlate with viral load or genotype. Our study demonstrates that, in perinatally infected children, the evolution of HCV quasispecies correlates with hepatic injury. The sequences reported in this paper have been deposited in the GenBank database (accession nos. DQ 504441-DQ 507112).

Alanine Transaminase↗

PubMed2006

Evolution of protein structural classes and protein sequence families.

In protein structure space, protein structures cluster into four elongated regions when mapped based solely on similarity among the 3D structures. These four regions correspond to the four major classes of present-day proteins defined by the contents of secondary structure types and their topological arrangement. Evolution of and restriction to these four classes suggest that, in most cases, the evolution of genes may have been constrained or selected to those genetic changes that results in structurally stable proteins occupying one of the four "allowed" regions of the protein structure space, "structural selection," an important component of natural selection in gene evolution. Our studies on tracing the "common structural ancestor" for each protein sequence family of known structure suggest that: (i) recently emerged proteins belong mostly to three classes; (ii) the proteins that emerged earlier evolved to gain a new class; and (iii) the proteins that emerged earliest evolved to become the present-day proteins in the four major classes, with the fourth-class proteins becoming the most dominant population. Furthermore, our studies also show that not all present-day proteins evolved from one single set of proteins in the last common ancestral organism, but new common ancestral proteins were "born" at different evolutionary times, not traceable to one or two ancestral proteins: "the multiple birth model" for the evolution of protein sequence families.

Evolution, Molecular↗

PubMed2006

Life-history evolution under a production constraint.

The recently formulated metabolic theory of ecology has profound implications for the evolution of life histories. Metabolic rate constrains the scaling of production with body mass, so that larger organisms have lower rates of production on a mass-specific basis than smaller ones. Here, we explore the implications of this constraint for life-history evolution. We show that for a range of very simple life histories, Darwinian fitness is equal to birth rate minus death rate. So, natural selection maximizes birth and production rates and minimizes death rates. This implies that decreased body size will generally be favored because it increases production, so long as mortality is unaffected. Alternatively, increased body size will be favored only if it decreases mortality or enhances reproductive success sufficiently to override the preexisting production constraint. Adaptations that may favor evolution of larger size include niche shifts that decrease mortality by escaping predation or that increase fecundity by exploiting new abundant food sources. These principles can be generalized to better understand the intimate relationship between the genetic currency of evolution and the metabolic currency of ecology.

Adaptation, Physiological↗

PubMed2001

Directed evolution of polymerase function by compartmentalized self-replication.

We describe compartmentalized self-replication (CSR), a strategy for the directed evolution of enzymes, especially polymerases. CSR is based on a simple feedback loop consisting of a polymerase that replicates only its own encoding gene. Compartmentalization serves to isolate individual self-replication reactions from each other. In such a system, adaptive gains directly (and proportionally) translate into genetic amplification of the encoding gene. CSR has applications in the evolution of polymerases with novel and useful properties. By using three cycles of CSR, we obtained variants of Taq DNA polymerase with 11-fold higher thermostability than the wild-type enzyme or with a >130-fold increased resistance to the potent inhibitor heparin. Insertion of an extra stage into the CSR cycle before the polymerase reaction allows its application to enzymes other than polymerases. We show that nucleoside diphosphate kinase and Taq polymerase can form such a cooperative CSR cycle based on reciprocal catalysis, whereby nucleoside diphosphate kinase produces the substrates required for the replication of its own gene. We also find that in CSR the polymerase genes themselves evolve toward more efficient replication. Thus, polymerase genes and their encoded polypeptides cooperate to maximize postselection copy number. CSR should prove useful for the directed evolution of enzymes, particularly DNA or RNA polymerases, as well as for the design and study of in vitro self-replicating systems mimicking prebiotic evolution and viral replication.

DNA-Directed DNA Polymerase↗

PubMed2002

Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates.

