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PubMed2005

Genetics and adaptation in structured populations: sex ratio evolution in Silene vulgaris.

Theoretical models suggest that population structure can interact with frequency dependent selection to affect fitness in such a way that adaptation is dependent not only on the genotype of an individual and the genotypes with which it co-occurs within populations (demes), but also the distribution of genotypes among populations. A canonical example is the evolution of altruistic behavior, where the costs and benefits of cooperation depend on the local frequency of other altruists, and can vary from one population to another. Here we review research on sex ratio evolution that we have conducted over the past several years on the gynodioecious herb Silene vulgaris in which we combine studies of negative frequency dependent fitness on female phenotypes with studies of the population structure of cytoplasmic genes affecting sex expression. This is presented as a contrast to a hypothetical example of selection on similar genotypes and phenotypes, but in the absence of population structure. Sex ratio evolution in Silene vulgaris provides one of the clearest examples of how selection occurs at multiple levels and how population structure, per se, can influence adaptive evolution.

Adaptation, Biological↗

PubMed1990

Reconstructing evolution of sequences subject to recombination using parsimony.

The parsimony principle states that a history of a set of sequences that minimizes the amount of evolution is a good approximation to the real evolutionary history of the sequences. This principle is applied to the reconstruction of the evolution of homologous sequences where recombinations or horizontal transfer can occur. First it is demonstrated that the appropriate structure to represent the evolution of sequences with recombinations is a family of trees each describing the evolution of a segment of the sequence. Two trees for neighboring segments will differ by exactly the transfer of a subtree within the whole tree. This leads to a metric between trees based on the smallest number of such operations needed to convert one tree into the other. An algorithm is presented that calculates this metric. This metric is used to formulate a dynamic programming algorithm that finds the most parsimonious history that fits a given set of sequences. The algorithm is potentially very practical, since many groups of sequences defy analysis by methods that ignore recombinations. These methods give ambiguous or contradictory results because the sequence history cannot be described by one phylogeny, but only a family of phylogenies that each describe the history of a segment of the sequences. The generalization of the algorithm to reconstruct gene conversions and the possibility for heuristic versions of the algorithm for larger data sets are discussed.

Algorithms↗

PubMed1989

The evolution of complex life.

In considering the probabilities that intelligent life might exist elsewhere in the Universe, it is important to ask questions about the factors governing the emergence of complex living organisms in the context of evolutionary biology, planetary environments and events in space. Two important problems arise. First, what can be learned about the general laws governing the evolution of complex life anywhere in space by studying its history on the Earth? Second, how is the evolution of complex life affected by events in space? To address these problems, a series of Science Workshops on the Evolution of Complex Life was held at the Ames Research Center. Included in this paper are highlights of those workshops, with particular emphasis on the first question, namely the evolution of complex extraterrestrial life.

Animals↗

PubMed1993

The evolution of virus diseases: their emergence, epidemicity, and control.

The evolution of virus diseases, both their emergence and disappearance, involves complex interactions between the agent, the host, and the environment. These themes are illustrated by three examples, poliomyelitis of humans, bovine spongiform encephalopathy of cattle, and AIDS of humans. Emergence may be due to evolution of the virus genome, such as probably occurred in parvovirus infection of dogs and human immunodeficiency virus infection of humans. However, emergence of some new viral diseases can be traced to host or environmental factors with no change in the agent. Poliomyelitis, an enteric infection, probably emerged as an epidemic disease due to improvements in personal hygiene and public sanitation which led to a delay in the occurrence of initial infections from the perinatal period (when maternal antibody protected against paralysis) to later childhood when passive immunity had waned. Bovine spongiform encephalopathy is a common source epidemic which was transmitted through nutritional supplements which became contaminated due to a change in the method of production of bone meal supplements in rendering plants. The reduction of disappearance of virus diseases usually involves human intervention, as exemplified by immunization for smallpox and other virus diseases of humans and animals. Naturally occurring immunity may lead to fadeout of a virus as seen with measles in isolated island populations. Evolution of a virus can also result in waning of a disease as seen with myxomatosis among rabbits in Australia. The evolution of virus diseases is a provocative scientific topic and carries lessons relevant to the control of important diseases of humans, animals, and plants.

Acquired Immunodeficiency Syndrome↗

PubMed1994

Cosmic radiation and evolution of life on earth: roles of environment, adaptation and selection.

