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At least 469 records · Page 26Linked to original sources
PubMed1999

Lack of evolutionary stasis during alternating replication of an arbovirus in insect and mammalian cells.

The evolution of vesicular stomatitis virus (VSV) in a constant environment, consisting of either mammalian or insect cells, has been compared to the evolution of the same viral population in changing environments consisting in alternating passages in mammalian and insect cells. Fitness increases were observed in all cases. An initial fitness loss of VSV passaged in insect cells was noted when fitness was measured in BHK-21 cells, but this effect could be attributed to a difference of temperature during VSV replication at 37 degrees C in BHK-21 cells. Sequencing of nucleotides 1-4717 at the 3' end of the VSV genome (N, P, M and G genes) showed that at passage 80 the number of mutations accumulated during alternated passages (seven mutations) is similar or larger than that observed in populations evolving in a constant environment (two to four mutations). Our results indicate that insect and mammalian cells can constitute similar environments for viral replication. Thus, the slow rates of evolution observed in natural populations of arboviruses are not necessarily due to the need for the virus to compromise between adaptation to both arthropod and vertebrate cell types.

Adaptation, Physiological↗
PubMed2026

Comparative Analysis of Chloroplast Genomes Reveals Molecular Evolution and Phylogenetic Relationships in Fraxinus (Fraxinus mandshurica).

Fraxinus mandshurica (Manchurian ash) is an ecologically and economically valuable hardwood tree native to Northeast Asia, yet its genomic resources remain limited. We assembled its complete chloroplast (cp) genome (155,559 bp) using hybrid PacBio and Illumina sequencing and performed comparative, phylogenetic, and evolutionary analyses. The cp genome exhibits a typical quadripartite structure encoding 132 gene copies, comprising 114 unique genes (80 protein-coding, 30 tRNA, and 4 rRNA genes), with 18 genes duplicated in the inverted repeat (IR) regions. Simple sequence repeat analysis revealed dominance of mononucleotide A/T repeats. Phylogenetic analysis of 53 complete cp genomes strongly supported the monophyly of Oleaceae and resolved F. mandshurica as sister to the North American F. nigra, consistent with previously proposed Miocene intercontinental dispersal scenarios between East Asia and North America. Most protein-coding genes were under strong purifying selection (Ka/Ks << 1), whereas petB, rpl2, and several ndh genes showed elevated Ka/Ks values that are suggestive of altered selective constraint but are based on very few substitutions and are therefore not, on their own, evidence of positive selection. Nucleotide diversity (Pi) analysis identified 15 hypervariable intergenic spacers (mean Pi = 0.067), among which trnM-CAU-rps14, ndhJ-ndhK, and petL-petG represent promising candidate barcode regions requiring further validation. This study provides a high-quality, fully annotated cp genome of F. mandshurica and a valuable genomic resource for future phylogenetic, population genetic, and conservation studies of this important genus.

Fraxinus↗
PubMed2003

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.

BACKGROUND: Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. RESULTS: We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs). We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes) of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains). We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain) are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA) of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties indicates that, even with a gain penalty of 1 (equal weights assigned to a gain and a loss), the set of 572 genes assigned to LUCA might be nearly sufficient to sustain a functioning organism. Under this gain penalty value, the numbers of horizontal gene transfer and gene loss events are nearly identical. This result holds true for two alternative topologies of the species tree and even under random shuffling of the tree. Therefore, the results seem to be compatible with approximately equal likelihoods of HGT and gene loss in the evolution of prokaryotes. CONCLUSIONS: The notion that gene loss and HGT are major aspects of prokaryotic evolution was supported by quantitative analysis of the mapping of the phyletic patterns of COGs onto a hypothetical species tree. Algorithms were developed for constructing parsimonious evolutionary scenarios, which include gene loss and gain events, for orthologous gene sets, given a species tree. This analysis shows, contrary to expectations, that the number of predicted HGT events that occurred during the evolution of prokaryotes might be approximately the same as the number of gene losses. The approach to the reconstruction of evolutionary scenarios employed here is conservative with regard to the detection of HGT because only patterns of gene presence-absence in sequenced genomes are taken into account. In reality, horizontal transfer might have contributed to the evolution of many other genes also, which makes it a dominant force in prokaryotic evolution.

Algorithms↗
PubMed1997

Phylogeny and rates of molecular evolution of planktonic foraminifera: SSU rDNA sequences compared to the fossil record.