An improved understanding of the evolution of gene function at the molecular level may provide significant insights into the origin of biological novelty and adaptation. With the approach of ancestral protein reconstruction, we here address the question of how a dramatically enhanced ribonucleolytic activity and the related antiviral activity evolved in a recently duplicated ribonuclease (eosinophil-derived neurotoxin) gene of higher primates. We show that the mother gene of the duplicated genes had already possessed a weak antiviral activity before duplication. After duplication, substitutions at two interacting sites (Arg-64-->Ser and Thr-132-->Arg) resulted in a 13-fold enhancement of the ribonucleolytic activity of eosinophil-derived neurotoxin. These substitutions are also necessary for the potent antiviral activity, with contributions from additional amino acid changes at interacting sites. Our observation that a change in eosinophil-derived neurotoxin function occurs only when both interacting sites are altered indicates the importance of complementary substitutions in protein evolution. Thus, neutral substitutions are not simply "noises" in protein evolution, as many have thought. They may play constructive roles by setting the intramolecular microenvironment for further complementary advantageous substitutions, which can lead to improved or altered function. Overall, our study illustrates the power of the "paleomolecular biochemistry" approach in delineating the complex interplays of amino acid substitutions in evolution and in identifying the molecular basis of biological innovation.

Adaptation, Biological↗

PubMed2003

Extensive gene gain associated with adaptive evolution of poxviruses.

Previous studies of genome evolution usually have involved one or two genomes and have thus been limited in their ability to detect the direction and rate of evolutionary change. Here, we use complete genome data from 20 poxvirus genomes to build a robust phylogeny of the Poxviridae and to study patterns of genome evolution. We show that, although there has been little gene order evolution, there are substantial differences between poxviruses in terms of genome content. Furthermore, we show that the rate of gene acquisition is not constant over time and that it has increased in the orthopox lineage (which includes smallpox and vaccinia). We also tested for positive selection on 204 groups of genes and show that a disproportionately high proportion of genes in the orthopox clade are under positive selection. The association of an increased rate of gene gain and positive selection is indicative of adaptive genome evolution. Many of the genes involved in these processes are likely to be associated with host-parasite coevolution.

Animals↗

PubMed2000

The transition from quantity to quality: a neglected causal mechanism in accounting for social evolution.

Students of social evolution are concerned not only with the general course it has followed, but also with the mechanisms that have brought it about. One such mechanism comes into play when the quantitative increase in some entity, usually population, reaching a certain threshold, gives rise to a qualitative change in the structure of a society. This mechanism, first recognized by Hegel, was seized on by Marx and Engels. However, neither they nor their current followers among anthropologists have made much use of it in attempting to explain social evolution. But as this paper attempts to show, in those few instances when the mechanism has been invoked, it has heightened our understanding of the process of social evolution. And, it is argued, if the mechanism were more widely applied, further understanding of the course of evolution could be expected to result.

Animals↗

PubMed1974

Two types of molecular evolution. Evidence from studies of interspecific hybridization.

To assess the significance of macromolecular sequence differences among species, we compared the serum albumins of 81 pairs of vertebrate species capable of producing viable hybrids. Micro-complement fixation experiments showed that the average difference between the albumins within such pairs was only 3 immunological distance units for placental mammals (31 pairs), but 36 units for frogs (50 pairs). Albumin immunological distance is strongly correlated with other measures of genetic distance, including those made with DNA annealing techniques. It therefore seems likely that mammalian species pairs capable of hybridization are far more similar at the macromolecular sequence level than is the case for most hybridizable frogs. We think the most likely explanation for the marked molecular restriction on hybridization among mammals is that the ratio of regulatory evolution to protein evolution is higher for mammals than for frogs. Mammals may have experienced unusually rapid regulatory evolution; indeed, this could be the factor responsible for their unusually rapid anatomical evolution.

Amino Acid Sequence↗

PubMed1974

On some principles governing molecular evolution.