The role of ionizing radiation in general, and cosmic radiation in particular, in the evolution of organisms on the earth by adaptation and natural selection is considered in a series of questions: (1) Are there times during the evolution of the earth and of life when genetic material could be exposed to heavy ion radiation? (2) Throughout the course of chemical and biological evolution on the earth, what fraction of environmental mutagenesis could be attributable to cosmic and/or solar ionizing radiation? (3) Is ionizing radiation an agent of adaptation or selection, or both? (4) What can the cladistics of the evolution of genetic repair tell us about the global history of genotoxic selection pressures? (5) How much genetic diversity can be attributed to the selection of radiation-damage repair processes?

Animals↗

PubMed1994

Heavy-ion induced genetic changes and evolution processes.

On Moon and Mars, there will be more galactic cosmic rays and higher radiation doses than on earth. Our experimental studies showed that heavy ion radiation can effectively cause mutation and chromosome aberrations and that high-LET heavy-ion induced mutants can be irreversible. Chromosome translocations and deletions are common in cells irradiated by heavy particles, and ionizing radiations are effective in causing hyperploidy. The importance of the genetic changes in the evolution of life is an interesting question. Through evolution, there is an increase of DNA content in cells from lower forms of life to higher organisms. The DNA content, however, reached a plateau in vertebrates. By increasing DNA content, there can be an increase of information in the cell. For a given DNA content, the quality of information can be changed by rearranging the DNA. Because radiation can cause hyperploidy, an increase of DNA content in cells, and can induce DNA rearrangement, it is likely that the evolution of life on Mars will be effected by its radiation environment. A simple analysis shows that the radiation level on Mars may cause a mutation frequency comparable to that of the spontaneous mutation rate on Earth. To the extent that mutation plays a role in adaptation, radiation alone on Mars may thus provide sufficient mutation for the evolution of life.

Animals↗

PubMed1981

Evolution of the control of pigment and plastid development in photosynthetic organisms.

How do bioenergetic organelles relate to the cells they are in and how was this relationship established over the course of evolution? Plastids and mitochondria are viewed as prokaryotic residents in eukaryotic cells. These organelles are semiautonomous: they perpetuate themselves by division but regulate and are subject to regulation by the cell in which they are residents. Although these organelles are usually constitutive, their development is arrested in certain organisms when an inducing substrate is absent (light, for example, in the case of the chloroplast) with the formation of precursor organelles such as proplastids. Various trends in the evolution of photo-control systems are discussed including those concerned with photoperception and photomorphogenesis. The photocontrol of chloroplast development by blue and red light is discussed in relation to its possible evolutionary origins in a system for finding the right light for photosynthesis. Models for various types of cellular regulation by light during chloroplast development are discussed. Also considered is the evolution of plastid pigments in response to available light. A parallel evolution of accessory pigments and chlorophylls is suggested which led to chlorophyll reaction centers serving as energy sinks for light absorbed by accessory pigments and, therefore, having their absorptions pushed to the longest possible wavelengths as accessory pigments evolved to fill the middle of the spectrum in response to ecological selection. An endosymbiotic origin of bioenergetic organelles is suggested based on polyphyletic origins of chloroplasts from a number of oxygenic procaryotic precursors. The similarity between proplastids and these oxygenic procaryotes suggests that the original invading organelle may have resembled a modern proplastid rather than a mature chloroplast.

Biological Evolution↗

PubMed1987

Punctualism, non-adaptationism, neutralism and evolution.

In its further development the theory of evolution will incorporate molecular biology, synergetics and the theory of information. Using a simple model it is shown that speciation can be similar to phase transition. This is a thermodynamical statement which does not say anything concerning the sharpness and kinetic features of transition. Hence there is no contradiction between punctuated equilibrium and phyletic gradualism. The notion of punctualism can be used in the sense of phase transition. Evolution is directional because of constraints of natural selection due to the structure of organisms already existing and to the possible pathways of development. Correspondingly many characters are non-adaptative. Not only are the structures of proteins important for speciation but also the exact answers to the questions: "how much", "where" and "when"? These answers can be obtained as the results of regulation of genes, particularly of homeiotic regulation. The basis features of the structure of proteins are considered and the sense of the neutral theory is discussed in connection with degeneracy of correlation between the primary structure of a protein, its spatial structure and biological function. Informational aspects of evolution are discussed. Punctualism, non-adaptationism and neutralism form the triad of internally connected features of evolution. The Darwinian theory preserves its fundamental significance.

