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PubMed1979

Rapid evolution of animal mitochondrial DNA.

Mitochondrial DNA was purified from four species of higher primates (Guinea baboon, rhesus macaque, guenon, and human) and digested with 11 restriction endonucleases. A cleavage map was constructed for the mitochondrial DNA of each species. Comparison of the maps, aligned with respect to the origin and direction of DNA replication, revealed that the species differ from one another at most of the cleavage sites. The degree of divergence in nucleotide sequence at these sites was calculated from the fraction of cleavage sites shared by each pair of species. By plotting the degree of divergence in mitochondrial DNA against time of divergence, the rate of base substitution could be calculated from the initial slope of the curve. The value obtained, 0.02 substitutions per base pair per million years, was compared with the value for single-copy nuclear DNA. The rate of evolution of the mitochondrial genome appears to exceed that of the single-copy fraction of the nuclear genome by a factor of about 10. This high rate may be due, in part, to an elevated rate of mutation in mitochondrial DNA. Because of the high rate of evolution, mitochondrial DNA is likely to be an extremely useful molecule to employ for high-resolution analysis of the evolutionary process.

Animals↗
PubMed1979

The evolution of the long and short repetitive DNA sequences in sea urchins.

The rates of evolution of purified long and short repetitive DNA sequences were examined by hybridisation analysis between the DNAs from several species of sea urchins. We find that the rates of nucleotide substitution are very comparable within mutually retained sequences for the two classes of repetitive DNA. The loss of hybridisable sequences between species also occurs at similar rates among both the short and long repetitive DNA sequences. Between species that separated less than 50 million years ago, hybridisable short repetitive sequences are lost all through the spectrum of reiteration frequencies. The long repeats contain a few sequences which are highly conserved within all of the species examined, and which amount to approximately 1% of the total genome. The short repetitive class, on the other hand, does not seem to contain any such highly conserved elements. The long repetitive sequences internally appear to contain short 'units' of reiteration, which may comprise families within the long repetitive class. We find no evidence to indicate that the majority of long and short repetitive sequences evolve by different mechanisms or at different rates.

Animals↗
PubMed1979

The amino acid sequence of mouse pancreatic ribonuclease. Extremely rapid evolutionary rates of the myomorph rodent ribonucleases.

The complete amino acid sequence of mouse pancreatic ribonuclease has been determined by analysis of tryptic, chymotryptic, thermolytic and CNBr peptides and by automatic sequence analysis of the intact protein. The sequence of mouse RNase differs in 20--30% of the positions from other RNase sequences. Three unique or neraly unique substitutions were found, viz. Gly-68 leads to Arg-68, Arg-85 leads to His-85 and Ser-123 leads to Thr-123. All these three residues might be involved in interactions with substrate molecules. A most parsimonious tree of the myomorph rodent RNase shows that after the divergence of rat and mouse, the ribonuclease of rat accumulated substitutions at a rate 2.5--4.3 times as high as the rates in other branches of the tree and 23 times as high as the average rate in the Bovidae ribonuclease evolution. These extreme fluctuations in substitution rate are difficult to reconcile with the hypothesis of the evolutionary clock. The high evolution rate of rat ribonuclease is thought to be caused by positive selection, leading to new functional properties of the enzyme.

Amino Acid Sequence↗
PubMed1975

Evolution of urinary flow rate with prostatectomy.

Urinary flow rate was studied before and after transurethral prostatectomy in 53 patients. An average of 43.8 percent improvement in maximum flow rate after transurethral prostatectomy was observed in this series. Improvement of maximum flow rate occurred in 71 per cent of patients. Half of the cases in which flow rate did not improve were chronic prostatitis. Uroflowmetry cannot be utilized as a quality index of a transurethral prostatic resection as long as the degree of detrusor deterioration is not assessed. There is a relationship between the degree of preoperative symptoms and the degree of postoperative urinary flow improvement. The degree of preoperative symptoms and urinary flow deviation are not related which suggests that uroflowmetry adds to the assessment of symptoms in the determination of the degree of obstruction. Patients presenting difficulty of urination have a greater chance to demonstrate urinary flow improvement after surgery than patients complaining of urinary frequency.

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↗
PubMed1977

Rapid speciation and chromosomal evolution in mammals.

