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PubMed2000

Replication orientation affects the rate and direction of bacterial gene evolution.

In many bacterial genomes, the leading and lagging strands have different skews in base composition; for example, an excess of guanosine compared to cytosine on the leading strand. We find that Chlamydia genes that have switched their orientation relative to the direction of replication, for example by inversion, acquire the skew of their new "host" strand. In contrast to most evolutionary processes, which have unpredictable effects on the sequence of a gene, replication-related skews reflect a directional evolutionary force that causes predictable changes in the base composition of switched genes, resulting in increased DNA and amino acid sequence divergence.

Base Composition↗
PubMed1995

Early cranial neural crest migration in the direct-developing frog, Eleutherodactylus coqui.

Direct development is a common reproductive mode in living amphibians characterized by absence of the free-living, aquatic larval stage. In Eleutherodactylus, a species-rich genus of New World frogs, evolution of direct development from the ancestral biphasic ontogeny is correlated with a comprehensive modification in embryonic cranial patterning, including the loss of many larval-specific components and the precocious formation of many adult (postmetamorphic) structures. We use scanning electron microscopy (SEM) to examine the emergence and early migration of cranial neural crest cells in Eleutherodactylus coqui to begin to assess the possible role of the neural crest in mediating these evolutionary changes. As in metamorphosing frogs, cranial crest cells emerge prior to neural fold closure and assemble into three streams: rostral otic, and caudal otic. These streams contribute to the face and first visceral (mandibular) arch, to the second (hyoid) arch, and to posterior (branchial) arches, respectively. Rostrocaudal position, morphology, and/or migration patterns distinguish subpopulations of cells within the rostral stream and caudal otic stream. With the possible exception of the small size of the rostral otic caudal otic streams, evolution of direct development in E. coqui has not altered basic patterns of neural crest emergence or early migration as assessed by SEM. If observed evolutionary changes in embryonic cranial patterning are mediated by the neural crest, then they likely involve later aspects of crest migration or more subtle features related to pattern formation such as cell behavior and commitment, or gene expression.

Animals↗
PubMed2001

How does a DNA interacting enzyme change its specificity during molecular evolution? A site-directed mutagenesis study at the DNA binding site of the DNA-(adenine-N6)-methyltransferase EcoRV.

The EcoRV DNA-(adenine-N6)-methyltransferase (MTase) recognizes GATATC sequences and modifies the first adenine residue within this site. Parts of its DNA interface show high sequence homology to DNA MTases of the dam family which recognize and modify GATC sequences. A phylogenetic analysis of M.EcoRV and dam-MTases suggests that EcoRV arose in evolution from a primordial dam-MTase in agreement to the finding that M.EcoRV also methylates GATC sites albeit at a strongly reduced rate. GATCTC sites that deviate in only one position from the EcoRV sequence are preferred over general dam sites. We have investigated by site-directed mutagenesis the function of 17 conserved and nonconserved residues within three loops flanking the DNA binding cleft of M.EcoRV. M.EcoRV contacts the GATATC sequence with two highly cooperative recognition modules. The contacts to the GAT-part of the recognition sequence are formed by residues conserved between dam MTases and M.EcoRV. Mutations at these positions lead to an increase in the discrimination between GATATC and GATC substrates. Our data show that the change in sequence specificity from dam (GATC) to EcoRV (GATATC) was accompanied by the generation of a second recognition module that contacts the second half of the target sequence. The new DNA contacts are formed by residues from all three loops that are not conserved between M.EcoRV and dam MTases. Mutagenesis at important residues within this module leads to variants that show a decreased ability to recognize the TC-part of the GATATC sequence.

Amino Acid Sequence↗
PubMed2002

Direct benefits and the evolution of female-biased cooperative breeding in Seychelles warblers.