Adaptation, Biological↗

PubMed1991

Directionality of evolution at molecular and organismic levels.

The molecular evolution theories of Eigen and Kimura are compared and their difference is explained. In terms of Eigen's theory for the evolution of macromolecules, the selection of genotypes occurs directly. The physical meaning of the neutral theory is the degeneracy of the correlation between a phenotype and a genotype at the molecular level. A model theory of evolution on a fitness landscape is proposed. The theory shows that the constraints of selection determined by the structure and dynamics of previous evolution stages increases its rate strongly.

Biological Evolution↗

PubMedDate not supplied

On the evolution of X-chromosome inactivation in mammals and the clinical consequences to man--a hypothesis.

A clinical analysis of abnormal sex chromosome states in man suggests that Lyon's recent X-Y translocation hypothesis for the evolution of X-chromosome inactivation in mammals most likely would have lead to an evolutionary dead-end. Therefore, as an alternate I have hypothesized that: X-chromosome inactivation in somatic cells of mammals could have evolved by a complementary process of one by one heterozygous physical deletion in males and heterozygous inactivation in females of genes for "somatic" traits scattered throughout the genome whose effective output had become 50% excessive during prior evolution. However, this complementary process could occur safely only if the genes so deleted or inactivated first segregated by chance onto the evolving sex-chromosomes via a one by one reciprocal exchange for non-sex related genes already there. The complementary process thereby would allow slow evolution of the Y-chromosome in the male and X-chromosome inactivation in the female. Evolution of X-chromosome inactivation in this manner is compatible with Ohno's observation of "conservation" of the X-chromosome in mammals; and the occurrance of clinical "somatic" abnormalities in the abnormal X or Y chromosome states of man despite X-chromosome inactivation.

Aneuploidy↗

PubMed2006

Flashback to the 1960s: utility of archived sera to explore the origin and evolution of Plasmodium falciparum chloroquine resistance in the Pacific.

The increasing frequencies of Plasmodium falciparum strains that are resistant to chloroquine (CQ) and other antimalarials are resulting in a global resurgence of malaria morbidity and mortality. CQ resistance (CQR) is associated with multiple mutations in the P. falciparum chloroquine resistance transporter (pfcrt) gene. The mode and tempo of the accumulation of substitutions leading to these complex CQR haplotypes remain speculative due to the dearth of samples temporally spanning the evolution of drug resistance. The origin and evolution of the CQR alleles of Papua New Guinea (PNG) is particularly ambiguous. It remains unclear whether the pfcrt haplotype in PNG resulted from an independent origin of a CQR haplotype identical in sequence to the South American haplotype, or if this haplotype originated in South America and recombined into a Southeast Asian-derived genome. We sequenced a segment of pfcrt exon 2 from 398 plasmid clones derived from archival human sera collected in the Pacific before and after the first reported cases of CQ treatment failure (n=251) and modern samples (n=147). None of the 251 pfcrt plasmid clones from nine archival samples displayed the C72S or the K76T mutations that are characteristic of CQR strains. In contrast, these two amino acid substitutions were present in all 147 pfcrt plasmid clones from five samples collected between 2001 and 2003; thus, the archival samples represent the baseline parasite genetic diversity before the evolution of CQR strains. We are currently expanding our analyses to include additional samples from the series described here and from series collected in the 1970s and the 1980s to evaluate the geographic origin of CQR strains in the Pacific and the validity of the sequential point mutation accumulation model of CQR evolution.

Amino Acid Sequence↗

PubMed2005

Whole plasmid mutagenic PCR for directed protein evolution.

Protein function can be engineered through iterated cycles of random mutagenesis and screening (directed evolution). Optimization of protein expression is essential for the development of sensitive and precise high throughput assays. Here we optimize the performance of a plasmid-borne Escherichia coli lacZ gene in two rounds of directed evolution. First, its promoter was "randomized" by whole plasmid polymerase chain reaction (PCR) and intra-molecular self-ligation. A genetically stable constitutive expression vector was isolated in an in vivo genetic selection. Second, the entire plasmid was randomly mutated in a slightly mutagenic long polymerase chain reaction. The PCR products were digested with a restriction enzyme, self-ligated by T4 DNA ligase and transformed into E. coli. The resulting library of beta-galactosidase (beta-gal) mutants consisted mostly ( approximately 80%) of hypomorphs, suggesting that the mutation rate was appropriate for directed evolution applications. We isolated and characterized 14 variants with increased activity in reactions with 5-bromo-4-chloro-3-indolyl-beta-d-galactopyranoside (X-gal). The purified protein derived from one clone exhibited a 100-fold improvement in k(cat) over its parent in reactions with para-nitrophenyl-beta-d-galactopyranoside (pNP-gal). This latter result clearly demonstrates the utility of whole plasmid mutagenic PCR for directed protein evolution.