THE FOLLOWING FIVE PRINCIPLES WERE DEDUCED FROM THE ACCUMULATED EVIDENCE ON MOLECULAR EVOLUTION AND THEORETICAL CONSIDERATIONS OF THE POPULATION DYNAMICS OF MUTANT SUBSTITUTIONS: (i) for each protein, the rate of evolution in terms of amino acid substitutions is approximately constant/site per year for various lines, as long as the function and tertiary structure of the molecule remain essentially unaltered. (ii) Functionally less important molecules or parts of a molecule evolve (in terms of mutant substitutions) faster than more important ones. (iii) Those mutant substitutions that disrupt less the existing structure and function of a molecule (conservative substitutions) occur more frequently in evolution than more disruptive ones. (iv) Gene duplication must always precede the emergence of a gene having a new function. (v) Selective elimination of definitely deleterious mutants and random fixation of selectively neutral or very slightly deleterious mutants occur far more frequently in evolution than positive Darwinian selection of definitely advantageous mutants.

Biological Evolution↗

PubMed1975

Group selection, altruism, reinforcement, and throwing in human evolution.

Evolution of altruism by group selection involves sacrifice of some individuals, not to the "group as a whole," but to other individuals in the group. Deme-group selection may establish strictly altruistic genes in a population, but only under limited conditions, and perhaps never among vertebrates, among which apparently altruistic behaviors may always potentially benefit the altruists. Responsive-group selection is a more effective mode of evolution of altruism, conspicuous in man. Evolutionary reinforcement increases the force of selection of advantageous behaviors, including altruistic ones, by making them pleasant or rewarding. It is probably involved also in ecological habitat selection, and may be the source of many human emotions, including esthetic ones. Throwing (of stones and weapons) exemplifies both the possible importance of a difficult-to-measure evolutionary factor and the role of reinforcement; in human evolution throwing may have been decisive in food-getting and fighting, in shifting emphasis from brute force to skill, and in inducing evolution of a brain able to handle three-body geometric problems precisely and thus preadapted for more complex functions.

Anthropology, Physical↗

PubMed1977

Is evolution gradual or rectangular? Evidence from living fishes.

The traditional view that most evolutionary change is gradual and cumulative within lineages (phyletic gradualism) has recently been challenged by the proposition that the majority of evolutionary change is concentrated within speciation events (rectangular evolution). The logical implications of these competing hypotheses for the means and variances of genetic distance among living members of rapidly and slowly speciating phylads are examined. An example of a critical test of gradual versus rectangular evolution is provided by electrophoretic analyses of genic composition in 69 species of North American Cyprinidae (minnows), and 19 species of Centrarchidae (sunfish). Rate of protein evolution appears somewhat decelerated, if anything, in the rapidly speciating minnows. Results are inconsistent with predictions of rectangular evolution, but are not demonstrably incongruent with predictions of phyletic gradualism.

Animals↗

PubMed1988

Effects of linkage on rates of molecular evolution.

When an advantageous mutation is fixed in a population by selection, a closely linked selectively neutral or mildly detrimental mutation may "hitchhike" to fixation along with it. It has been suggested that hitchhiking might increase the rate of molecular evolution. Computer simulations and a mathematical argument show that complete linkage to either advantageous or deleterious mutations does not affect the substitution of selectively neutral mutations. However, the simulations show that linkage to selected background mutations decreases the rate of fixation of advantageous mutations and increases the rate of fixation of detrimental mutations. This is true whether the linked background mutations are advantageous or detrimental, and it verifies and extends previous observations that linkage tends to reduce the effects of selection on evolution. These results can be interpreted in terms of the Hill-Robertson effect: a locus linked to another locus under selection experiences a reduction in effective population size. The interpretation of differences in evolutionary rates between different genomes or different regions of a genome may be confounded by the effects of strong linkage and selection. Recombination is expected to reduce the overall rate of molecular evolution while enhancing the rate of adaptive evolution.

Biological Evolution↗

PubMed1996

Molecular clock or erratic evolution? A tale of two genes.

