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PubMed2005

Loss of linkage disequilibrium and accelerated protein divergence in duplicated cytomegalovirus chemokine genes.

Human CMV (hCMV) encodes several captured chemokine ligand and chemokine receptor genes that may play a role in immune evasion. The adjacent viral alpha-chemokine genes UL146 and UL147 appear to have duplicated subsequent to a recent gene capture event. Sequence data from multiple hCMV isolates suggest accelerated protein evolution in one of the paralogues, UL146. Extensive sequence variation was noted throughout the more rapidly evolving paralogue, although significant variation was also observed within the more slowly evolving gene, especially within a region corresponding to a possible signal peptide. In contrast to the haplotype structure observed for other hCMV genes, the distribution of nucleotide variants indicates a marked loss of linkage disequilibrium within UL146 and to a lesser extent UL147. Despite evidence of accelerated protein evolution, the rate of nonsynonymous to synonymous substitutions (d(N)/d(S)) in the more rapidly evolving paralogue was not indicative of neutral evolution, but of moderate purifying selection. The data presented here provides a unique opportunity to study the mechanisms by which a recently duplicated pair of genes has diverged and suggests a role for recombination.

Animals↗
PubMed1993

Early electrocardiographic changes in acute myocardial infarction treated by streptokinase or alteplase: a randomized study with dynamic, multi-lead, electrocardiographic monitoring.

Patients with a patent coronary artery after reperfusion therapy show an increased rate of evolution of QRS changes and of resolution of S-T changes as compared to patients with a persistent occlusion. Dynamic vectorcardiography permits multi-lead monitoring of changes in QRS complex and S-T segment over time. We monitored 150 patients randomized to alteplase or streptokinase for 24 h after admission. Alteplase was associated with significantly more rapid evolution of electrocardiographic changes but also with an increased occurrence of recurrent S-T changes. This may indicate a higher rate of early reperfusion with alteplase but due to recurrent ischemia, an electrocardiographic catch-up is seen with similar extent of myocardial damage observed after 24 h of monitoring.

Aged↗
PubMed1999

Associations between amino acids in the evolution of HIV type 1 protease sequences under indinavir therapy.

Significant diversity exists in amino acid sequences encoding HIV-1 protease in individuals naive for protease inhibitors, which could influence the rate of evolution of resistance. High-level resistance to indinavir requires multiple substitutions among at least 11 amino acid sites, and no single substitution was observed in all of 29 resistant isolates obtained from patients on long-term indinavir monotherapy. We have analyzed the evolution of PR in these sequences. The divergence from the baseline amino acid sequence by week 24 was 4%, increasing more than 7% by week 60. The mean difference between sequences from different patients at baseline was 6% (3-9%), rising to 10% after 40 weeks (3-16%), although at all time points nonsynonymous substitutions were less frequent than synonymous nucleotide changes. Analysis of associations between variants at different amino acid sites using a mutual information statistic revealed four pairs of sites to be significantly associated. In three cases these associations included residue 82. Clusters of baseline and week 24 amino acid sequences identified by maximum parsimony did not correlate significantly with the IC95 to indinavir, although a weak correlation of baseline clusters with phenotype at the week 24 time point was suggested.

Amino Acid Sequence↗
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↗
PubMed2004

A Bayesian statistical analysis of human T-cell lymphotropic virus evolutionary rates.

HTLV is a genetically-stable retrovirus that is considered to have evolved partly in concert with human migrations. Its rate of evolution is low and therefore, difficult to estimate reliably. In the first part of this study, we provide an improved estimate of HTLV evolutionary rate using anthropological calibration of phylogenetic nodes. We investigate two different anthropological calibrations using a Bayesian method that implements a relaxed molecular clock model and can combine data from multiple genes. The analysis shows that the two calibrations are compatible. In the second part, we develop a Bayesian statistical model to combine and compare the anthropology-based estimates of evolutionary rate with a rate recently calculated using pedigree data from vertically HTLV-infected families. We compare the statistical power of the two estimates and show that the current pedigree estimate, although resulting in considerably higher evolutionary rates, is too statistically weak to warrant a re-examination of the commonly used anthropology-based estimates. Statistical uncertainty burdens HTLV rate estimates based on both anthropological calibrations and on pedigree data; the former method rests on an untested assumption, whilst that latter is affected by small sample sizes.