Planktonic foraminifera are marine protists, whose calcareous shells form oceanic sediments and are widely used for stratigraphic and paleoenvironmental analyses. The fossil record of planktonic foraminifera is compared here to their molecular phylogeny inferred from ribosomal DNA sequences. Eighteen partial SSU rDNA sequences from species representing all modern planktonic families (Globigerinidae, Hastigerinidae, Globorotaliidae, Candeinidae) were obtained and compared to seven sequences representing the major groups of benthic foraminifera. The phylogenetic analyses indicate a polyphyletic origin for the planktonic foraminifera. The Candeinidae, the Globorotaliidae, and the clade Globigerinidae + Hastigerinidae seem to have originated independently, at different epochs in the evolution of foraminifera. Inference of their relationships, however, is limited by substitution rates of heterogeneity. Rates of SSU rDNA evolution vary from 4.0 x 10(-9) substitutions/site/year in the Globigerinidae to less than 1.0 x 10(-9) substitutions/site/year in the Globorotaliidae. These variations may be related to different levels of adaptation to the planktonic mode of life. A clock-like evolution is observed among the Globigerinidae, for which molecular and paleontological data are congruent. Phylogeny of the Globorotaliidae is clearly biased by rapid rates of substitution in two species (G. truncatulinoides and G. menardii). Our study reveals differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera and demonstrates their effect on phylogenetic reconstructions.

Animals↗
PubMed2000

Molecular evolution in a multisite nearly neutral mutation model.

A simple nearly neutral mutation model of protein evolution was studied using computer simulation assuming a constant population size. In this model, a gene consists of a finite number of codons and there is no recombination within a gene. Each codon has two replacement and one silent sites. The fitness of a gene was determined multiplicatively by amino acids specified by codons (the independent multicodon model). Nucleotide diversity at replacement sites decreases as selection becomes stronger. A reduction of nucleotide diversity at silent sites also occurs as selection intensifies but the magnitude of the reduction is not a monotone function of the intensity of selection. The dispersion index is close to one. The average value of Tajima's and Fu and Li's statistics are negative and their absolute values increases as selection intensifies. However, their powers of detecting selection under the present model were not high unless the number of sites is large or mutation rate is high. The MK test was shown to detect intermediate selection fairly well. For comparison, the house-of-cards model was also investigated and its behavior was shown to be more sensitive to changes of population size than that of the independent multicodon model. The relevance of the present model for explaining protein evolution was discussed comparing its prediction and recent DNA data.

Amino Acid Substitution↗
PubMed1989

The rise and fall of Homo sapiens sapiens.

Human beings have broken the ecological 'law' that says that big, predatory animals are rare. Two crucial innovations in particular have enabled us to alter the planet to suit ourselves and thus permit unparalleled expansion: speech (which implies instant transmission of an open-ended range of conscious thoughts) and agriculture (which causes the world to produce more human food than unaided nature would do). However, natural selection has not equipped us with a long-term sense of self-preservation. Our population cannot continue to expand at its present rate for much longer, and the examples of many other species suggests that expansion can end in catastrophic collapse. Survival beyond the next century in a tolerable state seems most unlikely unless all religions and economies begin to take account of the facts of biology. This, if it occurred, would be a step in cultural evolution that would compare in import with the birth of agriculture.

Animals↗
PubMed1988

Comparative study of G- and C-banded chromosomes of five species of Microtidae: a chromosomal evolution analysis.

G-banded karyotypes were compared in the following species of Microtidae: Microtus nivalis, M. cabrerae, M. arvalis, and Arvicola sapidus. Previous observations on A. sapidus and A. terrestris were also incorporated in this study. The results show that Robertsonian translocations and pericentric inversions are common mechanisms involved in the karyotypic evolution of this group. Interspecific differences on the G-banding patterns were also analysed, and an attempt was made to establish a presumptive phylogenetic tree.

Animals↗
PubMed1999

Comparative biochemistry of CO2 fixation and the evolution of autotrophy.

Carbon dioxide fixation is a polyphyletic trait that has evolved in widely separated prokaryotic branches. The three principal CO2-assimilation pathways are (i) the reductive pentose-phosphate cycle, i.e. the Calvin-Benson cycle; (ii) the reductive citric acid (or Arnon) cycle; and (iii) the net synthesis of acetyl-CoA from CO/CO2, or Wood pathway. Sequence analysis and the comparative biochemistry of these routes suggest that all of them were shaped to a considerable extent by the evolutionary recruitment of enzymes. Molecular phylogenetic trees show that the Calvin-Benson cycle was a relatively late development in the (eu)bacterial branch, suggesting that some form(s) of carbon assimilation may have been operative before chlorophyll-based photosynthesis. On the other hand, the ample phylogenetic distribution of both the Arnon and the Wood pathways does not allow us to infer which one of them is older. However, different lines of evidence, including experimental reports on the NiS/FeS-mediated C-C bond formation from CO and CH3SH are used here to argue that the first CO2-fixation route may have been a semi-enzymatic Wood-like pathway.

