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Results for “convergent evolution”

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PubMed1997

Ape-like or hominid-like? The positional behavior of Oreopithecus bambolii reconsidered.

Comparative morphological and functional analyses of the skeletal remains of Oreopithecus bambolii, a hominoid from the Miocene Mediterranean island of Tuscany-Sardinia (Italy), provides evidence that bipedal activities made up a significant part of the positional behavior of this primate. The mosaic pattern of its postcranial morphology is to some degree convergent with that of Australopithecus and functionally intermediate between apes and early hominids. Some unique traits could have been selected only under insular conditions where the absence of predators and the limitation of trophic resources play a crucial role in mammalian evolution.

Animals↗
PubMed1999

In vitro evolution of preferred topoisomerase II DNA cleavage sites.

Topoisomerase II is an essential enzyme that is the target for several clinically important anticancer drugs. Although this enzyme must create transient double-stranded breaks in the genetic material in order to carry out its indispensable DNA strand passage reaction, the factors that underlie its nucleotide cleavage specificity remain an enigma. Therefore, to address the critical issue of enzyme specificity, a modified systematic evolution of ligands by exponential enrichment (SELEX) protocol was employed to select/evolve DNA sequences that were preferentially cleaved by Drosophila melanogaster topoisomerase II. Levels of DNA scission rose substantially (from 3 to 20%) over 20 rounds of SELEX. In vitro selection/evolution converged on an alternating purine/pyrmidine sequence that was highly AT-rich (TATATATACATATATATA). The preference for this sequence was more pronounced for Drosophila topoisomerase II over other species and was increased in the presence of DNA cleavage-enhancing anticancer drugs. Enhanced cleavage appeared to be based on higher rates of DNA scission rather than increased binding affinity or decreased religation rates. The preferred sequence for topoisomerase II-mediated DNA cleavage is dramatically overrepresented ( approximately 10,000-fold) in the euchromatic genome of D. melanogaster, implying that it may be a site for the physiological action of this enzyme.

Animals↗
PubMed2002

Exact stochastic mean-field approach to the fermionic many-body problem.

We investigate a reformulation of the dynamics of interacting fermion systems in terms of a stochastic extension of time-dependent Hartree-Fock equations. From a path-integral representation of the evolution operator, we show that the exact N-body state can be interpreted as a coherent average over Slater determinants evolving in a random mean-field. The imaginary time propagation is also presented and gives a similar scheme which converges to the exact ground state. In addition, the growth of statistical errors is examined to show the stability of this stochastic formulation.

Journal Article↗
PubMed2026

Unraveling evolutionary relationships in the Sida generic alliance (Malvaceae, Malvoideae): a phylogenetic and cytotaxonomic overview.

Sida (Malvaceae), the largest Malveae-Abutilinae member, has poorly defined morphological limits which overlaps with 11 phylogenetically closely related genera that comprises the "Sida generic alliance". The 12 genera are distributed in the tropics especially in Brazil where one third of its species diversity is found. Evolutionary relationships within Sida generic alliance remain unresolved due to morphological convergence, limited taxon sampling, and lack of integrative approaches including cytogenetic data. We reconstructed the phylogeny of Sida and allied genera using a multilocus dataset (nuclear ITS and seven plastid loci) including 193 species classified in 19 genera and analyzed chromosome evolution using cytogenetic data (chromosome number) for 79 species of the 19 genera. The phylogeny recovered seven clades-Abutilon, Bakeridesia, Callianthe, Gaya, and three Sida clades (I-III)-and confirmed the polyphyly of Sida, the largest genera. We detected reticulate evolution, with incongruence between nuclear and plastid topologies. Chromosome number ranged from 2n = 12 to 60 and represented synapomorphies for most clades. Ancestral character reconstruction indicated that ascending dysploidy and polyploidy predominated in karyotype evolution of Sida and allied genera. Our results reveal taxonomic incongruence in current classifications probably related to reticulate evolution. A generic-level taxonomic revision is necessary and should rely on integrated phylogenetic and karyotypic evidence. This study provides a framework for phylogenetic systematics and emphasizes the role of Brazil as a hotspot for plant genomic research.

Phylogeny↗
PubMed2003

Recent theoretical convergences in psychoanalysis and their epistemological importance.