Inclusive fitness benefits have been suggested to be a major selective force behind the evolution of cooperative breeding. We investigated the fitness benefits selecting for cooperative breeding in the Seychelles warbler, Acrocephalus sechellensis. A microsatellite-based genotyping method was used to determine the relatedness of subordinates to group offspring in an isolated population of Seychelles warblers. The indirect and direct breeding benefits accruing to individual subordinates were then calculated for every successful breeding event over a three-year period. We show that female subordinates frequently gained parentage and that this, combined with high levels of extragroup paternity, resulted in low levels of relatedness between subordinates and nondescendent offspring within a territory. Direct breeding benefits were found to be significantly higher than indirect kin benefits for both female and male subordinates. As predicted, female subordinates gained significantly more direct breeding opportunities and therefore higher inclusive fitness benefits by being a subordinate within a group than did males. This may explain why most subordinates in the Seychelles warbler are female.

Animals↗
PubMed1988

Directional selection and the evolution of breeding date in birds.

In many bird species, those pairs that breed earlier in the season have higher reproductive success than those that breed later. Since breeding date is known to be heritable, it is unclear why it does not evolve to an earlier time. Under assumptions outlined by Fisher, a model is developed that shows how breeding date may have considerable additive genetic variance, appear to be under directional selection, and yet not evolve. These results provide a general explanation for a persistent correlation of fitness with a variety of traits in natural populations.

Animals↗
PubMed1976

Evolution of DNA structure: direction, mechanism, rate.

On the basis of the results of an analysis of frequencies of pyrimidine oligonucleotides, the degree of pyrimidine clustering of DNA in species from different taxa has been determined. A tendency for an increase in the index of clustering of DNA was revealed in the sequence: invertebrates, fishes, amphibians, reptiles, birds, mammals. A mechanism is postulated, according to which the increase in the degree of clustering of DNA d-ring the evolution may be associated with the accumulation of mutations, Purine equalibrium Pyrimidine transversions, resulting in a selective enrichment of one of the chains of DNA with pyrimidines and the other- with purines, i.e. in an increase in the degree of purine-pyrimidine imbalance (asymmetry) of DNA complementary chains. This mechanism of DNA evolution is supported by the presence of positive correlation between the degree of clustering and the degree of the chain asymmetry of natural DNAs, as well as the character of the amino acid substitutions in cytochromes c in different species. The progressive evolution of different groups of organisms on the whole may have been accompanied by an acceleration of the rates of evolution of the DNA structure. On the basis of the amino acid sequence of cytochromes c in different species the degree of clustering and the degree of the chain asymmetry of the corresponding structural genes of DNA was found to have a general tendency towards an increase in the following order: invertebrates, fishes, amphibians, reptiles, birds, mammals. Thus, evolution of cytochrome c cistron is a vector process based on a selection of mutations which, on the one hand, are neurtral to protein, and, on the other hand, result in the sense chain of DNA being enriched with pyrimidines and the nonsense one (and the corresponding mRNA)- with purines. Hence, it is the polynucleotide template rather than protein, that must have been the "object of selection". The frequency of substitutions in cytochromes c cistron for vertebrates is 1.56x13(-9) per nucleotide per year. It is believed that the evolutionary modification of the DNA structure may be associated with an increase in the interference resistance of the translation, i.e. with selection for codons of highest readout stability.

Amino Acid Sequence↗
PubMed1991

Prebiotic co-evolution of self-replication and translation or RNA world?