Bayes Theorem↗
PubMed2003

Heterogeneous selection on LEGCYC paralogs in relation to flower morphology and the phylogeny of Lupinus (Leguminosae).

An analysis of the molecular evolution of two LEGCYC paralogs in Lupinus (Genisteae: Leguminosae) reveals a varied history of site-specific and lineage-specific evolutionary rates and selection both within and between loci. LEGCYC genes are homologous to regulatory loci known to control floral symmetry and adaxial flower organ identity in Antirrhinum and its relatives. Within Lupinus, L. densiflorus is unusual in having flowers with a proportionally smaller standard (upright adaxial petals) and larger wings (lateral petals) than other lupin species. Phylogenetic estimates of the nonsynonymous/synonymous substitution rate ratio, omega, suggest that along the L. densiflorus lineage, positive selection (omega > 1) acted at some codon sites of one paralog, LEGCYC1B, and greater purifying selection (omega < 1) acted at some sites of the other paralog, LEGCYC1A. Overall, LEGCYC1A appears to be evolving faster than LEGCYC1B, and both paralogs are evolving faster than the internal transcribed spacer (ITS) region of nr DNA. The predominant historical pattern inferred is a highly heterogeneous "selectional mosaic" which we suggest may be typical of the teosinte branched 1-cycloidea-PCF (TCP) class of transcriptional activators, and possibly other genes. Codon models that do not account for both site-specific and lineage-specific variation in omega do not detect positive selection at these loci. We suggest a modification of existing branch-site models involving an additional omega parameter along the foreground branch, to account for the effects of both greater positive selection and greater purifying selection at different codon sites along a particular branch. The higher rates of evolution and congruent phylogenetic signal of both LEGCYC paralogs show promise for the use of these genes as markers for phylogeny reconstruction at low taxonomic levels in Genisteae [corrected]

Amino Acid Substitution↗
PubMed1999

Evolutionary rate of a gene affected by chromosomal position.

Genes evolve at different rates depending on the strength of selective pressure to maintain their function. Chromosomal position can also have an influence [1] [2]. The pseudoautosomal region (PAR) of mammalian sex chromosomes is a small region of sequence identity that is the site of an obligatory pairing and recombination event between the X and Y chromosomes during male meiosis [3] [4] [5] [6]. During female meiosis, X chromosomes can pair and recombine along their entire length. Recombination in the PAR is therefore approximately 10 times greater in male meiosis compared with female meiosis [4] [5] [6]. The gene Fxy (also known as MID1 [7]) spans the pseudoautosomal boundary (PAB) in the laboratory mouse (Mus musculus domesticus, C57BL/6) such that the 5' three exons of the gene are located on the X chromosome but the seven exons encoding the carboxy-terminal two-thirds of the protein are located within the PAR and are therefore present on both the X and Y chromosomes [8]. In humans [7] [9], the rat, and the wild mouse species Mus spretus, the gene is entirely X-unique. Here, we report that the rate of sequence divergence of the 3' end of the Fxy gene is much higher (estimated at 170-fold higher for synonymous sites) when pseudoautosomal (present on both the X and Y chromosomes) than when X-unique. Thus, chromosomal position can directly affect the rate of evolution of a gene. This finding also provides support for the suggestion that regions of the genome with a high recombination frequency, such as the PAR, may have an intrinsically elevated rate of sequence divergence.

Animals↗
PubMed2001

Functional diversification of lepidopteran opsins following gene duplication.

