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PubMed2003

Phylogenetically nested comparisons for testing correlates of species richness: a simulation study of continuous variables.

Explaining the uneven distribution of species among lineages is one of the oldest questions in evolution. Proposed correlations between biological traits and species diversity are routinely tested by making comparisons between phylogenetic sister clades. Several recent studies have used nested sister-clade comparisons to test hypotheses linking continuously varying traits, such as body size, with diversity. Evaluating the findings of these studies is complicated because they differ in the index of species richness difference used, the way in which trait differences were treated, and the statistical tests employed. In this paper, we use simulations to compare the performance of four species richness indices, two choices about the branch lengths used to estimate trait values for internal nodes and two statistical tests under a range of models of clade growth and character evolution. All four indices returned appropriate Type I error rates when the assumptions of the method were met and when branch lengths were set proportional to time. Only two of the indices were robust to the different evolutionary models and to different choices of branch lengths and statistical tests. These robust indices had comparable power under one nonnull scenario. Regression through the origin was consistently more powerful than the t-test, and the choice of branch lengths exerts a strong effect on both the validity and power. In the light of our simulations, we re-evaluate the findings of those who have previously used nested comparisons in the context of species richness. We provide a set of simple guidelines to maximize the performance of phylogenetically nested comparisons in tests of putative correlates of species richness.

Phylogeny↗

PubMed1986

Marketing continuing education: a staff process.

State institutions of higher education are continually challenged to efficiently and effectively maximize every dollar spent. One means of realizing this goal is the development of an overall strategy to improve the marketing of continuing education programs. Because limited funds precluded hiring an individual to oversee marketing activities, one continuing education operation formed a steering committee of interested staff members to coordinate and expand its marketing efforts. This paper describes the evolution of staff involvement in an ongoing marketing process at a multidisciplinary center for continuing education and identifies some of the benefits of that involvement.

Academic Medical Centers↗

PubMed1997

The public health threat of emerging viral disease.

"Emerging diseases" are those that either have newly appeared in the population or are rapidly increasing their incidence or expanding their geographic range. Emerging viruses usually have identifiable sources, often existing viruses of animals or humans that have been given opportunities to infect new host populations ("viral traffic"). Environmental and social changes, frequently the result of human activities, can accelerate viral traffic, with consequent increases in disease emergence. Host factors, including nutrition, have often received less attention in the past but are of considerable importance. These factors, combined with the ongoing evolution of viral and microbial variants, make it likely that emerging infections will continue to appear and probably increase, emphasizing the need for effective surveillance.

Animals↗

PubMed2002

The energy-conserving and energy-dissipating processes in mitochondria isolated from wild type and nonripening tomato fruits during development on the plant.

Bioenergetics of tomato (Lycopersicon esculentum) development on the plant was followed from the early growing stage to senescence in wild type (climacteric) and nonripening mutant (nor, non-climacteric) fruits. Fruit development was expressed in terms of evolution of chlorophyll a content allowing the assessment of a continuous time-course in both cultivars. Measured parameters: the cytochrome pathway-dependent respiration, i.e., the ATP synthesis-sustained respiration (energy-conserving), the uncoupling protein (UCP) activity-sustained respiration (energy-dissipating), the alternative oxidase(AOX)-mediated respiration (energy-dissipating), as well as the protein expression of UCP and AOX, and free fatty acid content exhibited different evolution patterns in the wild type and nor mutant that can be attributed to their climacteric/nonclimacteric properties, respectively. In the wild type, the climacteric respiratory burst observed in vitro depended totally on an increse in the cytochrome pathway activity sustained by ATP synthesis, while the second respiratory rise during the ripening stage was linked to a strong increase in AOX activity accompanied by an overexpression of AOX protein. In wild type mitochondria, the 10-microM linoleic acid-stimulated UCP-activity-dependent respiration remained constant during the whole fruit development except in senescence where general respiratory decay was observed.

