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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↗
PubMed2002

Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus.

Myotragus balearicus was a dwarf artiodactyl endemic to the Eastern Balearic Islands, where it evolved in isolation for more than 5 million years before becoming extinct between 3640 and 2135 cal BC (calibrated years BC). Numerous unusual apomorphies obscure the relationship between Myotragus and the extant Caprinae. Therefore, genetic data for this species would significantly contribute to the clarification of its taxonomic position. In this study, we amplify, sequence, and clone a 338-base pair (bp) segment of the mitochondrial cytochrome b (cyt b) gene from a >9Kyr Myotragus subfossil from la Cova des Gorgs (Mallorca). Our results confirm the phylogenetic affinity of Myotragus with the sheep (Ovis) and the takin (Budorcas). In each tree, the Myotragus branch is long in comparison with the other taxa, which may be evidence of a local change in the rate of evolution in cyt b. This rate change may be due to in part to an early age of first reproduction and short generation time in Myotragus, factors that are potentially related to the extreme reduction in size of the adult Myotragus as compared to the other Caprinae.

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↗
PubMed2003

Investigating the role of atomic hydrogen on chloroethene reactions with iron using tafel analysis and electrochemical impedance spectroscopy.

Metallic iron filings are commonly employed as reducing agents in permeable barriers used for remediating groundwater contaminated by chlorinated solvents. Reactions of trichloroethylene (TCE) and tetrachloroethylene (PCE) with zerovalent iron were investigated to determine the role of atomic hydrogen in their reductive dechlorination. Experiments simultaneously measuring dechlorination and iron corrosion rates were performed to determine the fractions of the total current going toward dechlorination and hydrogen evolution. Corrosion rates were determined using Tafel analysis, and dechlorination rates were determined from rates of byproduct generation. Electrochemical impedance spectroscopy (EIS) was used to determine the number of reactions that controlled the observed rates of chlorocarbon disappearance, as well as the role of atomic hydrogen in TCE and PCE reduction. Comparison of iron corrosion rates with those for TCE reaction showed that TCE reduction occurred almost exclusively via atomic hydrogen at low pH values and via atomic hydrogen and direct electron transfer at neutral pH values. In contrast, reduction of PCE occurred primarily via direct electron transfer at both low and neutral pH values. At low pH values and micromolar concentrations, TCE reaction rates were faster than those for PCE due to more rapid reduction of TCE by atomic hydrogen. At neutral pH values and millimolar concentrations, PCE reaction rates were faster than those for TCE. This shift in relative reaction rates was attributed to a decreasing contribution of the atomic hydrogen reaction mechanism with increasing halocarbon concentrations and pH values. The EIS data showed that all the rate limitations for TCE and PCE dechlorination occurred during the transfer of the first two electrons. Results from this study show that differences in relative reaction rates of TCE and PCE with iron are dependent on the significance of the reduction pathway involving atomic hydrogen.

Electrochemistry↗
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↗
PubMed1997

Prospective randomized study comparing human serum albumin with fetal cord serum as protein supplement in culture medium for in-vitro fertilization.

The use of human serum albumin (HSA) instead of fetal cord serum (FCoS) as protein supplement highly simplifies the preparation of culture medium for human in-vitro fertilization (IVF) but whether they are equivalent in sustaining embryo development is still controversial. We performed a prospective randomized study of patients undergoing IVF or intracytoplasmic sperm injection (ICSI) where embryos were cultured in Earle's balanced salt solution containing either 8% (v/v) FCoS or 0.4% (w/v) HSA as protein source. Fertilization rates, morphological embryonic quality and pregnancy rates were compared. A total of 2189 oocytes from 210 cycles were cultured in medium supplemented with HSA in patient group 1 and 2109 oocytes from 203 cycles in medium supplemented with FCoS in patient group 2. The fertilization rate, defined as the presence of two nuclei, for microinjected oocytes was similar in both patient groups (77.4 and 76.7%, respectively). The fertilization rate for inseminated oocyte-cumulus complexes was significantly higher in the HSA group than in the FCoS group (62.9 versus 53.8%, P < 0.025). The embryonic quality was significantly better after culture in medium supplemented with HSA than with FCoS (13.7 versus 9.9% morphologically excellent embryos, P < 0.001). Implantation rates per transferred embryo were not significantly different (22.5 versus 18.2%), but there was a significantly higher pregnancy rate per embryo transfer in the HSA group (45.7 versus 35.9%, P < 0.05, respectively). Non-evolutive pregnancy rates were significantly different (27.4 and 16.7%). Our data demonstrate that the use of human serum albumin as a protein supplement for culture medium in human IVF programmes is associated with improved embryonic quality and significantly higher pregnancy rates. For this reason as well as the additional benefits of being virus-free and being purified, HSA is preferable to FCoS for the preparation of culture media in human IVF.