A comparative approach was taken for identifying amino acid substitutions that may be under positive Darwinian selection and are correlated with spectral shifts among orthologous and paralogous lepidopteran long wavelength-sensitive (LW) opsins. Four novel LW opsin fragments were isolated, cloned, and sequenced from eye-specific cDNAs from two butterflies, Vanessa cardui (Nymphalidae) and Precis coenia (Nymphalidae), and two moths, Spodoptera exigua (Noctuidae) and Galleria mellonella (Pyralidae). These opsins were sampled because they encode visual pigments having a naturally occurring range of lambda(max) values (510-530 nm), which in combination with previously characterized lepidopteran opsins, provide a complete range of known spectral sensitivities (510-575 nm) among lepidopteran LW opsins. Two recent opsin gene duplication events were found within the papilionid but not within the nymphalid butterfly families through neighbor-joining, maximum parsimony, and maximum likelihood phylogenetic analyses of 13 lepidopteran opsin sequences. An elevated rate of evolution was detected in the red-shifted Papilio Rh3 branch following gene duplication, because of an increase in the amino acid substitution rate in the transmembrane domain of the protein, a region that forms the chromophore-binding pocket of the visual pigment. A maximum likelihood approach was used to estimate omega, the ratio of nonsynonymous to synonymous substitutions per site. Branch-specific tests of selection (free-ratio) identified one branch with omega = 2.1044, but the small number of substitutions involved was not significantly different from the expected number of changes under the neutral expectation of omega = 1. Ancestral sequences were reconstructed with a high degree of certainty from these data. Reconstructed ancestral sequences revealed several instances of convergence to the same amino acid between butterfly and vertebrate cone pigments, and between independent branches of the butterfly opsin tree that are correlated with spectral shifts.

Amino Acid Sequence↗
PubMed2006

Phenotypic plasticity, sexual selection and the evolution of colour patterns.

When a population comes to occupy a new environment, phenotypically plastic responses alter the distribution of phenotypes, and hence affect both the direction and the intensity of selection. Rates of evolution can be accelerated or retarded compared to what would happen in the absence of plasticity. Plastic responses in one trait result in novel selection pressures on other traits, and this can lead to evolution in completely different directions than predicted in the absence of plasticity. In this paper I use the concept of the adaptive surface in order to identify conditions under which the various different outcomes are expected. I then discuss differences between sexually and naturally selected traits. Sexually selected traits are often expected to be plastic in their expression, with individuals in high condition developing greater elaboration. As examples of sexually selected traits I review the evolution of colour patterns in birds with a view to assessing the magnitude of plastic responses in their development, and to ask how such responses may have influenced genetic evolution. The common colour pigments in birds are carotenoids and melanins. Both are used in social signaling, and consequently are expected to evolve to be phenotypically plastic indicators of an individual's quality. Perhaps partly because they are condition indicators, the quantity of carotenoids in the plumage can be strongly influenced by diet. Examples are described where alterations of carotenoids in the diet are thought to have altered the phenotype, driving genetic evolution in novel directions. Melanin patterns seem to be less affected by diet, but the intensity of melanization after moult is affected by social interactions during the moult and by raising birds in humid conditions. Hormonal manipulations can have dramatic effects on both the kinds of melanin produced (eumelanin or phaeomelanin) as well as the patterns they form. Differences between species in melanin patterns resemble differences produced by environmental manipulations, as well as those produced by simple modulations of parameters in computer simulations of pattern formation. While phenotypic plasticity is one way that genetic change in plumage patterns (and other traits) could be driven, there are others, including the appearance of major mutations and selection on standing variation whose distribution is not altered in the new environment. I consider some evidence for the different alternatives, and ask when they might lead to qualitatively different evolutionary outcomes.

Adaptation, Physiological↗
PubMed2005

Evolutionary animation: how do molecular phylogenies compare to Mayr's reconstruction of speciation patterns in the sea?