A prebiotic scenario is proposed, based on the recent "domain hypothesis" model (Lahav, 1989, J. molec. Evol. 29, 475-479), suggested for domain propagation of RNA-like molecules in a fluctuating environment. The same system is suggested now not only for the evolution of ribozymes, but also for the evolution of directed peptide synthesis, as follows: Short, self-structured strands (termed prebioectons), each possessing a templatable domain which is chargeable by an amino acid, are the predecessors of tRNA (proto-tRNA). Complementary domains are formed on these prebioectons during an environmental cycle such as wetting-drying, followed by their dissociation from their template domain and ligation, to form the predecessor of mRNA (proto-mRNA). The evolution of directed peptide synthesis is suggested to be based on the ability of the charged prebioectons to attach preferentially to their complementary domains on the proto-mRNA. Two stages of this process are envisioned, namely: (a) Template-directed, random peptide synthesis taking place when non-specifically-charged prebioectons are sequentially attached each to its complementary domain on the proto-mRNA, followed by peptide bond formation. (b) Template-and-sequence-directed peptide synthesis, which can be realized after the "invention" of a catalytic molecule capable of specifically charging a proto-tRNA by an amino acid; this is the crucial evolutionary stage, where a crude genetic code becomes functional. Gradually, catalytic peptides and ribozymes are selected for their functions and evolve, while being encoded in the primitive "memory" of the emerging system. Thus, rather than the RNA monopoly postulated by the RNA World hypothesis, an early co-evolution of primitive enzymes and ribozymes is suggested.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2005

Evolution of host specificity in fleas: is it directional and irreversible?

Evolutionary trends in the evolution of host specificity have been the focus of much discussion but little rigorous empirical testing. On the one hand, specialization is often presumed to lead irreversibly into evolutionary dead ends and little diversification; this would mean that generalists might evolve into specialists, but not vice versa. On the other hand, low host specificity may limit the risk of extinction and provide more immediate fitness benefits to parasites, such that selection may favour evolution toward a generalist strategy. Here, we test for directionality in the evolution of host specificity using a large data set and phylogenetic information on 297 species of fleas parasitic on small mammals. The analyses determined whether host specificity, measured both as the number of host species exploited and their taxonomic diversity, was related to clade rank of the flea species, or the number of branching events between an extant species and the root of the phylogenetic tree (i.e., the total path length from the root of the tree to the species). Based on regression analyses, we found positive relationships between the number of host species used and clade rank across all 297 species, as well as within one (Hystrichopsyllidae) of four large families and one of seven large genera investigated separately; in addition, we found a positive relationship between the taxonomic diversity of host species used and clade rank in another of the seven genera. These results suggest a slight evolutionary trend of decreasing host specificity. Using a much more conservative likelihood ratio test, however, a random walk, or null model, of evolution could not be discarded in favour of the directional trends in all cases mentioned above. Still, these results suggest that host specificity may have tended to decrease in many flea lineages, a process that could have been driven by the benefits of exploiting a wide range of host species.

Adaptation, Biological↗
PubMed1998

Isolation and characterization of three mRNAs enriched in embryos of the direct-developing sea urchin Heliocidaris erythrogramma: evolution of larval ectoderm.

The Australian sea urchin Heliocidaris erythro-gramma utilizes a derived direct developmental mode that evolved 8-12 million years ago. From a differential screen we have isolated a small set of cDNAs corresponding to genes more greatly expressed in embryos of H. erythrogramma than in those of its indirect-developing nearest relative, H. tuberculata. The method was biased towards abundant transcripts and did not allow detection of modifications of usage of highly conserved gene family members. Three differentially expressed abundant transcripts were found that potentially encode secreted proteins. Two of these, the arylsulfatase HeARS and the putative lectin HeEL-1, were identifiable as homologues of known proteins. Another gene, HeET-1, may be exclusively expressed in the H. erythrogramma embryo. In situ hybridization experiments demonstrate that all three transcripts are localized to the ectoderm. Two of them, HeET-1 and HeEL-1, are transcribed in an identical domain comprising the larval ectoderm. This region of gene expression has acquired a novel columnar cytology during the evolution of the H. erythrogramma embryo. The third sequence, HeARS, encodes an arylsulfatase homologue. Its expression is uniform in the gastrula, but as the rudiment develops it accumulates to the greatest extent in the invaginating vestibular ectoderm. Through comparisons with indirect-developing species, we show that this concentration of arylsulfatase mRNA in the rudiment is a novel feature of H. erythrogramma development. These data suggest that H. erythrogramma has a unique arrangement of ectodermal gene expression territories. We propose that these reflect larval adaptations that have occurred in the lineage leading to H. erythrogramma, and enabled the evolution of direct development.

