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PubMed2003

Rapid appearance of epistasis during adaptive divergence following colonization.

Theory predicts that short-term adaptation within populations depends on additive (A) genetic effects, while gene-gene interactions 'epistasis (E)' are important only in long-term evolution. However, few data exist on the genetic architecture of adaptive variation, and the relative importance of A versus non-additive genetic effects continues to be a central controversy of evolutionary biology after more than 70 years of debate. To examine this issue directly, we conducted hybridization experiments between two populations of wild soapberry bugs that have strongly differentiated in 100 or fewer generations following a host plant shift. Contrary to expectation, we found that between-population E and dominance (D) have appeared quickly in the evolution of new phenotypes. Rather than thousands of generations, adaptive gene differences between populations have evolved in tens. Such complex genetic variation could underlie the seemingly extreme rates of evolution that are increasingly reported in many taxa. In the case of the soapberry bug, extraordinary ecological opportunity, rather than mortality, may have created hard selection for genetic variants. Because ultimate division of populations into genetic species depends on epistatic loss of hybrid compatibility, local adaptation based on E may accelerate macro-evolutionary diversification.

Acclimatization↗
PubMed2005

Dynamics of a quantum phase transition: exact solution of the quantum Ising model.

The Quantum Ising model is an exactly solvable model of quantum phase transition. This Letter gives an exact solution when the system is driven through the critical point at a finite rate. The evolution goes through a series of Landau-Zener level anticrossings when pairs of quasiparticles with opposite pseudomomenta get excited with a probability depending on the transition rate. The average density of defects excited in this way scales like a square root of the transition rate. This scaling is the same as the scaling obtained when the standard Kibble-Zurek mechanism of thermodynamic second order phase transitions is applied to the quantum phase transition in the Ising model.

Journal Article↗
PubMed2003

Estimating changes in mutational mechanisms of evolution.

By considering three DNA sequences simultaneously there is sufficient information to recover a full Markov model with three transition matrices from the root to each of the sequences. It is necessary to have relatively long sequences because, for nucleotides, the full model requires 39 parameters that are estimated from 63 observable values. This triplet Markov method is evaluated for the protein coding genes of mammalian vertebrate mitochondrial genomes, and, in addition, version for two-state-characters (such as R/Y coding) is implemented. A key finding is that some changes in mutational mechanism differentially affect the mutation rate between pairs of nucleotides: there does not appear to be a universal change in "rate" of evolution. It remains to be explored whether detecting changes in certain nucleotide interchanges can be localized to a particular part of the DNA replication/repair system. In order to estimate divergence dates it may eventually be advantageous to use the nucleotide interchanges that show little rate change.

Animals↗
PubMed1998

Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data.

The phylogenetic relationships of the African lungfish (Protopterus dolloi) and the coelacanth (Latimeria chalumnae) with respect to tetrapods were analyzed using complete mitochondrial genome DNA sequences. A lungfish + coelancanth clade was favored by maximum parsimony (although this result is dependent on which transition:transversion weights are applied), and a lungfish + tetrapod clade was supported by neighbor-joining and maximum-likelihood analyses. These two hypotheses received the strongest statistical and bootstrap support to the exclusion of the third alternative, the coelacanth + tetrapod sister group relationship. All mitochondrial protein coding genes combined favor a lungfish + tetrapod grouping. We can confidently reject the hypothesis that the coelacanth is the closest living relative of tetrapods. When the complete mitochondrial sequence data were combined with nuclear 28S rRNA gene data, a lungfish + coelacanth clade was supported by maximum parsimony and maximum likelihood, but a lungfish + tetrapod clade was favored by neighbor-joining. The seeming conflicting results based on different data sets and phylogenetic methods were typically not statistically strongly supported based on Kishino-Hasegawa and Templeton tests, although they were often supported by strong bootstrap values. Differences in rate of evolution of the different mitochondrial genes (slowly evolving genes such as the cytochrome oxidase and tRNA genes favored a lungfish + coelacanth clade, whereas genes of relatively faster substitution rate, such as several NADH dehydrogenase genes, supported a lungfish + tetrapod grouping), as well as the rapid radiation of the lineages back in the Devonian, rather than base compositional biases among taxa seem to be directly responsible for the remaining uncertainty in accepting one of the two alternate hypotheses.