Ernst Mayr used the geography of closely related species in various stages of increasing divergence to "animate" the process of geographic, or allopatric, speciation. This approach was applied to a wide set of taxa, and a seminal paper by Mayr used it to explore speciation patterns in tropical sea urchins. Since then, taxonomic information in several of these genera has been augmented by detailed molecular phylogenies. We compare Mayr's animation with the phylogenies of eight sea urchin genera placed by Mayr into four speciation groups. True to Mayr's predictions, early-stage genera have on average lower species divergence and more polytypic species than genera in later stages. For six of these genera, we also have information about the evolution of the gamete recognition protein bindin, which is critical to reproductive isolation. These comparisons show that later-stage genera with many sympatric species tend to be those with rapid bindin evolution. By contrast, early-stage genera with few sympatric species are not necessarily earlier in the divergence process; they happen to be those with slow rates of bindin evolution. These results show that the rate of speciation in sea urchins does not only depend on the steady accumulation of genome divergence over time, but also on the rate of evolution of gamete recognition proteins. The animation method used by Mayr is generally supported by molecular phylogenies. However, the existence of multiple rates in the acquisition of reproductive isolation complicates placement of different genera in an evolutionary series.

Animals↗
PubMed1992

Cranial capacity evolution in Homo erectus and early Homo sapiens.

This paper investigates patterns of cranial capacity evolution in Homo erectus, early Homo sapiens, and in regional subsamples of H. erectus. Specifically, models explaining evolution of cranial capacity in these taxa are evaluated with statistical techniques developed for the analysis of time series data. Regression estimates of rates of evolution in cranial capacity are also obtained. A non-parametric test for trend suggests that cranial capacity in both H. erectus and early H. sapiens may increase significantly through time. Cranial capacity in an Asian subsample of H. erectus (comprised of Chinese and Indonesian specimens) increases significantly through time. Other subsamples of H. erectus (African, Chinese, and Indonesian) do not appear to increase significantly through time. Regression results generally corroborate results of the test for trend. Spatial and temporal variation may characterize evolution of cranial capacity in H. erectus. Different patterns of cranial capacity evolution may distinguish H. erectus from early H. sapiens.

Africa↗
PubMed1979

Model of effectively neutral mutations in which selective constraint is incorporated.

Based on the idea that selective neutrality is the limit when the selective disadvantage becomes indefinitely small, a model of neutral (and nearly neutral) mutations is proposed that assumes that the selection coefficient (s') against the mutant at various sites within a cistron (gene) follows a Gamma distribution; f(s') = alpha(beta)e(-alphas')s'(beta-1)/Gamma(beta), in which alpha = beta/ s' and s' is the mean selection coefficient against the mutants ( s' > 0; 1 [unk] beta > 0). The mutation rate for alleles whose selection coefficients s' lie in the range between 0 and 1/(2N(e)), in which N(e) is the effective population size, is termed the effectively neutral mutation rate (denoted by v(e)). Using the model of "infinite sites" in population genetics, formulas are derived giving the average heterozygosity ( h(e)) and evolutionary rate per generation (k(g)) in terms of mutant substitutions. It is shown that, with parameter values such as beta = 0.5 and s' = 0.001, the average heterozygosity increases much more slowly as N(e) increases, compared with the case in which a constant fraction of mutations are neutral. Furthermore, the rate of evolution per year (k(1)) becomes constant among various organisms, if the generation span (g) in years is inversely proportional to radicalN(e) among them and if the mutation rate per generation is constant. Also, it is shown that we have roughly k(g) = v(e). The situation becomes quite different if slightly advantageous mutations occur at a constant rate independent of environmental conditions. In this case, the evolutionary rate can become enormously higher in a species with a very large population size than in a species with a small population size, contrary to the observed pattern of evolution at the molecular level.

Journal Article↗
PubMed2002

Fixation of deleterious alleles, evolution and human aging.