Amino Acid Sequence↗
PubMed2006

Temporal evolution of 2-dimensional direction signals used to guide eye movements.

The smooth pursuit system must integrate many local motion measurements into a coherent estimate of target velocity. Several laboratories have studied this integration process using eye movements elicited by targets, such as tilted bars, containing conflicts between local motion signals measured along contours [one dimensional (1D)] and those measured at the bar's endpoints, or terminators [two dimensional (2D)]. The general finding is that 1D signals dominate early responses, whereas later components of the behavior are determined by 2D signals. We studied the dynamics of the integration process in macaque monkeys by systematically varying the relative proportions of 1D and 2D signals and the retinal eccentricities at which they appeared. Predictably, longer bars produced greater and longer-lasting contour-induced deviations. The evolution of the 2D response occurred over a period of 50-400 ms, depending on the relative proportions of 1D and 2D signals. As contours were displaced from the fovea the deviation decreased but much less so for early (1st 40 ms) than for late (subsequent 40 ms) pursuit initiation. These bottom-up effects could be overcome to a limited extent by the top-down influence of predictability. Finally, we observed that when animals were free to track any part of the bar, they spontaneously made short-latency saccades to the terminators on most trials, especially when the bars were tilted. This suggests an increased saliency of moving terminators, particularly when discrepancies exist among local motion signals.

Adaptation, Ocular↗
PubMed1976

Evolution of continuous variation: direct approach through joint distribution of genotypes and phenotypes.

The evolutionary dynamics of the joint distribution of genotypes and phenotypes is studied. The model, originally devised to study the joint effects of Mendelian and other types of transmissions, provides results of interest also to the theory of direct Mendelian transmission with natural selection. Assuming bivariate normal distributions, it is shown that in the latter case genotypic and phenotypic means and variances, and genotype-phenotype correlation can be expressed recursively as functions of the parameters for the selection, environmental, and mutation variance. Equilibria and rates of approach for these moments are calculated. It is also proved that in the presence of selection the heritability,defined as the ratio of expected genotypic to expected phenotypic variance after selection, is greater than that before selection by a predictable amount and that it can be greater than unity.

Biological Evolution↗
PubMed2003

Efficient display of two enzymes on filamentous phage using an improved signal sequence.

Directed protein-evolution strategies generally make use of a link between a protein and the encoding DNA. In phage-display technology, this link is provided by fusion of the protein with a coat protein that is incorporated into the phage particle containing the DNA. Optimization of this link can be achieved by adjusting the signal sequence of the fusion. In a previous study, directed evolution of signal sequences for optimal display of the Taq DNA polymerase I Stoffel fragment on phage yielded signal peptides with a 50- fold higher incorporation of fusion proteins in phage particles. In this article, we show that for one of the selected signal sequences, improved display on phage can be generalized to other proteins, such as adenylate cyclases from Escherichia coli and Bordetella pertussis, and that this is highly dependent on short sequences at the C-terminus of the signal peptide. Further, the display of two enzymes on phage has been achieved and may provide a strategy for directing coevolution of the two proteins. These findings should be useful for display of large and cytoplasmic proteins on filamentous phage.

Adenylyl Cyclases↗
PubMed1992

Human cytochromes P450: evolution and cDNA-directed expression.