Adult↗
PubMed1993

Analysis of the evolution and variation of the human influenza A virus nucleoprotein gene from 1933 to 1990.

This study examined the evolution and variation of the human influenza virus nucleoprotein gene from the earliest isolates to the present. Phylogenetic reconstruction of the most parsimonious evolutionary path connecting 49 nucleoprotein sequences yielded a single lineage. The average calculated rate of mutation was 3.6 nucleotide substitutions per year (2.3 x 10(-3) substitutions per site per year). Thirty-two percent of these mutations resulted in amino acid substitutions, and the remainder were silent mutations. Analysis of virus isolates from China and elsewhere showed no significant differences in their rate of evolution, genetic diversity, or mean survival time. The nearly constant rate of change was maintained through the two antigenic shifts, and there were no obvious changes in the number or types of mutations associated with the changes in the surface proteins. A detailed comparison of the changes that have occurred on the main evolutionary path with those that have occurred on the side branches of the phylogenetic tree was made. This showed that while 35% of the mutations on the side branches resulted in amino acid changes, only 21% of those on the main path affected the protein sequence. These results suggest that although the rate of change of the human influenza virus nucleoprotein is much higher than that previously described for avian influenza viruses, there are measurable constraints on the evolution of the surviving virus lineage. Comparison of the nucleoproteins of virus isolates adapted to chicken embryos with the nucleoproteins of those grown only in MDCK cells revealed no consistent differences between the virus pairs. Thus, although the nucleoprotein is known to be critical for host specificity, its adaptation to growth in eggs apparently involves no immediate selective pressures, such as are found with hemagglutinin.

Amino Acid Sequence↗
PubMed1998

Large-subunit ribosomal RNA systematics of symbiotic dinoflagellates: morphology does not recapitulate phylogeny.

Biochemical, histological, physiological, and genetic evidence indicates that dinoflagellates symbiotic with marine invertebrates are a heterogeneous complex of taxa, representing at least five genera in three orders. Despite a wealth of data regarding morphological, biochemical, and behavioral differences among symbiotic dinoflagellates, knowledge concerning patterns of diversification is limited. I analyzed approximately 900 bp of the 5' end of the large-subunit ribosomal RNA gene from 14 dinoflagellate isolates: six cultured Symbiodinium specimens, two cultured symbiotic Gymnodinium, two algal samples isolated from reef-building corals, an algal sample obtained from cultures of the jellyfish Cassiopea xamachana, and three free-living Gymnodinium isolates. Results show that morphological similarities among the examined symbiotic taxa do not necessarily correspond with molecular phylogeny. The included Symbiodinium taxa represent a paraphyletic assemblage while Gymnodinium is reconstructed as a polyphyletic assemblage. Analysis indicates that all the included symbiotic dinoflagellates descended from a common, symbiotic ancestor (though within the dinoflagellates, symbiosis is a polyphyletic trait). Additionally, two free-living dinoflagellates emerge within the symbiotic clade, suggesting that the symbiotic lifestyle has been lost at least once in this group. It has been hypothesized that rates of evolution within mutualistic endosymbioses should be reduced relative to free-living taxa. However, results indicate that rates of molecular, morphological, biochemical and behavioral change are similar among branches leading to symbiotic and free-living dinoflagellates.

Animals↗
PubMedDate not supplied

Neuromediators and neuromodulators. Evolution of compounds and evolution of hypotheses.

The probable features of the evolution of neuromediators (NM) and neuromodulators (NR) of different types are discussed. The assumption concerning the high rate of evolution of peptide NM and NR and the greater potentialities of the formation of new NM and NR of this type is substantiated. Monomolecular NM and NR are presumably more conservative, but have an advantage as regards the strict individualism of the systems of synthesis and degradation. Peptides, individual amino acids, and ATP are probably among the oldest NM and NR.

Adenosine Triphosphate↗
PubMed2006

Rapid progression of carotid lesions in HAART-treated HIV-1 patients.

To obtain data on the evolution of carotid lesions, we evaluated 133 patients at their first antiretroviral regimen, followed for at least 2 years; 77 treated with protease inhibitors (PIs): Group A and 56 with non-nucleosidic reverse transcriptase inhibitors (NNRTIs): Group B. All patients were subjected to carotid ultrasonography. In Group A, among the previously normal patients 22.5% developed lesions, 40% remained normal, 37.5% shifted to other antiretroviral regimens. Among the 37 previously pathologic patients, 46% worsened, 19% were stable, in 8% the lesions had disappeared, 27% shifted. In Group B, among the previously normal patients, 12.7% developed lesions, 80.8% remained unaltered, 6.5% shifted. Among the previously pathologic patients, 12.5% worsened, lesions reversed in 25%, remained stable in 50% and 12.5% shifted to PI. At statistical analysis, in Group A both the percentage of patients developing new lesions and the percentage of patients who worsened was significantly higher. In conclusion, we evidenced a more rapid onset of lesions in patients treated with PIs with respect to patients treated with NNRTIs and towards a more rapid evolution of the previous lesions. The shift from PIs to NNRTI/3 NRTI seems related to a lower rate of evolution. Interestingly, a disappearance of lesions was detected in both groups.