Animals↗
PubMed1985

Quantitative models of hybrid dysgenesis: rapid evolution under transposition, extrachromosomal inheritance, and fertility selection.

A model of the P-M system of hybrid dysgenesis is presented which incorporates single-site transposition of P factors in M cytotype, determination of offspring cytotype by both maternal cytotype and maternal or offspring nuclear genotype, and strong fertility selection in dysgenic individuals. The conditions required for the initial invasion of P factors into a pure M population, information concerning stable polymorphisms, and results of numerical iterations depicting the dynamic, nonequilibrium behavior of the system are summarized. While conditions for initial increase are independent of the rate of cytotype switching, the rate of evolution is accelerated by increased production of dysgenic individuals. If the transposition rate is sufficiently high to overcome the fertility barrier opposing P factors introduced into M populations, then convergence to high frequencies of the P factor occurs very rapidly. Under intense fertility depression, the phase of rapid increase may be preceded by an extended period of gradual increase at low frequencies.

Animals↗
PubMed2001

Rapid evolution of wing size clines in Drosophila subobscura.

Parallel latitudinal clines across species and continents provide dramatic evidence of the efficacy of natural selection, however little is known about the dynamics involved in cline formation. For example, several drosophilids and other ectotherms increase in body and wing size at higher latitudes. Here we compare evolution in an ancestral European and a recently introduced (North America) cline in wing size and shape in Drosophila subobscura. We show that clinal variation in wing size, spanning more than 15 degrees of latitude, has evolved in less than two decades. In females from Europe and North America, the clines are statistically indistinguishable however the cline for North American males is significantly shallower than that for European males. We document that while overall patterns of wing size are similar on two continents, the European cline is obtained largely through changing the proximal portion of the wing, whereas the North American cline is largely in the distal portion. We use data from sites collected in 1986/1988 (Pegueroles et al. 1995) and our 1997 collections to compare synchronic (divergence between contemporary populations that share a common ancestor) and allochronic (changes over time within a population) estimates of the rates of evolution. We find that, for these populations, allochronically estimated evolutionary rates within a single population are over 0.02 haldanes (2800 darwins), a value similar in magnitude to the synchronic estimates from the extremes of the cline. This paper represents an expanded analysis of data partially presented in Huey et al. (2000).

Animals↗
PubMed1996

Mitochondrial gene sequences and the molecular systematics of the artiodactyl subfamily bovinae.

Nucleotide sequence evolution of the mitochondrial cytochrome c oxidase subunit II (COII) gene was used to examine the molecular phylogenetics and evolution of the Bovinae, a subfamily within the mammalian order Artiodactyla. The COII gene was sequenced in representatives of three bovine tribes (Bovini, Boselaphini, and Tragelaphini) and the outgroup taxon Capra (subfamily Caprinae). Although the phylogenetic analyses grouped Bison as sister to Bos, the genus Bison was paraphyletic, with the American bison being most closely related to species of Bos rather than to the European bison. COII data also supported a close relationship between African (Syncerus) and Asian (bubalus) buffaloes, the monophyly of the tribe Bovini, and a sister-group relationship between the tribes Bovini and Boselaphini. Analysis of nucleotide substitutions in the COII gene prompted a system of differential weighting of nucleotide substitutions for inferring phylogenetic relationships across the range of divergence times examined here (2-20 million years). Rates of evolution in the COII gene are examined and compared to evolutionary rates in mtDNA tRNA/rRNA genes and the D-loop among other artiodactyl taxa.