In this paper, the author starts by examining the recent occurrence of an increasing receptivity and critical exchange between different schools of psychoanalytical thought. Among its consequences have been convergences in the understanding of countertransference, especially through the hypotheses of projective identification and countertransferential enactment. The prevalence of these hypotheses points towards the fact that the community of analysts is bringing about an informal and convergent clinical research conducted by a wide and heterogeneous range of its members. The importance and epistemological relevance of this kind of 'informal clinical research' for the construction of psychoanalytical knowledge is emphasised. This process in psychoanalysis is compared with the evolution of knowledge in other scientific areas, highlighting their similarities and their differences. The author shows how Freud's 'mystic writing-pad'model can be expanded to represent the object of psychoanalytical investigation and to bring a better understanding of the reason why the hypotheses of projective identification and countertransferential enactment occupy such a central position in psychoanalysis. In addition, consideration is given to how this kind of research can help in the difficult task of finding criteria for the evaluation of different psychoanalytical concepts. Finally, the author demonstrates how, using this approach, some of the important divergences in contemporary psychoanalysis can be viewed from a new perspective.

Biomedical Research↗
PubMed1984

[Trial of folic acid treatment in fragile X syndrome].

Forty-two patients with the fragile-X syndrome have been treated with oral folic acid, 0.5 mg/kg/d. An improvement of the behavior was observed in the majority of the cases, and evolution of the IQ showed a favorable tendency at the border of statistical significance. On the contrary, the addition to the treatment regime of methionine or of carnitine (carriers of methyl radicals) had unfavorable effects. In view of the few preliminary convergent observation recorded in literature, a continued trial of folic acid treatment seems justified. Simultaneously, however, research is indicated on monocarbon metabolism, probably affected in these patients.

Behavior↗
PubMed1995

Nutritional change and economic crisis in an urban Congolese community.

BACKGROUND: In 1986, the government of Congo undertook a structural adjustment programme to cope with the economic crisis. We present the results of a study whose objectives were to assess the evolution of nutritional status of an urban community between 1986 and 1991 and to identify specific groups for which the nutritional status may have worsened. METHODS: Two cross-sectional surveys were carried out on representative samples of Brazzaville children < 6 years old: 2295 children were surveyed in 1986 and 2373 in 1991. Anthropometric assessment of nutritional status was performed. For children, weight-for-height and height-for-age indices were used according to WHO recommendations. Wasting and stunting were respectively defined as indices under -2 z-scores. Body mass index of mothers was calculated and risk of chronic energy deficiency (CED) was defined as < 18.5 kg/m2. Socioeconomic data relative to the households were also collected. Multivariate statistical methods were used to obtain adjusted estimates of nutritional changes in the community. RESULTS: Data analysis led to several converging results: increase in the percentage of low birthweight (10.2% in 1985 versus 18.7% in 1990), increase in the percentage of CED (from 7.9% to 10.5%), and increase in the prevalence of wasting (from 2.9% to 4.2%). By contrast, the overall prevalence of stunting decreased from 13.9% to 11.0%. After statistical adjustment, the factors found to influence the evolution of anthropometric status were: age of child, age of mother, schooling of mother and household characteristics such as number of preschool children, economic level and head of household's occupation. CONCLUSIONS: The study enables the negative effects of the economic crisis to be quantified. Body mass index is shown to be sensitive to economic changes. It could be recommended as a possible indicator for monitoring the nutritional status at population level. The results also call for a new impetus in preventive health programmes and the implementation of nutritional surveillance activities.

Adolescent↗
PubMed2003

The mind of primitive anthropologists: hemoglobin and HLA, patterns of molecular evolution.

Frank Livingstone played a central role in defining the population genetics of the sickle cell mutation at position 6 of the human beta globin gene, the most famous amino acid substitution in evolutionary biology. Its discovery occurred at a time when traditional, 19th-century principles of natural selection were being joined with the newly discovered mechanics of DNA structure and protein synthesis to produce Neo-Darwinian theory. When combined with the epidemiology of malaria in Africa, differential mortality for both homozygotes, and the resulting advantage of the heterozygote, sickle cell became the classic balanced polymorphism. Human HLA-A has 237 molecular alleles. The histocompatibility system has as its primary function the presentation of peptides to T-cell receptors and plays an essential role in the immune system. Nearly all of the alleles are codominant and fully functional. Despite almost 30 years of disease-association studies with HLA-A, no convincing evidence has been found for differential fertility or mortality at this locus. Yet the dogma in the histocompatibility field is that this extensive human polymorphism is maintained by "balancing selection." Explaining HLA-A polymorphism is what one might call the sickle-cell-effect. This one mutation, coming as it did at the historical convergence of Darwinian theory and modern genetics, and carrying with it the strong relationship between mutation, disease, and allele frequency, has conditioned our discussion of human genetic variation and population genetics. Has the strength of this early idea made evolutionary biologists uncritical of systems like HLA-A and retarded the search for new mechanisms of molecular evolution? Is it now time to move away from a focus on mutation and polymorphism in evolutionary genetics and toward a systems theory that would explain the origin and evolution of hemoglobin and HLA-A and the biochemical pathways that surround them?