We have investigated the evolution of glycerol-3-phosphate dehydrogenase (Gpdh). The rate of amino acid replacements is 1 x 10(-10)/site/year when Drosophila species are compared. The rate is 2.7 times greater when Drosophila and Chymomyza species are compared; and about 5 times greater when any of those species are compared with the medfly Ceratitis capitata. This rate of 5 x 10(-10)/site/year is also the rate observed in comparisons between mammals, or between different animal phyla, or between the three multicellular kingdoms. We have also studied the evolution of Cu,Zn superoxide dismutase (Sod). The rate of amino acid replacements is about 17 x 10(-10)/site/year when comparisons are made between dipterans or between mammals, but only 5 x 10(-10) when animal phyla are compared, and only 3 x 10(-10) when the multicellular kingdoms are compared. The apparent decrease by about a factor of 5 in the rate of SOD evolution as the divergence between species increases can be consistent with the molecular clock hypothesis by assuming the covarion hypothesis (namely, that the number of amino acids that can change is constant, but the set of such amino acids changes from time to time and from lineage to lineage). However, we know of no model consistent with the molecular clock hypothesis that would account for the increase in the rate of GPDH evolution as the divergence between species increases.

Amino Acid Sequence↗

PubMed1996

Accelerated evolution and Muller's rachet in endosymbiotic bacteria.

Many bacteria live only within animal cells and infect hosts through cytoplasmic inheritance. These endosymbiotic lineages show distinctive population structure, with small population size and effectively no recombination. As a result, endosymbionts are expected to accumulate mildly deleterious mutations. If these constitute a substantial proportion of new mutations, endosymbionts will show (i) faster sequence evolution and (ii) a possible shift in base composition reflecting mutational bias. Analyses of 16S rDNA of five independently derived endosymbiont clades show, in every case, faster evolution in endosymbionts than in free-living relatives. For aphid endosymbionts (genus Buchnera), coding genes exhibit accelerated evolution and unusually low ratios of synonymous to nonsynonymous substitutions compared to ratios for the same genes for enterics. This concentration of the rate increase in nonsynonymous substitutions is expected under the hypothesis of increased fixation of deleterious mutations. Polypeptides for all Buchnera genes analyzed have accumulated amino acids with codon families rich in A+T, supporting the hypothesis that substitutions are deleterious in terms of polypeptide function. These observations are best explained as the result of Muller's ratchet within small asexual populations, combined with mutational bias. In light of this explanation, two observations reported earlier for Buchnera, the apparent loss of a repair gene and the overproduction of a chaperonin, may reflect compensatory evolution. An alternative hypothesis, involving selection on genomic base composition, is contradicted by the observation that the speedup is concentrated at nonsynonymous sites.

Animals↗

PubMed1998

Slow rate of molecular evolution in high-elevation hummingbirds.

Estimates of relative rates of molecular evolution from a DNA-hybridization phylogeny for 26 hummingbird species provide evidence for a negative association between elevation and rate of single-copy genome evolution. This effect of elevation on rate remains significant even after taking into account a significant negative association between body mass and molecular rate. Population-level processes do not appear to account for these patterns because (i) all hummingbirds breed within their first year and (ii) the more extensive subdivision and speciation of bird populations living at high elevations predicts a positive association between elevation and rate. The negative association between body mass and molecular rate in other organisms has been attributed to higher mutation rates in forms with higher oxidative metabolism. As ambient oxygen tensions and temperature decrease with elevation, the slow rate of molecular evolution in high-elevation hummingbirds also may have a metabolic basis. A slower rate of single-copy DNA change at higher elevations suggests that the dynamics of molecular evolution cannot be separated from the environmental context.

Animals↗

PubMed1998

Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline.

Evolution of HIV-1 env sequences was studied in 15 seroconverting injection drug users selected for differences in the extent of CD4 T cell decline. The rates of increase of either sequence diversity at a given visit or divergence from the first seropositive visit were both higher in progressors than in nonprogressors. Viral evolution in individuals with rapid or moderate disease progression showed selection favoring nonsynonymous mutations, while nonprogressors with low viral loads selected against the nonsynonymous mutations that might have resulted in viruses with higher levels of replication. For 10 of the 15 subjects no single variant predominated over time. Evolution away from a dominant variant was followed frequently at a later time point by return to dominance of strains closely related to that variant. The observed evolutionary pattern is consistent with either selection against only the predominant virus or independent evolution occurring in different environments within the host. Differences in the level to which CD4 T cells fall in a given time period reflect not only quantitative differences in accumulation of mutations, but differences in the types of mutations that provide the best adaptation to the host environment.

Base Sequence↗