Animals↗
PubMed1979

Photosynthetic oxygen reduction in isolated intact chloroplasts and cells in spinach.

The time course of light-induced O(2) exchange by isolated intact chloroplasts and cells from spinach was determined under various conditions using isotopically labeled O(2) and a mass spectrometer. In dark-adapted chloroplasts and cells supplemented with saturating amounts of bicarbonate, O(2) evolution began immediately upon illumination. However, this initial rate of O(2) evolution was counterbalanced by a simultaneous increase in the rate of O(2) uptake, so that little net O(2) was evolved or consumed during the first approximately 1 minute of illumination. After this induction (lag) phase, the rate of O(2) evolution increased 3- to 4-fold while the rate of O(2) uptake diminished to a very low level. Inhibition of the Calvin cycle, e.g. with dl-glyceraldehyde or iodoacetamide, had negligible effects on the initial rate of O(2) evolution or O(2) uptake; both rates were sutained for several minutes, and about balanced so that no net O(2) was produced. Uncouplers had an effect similar to that observed with Calvin cycle inhibitors, except that rates of O(2) evolution and photoreduction were stimulated 40 to 50%.These results suggest that higher plant phostosynthetic preparations which retain the ability to reduce CO(2) also have a significant capacity to photoreduce O(2). With near-saturating light and sufficient CO(2), O(2) reduction appears to take place primarily via a direct interaction between O(2) and reduced electron transport carriers, and occurs principally when CO(2)-fixation reactions are suboptimal, e.g. during induction or in the presence of Calvin cycle inhibitors. The inherent maximum endogenous rate of O(2) reduction is approximately 25 to 50% of the maximum rate of noncyclic electron transport coupled to CO(2) fixation. Although the photoreduction of O(2) is coupled to ion transport and/or phosphorylation, this process does not appear to supply significant amounts of ATP directly during steady-state CO(2) fixation in strong light.

Journal Article↗
PubMed2006

Survival of cancer patients in France: a population-based study from The Association of the French Cancer Registries (FRANCIM).

We present the main results of the first population-based cancers survival study gathering all French registry data. Survival data on 205,562 cancer cases diagnosed between 01/01/1989 and 31/12/1997 were analysed. Relative survival was estimated using an excess rate model. The evolution of the excess mortality rate over the follow-up period was graphed. The analysis emphasised the effect of age at diagnosis and its variation with time after diagnosis. For breast and prostate cancers, the age-standardised five-year relative survivals were 84% and 77%, respectively. The corresponding results in men and women were 56% versus 58% for colorectal cancer and 12% versus 16% for lung cancer. For some cancer sites, the excess mortality rate decreased to low values by five years after diagnosis. For most cancer sites, age at diagnosis was a negative prognostic factor but this effect was often limited to the first year after diagnosis.

Adolescent↗
PubMed1991

Mammalian DNA replication: mutation biases and the mutation rate.

Experimental studies have shown that the fidelity of DNA replication can be affected by the concentrations of free deoxyribonucleotides present in the cell. Replication of mammalian chromosomes is achieved using pools of newly-synthesized deoxyribonucleotides which fluctuate during the cell cycle. Since regions of mammalian chromosomes are replicated sequentially, there is the potential for differences among mammalian loci in both the relative and absolute frequencies of the various transitional and transversional mutations which may occur. Where these mutations are effectively neutral, at silent sites in genes and in non-coding sequences, this may result in different rates of evolution and in different base compositions, as have been observed in data from mammalian genes. A simple model of the DNA replication process is developed to describe how the mutation rate could be affected by the G + C contents of the deoxyribonucleotide pools and of the replicating DNA. Mutation rates are predicted to vary from locus to locus; only in the particular case of identical G + C contents in the DNA locus and the deoxyribonucleotide pools, and no proofreading, will the mutation rate be uniform over all loci.