As the first step in the process of carcinogenesis, most chemical carcinogens require metabolic activation by cytochromes P450 for conversion to highly reactive electrophiles that bind covalently to DNA. Studies in rodents suggest that low or high levels of expression of a single P450 can determine susceptibility or resistance to chemically induced cancer. Although rodent systems have been used to explore the molecular basis of chemical carcinogenesis and to identify chemicals capable of damaging genes and causing cancer, it has been understood that marked species differences exist in the expression, regulation, and catalytic activities of different P450s. Thus, large efforts are underway to study the catalytic activities of human P450s directly by expression of their cDNAs in cultured cells. Two systems are being used: a) transient high-level P450 production in HepG2 cells for analysis of catalytic activities, and b) stable expression in human B-lymphoblastoid cells to study promutagen and procarcinogen activation. These studies define the relative contributions of individual P450 forms to the activation of various chemical carcinogens. The B-lymphoblastoid cDNA expression system can also be used to determine whether a chemical will be hazardous or toxic to humans. The most intriguing aspects of P450s are the occurrence of human genetic polymorphisms in P450 expression, which could be a risk factor for chemical carcinogenesis. The best-studied P450 genetic polymorphism is the debrisoquine/sparteine polymorphism which is due to mutant CYP2D6 alleles. Four mutant alleles have been characterized that account for most of the defective CYP2D6 genes in Caucasians. These can be detected by polymerase chain reaction assays.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

Practical evolution and application of direct intracytoplasmic sperm injection for male factor and idiopathic fertilization failure infertilities.

OBJECTIVE: To analyze the introduction of a new assisted fertilization technique for the treatment of severe male factor and idiopathic fertilization failure infertilities. DESIGN: Retrospective analysis of 16-month clinical application of IVF-ET where insemination was performed solely by direct intracytoplasmic sperm injection. SETTING: Clinical IVF-ET program. PATIENTS: Ninety-two couples undergoing 105 cycles of sperm injection. RESULTS: One hundred embryo transfers yielded 28 viable pregnancies (28%) from which eight normal deliveries have occurred to date. Complete cleavage arrest or fertilization failure occurred in four cycles, and one couple had all embryos cryopreserved. One thousand one hundred forty-three eggs were injected of which 173 (15%) degenerated. Four hundred seventy-nine of the surviving 970 eggs became normally fertilized (49%), and 381 of these zygotes (79.5%) developed suitably for cryopreservation or for transfer. Thirty-four of 310 embryos transferred implanted, yielding an implantation rate of 11%. Both testicular and epididymal sperm were used successfully to achieve fertilization and pregnancies, as was sperm retrieved by electroejaculation. Older women and couples suffering from prior idiopathic fertilization failure had a markedly poorer outcome. CONCLUSIONS: These results confirm that the intracytoplasmic sperm injection technique is a successful form of assisted fertilization that can be applied to a wide range of couples at significant risk from fertilization failure.

Adult↗
PubMed2026

Direct link between convergent evolution at sequence level and phenotypic level of septal pore cap in Agaricomycotina.

Several homologous morphological characters, despite sharing apparently similar features, are known to have independently evolved in different lineages multiple times. However, the genetic backgrounds of such morphological convergences remain poorly understood. To detect any correlated amino acid substitutions potentially responsible for morphological convergence at the phenotypic level, we focused on the morphology of the septal pore cap (SPC), a structure involved in mycelia's complex multicellularity in fungi. SPCs are classified into 3 morphological types: perforate, imperforate, and vesiculate. To understand the evolutionary events that occurred at the sequence level during the morphological convergence of perforate SPCs in Agaricomycotina, we examined sequence differences among species with different SPC types by comparative genomic analysis using a single-copy gene dataset from 12 Agaricomycotina genomes with morphological literature of SPC. Our analysis revealed that sequences of 8 genes, including an SPC-related gene spc33, were clustered based on SPC morphology rather than species relationship. Additionally, same amino acid substitutions independently occurred in both lineages in which species with perforate SPCs emerged. These findings suggest that specific amino acid substitutions in spc33 were critical for the emergence of perforate SPCs in multiple lineages. Further, our gene search for spc33 across organisms suggests that spc33 evolved shortly before the emergence of imperforate SPC. This study represents the first step toward elucidating the genetic basis of the morphological evolution of SPC. It contributes to both clarifying the genetic basis underlying morphological convergence and advances the study of fungal evolutionary morphology.

Evolution, Molecular↗