To test the hypothesis that population subdivision into small demes promotes both rapid speciation and evolutionary changes in gene arrangement by inbreeding and drift, we estimated rates of speciation and rates of chromosomal evolution in 225 genera of vertebrates. Rates of speciation were estimated by considering the number of living species in each genus and the fossil record of each genus as well as information about extinction rates. Speciation rate was strongly correlated with rate of chromosomal evolution and average rates of speciation in lower vertebrate genera were one-fifth those in mammalian genera. Genera with high karyotypic diversity and rapid speciation rates may generally have small effective population size (Ne), whereas large Ne values may be associated with karyotypically uniform genera and slow rates of speciation. Speciation and chromosomal evolution seem fastest in those genera with species organized into clans or harems (e.g., some primates and horses) or with limited adult vagility and juvenile dispersal, patchy distribution, and strong individual territoriality (e.g., some rodents). This is consistent with the above hypothesis regarding the evolutionary importance of demes.

Animals↗
PubMed1978

Carbon dioxide evolution during the cell cycle of the fission yeast Schizosaccharomyces pombe.

The rate of CO2 evolution was measured in synchronous cultures of the fission yeast Schizosaccharomyces pombe growing in a minimal medium. The rate of CO2 evolution was found to double sharply at about the time of nuclear division (0.75 of the way through the cell cycle). For the remainder of the cell cycle the rate remained constant. Addition of inhibitors of DNA synthesis or nuclear division did not affect the pattern of CO2 evolution in synchronous cultures. Similarly, in an induced synchronous culture, in which DNA synthesis, nuclear division and cell division--but not growth, were synchronized, CO2 evolution showed a continuous pattern and not the step-wise increase associated with the normal synchronous cultures. When S. pombe was grown in a complete medium, the evolution of CO2 in a synchronous cultures was shown to increase in a continuous manner but at a rate faster than the growth of the culture.

Ascomycota↗
PubMed1979

The time-course of energy balance in an isometric tetanus.

Unpoisoned sartorius muscles of Rana temporaria were stimulated tetanically in isometric contractions lasting up to 20 s at 0 degrees C. The observed enthalpy (heat + work) production and the chemical changes in these contractions were measured, and a comparison was made between the observed enthalpy and the enthalpy that could be explained by the chemical changes. Like earlier workers, we found that the only net known reaction of energetic significance that occurred was dephosphorylation of n-phosphoryl creatine (PC), and we found a significant evolution of unexplained enthalpy (UE), a portion of the observed enthalpy which could not be explained by the extent of PC dephosphorylation. We measured the total quantity and the rate of production of the UE, and we found that its rate of evolution, which was most rapid during the first 750 ms of contraction, fell progressively to zero by the 8th s of contraction: i.e., after 8 s of contraction, all the observed enthalpy is adequately explained by PC dephosphorylation. The time-course of evolution of the UE was slower than that of the labile enthalpy (a component of the enthalpy evolved in isometric contraction whose rate of production declines exponentially at approximately 1 s-1). We conclude that, although the magnitudes of these enthalpy quantities may be similar, they are not derived from the same chemical reaction in muscle.

Animals↗
PubMed2025

A General Principle of Neuronal Evolution Reveals a Human-Accelerated Neuron Type Potentially Underlying the High Prevalence of Autism in Humans.

The remarkable ability of a single genome sequence to encode a diverse collection of distinct cell types, including the thousands of cell types found in the mammalian brain, is a key characteristic of multicellular life. While it has been observed that some cell types are far more evolutionarily conserved than others, the factors driving these differences in the evolutionary rate remain unknown. Here, we hypothesized that highly abundant neuronal cell types may be under greater selective constraint than rarer neuronal types, leading to variation in their rates of evolution. To test this, we leveraged recently published cross-species single-nucleus RNA-sequencing datasets from three distinct regions of the mammalian neocortex. We found a strikingly consistent relationship where more abundant neuronal subtypes show greater gene expression conservation between species, which replicated across three independent datasets covering >106 neurons from six species. Based on this principle, we discovered that the most abundant type of neocortical neurons-layer 2/3 intratelencephalic excitatory neurons-has evolved exceptionally quickly in the human lineage compared to other apes. Surprisingly, this accelerated evolution was accompanied by the dramatic down-regulation of autism-associated genes, which was likely driven by polygenic positive selection specific to the human lineage. In summary, we introduce a general principle governing neuronal evolution and suggest that the exceptionally high prevalence of autism in humans may be a direct result of natural selection for lower expression of a suite of genes that conferred a fitness benefit to our ancestors while also rendering an abundant class of neurons more sensitive to perturbation.