Animals↗
PubMed2002

Retrospective multicentre study on mechanical and enzymatic preparation of fresh and cryopreserved testicular biopsies.

BACKGROUND: Isolation of sperm suitable for ICSI from fresh or frozen-thawed testicular sperm extraction (TESE) can be facilitated by mechanical or enzymatic processing of the samples. METHODS: A retrospective multicentre study was initiated to compare these two approaches. Eleven German centres provided data on their TESE cycles performed during the period 1996/1997. Quality of retrieved sperm, fertilization rates of injected oocytes, embryo quality, resulting pregnancy rates and evolution of pregnancies were evaluated. RESULTS: The percentage of cycles with at least some motile sperm available for injection was higher after mechanical preparation. Independent of the preparation method, fertilization rates were higher for motile compared with immotile sperm or elongated spermatids in all groups and in general higher for cryopreserved versus fresh samples. Embryo quality was significantly better after injection of motile sperm for all treatments and in particular after enzymatic versus mechanical processing of biopsies. Pregnancy rates were identical for embryos derived from sperm prepared mechanically or enzymatically from fresh or cryopreserved testicular samples. The abortion rate (32/172, 18.6%) and the rate of multiple implantations (32/140, 22.9%) were not different from results reported in the literature for ICSI using ejaculated sperm. CONCLUSION: In this retrospective multicentre study, no unequivocal advantage of one over the other preparation method could be identified in 839 ICSI cycles using testicular sperm from 549 patients.

Abortion, Spontaneous↗
PubMed1997

Reduced turnover of the D1 polypeptide and photoactivation of electron transfer in novel herbicide resistant mutants of Synechocystis sp. PCC 6803.

Two missense mutants, A263P and S264P, and a deletion mutant des-Ala263, Ser264, have been constructed in the D1 protein of the cyanobacterium Synechocystis sp PCC 6803. All were expected to induce a significant conformational change in the QB-binding region of photosystem II (PSII). Although the des-Ala263, Ser264-D1 mutant accumulated some D1 protein in the thylakoid membrane it was unable to grow photoautotrophically or evolve oxygen. Thermoluminescence and chlorophyll fluorescence studies confirmed that this deletion mutant did not show any functional PSII activity. In contrast, [S264P]D1 was able to grow photoautotrophically and give light-saturated rates of oxygen evolution at 60% of the rate of the wild-type control strain, TC31. The A263P missense mutant was also able to evolve oxygen at 50% of TC31 rates although it did not readily grow photoautotrophically. Thermoluminescence, flash oxygen yield and chlorophyll fluorescence measurements indicated that in both missense mutants electron transfer from QA to QB was significantly impaired in dark adapted cells. However, QA to QB electron transfer could be photoactivated in the mutants by background illumination. Both the A263P and S264P mutants also showed an increase in resistance to the s-triazine family of herbicides although this feature did not hold for the phenolic herbicide, ioxynil. Of particular interest was that the two missense mutants, especially S264P, possessed a slower rate of turnover of the D1 protein compared with TC31 and in vivo contained detectable levels of a 41-kDa adduct consisting of D1 and the alpha subunit of cytochrome b559. When protein synthesis was blocked by the addition of lincomycin, D1 degradation was again slower in S264P than TC31. The results are discussed in terms of structural changes in the QB-binding region which affect herbicide and plastoquinone binding and perturb the normal regulatory factors that control the degradation of the D1 protein and its synchronisation with the synthesis of a replacement D1 protein.

Binding Sites↗
PubMed1998

Conservation of pericentromeric duplications of a 200-kb part of the human 21q22.1 region in primates.

