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PubMed1997

Evolution of the structural repertoire of the human V(H) and Vkappa germline genes.

Variable genes of human Ig are classified in families and clans which reflect the early events of gene duplication in the evolution of the locus. This organization in multiple copies of variable genes plus the somatic processes of recombination and hypermutation allows the immune system to generate an antibody repertoire of great diversity. At present the role that somatic processes play in the generation of that diversity is understood with some detail. It is a matter of hard controversy, however, which selective pressures have shaped the evolution of the germline genes of Ig and, consequently, what the role of this germline component in the generation of the antibody diversity actually is. Previous studies of our group have showed that the structural repertoire of Ig-determined by the canonical structures-is an important factor to determine the recognition properties of the antibodies. Complete knowledge of the sequences of the human V(H) and Vkappa loci is available to analyze the evolution of the structural repertoire of these loci. Two phylogenetic gene trees were built from the functional germline genes and the evolution of the structural repertoire was studied. We report that for both loci the canonical structures are not randomly distributed within the tree. Conversely, it is shown that the evolution of the structural repertoire follows a gradual process of diversification. This indicates a correlation between the evolution of genes and the structural repertoire, although important differences are found in the patterns of evolution of the structural repertoire between V(H) and Vkappa. Based on those results we propose a primordial structural repertoire for V(H) and Vkappa. The general properties and an outline of the three-dimensional structure of this primordial repertoire are given.

Amino Acid Sequence↗

PubMed1981

On the evolution of neurochemical transmission.

A discussion of the evolution of neurochemical transmission is divided into three main topics: evolution of biochemical signalling devices, evolution of neurotransmitter substances, and evolution of signal meaning. Models of signalling devices are developed from a primitive chemoceptive process through open and closed loop communications to a neuronal communications network and to its development into a symbolic logic exchange. The evolution of neurotransmitter substances is extrapolated from experimental evidence which has been obtained under primitive earth atmosphere conditions. Examples from comparative biology suggest that the evolution of transmitter use was not unidirectional and that purine derivatives may well have been the primordial transmitter substances. The classical neurotransmitters, such as acetylcholine and norepinephrine have a limited information content in their molecular structure, whereas inherent message content of peptidergic transmitters is potentially significant. If there are mnemotypic genes, they may be expressed as informational macromolecules which specify behavioral patterns. Such information transfer would represent a second order of neurochemical transmission and its evolution would be closely coupled to that of molecules which contain a universal meaning.

Acetylcholine↗

PubMed1998

Viral genetic evolution in macaques infected with molecularly cloned simian immunodeficiency virus correlates with the extent of persistent viremia.

Genetic evolution of the simian immunodeficiency virus (SIV) envelope glycoprotein was evaluated in a group of six macaques (Macaca nemestrina) infected with the molecularly cloned, moderately pathogenic SIVsm62d. The extent of envelope evolution was subsequently evaluated within the context of the individual pattern of viremia and disease outcome. Two macaques in this cohort developed AIDS by 1.5 years postinoculation (progressors), whereas the remaining four macaques remained asymptomatic (nonprogressors). Compared with the nonprogressor macaques, the two progressor macaques exhibited higher persistent plasma viremia, higher homologous neutralizing antibody titers, and more extensive mutation and evolution in the V1 region of envelope. Although clearly distinct in each of these parameters from the progressors, the four nonprogressors exhibited more individual variability with respect to the extent of persistent viremia and genetic evolution of the V1 region of envelope. The extent of V1 envelope varied from no apparent V1 evolution in a macaque with good viral containment to extensive evolution in one macaque with persistent viremia. This study underscores the critical role of persistent replication in the genetic evolution of SIV.

Amino Acid Sequence↗

PubMed2000

The development and evolution of exaggerated morphologies in insects.