Humans↗
PubMedDate not supplied

[Evolution of the DNA structure: direction, mechanism, rate].

On the basis of the analysis of frequencies of occurence of pyrimidines of different length, the degree of clustering of DNA of a hundred species belonging to different taxons has been determined. A tendency towards increase in the index of DNA clustering was revealed in the sequence: bacteria, invertebrates, fishes, amphibians, reptiles, birds, mammals. A mechanism is postulated, according to which an increase in the degree of clustering of DNA in the process of progressive evolution of species may be due to accumulation of mutations, Pyr in equilibrium Pur transversions, resulting in an increase in the degree of asymmetry of the complementary chains of DNA. That this mechanism does exist is proved by a positive correlation between the degree of clustering of DNA and the degree of asymmetry of natural DNA chains. The mean frequency of mutation of vertebrates is about 4,6-10(-8) substitutions per nucleotide per year. Evolution of different groups of organisms may be accompanied with an increase in the rate of evolution of DNA structure. With the help of a special computer program, proceeding from the amino acid sequence of cytochromes c in 40 species belonging to different taxons, the degree of clustering of pyrimidines and the degree of asymmetry of complementary chains of DNA cistrons coding for cytochrome c was determined. A general tendency towards an increase in the mean values of the corresponding parametres of structure was found in the following: bacteria, invertebrates, fishes, amphibians, reptiles, birds and mammals. Thus, it was established that "neutral" amino acid substitutions in cytochromes are based on the selection of mutations leading to accumulation of pyrimidines in sense H-chain of DNA, and purines--in the corresponding mRNA. The frequency of mutation in cytochrome c of chordates is about 5,2-10(-8) of amino acid residues per year. It is assumed that the evolution modification of DNA structure may be due to increase in the disturbance stability of translation.

Amino Acids↗
PubMed2024

An Orthogonal T7 Replisome for Continuous Hypermutation and Accelerated Evolution in E. coli.

Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can dramatically accelerate the evolution of new or enhanced protein functions. We describe an orthogonal DNA replication system in E. coli based on the controlled expression of the replisome of bacteriophage T7. The system replicates circular plasmids that enable high transformation efficiencies and seamless integration into standard molecular biology workflows. Engineering of T7 DNA polymerase yielded variant proteins with mutation rates of 1.7 × 10 -5 substitutions per base in vivo - 100,000-fold above the genomic mutation rate. Continuous evolution using the mutagenic T7 replisome was demonstrated by expanding the substrate scope of TEM-1 β-lactamase and increase activity 1,000-fold against clinically relevant monobactam and cephalosporin antibiotics in less than one week.

Journal Article↗
PubMed1975

Evolution of type C viral genes: preservation of ancestral murine type C viral sequences in pig cellular DNA.

Domestic pigs (Sus scrofa) and other members of the family Suidae have multiple copies of type C viral gene sequences in the cellular DNA of all their tissues. Partially homologous viral gene sequences are also found in cellular DNA of rodents, particularly Muridae. The results lead to the conclusion that type C viral genes were introduced into the Suidae lineage as a result of trans-species infection by an ancestral xenotropic murine virus. The rate of evolution of the virogene sequences in the pig appears to be much slower than that of genes that have remained in the rodent lineage; this may be a consequence of transfer from a shorter-lived animal (the rodent) to a longer-lived one (the pig). We estimate the time of gene transmission as 5-10 million years ago and conclude that the present-day porcine type C virogenes most closely approximate the viral genes as they were several million years ago in the rodent lineage.

Animals↗
PubMed1979

From extracellular to intracellular: the establishment of a symbiosis.