We analyzed the conservation of large paralogous regions (more than 200 kb) on human chromosome regions 21q22.1 and 21q11.2 and on pericentromeric regions of chromosomes 2, 13, and 18 in three nonhuman primate species. Orthologous regions were found by FISH analysis of metaphase chromosomes from Gorilla gorilla, Pan troglodytes, and Pongo pygmaeus. Only one orthologous region was detected in chromosomes of P. pygmaeus, showing that the original locus was at 21q22.1 and that the duplication arose after the separation of Asian orangutans from the other hominoids. Surprisingly, the paralogous regions were more highly conserved in gorilla than in chimpanzee. PCR amplification of STSs derived from sequences of the chromosome 21 loci and low-stringency FISH analysis showed that this duplication occurred recently in the evolution of the genome. Different rates of sequence evolution through substitutions or deletions, after the duplication, may have resulted in diversity between closely related primates.

Animals↗
PubMed2005

[Endocrine tumors: biology and physiopathology].

Endocrine tumors are defined as neoplastic lesions resulting from the proliferation of cells engaged in an endocrine differentiation pathway, as shown by their expression of a set of specific markers, including true endocrine markers (such as chromogranine A) and neuro-endocrine markers, shared between neurons and endocrine cells (such as synaptophysin). The demonstration of the synthesis and secretion of one or several hormones is not necessary for the assessment of the endocrine nature of a tumor; only tumors associated with a clinical syndrome resulting from hormone overproduction can be said functioning endocrine tumors. Beyond their common features, endocrine tumors are characterized by a marked diversity, which results from the large functional, structural and embryological heterogeneity of normal endocrine cells. The natural history of endocrine tumors is also characterized by a marked heterogeneity in their evolution and rate of progression. While most endocrine tumors are locally and slowly evolving, some of them behave as truly malignant tumors, as shown by their capacity of metastatic dissemination and their fatal evolution. A better understanding of the cellular and molecular mechanisms involved in tumor progression and metastatic dissemination is necessary for the identification of new prognostic tools and novel therapeutic targets.

Cell Division↗
PubMed1981

Effect of treatment of soil with keratinaceous material on soil fungi.

In the early periods of soil storage, the total number of fungi almost regularly and significantly increased with the concentration of keratinaceous material (ground buffalo hooves) between 1% and 10%. A concentration of 20% was stimulative after 7 days and became toxic after 15 days and remained so through the end of the experiment. With increase in the storage period, the beneficial effect of all concentrations was lost and in the case of high concentrations (5-20%) toxic ammonia was produced. The occurrence of Scopulariopsis brevicaulis, Cephalosporium acremonium, Chrysosporium tropicum, C. indicum, and C. keratinophilum increased markedly, especially at the higher concentrations of the keratinaceous material and after long periods of incubation. With increase in the concentration of keratinaceous material, the rate of evolution of ammonia from the soil sharply increased during the second week after treatment and fell off sharply during the third and fourth weeks. In soil stored at 35 C, the rate of decline in total fungi after longer periods of incubation was sharper at 35 C than at 25 C. Also the amount of evolved ammonia during the first and the second weeks was almost always higher at 35 C than at 25 C. Fourteen species were tested for keratinolytic activity. Three of them were highly keratinolytic and five moderately so.

Animals↗
PubMed1996

Patterns of divergence during evolution of alpha 1-proteinase inhibitors in mammals.

alpha 1-Proteinase inhibitor (alpha 1-PI), a member of the serine proteinase inhibitor superfamily, has a primary role in controlling neutrophil elastase activity within the mammalian circulation. Several studies have indicated that the reactive center region of alpha 1-PI, the amino acid sequence of which is critical to recognition of and binding to target proteinases, is highly divergent within and among species. This appears to be a consequence of accelerated rates of evolution that may have been driven by positive Darwinian selection. In order to examine this and other features of alpha 1-PI evolution in more detail, we have isolated and sequenced cDNAs representing alpha 1-PI mRNAs of the mouse species Mus saxicola and Mus minutoides and have compared these with a number of other mammalian alpha 1-PI mRNAs. Relative to other mammalian mRNAs, the extent of nonsynonymous substitution is generally high throughout the alpha 1-PI mRNA molecule, indicating greater overall rates of amino acid substitution. Within and among mouse species, the 5'-half of the mRNA, but not the 3'-half, has been homogenized by concerted evolution. Finally, the reactive center is under diversifying or positive Darwinian selection in murid rodents (rats, mice) and guinea pigs yet is under purifying selection in primates and artiodactyls. The significance of these findings to alpha 1-PI function and the possible selective forces driving evolution of serpins in general are discussed.