We discuss a framework for studying the evolution of morphology in insects, based on the concepts of "phenotypic plasticity" and "reaction norms." We illustrate this approach with the evolution of some of the most extreme morphologies in insects: exaggerated, sexually selected male ornaments and weapons, and elaborate social insect soldier castes. Most of these traits scale with body size, and these scaling relationships are often nonlinear. We argue that scaling relationships are best viewed as reaction norms, and that the evolution of exaggerated morphological traits results from genetic changes in the slope and/or shape of these scaling relationships. After reviewing literature on sexually selected and caste-specific structures, we suggest two possible routes to the evolution of exaggerated trait dimensions: (a) the evolution of steeper scaling relationship slopes and (b) the evolution of sigmoid or discontinuous scaling relationship shapes. We discuss evolutionary implications of these two routes to exaggeration and suggest why so many of the most exaggerated insect structures scale nonlinearly with body size. Finally, we review literature on insect development to provide a comprehensive picture of how scaling relationships arise and to suggest how they may be modified through evolution.

Animals↗

PubMed2000

Genetic and developmental bases of serial homology in vertebrate limb evolution.

Two sets of paired appendages are a characteristic feature of the body plan of jawed vertebrates. While the fossil record provides a good morphological description of limb evolution, the molecular mechanisms involved in this process are only now beginning to be understood. It is likely that the genes essential for limb development in modern vertebrates were also important players during limb evolution. In recent years, genes from a number of gene families have been described that play important roles both in limb induction and in later patterning processes. These advances facilitate inquiries into several important aspects of limb evolution such as their origin, position along the body axis, number and identity. Integrating paleontological, developmental and genetic data, we propose models to explain the evolution of paired appendages in vertebrates. Whereas previous syntheses have tended to focus on the roles of genes from a single gene family, most notably Hox genes, we emphasize the importance of considering the interactions among multiple genes from different gene families for understanding the evolution of complex developmental systems. Our models, which underscore the roles of gene duplication and regulatory 'tinkering', provide a conceptual framework for elucidating the evolution of serially homologous structures in general, and thus contribute to the burgeoning field seeking to uncover the genetic and developmental bases of evolution.

Animals↗

PubMed2025

Experimental evolution of a pathogen confronted with innate immune memory increases variation in virulence.

Understanding the drivers and mechanisms of virulence evolution is still a major goal of evolutionary biologists and epidemiologists. Theory predicts that the way virulence evolves depends on the balance between the benefits and costs it provides to pathogen fitness. Additionally, host responses to infections, such as resistance or tolerance, play a critical role in shaping virulence evolution. But, while the evolution of pathogens has been traditionally studied under the selection pressure of host adaptive immunity, less is known about their evolution when confronted to simpler and less effective forms of immunity such as immune priming. In this study, we used a well-established insect model for immune priming - red flour beetles and their bacterial pathogen Bacillus thuringiensis tenebrionis - to test how this form of innate immune memory drives the pathogen evolution. Through controlled experimental evolution of the pathogen in primed versus non-primed hosts, we found no change in average virulence after eight selection cycles in primed host. Nonetheless, we observed a notable rise in the variability of virulence, defined as the ability to kill hosts, among independent pathogen lines that evolved in primed hosts, and the bacteria were unable to develop resistance to host priming. Whole genome sequencing revealed increased activity in the bacterial mobilome (prophages and plasmids). Expression of the Cry toxin - a well-known virulence factor - was linked to evolved differences in copy number variation of the cry-carrying plasmid, though this did not correlate directly with virulence. These findings highlight that innate immune memory can drive variability in pathogen traits, which may favor adaptation to variable environments. This underscores the need to consider pathogen evolution in response to innate immune memory when applying these mechanisms in medicine, aquaculture, pest control, and insect mass production.

Animals↗

PubMed2000

Genome evolution in polyploids.

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

Evolution, Molecular↗

PubMed1985

The myelodysplastic syndromes: different evolution patterns based on sequential morphological and cytogenetic investigations.