Acquired Immunodeficiency Syndrome↗
PubMed2004

Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis.

To explain why informational genes (i.e., those involved in transcription, translation, and related processes) are less likely than housekeeping genes to be horizontally transferred, Jain and coworkers proposed the complexity hypothesis. The underlying idea is that informational genes belong to large, complex systems of coevolving genes. Consequently, the likelihood of the successful horizontal transfer of a single gene from such an integrated system is expected to be low. Here, this hypothesis is extended to explain some of the determinants of the mode of evolution of coding sequences. It is proposed that genes belonging to complex systems are relatively less likely to be under adaptive evolution. To evaluate this "extended complexity hypothesis," 2,428 families and protein domains were analyzed. This analysis found that genes whose products are highly connected, located in intracellular components, and involved in complex processes and functions were more conserved and less likely to be under adaptive evolution than are other gene products. The extended complexity hypothesis suggests that both the mode and the rate of evolution of a protein are influenced by its gene ontology (localization, biological process, and molecular function) and by its connectivity.

Adaptation, Biological↗
PubMed1984

The molecular clock may be an episodic clock.

It is argued that the apparent constancy of the rate of molecular evolution may be an artifact due to the very slow rate of evolution of individual amino acids. A statistical analysis of protein evolution using a stationary point process as the null hypothesis leads to the conclusion that molecular evolution is episodic, with short bursts of rapid evolution followed by long periods of slow evolution. Such dynamics are incompatible with the neutral allele theory and require a revision of the standard interpretation of the molecular clock.

Alleles↗
PubMed1998

Rates and patterns of mitochondrial DNA sequence evolution in fringilline finches (fringilla spp.) and the greenfinch (Carduelis chloris).

Rates and patterns of evolution in partial sequences of five mitochondrial genes (cytochrome b, ATPase 6, NADH dehydrogenase subunit 5, tRNA(Glu), and the control region) were compared among taxa in the passerine bird genera Fringilla and Carduelis. Rates of divergence do not vary significantly among genes, even in comparisons with the control region. Rate variation among lineages is significant only for the control region and NADH dehydrogenase subunit 5, and patterns of variation are consistent with the expectations of neutral theory. Base composition is biased in all genes but is stationary among lineages, and there is evidence for directional mutation pressure only in the control region. Despite these similarities, patterns of substitution differ among genes, consistent with alternative regimes of selective constraint. Rates of nonsynonymous substitution are higher in NADH dehydrogenase subunit 5 than in other protein-coding genes, and transitions exist in elevated proportions relative to transversions. Transitions appear to accumulate linearly with time in tRNA(Glu), and despite exhibiting the highest overall rate of divergence among species, there are no transversional changes in this gene. Finally, for resolving phylogenetic relationships among Fringilla taxa, the combined protein-coding data are broadly similar to those of the control region in terms of phylogenetic informativeness and statistical support.

Animals↗
PubMed1994

The effect of background selection against deleterious mutations on weakly selected, linked variants.

This paper analyses the effects of selection against deleterious alleles maintained by mutation ('background selection') on rates of evolution and levels of genetic diversity at weakly selected, completely linked, loci. General formulae are derived for the expected rates of gene substitution and genetic diversity, relative to the neutral case, as a function of selection and dominance coefficients at the loci in question, and of the frequency of gametes that are free of deleterious mutations with respect to the loci responsible for background selection. As in the neutral case, most effects of background selection can be predicted by considering the effective size of the population to be multiplied by the frequency of mutation-free gametes. Levels of genetic diversity can be sharply reduced by background selection, with the result that values for sites under selection approach those for neutral variants subject to the same regime of background selection. Rates of fixation of slightly deleterious mutations are increased by background selection, and rates of fixation of advantageous mutations are reduced. The properties of sex-linked and autosomal loci in random-mating populations are compared, and the effects of background selection on asexual and self-fertilizing populations are considered. The implications of these results for the interpretation of studies of molecular evolution and variation are discussed.

Animals↗
PubMed2001

Toxicity in animals. Trends in evolution?