Alleles↗
PubMed2001

SELEX for tubulin affords specific T-rich DNA aptamers. Systematic evolution of ligands by exponeential enrichment.

We succeeded in acquiring two DNA aptamers that selectively recognize tubulin by the SELEX method. A pool of single-stranded oligo-DNAs including a random region of 59 nucleotides was screened by SELEX for tubulin purified from calf-brain as a target. After 20 repetitions of selection round, the library converged on specific T-rich sequences. The binding activity of T-rich clones was analyzed by the SPR sensor to determine their dissociation constants to be in the order of 10 microM.

Animals↗
PubMed1992

Evolutionary conservation pattern of zinc-finger domains of Drosophila segmentation genes.

A number of genes of the developmental gene hierarchy in Drosophila encode transcription factors containing Cys2His2 zinc finger domains as DNA-binding motifs. To learn more about the evolution of these genes, it is necessary to clone the homologs, or more correctly the orthologs, from different species. Using PCR, we were able to obtain apparently orthologous fragments of hunchback (hb), Krüppel (Kr), and snail (sna) from a variety of arthropods and partly also from other animal phyla. Sequence alignments of these fragments show that the amino acid differences can normally not be correlated with the evolutionary distances of the respective species. This is due to an apparent saturation of potential replacements within the finger domains, which is also evident from the frequent occurrence of convergent replacements. Another recurrent feature of these alignments is that those amino acids that are directly involved in determining the DNA-binding specificity of the fingers are most conserved. Using in vitro bandshift experiments we can indeed show that the binding specificity of a hunchback finger fragment from different species is not changed. This implies that there is a high selective pressure to maintain the regulatory target elements of these genes during evolution.

Amino Acid Sequence↗
PubMed2004

Evolutionary dynamics of complex biomechanical systems: an example using the four-bar mechanism.

Like many phenotypic traits, biomechanical systems are defined by both an underlying morphology and an emergent functional property. The relationship between these levels may have a profound impact on how selection for functional performance is translated into morphological evolution. In particular, complex mechanical systems are likely to be highly redundant, because many alternative morphologies yield equivalent functions. We suggest that this redundancy weakens the relationship between morphological and functional diversity, and we illustrate this effect using an evolutionary model of the four-bar lever system of labrid fishes. Our results demonstrate that, when traits are complex, the morphological diversity of a clade may only weakly predict its mechanical diversity. Furthermore, parallel or convergent selection on function does not necessarily produce convergence in morphology. Empirical observations suggest that this weak form-function relationship has contributed to the morphological diversity of labrid fishes, as functionally equivalent species may nevertheless possess morphologically distinct jaws. We suggest that partial decoupling of morphology and mechanics due to redundancy is a major factor in morphological diversification.

Animals↗
PubMed2006

Some aspects of E. coli promoter evolution observed in a molecular evolution experiment.

We devised a molecular evolution procedure to evolve E. coli promoter sequences and applied it to observe an arbitrary, nonfunctional sequence evolving into functional promoters. In the experiments, DNA sequence variations were generated with error-prone PCR and were inserted in the promoter region of the cat (chloramphenicol acetyl transferase) gene on a plasmid. Upon transforming the cells, functional promoters on the plasmid were selected according to the chloramphenicol resistance. Within a few cycles of mutation-selection, promoters emerged, and the sequences converged into a small number of groups. In the process, the extended minus 10 type of promoters emerged quickly, and small deletions were often involved in adjusting the length between the -35 and the -10 elements. Our results also suggest a possible selection for promoter stability against mutation.

Base Sequence↗
PubMed2005

Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes.