Adenosine Triphosphate↗

PubMed2025

Tracing the evolution and genomic dynamics of mating-type loci in Cryptococcus pathogens and closely related species.

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in C. decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in K. mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

MAT genes↗

PubMed2025

The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella.

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in Cryptococcus decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in Kwoniella mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

Genes, Mating Type, Fungal↗

PubMed1979

Dynamics of density- and frequency-dependent selection.

The evolution of a multiallelic locus in a diploid monoecious population is investigated for weak selection in both discrete and continuous time. It is assumed that in the absence of selection the rate of change of population size N is a function only of N, and N converges exponentially to a unique, globally stable equilibrium, ;N. With arbitrary density- and frequency-dependent selection, after several generations have elapsed, N differs from ;N by terms of O(s) (i.e., bounded by a constant times s), where s is the selection intensity. The mean absolute fitness deviates from its equilibrium value (1 in discrete, 0 in continuous time) by only O(s(2)); its rate of change is O(s(3)). The evolution of the gene frequencies may be approximated with an error of O(s) by assuming that N = ;N and Hardy-Weinberg proportions obtain. When the frequency dependence is weaker than the selection intensity, the mean absolute fitness generally exceeds its equilibrium value by a quantity approximately proportional to the genic variance, the constant of proportionality being simply related to the rate of convergence of N to ;N in the absence of selection. Thus, after a short time, the population generally increases, and the rate of growth is proportional to the genic variance.

Journal Article↗

PubMed2005

Germline and somatic diversification of immune recognition elements in Metazoa.

The histories of the immune systems of Metazoa during evolution are envisaged like as many adaptations to the continuous diversification of immune receptors and effectors genes under the pressure of changing environments. A basic diversity of potential immune receptor genes existed in primitive Metazoa. Their subsequent recruitment into immunity, their diversification revolving around the conservation of signaling cascades was paralleled by cell specialization and the introduction of regulatory networks. Polymorphism, duplication and somatic mechanisms of diversification affected independently and still affect different gene families in many phyla, creating a greater variety of immune system exhibiting sometimes little homology but much analogy to one another. Diversity and multiplicity of receptors was generated by duplication and creation of multigene families. Independently in several phyla further diversity is created somatically by alternate splicing, somatic mutation, gene conversion and gene rearrangement. In several instances combinatorial usage of polypeptide chains or genes segments increases the repertoire of the recognition structures. Metazoa had to adapt to the conditions generated by this diversity: the control of expression of multiple genes and the risk of autoimmunity.

Adaptation, Physiological↗

PubMed1990

Chemical evolution and the origin of life: cumulative keyword subject index 1970-1986.

This cumulative subject index encompasses the subject indexes of the bibliographies on Chemical Evolution and the Origin of Life that were first published in 1970 and have continued through publication of the 1986 bibliography supplement. Early bibliographies focused on experimental and theoretical material dealing directly with the concepts of chemical evolution and the origin of life, excluding the broader areas of exobiology, biological evolution, and geochemistry. In recent years, these broader subject areas have also been incorporated as they appear in literature searches relating to chemical evolution and the origin of life, although direct attempts have not been made to compile all of the citations in these broad areas. The keyword subject indexes have also undergone an analogous change in scope. Compilers of earlier bibliographies used the most specific term available in producing the subject index. Compilers of recent bibliographies have used a number of broad terms relating to the overall subject content of each citation and specific terms where appropriate. The subject indexes of these 17 bibliographies have, in general, been cumulatively compiled exactly as they originally appeared. However, some changes have been made in an attempt to correct errors, combine terms, and provide more meaningful terms.

Exobiology↗

PubMedDate not supplied

[Critical analysis of the evolution of commercial preparations for enteral nutrition during 1988-1996].