Animals↗
PubMed2002

Determinants of extinction in the fossil record.

The causes of mass extinctions and the nature of biological selectivity at extinction events are central questions in palaeobiology. It has long been recognized, however, that the amount of sedimentary rock available for sampling may bias perceptions of biodiversity and estimates of taxonomic rates of evolution. This problem has been particularly noted with respect to the principal mass extinctions. Here we use a new compilation of the amount of exposed marine sedimentary rock to predict how the observed fossil record of extinction would appear if the time series of true extinction rates were in fact smooth. Many features of the highly variable record of apparent extinction rates within marine animals can be predicted on the basis of temporal variation in the amount of exposed rock. Although this result is consistent with the possibility that a common geological cause determines both true extinction rates and the amount of exposed rock, it also supports the hypothesis that much of the observed short-term volatility in extinction rates is an artefact of variability in the stratigraphic record.

Animals↗
PubMed1993

Role of Oxygen in the Limitation and Inhibition of Nitrogenase Activity and Respiration Rate in Individual Soybean Nodules.

Although infected cell O2 concentration (Oi) is known to limit respiration and nitrogenase activity in legume nodules, techniques have not been available to measure both processes simultaneously in an individual legume nodule. Consequently, details of the relationship between nitrogenase activity and Oi are not fully appreciated. For the present study, a probe was designed that allowed open circuit measurements of H2 evolution (nitrogenase activity) and CO2 evolution (respiration rate) in a single attached soybean nodule while simultaneously monitoring fractional oxygenation of leghemoglobin (and thereby Oi) with a nodule oximeter. Compared to measurements of whole nodulated roots, use of the probe led to inhibition of nitrogenase activity in the single nodules. During oximetry measurements, total nitrogenase activity (TNA; peak H2 evolution in Ar/O2) in the single nodules was 16% of that in whole nodulated roots and 48% of nodulated root activity when Oi was not being measured simultaneously. This inhibition did not affect the nodules' ability to regulate Oi, because exposure to Ar/O2 (80:20, v/v) caused nitrogenase activity and respiration rate to decline, and this decline was linearly correlated with a concurrent decrease in Oi. When the nodules were subsequently exposed to a linear increase in external pO2 from 20 to 100% O2 at 2.7% O2/min, fractional leghemoglobin oxygenation first increased gradually and then more rapidly, reaching saturation at a pO2 between 76 and 100% O2. Plots of nitrogenase activity and respiration rate against Oi showed that rates increased with Oi up to a value of 57 nM, with half-maximal rates being attained at Oi values between 10 and 14 nM O2. The maximum nitrogenase activity achieved during the increase in pO2 (potential nitrogenase activity) was 30 to 57% of that measured in intact nodulated roots, showing that O2 limitation of nitrogenase activity could account for a significant proportion of the inhibition of TNA associated with the use of the probe. However, some factor(s) in addition to O2 must have limited the activity of single nodules at both subsaturating and saturating Oi. At Oi values greater than about 57 nM, nitrogenase activity and nodule respiration were inhibited, but, because this inhibition has been shown previously to be readily reversible when the Oi was lowered, it was not attributed to direct O2 inactivation of the nitrogenase protein. These results indicate that maximum nitrogenase activity in legume nodules is supported by a narrow range of Oi values. Possible biochemical mechanisms are discussed for both O2 limitation of nitrogenase activity at low Oi and inhibition of nitrogenase activity at high Oi.

Journal Article↗