Acetyl Coenzyme A↗
PubMedDate not supplied

Flow rate dependent ex vivo deheparinization with immobilized cationic ligand.

The Heparin Removal Device is a deheparinization system that provides a good alternative when adverse reaction to protamine is suspected or when a heparin coated device is employed for cardiopulmonary bypass. In a bovine model, after systemic heparinization with 300 IU/kg body wt, the authors investigated the rate of deheparinization using this plasmapheresis system that allows exposition of heparinized plasma to an immobilized cationic ligand. Blood was shunted through a heparin coated veno-venous circuit to the plasma separator at a flow rate of 500 ml/min (n = 3, body wt 68 +/- 4 kg) or 1,000 ml/min (n = 3, body wt 57 +/- 4 kg). All plasma separators remained patent without any failure of the devices. Blood samples were drawn at regular intervals for coagulation parameters. The evolution of the activated coagulation time (ACT) was measured during the first 60 min of the deheparinization procedure, and results were compared with spontaneous evolution in a control group (n = 3, body wt 73 +/- 5 kg) without reversal of heparinization. After heparin administration, mean ACT was longer than 1,000 sec in the three groups. Fifteen minutes later it was still > 1,000 sec in the control group, whereas it was 427 +/- 8 sec in the slow flow group (500 ml/min) and 340 +/- 26 sec in the high flow group (1,000 ml/min). At 30 min it was 1,000, 367 +/- 26, and 200 +/- 24 sec, respectively, in the three groups. A regression curve was calculated for each group, and areas under the curves were compared. Ex vivo deheparinization was efficient in normalization of ACT, but removal of heparin appeared to be flow rate dependent. Increased blood flow from 500 to 1,000 ml/min across the deheparinization system resulted in significant acceleration of ACT normalization (p < 0.05).

Animals↗
PubMedDate not supplied

The evolution of postoperative ileus after laparoscopic cholecystectomy. A comparative study with conventional cholecystectomy and sympathetic blockade treatment.

Our study is prompted by the arrival of laparoscopic cholecystectomy in connection with the evolution of postoperative ileus (PI) and by its avoidance of the intraabdominal handling implied in conventional cholecystectomy. With this aim a prospective, controlled, randomized, and blind clinical trial was designed using 100 patients divided into five groups (n = 20): I, conventional cholecystectomy (CC): II, CC+injection of 20 ml bupivacaine 0.5% into the mesentery root; III, CC + 7.5 mg propranolol i.v. and 0.5 mg neostigmine s.c., postoperatively until the first defecation; IV, II+III; and V, laparoscopic cholecystectomy. The shortest period of PI was observed in group V. This period increases notably in group IV (53 h), group II (72 h), and group III (84 h) relative to the control group with (89 h). This reduction in PI time runs parallel with an improvement in the patient's general state of well-being. We concluded that after laparoscopic cholecystectomy PI is nonexistent. Furthermore, this study confirms the correlation between the avoidance of intraabdominal manipulation and the evolution of postoperative ileus.

Autonomic Nerve Block↗
PubMedDate not supplied

Trends in comparative genetics and their potential impacts on wheat and barley research.

We review some general points about comparative mapping, the evolution of gene families and recent advances in the understanding of angiosperm phylogeny. These are considered in relation to studies of large-genome cereals, particularly barley (Hordeum vulgare) and wheat (Triticum aestivum), with reference to methods of gene isolation. The relative merits of direct map-based cloning in barley and wheat, utilization of the smaller genome of rice (Oryza sativa) and gene homology methods that utilize information from model species such as Arabidopsis thaliana are briefly discussed.

Chromosome Mapping↗
PubMed2000

Evolution of the basal ganglia: new perspectives through a comparative approach.