Serial morphological and cytogenetic investigations were performed in 46 patients with the myelodysplastic syndrome (MDS). Twenty-one patients (45.5%) progressed to AML (greater than 30% blasts in bone marrow smears). Based on sequential determinations of percentages of bone marrow blasts, three patterns of evolution were observed in MDS. Patients with evolution pattern A (48%) had an apparently stable disease with minimal or no increase in bone marrow blasts. Exceptionally they developed new or additional chromosomal anomalies during the course of their disease. Cases in this group, who showed no abnormal localization of immature myeloid precursors (ALIP) at time of diagnosis experienced prolonged survival (median: 43 months), while ALIP positive patients had shorter survival times (median: 14 months), with high probability of early death from infections and/or bleeding problems. Patients with evolution pattern B (28%) initially had a morphologically stable disease, comparable to cases with evolution pattern A, but showed an abrupt shift from MDS to AML. Most of these patients (82%) were ALIP positive and a substantial proportion (46%) showed karyotype anomalies at diagnosis. The abrupt shift to AML in these patients was frequently (61.5%) associated with additional cytogenetic anomalies. Patients with evolution pattern C (24%) showed a gradual increase in bone marrow blasts. The majority of these cases (8/11) ultimately developed acute myeloid leukaemia (gradual progression to AML), whereas some patients (3/11) died from infections and/or haemorrhagic complications before they had reached the level of clinical AML. All of these patients were ALIP positive at diagnosis and no additional cytogenetic alterations occurred during evolution. Acquisition of new karyotypic anomalies during the course of MDS was almost invariably associated with abrupt shift to AML. From this retrospective study we conclude that evolution in MDS shows two important aspects, which seem to be preponderant in determining the course and outcome of the disease: one is the proliferative capacity and resulting growth advantage of the neoplastic clone over normal haematopoiesis, as measured by increasing percentages of bone marrow blasts in sequential aspirates; the other one is instability of the clone. Unstable clones have a high propensity to further intraclonal changes; they are expressed morphologically by the abrupt increase in bone marrow blasts and cytogenetically by the acquisition of new or additional karyotype anomalies.(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗

PubMed1996

Significance of cytogenetic clonal evolution in chronic myelogenous leukemia.

PURPOSE: To describe the incidence and significance of clonal evolution patterns. PATIENTS AND METHODS: We analyzed 264 patients with Philadelphia chromosome (Ph)-positive chronic myelogenous leukemia (CML) who developed clonal evolution between 1967 and 1993. RESULTS: The median survival time following clonal evolution was 19 months. Factors associated with worse survival (P < .01) were as follows: chromosome 17 abnormality or chromosomal translocations other than Ph, high percentage of abnormal metaphases, longer time to clonal evolution, and presence of other accelerated-phase features. A recursive partitioning technique (CART) identified different risk groups. The best group (37 patients; no chromosome 17 abnormality, abnormal metaphases < 16%, and interval to clonal evolution < or = 24 months) had an estimated median survival time of 54 months. The worst two groups included 27 patients with chromosome 17 abnormalities and > or = 36% abnormal metaphases (estimated median survival time, 6 months), and 22 patients with other accelerated features and > or = 16% abnormal metaphases (estimated median survival time, 7 months). The intermediate group had an estimated median survival time that ranged from 13 to 24 months. Prior interferon therapy evaluated within risk groups showed a significant survival advantage only in the intermediate-risk group. A multivariate analysis showed similar results, and identified the following independent poor prognostic variables: chromosome 17 abnormality, percentage of abnormal metaphases (cutoff, 24%), longer time to clonal evolution (cutoff, 24 months), other accelerated-phase features, and no prior interferon therapy. Patients with none, one, two, three, or more of the first four features had median survivals times of 51, 24, 14, and 7 months, respectively. CONCLUSION: The prognostic significance of clonal evolution in CML is not uniform and is related to the specific abnormality, time to its development, its predominance in metaphases, and the presence of other accelerated features, and it may be modified by specific therapies.

Bone Marrow Transplantation↗

PubMed1976

Effect of hydrogen ion buffers on photosynthetic oxygen evolution in the blue-green alga, Agmenellum quadruplicatum.