Enteral nutrition is a form of nutritional support that is continually growing and expanding, and within this area especially the enteral preparations or formulae. The object of the present is to analyze the evolution of the commercially available nutritionally complete enteral preparations between 1988 and 1997, illustrating the variations that have occurred both from the quantitative and form the qualitative points of view. A progressive increase is seen in the absolute number of available enteral formulae, with the increase in both polymeric formulae with dietary fiber, and that of formulae designed for specific diseases being significant (p < 0.05). The standard polymeric formulae and the oligomeric formulae decrease, but not in a significant manner. There is a special discussion or the characteristic and the usefulness of the polymeric formulae with dietary fiber ad the formulae designed especially for specific diseases. The clinical efficacy of most of these special formulae is controversial, with there not being sufficient objective clinical evidence at present that justifies their routine use.

Dietary Fiber↗

PubMed2002

Perspectives on dental education in the Nordic countries.

The object of this review is to discuss the state of dental education and describe current developments at dental schools in the Nordic countries. The main focus is the undergraduate dental education; however, the postgraduate system will also be addressed. The curriculum model for undergraduate dental education in the Nordic countries is based upon the odontological tradition. The influence of biomedicine on dental education is increasing at present due to scientific and medico-technological developments and the altered disease profiles of oral and systemic diseases. These circumstances create new possibilities for dental education, but at the same time they raise some problems. In the long-term, the strong biomedical influence on dental education will be an advantage to future dentists' function and tasks in health care systems in the Nordic countries. In the short term, it may result in an identity crisis for dental schools, students, and our profession, as we experience the evolution from the traditional odontological curriculum model to one significantly influenced by ongoing changes in the biomedical field. Continuing professional education and advanced training in clinical specialties are likely to play important roles in this evolution.

Biomedical Research↗

PubMed2006

Genospecies of Borrelia burgdorferi sensu lato in Ixodes ricinus ticks from the Autonomous Province of Trento, Italy.

Sequences of the variable intergenic spacer region 5S (rrfA) 23S (rrlB) rRNA were used to identify Borrelia genospecies present in Ixodes ricinus nymphs collected from the Lamar Lakes area of the Province of Trento, Italy (overall prevalence=6.3%). Four genospecies were identified, one for the first time in this Province (B. valaisiana), and three which have been noted previously (B. afzelii, B. garinii, and B. burgdorferi s.s.). In order to compare the genetic variability of these genospecies in Trento with that at a European level, our 21 sequences (15 new haplotypes) and all appropriate European Borrelia sequences registered in GenBank (up to the end of 2004) were subjected to a phylogenetic analysis (for a total of 73 sequences and 43 haplotypes). Clusters of sequences representing the five main European genospecies (afzelii, garinii, burgdorferi s.s., valaisiana, lusitaniae) are well-supported. At least two other groups of haplotypes (genospecies) are suggested by our analysis; moreover, divergent evolution may be occurring in several genospecies. The maximum uncorrected pairwise differences between sequences within genospecies ranges from 1.5% (B. burgdorferi s.s.), to 2.3% (B. garinii and B. valaisiana) to 4.7% (B. afzelii), and are not correlated with geographical distribution. Within the Province of Trento, these values for the same genospecies are 1.5%, 2.3%, 0.9%, 1.9%, respectively. These high mutation rates within genospecies suggest that the sequencing of haplotypes should continue if we are to fully understand and monitor the evolution and epidemiology of Borrelia.

Animals↗

PubMed2025

Adaptive laboratory evolution of Micrococcus luteus and identification of genes associated with radioresistance through genome-wide association study.