The basal ganglia (BG) have received much attention during the last 3 decades mainly because of their clinical relevance. Our understanding of their structure, organisation and function in terms of chemoarchitecture, compartmentalisation, connections and receptor localisation has increased equally. Most of the research has been focused on the mammalian BG, but a considerable number of studies have been carried out in nonmammalian vertebrates, in particular reptiles and birds. The BG of the latter 2 classes of vertebrates, which together with mammals constitute the amniotic vertebrates, have been thoroughly studied by means of tract-tracing and immunohistochemical techniques. The terminology used for amniotic BG structures has frequently been adopted to indicate putative corresponding structures in the brain of anamniotes, i.e. amphibians and fishes, but data for such a comparison were, until recently, almost totally lacking. It has been proposed several times that the occurrence of well developed BG structures probably constitutes a landmark in the anamniote-amniote transition. However, our recent studies of connections, chemoarchitecture and development of the basal forebrain of amphibians have revealed that tetrapod vertebrates share a common pattern of BG organisation. This pattern includes the existence of dorsal and ventral striatopallidal systems, reciprocal connections between the striatopallidal complex and the diencephalic and mesencephalic basal plate (striatonigral and nigrostriatal projections), and descending pathways from the striatopallidal system to the midbrain tectum and reticular formation. The connectional similarities are paralleled by similarities in the distribution of chemical markers of striatal and pallidal structures such as dopamine, substance P and enkephalin, as well as by similarities in development and expression of homeobox genes. On the other hand, a major evolutionary trend is the progressive involvement of the cortex in the processing of the thalamic sensory information relayed to the BG of tetrapods. By using the comparative approach, new insights have been gained with respect to certain features of the BG of vertebrates in general, such as the segmental organisation of the midbrain dopaminergic cell groups, the occurrence of large numbers of dopaminergic cell bodies within the telencephalon itself and the variability in, among others, connectivity and chemoarchitecture. However, the intriguing question whether the basal forebrain organisation of nontetrapods differs essentially from that observed in tetrapods still needs to be answered.

Amphibians↗
PubMed1992

Pineal "synaptic" ribbons evolution over a 24 hour period during two different photoluminous seasons, a comparative and statistical analysis.

A comparative statistical analysis of "synaptic ribbons" evolution over a 24 hour period during two different photoluminous seasons (September, and winter) is carried out. Seventy male rats were used. Statistical analysis involved the Kolmogorov-Smirnov test, variance analysis, the Student t-test and Pearson's correlation test. The results show that "synaptic ribbons" evolve during the circadian phase and through two different seasons, with a clear and marked influence of point-time (p < 0.0001) and season (p < 0.0001).

Analysis of Variance↗
PubMed2000

Variations on a theme: flower development and evolution.

A recent study, comparing the maize SILKY1 gene to its well-characterized homolog APETALA3 from Arabidopsis, has provided some of the first evidence pointing to conservation of homeotic gene function between monocots and dicots.

Arabidopsis↗
PubMed2002

Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man.

The major histocompatibility complex (MHC) genomic region is composed of a group of linked genes involved functionally with the adaptive and innate immune systems. The class I and class II genes are intrinsic features of the MHC and have been found in all the jawed vertebrates studied so far. The MHC genomic regions of the human and the chicken (B locus) have been fully sequenced and mapped, and the mouse MHC sequence is almost finished. Information on the MHC genomic structures (size, complexity, genic and intergenic composition and organization, gene order and number) of other vertebrates is largely limited or nonexistent. Therefore, we are mapping, sequencing and analyzing the MHC genomic regions of different human haplotypes and at least eight nonhuman species. Here, we review our progress with these sequences and compare the human MHC structure with that of the nonhuman primates (chimpanzee and rhesus macaque), other mammals (pigs, mice and rats) and nonmammalian vertebrates such as birds (chicken and quail), bony fish (medaka, pufferfish and zebrafish) and cartilaginous fish (nurse shark). This comparison reveals a complex MHC structure for mammals and a relatively simpler design for nonmammalian animals with a hypothetical prototypic structure for the shark. In the mammalian MHC, there are two to five different class I duplication blocks embedded within a framework of conserved nonclass I and/or nonclass II genes. With a few exceptions, the class I framework genes are absent from the MHC of birds, bony fish and sharks. Comparative genomics of the MHC reveal a highly plastic region with major structural differences between the mammalian and nonmammalian vertebrates. Additional genomic data are needed on animals of the reptilia, crocodilia and marsupial classes to find the origins of the class I framework genes and examples of structures that may be intermediate between the simple and complex MHC organizations of birds and mammals, respectively.

Animals↗
PubMed1985

Evolution of antibody structure and effector functions: comparative hemolytic activities of monomeric and tetrameric IgM from rainbow trout, Salmo gairdnerii.

Monomeric and tetrameric IgM anti-haptin antibodies isolated from the sera of rainbow trout (S. gairdnerii) by immunoaffinity chromatography were compared both immunochemically and with regard to their functional abilities to lyse haptenated trout erythrocytes in the presence of trout complement. The two populations had similar binding affinities for hapten and apparently identical L chains, but differed in H chain peptide maps and immunoreactivity with rabbit anti-trout H chain serum. These differences could not be attributed to J-chain. The abilities of the two antibody subpopulations to activate C to lyse haptenated trout erythrocytes also differed dramatically. Such functional differences are not simply explained by the greater avidity of the tetrameric form since preliminary studies show that the monomeric form of trout IgM activates C via an alternative pathway mechanism while the tetrameric form activates both classical and alternative pathway mechanisms. Results suggest divergent evolution of antibody structures involved in the familiar effector functions (C activation, transport, etc.).

Animals↗