The photosynthetic oxygen evolution capacity of Agmenelium quadruplication suspended in four hydrogen ion buffers (pH 7.4, 0.05 M) and its synthetic marine growth medium was measured with an oxygen electrode. High rates of oxygen evolution were obtained in the growth medium and N-tris(hydroxymethyl)-methylglycine (Tricine) buffer. Compared to oxygen evolution in the growth medium, rates in phosphate buffer and N-tris(hydroxymethyl)-2-aminoethanesulphonic acid (TES) buffer were sometimes reduced by up to 30% and rates in tris (hydroxymethyl) amino-methane (Tris) were consistently reduced by 50%. An incubation-rinsing procedure caused inhibition of oxygen evolution in TES, phosphate, and Tris by 50 to 100%. Oxygen evolution could be restored to cells rinsed in TES or phosphate by resuspension in growth medium or in buffer plus magnesium and calcium ions. Bezoquinone-supported oxygen evolution was not affected by rinsing with any buffer tested except Tris. Ferricyanide was photoreduced at a low rate by cells rinsed in Tes but at a high rate in TES plus magnesium and calcium ions. We interpreted our results to mean that, in Agmenellum quadruplicatum, inhibition of photosynthetic oxygen evolution by Tris occurs at the level of photosystem 2 while the effects of TES and phosphate are on electron-transport occurring after the rate-limiting reaction.

Buffers↗

PubMed1993

[Changes in the pancreatic and respiratory functions in cystic fibrosis. The influence of the time of the evolution of the disease].

BACKGROUND: Cystic fibrosis is the most frequent congenital disease in Caucasian and is transmitted by recessive autosomic inheritance. It is characterized by affection of different glands of exocrine secretion, particularly the pancreas and the lung. The aim of this study was to analyze the degree of alteration of pulmonary and pancreatic exocrine function in a group of patients with cystic fibrosis in relation to the time of disease evolution. METHODS: Twenty-one patients between 9 and 31 years of age were studied; 11 with an evolution of lower than or equal to 158 months and 10 with an evolution of higher than 158 months (median of the total patients). To study pancreatic exocrine function the BT-PABA test immunoreactive serum trypsin test were used. To evaluate respiratory function FEV1, FVC, FEV1/FVC ratio and PaO2 were used. RESULTS: The results obtained demonstrated that in the group with a lower time of evolution the diagnosis had been carried out at earlier ages (17 +/- 17 months versus 84 +/- 60 months; p = 0.002) and presented a significantly more altered pancreatic exocrine function (BT-PABA: 13 +/- 12% versus 35 +/- 23%; p = 0.013). However, respiratory function was altered in the group with longer time of evolution (FEV1: 68 +/- 20% versus 36 +/- 23%; p = 0.003; FVC: 74 +/- 9 versus 52 +/- 25%; p = 0.013; FEV1/FEV: 77 +/- 19 versus 50 +/- 9%; p < 0.001; PaO2: 84 +/- 16 versus 58 +/- 11%; p < 0.001). CONCLUSIONS: Pancreatic exocrine function is most intensely affected in patients diagnosed with cystic fibrosis at earlier and with shorter times of evolution while patients who have the longest time of evolution and who were diagnosed later in life presented greater changes in respiratory function.

Adolescent↗

PubMed1998

[Prostate cancer in Isère and Tarn (France) between 1985 and 1995: evolution of therapeutic indications].