Buffalograss (Buchloë dactyloides (Nutt.) Englem), a C4 turfgrass species, is native to the Great Plains region of North America. The evolutionary implications of buffalograss are unclear. Sequencing of rbcL and matK genes from plastid and the cob gene from mitochondrial genomes was examined to elucidate buffalo grass evolution. This study is the first to report sequencing of these genes from organelle genomes in the genus Buchloë. Comparisons of sequence data from the mitochondrial and plastid genome revealed that all genotypes contained the same cytoplasmic origin. There were some rearrangements detected in mitochondrial genome. The buffalograss genome appears to have evolved through the rearrangements of convergent subgenomic domains. Combined analyses of plastid genes suggest that the evolutionary process in Buchloë accessions studied was monophyletic rather than polyphyletic. However, since plastid and mitochondrial genomes are generally uniparentally inherited, the evolutionary history of these genomes may not reflect the evolutionary history of the organism, especially in a species in which out-crossing is common. The sequence information obtained from this study can be used as a genome-specific marker for investigation of the buffalograss polyploidy complex and testing of the mode of plastid and mitochondrial transmission in genus Buchloë.

Chloroplasts↗
PubMed2000

Gene conversions may obscure actin gene family relationships.

Phylogenetic hypotheses of muscle actin evolution are significantly different when a sea urchin is used as a representative echinoderm than when a sea star is used. While sea urchin muscle actins support an echinoderm-chordate sister relationship, sea star sequences suggest that echinoderm muscle actins are convergent with chordate muscle actins. Our results suggest that gene conversion in the sea star muscle actin may be responsible for these discordant results.

Actins↗
PubMed2005

Robustness, evolvability, and optimality of evolutionary neural networks.

In a typical optimization problem, the main goal is to search for the appropriate values of the variables that provide the optimal solution of the given function. In artificial neural networks (ANN), this translates to the minimization of the error surface during training such that misclassification is minimized during generalization. However, since optimal training performance does not necessarily imply optimal generalization due to the possibility of overfitting or underfitting, we developed SEPA (Structure Evolution and Parameter Adaptation) which addressed these issues by simultaneously evolving ANN structure and weights. Since SEPA primarily relies on the perturbation function to bring variation in its population, this follow-up study aims to find out SEPAs evolvability, optimality, and robustness in other perturbation functions. Our findings indicate that SEPAs optimal generalization performances are stable and robust from the effect of the different perturbation functions. This is due to the feedback loop between its architecture evolution and weight adaptation such that any shortcoming of the former is compensated by the latter, and vice versa. Our results strongly suggest that proper ANN design requires simultaneous adaptation of ANN structure and weights to avoid one-sided or bias convergence to either the weight or architecture space.

Algorithms↗
PubMed2002

The Jak/STAT pathway in model organisms: emerging roles in cell movement.

The JAK/STAT pathway was originally identified in mammals. Studies of this pathway in the mouse have revealed that JAK/STAT signaling plays a central role during hematopoeisis and other developmental processes. The role of JAK/STAT signaling in blood appears to be conserved throughout evolution, as it is also required during fly hematopoeisis. Studies in Dictyostelium, Drosophila, and zebrafish have shown that the JAK/STAT pathway is also required in an unusually broad set of developmental decisions, including cell proliferation, cell fate determination, cell migration, planar polarity, convergent extension, and immunity. There is increasing evidence that the versatility of this pathway relies on its cooperation with other signal transduction pathways. In this review, we discuss the components of the JAK/STAT pathway in model organisms and what is known about its requirement in cellular and developmental processes. In particular, we emphasize recent insights into the role that this pathway plays in the control of cell movement.

Animals↗
PubMed2005

Irritable bowel syndrome and inflammatory bowel disease: interrelated diseases?

In the past inflammatory bowel disease (IBD), celiac disease and irritable bowel syndrome (IBS) were regarded as completely separate disorders. Now, with the description of inflammation, albeit low-grade, in IBS, and of symptom overlap between IBS and celiac disease, this contention has come under question. Is there true overlap between these disorders? Despite the limitations of available data one cannot but be struck by some areas of apparent convergence: IBD and celiac disease in remission, lymphocytic colitis and microscopic inflammation in IBS, in general, and, especially, in the post-infectious IBS category. The convergence between latent celiac disease and sub-clinical IBD, on the one hand, and IBS, on the other, appears, based on available evidence, to be somewhat spurious and may largely relate to misdiagnosis, a phenomenon which may also explain the apparent evolution of IBS into IBD in some studies. Similarities between IBS and lymphocytic colitis are more striking and less readily dismissed; as for IBS, well documented instances of progression of lymphocytic colitis to full-blown IBD are infrequent, suggesting a true separation between this disorder and classical IBD. Do IBS and lymphocytic colitis represent different responses to similar triggers? Will some of the 'inflamed' IBS subgroup be reclassified as part of the spectrum of lymphocytic colitis in the future? Will inflammation emerge as a common underlying factor in the pathogenesis of IBS? The answer to these and many questions must await further study of this fascinating area.

Environment↗