Cloning, Molecular↗

PubMed2005

Directed evolution of enzyme stability.

Modern enzyme development relies to an increasing extent on strategies based on diversity generation followed by screening for variants with optimised properties. In principle, these directed evolution strategies might be used for optimising any enzyme property, which can be screened for in an economically feasible way, even if the molecular basis of that property is not known. Stability is an interesting property of enzymes because (1) it is of great industrial importance, (2) it is relatively easy to screen for, and (3) the molecular basis of stability relates closely to contemporary issues in protein science such as the protein folding problem and protein folding diseases. Thus, engineering enzyme stability is of both commercial and scientific interest. Here, we review how directed evolution has contributed to the development of stable enzymes and to new insight into the principles of protein stability. Several recent examples are described. These examples show that directed evolution is an effective strategy to obtain stable enzymes, especially when used in combination with rational or semi-rational engineering strategies. With respect to the principles of protein stability, some important lessons to learn from recent efforts in directed evolution are (1) that there are many structural ways to stabilize a protein, which are not always easy to rationalize, (2) that proteins may very well be stabilized by optimizing their surfaces, and (3) that high thermal stability may be obtained without forfeiture of catalytic performance at low temperatures.

Animals↗

PubMed2004

Interactions between learning and evolution: the outstanding strategy generated by the Baldwin effect.

The Baldwin effect is known as an possible interaction between learning and evolution, where individual lifetime learning can influence the course of evolution without using any Lamarckian mechanism. Our concern is to consider the Baldwin effect in dynamic environments, especially when there is no explicit optimal solution through generations and this solution depends only on interactions among agents. We adopted the iterated Prisoner's Dilemma as a dynamic environment, introduced phenotypic plasticity into its strategies, and conducted computational experiments, in which phenotypic plasticity is allowed to evolve. The Baldwin effect was observed in the experiments as follows: First, strategies with enough plasticity spread, which caused a shift from defect-oriented populations to cooperative populations. Second, these strategies were replaced by a strategy with a modest amount of plasticity generated by interactions between learning and evolution. By making three kinds of analysis, we have shown that this strategy provides outstanding performance in comparison with other deterministic strategies. Further experiments towards open-ended evolution have also been conducted so as to generalize our results.

Adaptation, Physiological↗

PubMed2005

The evolution of the language faculty: clarifications and implications.

In this response to Pinker and Jackendoff's critique, we extend our previous framework for discussion of language evolution, clarifying certain distinctions and elaborating on a number of points. In the first half of the paper, we reiterate that profitable research into the biology and evolution of language requires fractionation of "language" into component mechanisms and interfaces, a non-trivial endeavor whose results are unlikely to map onto traditional disciplinary boundaries. Our terminological distinction between FLN and FLB is intended to help clarify misunderstandings and aid interdisciplinary rapprochement. By blurring this distinction, Pinker and Jackendoff mischaracterize our hypothesis 3 which concerns only FLN, not "language" as a whole. Many of their arguments and examples are thus irrelevant to this hypothesis. Their critique of the minimalist program is for the most part equally irrelevant, because very few of the arguments in our original paper were tied to this program; in an online appendix we detail the deep inaccuracies in their characterization of this program. Concerning evolution, we believe that Pinker and Jackendoff's emphasis on the past adaptive history of the language faculty is misplaced. Such questions are unlikely to be resolved empirically due to a lack of relevant data, and invite speculation rather than research. Preoccupation with the issue has retarded progress in the field by diverting research away from empirical questions, many of which can be addressed with comparative data. Moreover, offering an adaptive hypothesis as an alternative to our hypothesis concerning mechanisms is a logical error, as questions of function are independent of those concerning mechanism. The second half of our paper consists of a detailed response to the specific data discussed by Pinker and Jackendoff. Although many of their examples are irrelevant to our original paper and arguments, we find several areas of substantive disagreement that could be resolved by future empirical research. We conclude that progress in understanding the evolution of language will require much more empirical research, grounded in modern comparative biology, more interdisciplinary collaboration, and much less of the adaptive storytelling and phylogenetic speculation that has traditionally characterized the field.