Micrococcus luteus (V017) is a Gram-positive bacterium that was isolated from a sterilization area exposed to 60Co radiation. In this study, we performed an adaptive laboratory evolution experiment with M. luteus, exposing it to 24 continuous cycles of gamma irradiation at four different doses (1.5 kGy, 3.5 kGy, 5.5 kGy, and 7.5 kGy). This led to the creation of four evolved populations with different levels of radioresistance, which were positively correlated with the radiation dose applied. The survival rate of the evolved population that underwent adaptive treatment at the highest dose (7.5 kGy) was 0.69% after exposure to 5.5 kGy, which is about five orders of magnitude higher than that of the original strain V017. Furthermore, 76 evolved strains were selected from these populations, and their genomes were re-sequenced, uncovering a total of 3072 mutations. A genome-wide association study identified 56 single nucleotide polymorphisms (SNPs) significantly associated with radioresistance, linked to 62 candidate genes. Ultimately, 9 genes were selected for functional validation. Inactivating 6 of these genes, including H0H31_RS03855 (SMC family ATPase, SbcC), H0H31_RS04250 (ribonuclease HII), H0H31_RS04570 (endonuclease VIII), H0H31_RS07595 (bifunctional 3'-5' exonuclease/DNA polymerase I), H0H31_RS00170 (serine/threonine phosphatase PPP), and H0H31_RS05860 (CBS-domain-containing protein), significantly increased sensitivity to gamma radiation, underscoring their importance in radioresistance.

Micrococcus luteus↗

PubMed2002

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗

PubMed1987

Cellular origin and evolution of neochondrogenesis in major full-thickness defects of a joint surface treated by free autogenous periosteal grafts and subjected to continuous passive motion in rabbits.

A graft of periosteum from the tibia of 27 rabbits was incubated in vitro with tritiated thymidine for 24 hours and then transplanted into a full-thickness defect in the patellar groove. The rabbits were managed after the operation on continuous passive motion (CPM), and the joints excised at intervals of two to 21 days. After one week the cells had begun to synthesize glycosaminoglycan and by two weeks the tissue resembled immature hyaline cartilage. Thymidine-labeled cells were seen throughout the entire regenerated tissue. The cellular origin of the hyaline-like tissue that filled the defects was the progenitor cells of the periosteal graft.

Animals↗

PubMed1987

Polymorphism of the vitamin D binding protein (DBP) among primates: an evolutionary analysis.

The distribution of the DBP (vitamin D binding protein) polymorphism is now well characterized among human populations but for primates only limited results are known. The aim of this paper is to describe the electrophoretic polymorphism of this protein among various species. Using three different electrophoretic methods, we are able to detect an unknown polymorphism and to classify the different alleles observed. These results may be used to set an international nomenclature for further comparisons. The different electrophoretic mobilities between Old and New World Monkeys show that: 1) the Cercopithecoïdea are presenting the largest genetic heterogeneity; 2) the DBP among the Galago corresponds to the lowest isoelectric points observed among Primates; 3) during the evolution from nonhuman Primates to Man, the DBP is able to keep its affinity for vitamin D derivatives despite the occurrence of significant molecular modifications; 4) among Anthropoïdea, the electrophoretic patterns of DBP are very close to the human Gc1 proteins. These results show that evolution at the DBP level can be considered as a continuous mechanism of structural modifications. A significant transition occurs during the differentiation between Cercopithecoïdea and Anthropoïdea. It is not too speculative to consider that some electrophoretic forms detected among Gorilla, Pongo, or Pan may be identical to rare variants observed among humans.

Animals↗

PubMed1977

[Biological bases of aging].

The author discusses ageing with special regard to evolution processes. Accelaration and retardation of certain ontogenetic phases or the whole ontogenesis have developed during phylogenesis and have been fixed genetically as a special reaction norm. The limitation of life span in highly differentiated organisms after reproduction is perfected has to be considered as one of the preconditions of evolution. Considering the phylogenesis, those hypotheses which interpret ageing as a continuous accumulation of cell damage, are no longer admissable. The different theories of the genetic control for ontogenesis are discussed on the basis of international literature.

Aging↗

PubMed2001

[Potential functional differentiation of genome in the course of evolution and approaches to its study. I. Neontological annals of evolution and its analysis].

It is shown that the division of phylogenetical branches descends anisotomically. One new branch becomes evolutionary not active. Another one continues actively to develop. It allows to consider a system of present-day organisms as neonatological annals of evolution. A question arises on distinctions in the constitution of genomes of organisms belonging to active and inactive phylogenetic branches.

Evolution, Molecular↗