Human aging, like everything else in biology, only makes sense in the context of evolution. There is substantial agreement among evolutionary geneticists regarding the evolutionary underpinnings of one of the main questions of human aging i.e. 'Why do we age?', which involves the higher rate of fixation of alleles that cause deleterious post-reproductive phenotypes vs. alleles that cause deleterious pre-reproductive phenotypes. Even higher rates of fixation of deleterious mutations are predicted to occur on population genetic grounds in two non-recombinant genomes in humans i.e. the Y chromosome, and the mitochondrial genome. The added burden of deleterious mutations on the Y may explain the reduced average lifespan of males vs. females. A high predicted fixation rate of the mitochondrial genome may explain its fast rate of evolution, and the high frequency of mitochondrial disease in relationship to this genomes' small size, and may underlie the transfer of mitochondrial genes over evolutionary time to the nucleus. Thus a molecular evolutionary model of aging which focuses on increased fixation rates of (1) nuclear alleles which only have deleterious effects post-reproduction, (2) deleterious genes on the Y chromosome, and (3) deleterious genes on the mitochondrial genome, makes multiple testable predictions about the causes and mechanisms of aging.

Aging↗
PubMed2004

Prognostic value of clinical and morphologic findings in short-term evolution of aortic intramural haematoma. Therapeutic implications.

AIMS: Intramural haematoma (IMH) forms part of the acute aortic syndrome presenting physiopathologic and evolutive patterns different from those of aortic dissection. The aim of this study was to determine the mortality and predictive factors of IMH in the first 3 months of evolution. METHODS AND RESULTS: Sixty-eight consecutive patients diagnosed of IMH (12 type A, 56 type B) were prospectively studied. Ten patients (eight type A, two type B) were surgically treated for clinical or haemodynamic evolution. Mortality rate was 19% (six type A and seven type B): five surgically treated (three type A, two type B) and eight medically treated (three type A, five type B). No relationship was observed between clinical variables and evolution. Maximum aortic diameter was greater in the group of patients who died (65.5+/-14.4 mm vs 46.0+/-7.6 mm; P<0.0001). Mortality rate in patients with aortic diameter >50 mm was 50% (P<0.0001). Significant periaortic bleeding was mortality-related (47%; P<0.005). Multivariate analysis showed only a significant relationship between mortality and maximum aortic diameter >50 mm (OR=11.33; P<0.005) and ascending aorta involvement (OR=11.18; P<0.05). CONCLUSION: Intramural haematoma mortality in the first 3 months of evolution is high (19%). Maximum aortic diameter >50 mm and ascending aorta involvement are predictive of early mortality.

Aged↗
PubMed1997

The probability of fixation in populations of changing size.

The rate of adaptive evolution of a population ultimately depends on the rate of incorporation of beneficial mutations. Even beneficial mutations may, however, be lost from a population since mutant individuals may, by chance, fail to reproduce. In this paper, we calculate the probability of fixation of beneficial mutations that occur in populations of changing size. We examine a number of demographic models, including a population whose size changes once, a population experiencing exponential growth or decline, one that is experiencing logistic growth or decline, and a population that fluctuates in size. The results are based on a branching process model but are shown to be approximate solutions to the diffusion equation describing changes in the probability of fixation over time. Using the diffusion equation, the probability of fixation of deleterious alleles can also be determined for populations that are changing in size. The results developed in this paper can be used to estimate the fixation flux, defined as the rate at which beneficial alleles fix within a population. The fixation flux measures the rate of adaptive evolution of a population and, as we shall see, depends strongly on changes that occur in population size.

Alleles↗
PubMed1992

Complete congruence between morphological and rbcL-based molecular phylogenies in birches and related species (Betulaceae).