The objective is to describe the evolution of therapeutic practices of prostate carcinoma in the departements of Tarn and Isère in France for the 1985-1995 period. This retrospective study is based on patient folders for whom a prostate carcinoma has been diagnosed between 1985 and 1995. A sample of 871 patients have been included after randomisation stratified on the year and the department of the diagnostic in the files of the cancer registries of Tarn and Isère. Therapeutic practices of the prostate cancer have significantly evolved between 1985 and 1989. The rate of radical prostatectomies increased from 1986 whereas the rate of radiotherapy remained stable. This evolution has been made to the detriment of non curative treatments with the decrease of the rate of hormonotherapies. This is due to the important development of diagnostic technics which led to an earlier diagnostic of these cancers; but, the evolution of therapeutic technics and particularly of the radical prostatectomy allowed the evolution of indications for the treatment of this cancer, with the increase of the rate of radical prostatectomies and the decrease of the rate of radiotherapies at the same stage of disease evolution. For 1990 to 1995, there was no major evolution. Some indications are discussed in this disease touching old man, with a slow evolution.

Adenocarcinoma↗

PubMed2025

Phylogenomics Unveils the Complex Evolution of Retroviruses in Birds.

The rise of birds represents one of the major evolutionary transitions in the history of life. Yet, much remains obscure about the origins and diversification of viruses in birds. Endogenous retroviruses (ERVs), relics of past retroviral infections, provide molecular fossils for interrogating the evolution and ecology of retroviruses. Here, we perform phylogenomic mining of ERVs within the genomes of 758 bird species and identify more than 470,000 ERVs, revealing a highly diverse and complex retrovirus repertoire in birds. These ERVs greatly expand the diversity of retroviruses in birds, indicating that exogenous retroviruses characterized in birds to date are highly underestimated. The evolution of retroviruses in birds is shaped by both coevolution and cross-species transmission. Tens of retrovirus lineages originated during the early evolution of birds, four of which contribute to more than 90% of complete ERVs in birds. We also observe recent ERV activity across the bird phylogeny (particularly in Passeriformes). Moreover, we find that ERVs can mediate genome rearrangements, potentially facilitating the genome evolution of birds. Many bird retroviruses recruited genes of cellular provenience, which might drive the evolution of the genome complexity of retroviruses. Together, these results unveil a diverse and complex retrovirosphere in birds and provide insights into the intricate evolution of retrovirus-bird interaction.

Animals↗

PubMed2000

Evolution of vertebrate immunoglobulin variable gene segments.

Evolution of Ig V gene segments are generally characterized by (a) evolution by "the birth and death process" and (b) diversifying selection. However, the detailed evolutionary pattern of V gene segments varies among species due to the fact that the humoral immune system itself has changed during vertebrate evolution. The change in somatic diversification system coupled with the change in lymphocyte development has imposed a significant impact on the evolution of Ig genes. In order to understand the evolution of immunological genes it is important to view it in the context of the evolution of the entire immune system itself.

Animals↗

PubMed1993

Characterization of the cow stomach lysozyme genes: repetitive DNA and concerted evolution.

Cow stomach lysozyme genes have evolved in a mosaic pattern. The majority of the intronic and flanking sequences show an amount of sequence difference consistent with divergent evolution since duplication of the genes 40-50 million years ago. In contrast, exons 1, 2, and 4 and immediately adjacent intronic sequences differ little between genes and show evidence of recent concerted evolution. Exon 3 appears to be evolving divergently. The three characterized genes vary from 5.6 to 7.9 kilobases in length. Different distributions of repetitive DNA are found in each gene, which accounts for the majority of length differences between genes. The different distributions of repetitive DNA in each gene suggest the repetitive elements were inserted into each gene after the duplications that give rise to these three genes and provide additional support for divergent evolution for the majority of each gene. The observation that intronic and flanking sequences are evolving divergently suggests that the concerted evolution events involved in homogenizing the coding regions of lysozyme genes involve only one exon at a time. This model of concerted evolution would allow the shuffling of exon-sized pieces of information between genes, a phenomenon that may have aided in the early adaptive evolution of stomach lysozyme.

Animals↗

PubMed1981

Simulation of protein evolution by random fixation of allowed codons.