Biological Evolution↗

PubMed2006

Natural selection drives extremely rapid evolution in antiviral RNAi genes.

RNA interference (RNAi) is perhaps best known as a laboratory tool. However, RNAi-related pathways represent an antiviral component of innate immunity in both plants and animals. Since viruses can protect themselves by suppressing RNAi, interaction between RNA viruses and host RNAi may represent an ancient coevolutionary "arms race." This could lead to strong directional selection on RNAi genes, but to date their evolution has not been studied. By comparing DNA sequences from different species of Drosophila, we show that the rate of amino acid evolution is substantially elevated in genes related to antiviral RNAi function (Dcr2, R2D2, and Ago2). They are among the fastest evolving 3% of all Drosophila genes; they evolve significantly faster than other components of innate immunity and faster than paralogous genes that mediate "housekeeping" functions. Based on DNA polymorphism data from three species of Drosophila, McDonald-Kreitman tests showed that this rapid evolution is due to strong positive selection. Furthermore, Dcr2 and Ago2 display reduced genetic diversity, indicative of a recent selective sweep in both genes. Together, these data show rapid adaptive evolution of the antiviral RNAi pathway in Drosophila. This is a signature of host-pathogen arms races and implies that the ancient battle between RNA viruses and host antiviral RNAi genes is active and significant in shaping RNAi function.

Amino Acid Sequence↗

PubMed2004

Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes.

The Structurally Constrained Protein Evolution (SCPE) model simulates protein evolution by introducing random mutations into the evolving sequences and selecting them against too much structural perturbation. Given a single protein structure, the SCPE model can be used to obtain a whole set of site-dependent amino acid substitution matrices. The set of SCPE substitution matrices for a given protein family can be seen as an independent-sites model of evolution for that family. Thus, these matrices can be compared with other substitution-matrix-based models of evolution. So far, SCPE has been tested only on left-handed parallel beta helix (LbetaH) proteins. Here, we address the question of generality by assessing the SCPE model on representatives of the four main classes of folds: alpha, beta, alpha+beta, and alpha/beta. We compare with other models using the likelihood ratio test with parametric bootstrapping. We show that SCPE performs better than the popular JTT model for all cases considered. Furthermore, by considering the relative contributions of mutation and selection, we found that the key to the success of the SCPE model is the selection step.

Algorithms↗

PubMed2005

Sequence evolution, processing, and posttranslational modification of zonadhesin D domains in primates, as inferred from cDNA data.

Zonadhesin is a mammalian transmembrane sperm ligand. Precursor zonadhesin essentially consists of MAM (meprin/A5 antigen/mu receptor tyrosine phosphatase) domains, a mucin-like repeat, and D domains (homologous to von Willebrand D). Recent immunovisualization and binding assays indicate that zonadhesin D domains 1-3 bind postacrosomally to the zona pellucida. This feature has attracted considerable interest in the evolution of zonadhesin and its possible biological and biomedical implications. Previous molecular evolutionary analyses, however, were confined to cDNA sequences of only few distantly related species. Moreover, except for rabbit and pig, little is known about zonadhesin's processing. To delineate the situation in primates including humans, we analyze here the evolution of zonadhesin on the basis of D domain encoding cDNAs of about 4900 base pairs (bp) length from a representative primate sampling (1 Strepsirhini, 3 Cercopithecidae, 3 Platyrrhini, and human; 7 new sequences) plus GenBank data from mouse, rabbit, and pig. Site-specific (CODEML and HyPhy) analysis indicates positive evolution of zonadhesin. Moreover, moving window analysis (CRANN) points to a positive correlation of sequence evolution and sperm-competition. Significant accumulations of positively selected sites across interspecifically variable motifs (identified by PROSITE) suggest that positive selection promotes differences between species by amino acid exchanges and changes in posttranslational modification. In the case of zonadhesin D domains, positive selection might thus contribute to the species-specific binding of zonadhesin and zona pellucida. A high conservation of processing and dimerization motifs of primate zonadhesin in analogy to pig, on the other hand, illustrates that zonadhesin's backbone needs to meet basic requirements in order to retain function.

Amino Acid Sequence↗