Estimations of phylogenies from morphological and molecular data often show contrasting results. We compared morphological and molecular phylogenies in an ancient family of woody dicots, the Betulaceae (birch family). The phylogeny of the family was estimated from parsimony analysis of morphological characters in the genera Alnus, Betula, Carpinus, Corylus, Ostrya, and Ostryopsis and from parsimony and distance-matrix analyses of DNA sequences of the chloroplast gene encoding the large subunit of ribulose-1,5-biphosphate carboxylase (rbcL) in the genera Alnus, Betula, Carpinus, Corylus, and Ostrya and in two outgroups, Quercus and Liquidambar. The topologies obtained by the different methods were completely congruent, and bootstrapping strongly supported the division of the family Betulaceae into two major clades, Betuleae (Alnus and Betula) and Coryleae (other members). Only slightly more homoplasy was present in the rbcL sequence data set than in the morphological set. Relative-rate tests indicated that the Coryleae clade had a faster rate of rbcL evolution than did the Betuleae clade. Heterogeneity of rates of morphological evolution also paralleled those for rbcL.

Base Sequence↗
PubMed1989

Lipoprotein lipase and hepatic lipase mRNA tissue specific expression, developmental regulation, and evolution.

Lipoprotein lipase (LPL) and hepatic lipase (HL) enzyme activities were previously reported to be regulated during development, but the underlying molecular events are unknown. In addition, little is known about LPL evolution. We cloned and sequenced a complete mouse LPL cDNA. Comparison of sequences from mouse, human, bovine, and guinea pig cDNAs indicated that the rates of evolution of mouse, human, and bovine LPL are quite low, but guinea pig LPL has evolved several times faster than the others. 32P-Labeled mouse LPL and rat HL cDNAs were used to study lipase mRNA tissue distribution and developmental regulation in the rat. Northern gel analysis revealed the presence of a single 1.87 kb HL mRNA species in liver, but not in other tissues including adrenal and ovary. A single 4.0 kb LPL mRNA species was detected in epididymal fat, heart, psoas muscle, lactating mammary gland, adrenal, lung, and ovary, but not in adult kidney, liver, intestine, or brain. Quantitative slot-blot hybridization analysis demonstrated the following relative amounts of LPL mRNA in rat tissues: adipose, 100%; heart, 94%; adrenal, 6.6%; muscle, 3.8%; lung, 3.0%; kidney, 0%; adult liver, 0%. The same quantitative analysis was used to study lipase mRNA levels during development. There was little postnatal variation in LPL mRNA in adipose tissue; maximal levels were detected at the earliest time points studied for both inguinal and epididymal fat. In heart, however, LPL mRNA was detected at low levels 6 days before birth and increased 278-fold as the animals grew to adulthood.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1997

The Optimum Recombination Rate That Realizes the Fastest Evolution of a Novel Functional Combination of Many Genes

The effect of genetic recombination (or crossover) by sexual reproduction on the time until a novel set of genes performing a combined function appears, spreads, and becomes fixed is studied. First, we study a haploid finite population with many binary loci, in which only one sequence (called a functional gene set) is significantly advantageous over the others. The time for evolution of the function (Td) is defined as the mean number of generations until the advantageous sequence dominates in an initially random population. When the sequence diversity is initially stored sufficiently, the evolution time Td is roughly the product of the waiting time until the appearance of the advantageous sequence (creation time Tc) and the average number of appearances of the advantageous sequence from its absence until its fixation (destruction number Nd). Mutation and crossover reduce the former but enlarge the latter. If the mutation rate is low, there is an intermediate optimal rate of crossover that achieves the minimum Td. In contrast, if the mutation rate is sufficiently high, Td is smallest without crossover. Second, the breakdown of established functions by recurrent deleterious mutation in an infinite population is examined. The number of functional genes maintained decreases monotonically with the recurrent deleterious mutation rate. Thus in higher organisms having many functional sets of genes in the genome, the mutation rate must be kept very low to preserve them, and hence a high crossover rate made possible by sexual reproduction is important in accelerating the evolution of novel functional sets of genes. Implications of this long-term advantage of recombination in the maintenance of sexual reproduction in higher organisms are discussed.

Journal Article↗