The colonization of host cells by modern symbionts is surveyed. The morphological distinction between extracellular and intracellular symbionts is not sharp, and the various kinds of association can be arranged in a graded series of increasing morphological integration of the symbiont into the host cell. Apart from some aggressive parasitic infections, the great majority of symbionts are enclosed by a host membrane in a vacuole. Those not enclosed in a host vacuole usually cannot be cultivated outside the cell. It is therefore surmised that encirclement by a vacuolar membrane would only disappear, if at all, in the later stages of the evolution of intracellular symbiosis. Recognition mechanisms between host and symbiont occur, but have been little studied. In some associations, recognition at surface contact occurs, and there is evidence for the involvement of lectins in certain cases. In other associations, recognition may occur wholly or in part after the entry of symbiont into host cells. After entry, special mechanisms for the biotrophic transfer of nutrients from symbiont to host develop. Both the symbiont population size and its rate of increase are strictly regulated by the host cell; symbiont metabolism may be controlled likewise. Rates of evolution of intracellular symbionts are probably very rapid, owing in part to responses of the host cell to its symbiont.

Animals↗
PubMed1978

Hydrogen evolution by chloroplast-hydrogenase systems: improvements and additional observations.

An in vitro system containing isolated chloroplasts, ferredoxin and bacterial hydrogenase on illumination evolves H2 and O2 from water. Maximum rate of hydrogen production so far achieved is two litres H2 per g. chlorophyll per h. The rate of H2 evolution per mg chlorophyll is dependent on concentrations of chlorophyll and ferredoxin in the reaction mixture. The rates as well as duration of H2 production are enhanced by the presence of oxygen scavengers and bovine serum albumin in the system. Hydrogenases and ferredoxins vary in their degree of cross reactivity in the chloroplast system; with some hydrogenases the H2 evolution rates were increased by the presence of additional biological electron carriers. Attempts to couple algal hydrogenases to the chloroplasts system have not succeeded so far.

Bacteria↗
PubMed1979

Contrasted modes of evolution in the same genome: allozymes and adaptive change in Heliconius.

Butterflies in the South American genus Heliconius have undergone a spectacular adaptive radiation (with convergent evolution between some lines) in their color patterns; this has been produced by natural selection for muellerian mimicry. The genetic basis of this radiation, shown by crossing highly differentiated races within two of the species, is homozygosity for alternative alleles at some half dozen loci. In complete contrast, allozyme loci in these butterflies are strongly heterozygous and show only frequency differences (never amounting to homozygosity of alternative alleles) between races; the amount of allozyme divergence is the same between races of H. erato and H. sara, although in color pattern the first forms marked races and the other does not. For the allozymes, there is a strong correlation over loci for rate of divergence between species and average heterozygosity. This is not true of the genes controlling color pattern. Heterozygosity of the enzymes is correlated with subunit molecular weight. Thus, different parts of the genome can evolve in different ways simultaneously; genes controlling color pattern in the "classical" mode, and allozymes in a different mode in which the rate of evolution is related to their heterozygosity (a "balance" or "neutral" mode).

Animals↗
PubMed2026

Building phenotypic character matrices for phylogenetic inference: exploration of 35 years of practice.

Recent methodological development in phylogenetic inference has focused predominantly on molecular data. However, renewed interest in other data types, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. However, attention has largely focused on the improvement of models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference. We present a systematic review of 164 phylogenetic analyses conducted over the last 35 years and focused on a diverse group of extinct arthropods: trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Not surprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data are missing for many tips, providing support against the exclusion of characters because of missing data. In consideration of this, as well as advances in the study of developmental biology and variational complexity, we identify several avenues for increasing the quality and quantity of morphological data going forward.

Phylogeny↗
PubMed1978

Quantitative subunit hybridization of drosophila alpha-glycerophosphate dehydrogenase.

The dimeric enzyme, alpha-Glycerophosphate dehydrogenase, was purified from eight Drosophila species by the method of Collier et al. (1976). The enzymes were inactivated at high pH and the conditions sufficient for reactivation were established. Electrophoretic patterns of reactivated alpha-glycerophosphate dehydrogenases which were mixed following inactivation of two species' enzymes, demonstrate that high pH dissociates the enzyme into its constituent subunits and reactivation involves subunit reassociation. Twenty interspecific combinations of dissociated enzymes were allowed to reassociate, and the amounts of both heterospecific and homospecific enzyme activity and protein were determined by densitometry. In all 20 tests there were no differences between observed and expected heterospecific:homospecific enzyme ratios. These results are consistent with the very slow rate of evolution of this enzyme in the family Drosophilidae (Collier and MacIntyre, 1977).

Animals↗