Animals acquire toxicity either by metabolic synthesis of toxins (secondary metabolites), by expression of toxin genes or by the uptake, storage and sequestration of toxins produced by other organisms, i.e., microbes, plants or other animals. Variability of toxin structure and function is high. Peptide toxins in particular, although relying on a limited number of structural frameworks, often exhibit considerable structural hypervariability. An accelerated rate of evolution in the toxin gene structure (conserved introns, but high substitution rates in the exons) leads to the functional diversity of these peptides or proteins. The selective forces which may drive toxin evolution are unknown. Venomousness or the possession of toxins can be essential for survival, but the advantage of toxin biosynthesis may also be of minor importance or has been lost during evolution.

Animals↗
PubMed2002

The pattern of amino acid replacements in alpha/beta-barrels.

The determinants of site-to-site variability in the rate of amino acid replacement in alpha/beta-barrel enzyme structures are investigated. Of 125 available alpha/beta-barrel structures, only 25 meet a variety of phylogenetic and statistical criteria necessary to ensure sufficient data for reliable analysis. These 25 enzyme structures (from a wide variety of taxa with diverse lifestyles in diverse habitats) differ greatly in size, number, and topology of domains in addition to the alpha/beta-barrel, quaternary structure, metabolic role, reaction catalyzed, presence of prosthetic groups, regulatory mechanisms, use of cofactors, and catalytic mechanisms. Yet, with the exception of ribulose-1,5-bisphosphate carboxylase, all structures have similar frequency distributions of amino acid replacement rates. Hence, site-specific variability in rates of evolution is largely independent of differences in biology, biochemistry, and molecular structure. A correlation between site-specific rate variation and (1) distance from the active site, (2) solvent accessibility, and (3) treating glycines in unusual main-chain conformations as a separate class, explains approximately half the causal variation. Secondary structure exerts little influence on the pattern and distribution of replacements. Additional domains and subunits, side-chain hydrogen bonds, unusual side-chain rotamers, nonplanar peptide bonds, strained main-chain conformations, and buried hydrophilic-charged residues contribute little to variability among sites because they are rare. Nonlinear models do not improve the fits. In several enzymes, deviations from the typical pattern of replacements suggest the possible action of natural selection. A statistical analysis shows that, in all cases, much of the remaining unexplained variation is not attributable to chance and that other, as yet unidentified, causal relations must exist.

Amino Acid Sequence↗
PubMed2001

Tempo and mode of evolution in an orthologous Can SINE.

Tempo and mode of nucleotide change were examined in an orthologous carnivoran nuclear repetitive DNA element (Can SINE), and compared with those of the transthyretin intron I (TR-i-I) sequence in which it is embedded, by using a phylogenetic framework. The Can SINE is found in representatives of all living caniform carnivoran families, but no living feliform families. This suggests insertion 40-65 MYA, after the two lineages split, but before the caniform radiation. Despite linkage and a long shared evolutionary history, both parsimony and likelihood analyses showed the Can SINE to be significantly different from TR-i-I in rates of evolution and phylogenetic hypotheses supported. The substitution rate is significantly higher in Can SINE than in TR-i-I, and this is attributable to the tRNA-related region of the insertion. While the incongruence length difference test revealed significant conflict between the Can SINE and TR-i-I partitions, the test was shown to be sensitive to the distribution of homoplasy within partitions. The conflicting phylogenies are likely the result of differences in phylogenetic accuracy (homoplasy distribution) rather than in phylogenetic history (gene trees). The base composition of Can SINE contains a significantly higher GC percentage than TR-i-I. Our results indicate that differences between the two partitions may be the result of homoplasy introduced by an increased substitution rate in the tRNA-related region of Can SINE owing to CpG hypermutability.

Animals↗
PubMed2004

Rapid evolution of a sexually selected trait following population establishment in a novel habitat.

Colonization of novel environments creates new selection pressures. Sexually selected traits are affected by the physical and social environment and should be especially susceptible to change, but this has rarely been studied. In southern California, dark-eyed juncos, (Junco hyemalis) naturally breed in mixed-coniferous temperate forests, typically from 1500 m to 3000 m in elevation. In the early 1980s, a small population became established in a coastal habitat, the University of California, San Diego campus, which has a mild, Mediterranean climate. I show that a sexually and socially selected signaling trait--the amount of white in the tail--has declined by approximately 22% as compared to mountain juncos. I address three main factors that could explain the difference between mountain and coastal juncos: phenotypic plasticity, genetic drift, and selection. Results indicate that the first two can be ruled out as the sole cause of the plumage change, which implies that selection contributed to the genetic differentiation from the mountain population. The estimated rate of evolution is about 0.2 haldanes, comparable with rates of change in systems where individuals have been artificially introduced into new environments (e.g., guppies and Drosophila). This is the first study to demonstrate evolution of a sexually selected trait after only several generations resulting from a natural invasion into a novel environment.

Animals↗