Computer simulation of protein evolution is based on a simple model consisting of random fixation of allowed codons (RFAC). Random replacement of single nucleotides occurs in a DNA sequence. If this results in any of the synonomous codons for allowed amino acids the mutation is fixed, if not, there is no change in the DNA and the cycle is repeated. Multiple fixations at the same nucleotide site, back mutations, degenerate fixations and coincidental identity of amino acids all occur. RFAC simulation begins with a single DNA sequence and follows a phylogeny based on the fossil record. The rate of fixation at the level of DNA is constant. The model upon which RFAC simulation is based is the same as the neutral theory of molecular evolution. The simulation is therefore a test of this theory. The results of simulated and real evolution are compared for fibrinopeptides A in mammals and cytochromes C and hemoglobin alpha and beta chains in vertebrates. In each case the allowed variation at each site has been set equal to that observed, twice that observed and all protein amino acids. Rates of fixation vary from 2.4 X 10(-10) to 10(-8) accepted nucleotide fixations per codon per year. There is some, although never excellent, agreement between real and simulated evolution, the better fits are obtained in the cases of fibrinopeptides A and cytochromes C. The major source of discrepancy between real evolution and simulation is irregularities in the rates of real evolution. RFAC simulation is compared with the random evolutionary hit (REH) model, augmented maximum parsimony and the accepted point mutations (PAM) approach.

Amino Acids↗

PubMed1991

Elements in microbial evolution.

Spontaneous mutation, selection, and isolation are key elements in biological evolution. Molecular genetic approaches reveal a multitude of different mechanisms by which spontaneous mutants arise. Many of these mechanisms depend on enzymes, which often do not act fully at random on the DNA, although a large number of sites of action can be observed. Of particular interest in this respect are DNA rearrangement processes, e.g., by transposition and by site-specific recombination systems. The development of gene functions has thus to be seen as the result of both DNA rearrangement processes and sequence alterations brought about by nucleotide substitutions and small local deletions, insertions, and duplications. Prokaryotic microorganisms are particularly appropriate for studying the effects of spontaneous mutation and thus microbial evolution, as they have haploid genomes, so that genetic alterations become rapidly apparent phenotypically. In addition, bacteria and their viruses and plasmids have relatively small genomes and short generation times, which also facilitate research on evolutionary processes. Besides the strategy of development of gene functions in the vertical transmission of genomes from generation to generation, the acquisition of short DNA segments from other organisms appears to be an important strategy in microbial evolution. In this process of horizontal evolution natural vector DNA molecules are often involved. Because of acquisition barriers, the acquisition strategy works best for relatively small DNA segments, hence at the level of domains, single genes, or at most operons. Among the many enzymes and functional systems involved in vertical and horizontal microbial evolution, some may serve primarily for essential life functions in each individual and only secondarily contribute to evolution.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1996

A theory of evolution that includes prebiotic self-organization and episodic species formation.

A theory has been proposed that encompasses pre-replication changes in RNA synthesis and non-gradual variant formation, in addition to competitive replication. Using a fundamental theorem of natural selection and maximum principle scaled to nucleotide condensation, evolution in vitro was demonstrated to maximally damp both kinetic and thermodynamic forces driving this reaction, from its pre-replication stage. This led to the finding that evolution follows a path of least action. These principles form the framework for a general theory of evolution, whose scope extends beyond evolution modeled by synthesis of non-interacting RNA molecules. It applies, in particular, to standard processes, such as competitive crystallization. In calculations simulating de novo formation of self-replicating RNA molecules in the Qbeta replicase system, spontaneous changes in strand secondary structure promoted the transition from random copolymerization to template-directed polymerization. This finding indicates selection preceded genome self-propagation. Non-gradual species formation was attributed to the presence of heterogeneous thermodynamic forces. Growth unconstrained by competition follows mutation to a variant able to utilize a free energy source alien to its progenitors. Evolution in a heterogeneous system can, therefore, exhibit discontinuous rates of species formation and spawn new species populations. Natural selection among competing self-propagators thus gives way to a principle of wider scope stating that evolution optimally damps the physicochemical forces causing change within an evolving system.

Biological Evolution↗