Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “parallel evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,315 records · Page 73Linked to original sources

From movement to transitivity: the role of hippocampal parallel maps in configural learning.

Whether spatial learning is a special case of configural or relational learning, or whether abstract principles evolved from the concrete need to navigate in space, is a question of long-standing debate. The parallel map theory of hippocampal function offers a resolution of the debate by redefining 'spatial learning' as two parallel, geometric processes, Euclidean metric and topological. Moreover, these processes are subserved by independent hippocampal subfields that underlie two ways of representing space, the bearing and the sketch map. It is possible that configural and relational learning, like spatial learning, should also be distinguished in this way. Transitive inference, requiring the construction of a value gradient, could be analyzed as a Euclidean metric problem. In contrast, transverse patterning could be seen as a topological analysis of the relationships among discrete objects. If this interpretation is correct, lesions to the primary bearing map structure (dentate gyrus) should impair transitivity while lesions to the primary sketch map structure (CA1) should impair transverse patterning and similar topological tasks. Recent results from diverse species and tasks lend support to these predictions, suggesting that the hippocampus not only creates parallel maps but uses these maps to solve more abstract configural or relational problems.

Animals↗

Nemo: an evolutionary and population genetics programming framework.

UNLABELLED: Nemo is an individual-based, genetically explicit and stochastic population computer program for the simulation of population genetics and life-history trait evolution in a metapopulation context. It comes as both a C++ programming framework and an executable program file. Its object-oriented programming design gives it the flexibility and extensibility needed to implement a large variety of forward-time evolutionary models. It provides developers with abstract models allowing them to implement their own life-history traits and life-cycle events. Nemo offers a large panel of population models, from the Island model to lattice models with demographic or environmental stochasticity and a variety of already implemented traits (deleterious mutations, neutral markers and more), life-cycle events (mating, dispersal, aging, selection, etc.) and output operators for saving data and statistics. It runs on all major computer platforms including parallel computing environments. AVAILABILITY: The source code, binaries and documentation are available under the GNU General Public License at http://nemo2.sourceforge.net.

Biological Evolution↗

Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera.

Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprinid fish Cyprinella spiloptera. Variation at different nucleotide positions in individual repeats supported different models of repeat evolution. One set of characters included several nucleotide variants found in all copies from a limited number of individuals, while the other set included an 8-bp deletion found in a limited number of copies in all individuals. The deletion and an associated nucleotide change appear to be the result of a deterministic, rather than stochastic, mutation process. Parallel origins of repeat arrays in different mitochondrial lineages, possibly coupled with a homogenization mechanism, best explain the distribution of nucleotide variation.

Animals↗

Relationships and evolution of the North African geckos, Geckonia and Tarentola (Reptilia: Gekkonidae), based on mitochondrial and nuclear DNA sequences.

Mitochondrial (cytochrome b and 12S rRNA) and nuclear (c-mos) genes, analyzed by a variety of methods, indicate that the distinctive northwest African gecko Geckonia chazaliae is a member of the Tarentola clade, being most closely related to the species of the western Canary and Cape Verde islands. Relationships in Tarentola as a whole are as follows: (T. americana ((T. mauritanica, T. angustimentalis) ((T. deserti, T. boehmei) ((T. b. boettgeri-South (T. b. boettgeri-North (T. b. bischoffi, T. b. hierrensis))) ((T. annularis, T. ephippiata) (Geckonia, T. delalandii, T. gomerensis, Cape Verde species)))))); nearly all nodes have high bootstrap support. Results confirm that T. americana of Cuba and the Bahamas separated at the most basal dichotomy of the phylogeny and give no positive support for the monophyly of the subgenera Tarentola s. str. and Makariogecko. The latter includes Geckonia and the subgenus Sahelogecko. Continental Tarentola appear to have invaded the Sahara desert from its northern edge. They have also colonized groups of Atlantic islands five times: a single invasion of the West Indies and three of the Canary islands, one of which then went on to invade the Cape Verde archipelago. The phylogeny corroborates anatomical evidence that the ground-dwelling Geckonia had a climbing ancestry, something that is paralleled in some southern African terrestrial gekkonids related to Pachydactylus. Distinctive derived features of Geckonia occur in other gekkonids that are ground dwelling in arid habitats and may be functionally related to this environment. The evolution of such features indicates that, although Tarentola is generally very uniform and may have been so for over 10 million years, this is not due to any overwhelming phylogenetic constraint. G. chazaliae should be included in Tarentola, as Tarentola chazaliae.

Africa, Northern↗

Précis of Foundations of language: brain, meaning, grammar, evolution.

The goal of this study is to reintegrate the theory of generative grammar into the cognitive sciences. Generative grammar was right to focus on the child's acquisition of language as its central problem, leading to the hypothesis of an innate Universal Grammar. However, generative grammar was mistaken in assuming that the syntactic component is the sole course of combinatoriality, and that everything else is "interpretive." The proper approach is a parallel architecture, in which phonology, syntax, and semantics are autonomous generative systems linked by interface components. The parallel architecture leads to an integration within linguistics, and to a far better integration with the rest of cognitive neuroscience. It fits naturally into the larger architecture of the mind/brain and permits a properly mentalistic theory of semantics. It results in a view of linguistic performance in which the rules of grammar are directly involved in processing. Finally, it leads to a natural account of the incremental evolution of the language capacity.

Biological Evolution↗

Evolutionary processes in the genus Coreocarpus: insights from molecular phylogenetics.

A molecular phylogenetic study of the plant genus Coreocarpus was conducted using nuclear (ITS) and plastid (rpl16 intron) DNA sequences, with phylogenies of the nuclear and plastid sequences highly congruent in defining a monophyletic group of six species (core Coreocarpus), although three other species often placed within the genus were excluded. Relationships within the genus are largely but not totally concordant with prior biosystematic studies. Despite strong molecular support, no morphological characters uniting the six species of core Coreocarpus have been identified; retention of plesiomorphic characters and the genetic lability of characters are two probable factors contributing to lack of consistent defining characters. The age of the core Coreocarpus is estimated at 1 million years because the basal species is endemic to a volcanic island that emerged in the past million years. Mapping the results of earlier breeding studies on the molecular phylogeny showed that use of cross-compatibility as a criterion for species delimitation would result in the recognition of paraphyletic species. Prior field, morphological, and biosystematic studies provided no indication of past hybridization in the evolution of Coreocarpus, and species in the genus appeared to be well defined morphologically. However, three instances of incongruence were observed. Two of these were between the nuclear and plastid partitions, and the third was between the morphological species assignment of one accession and the molecular data. If hybridization accounts for incongruence between the nuclear and plastid data, it occurred between species that now appear to be cross-incompatible and allopatric. The incongruence between morphological species assignment and the molecular data could be the result of parallel fixation of characters that have a simple genetic basis. This study suggests that the evolutionary history of Coreocarpus is much more complex than indicated from prior biosystematic investigations and that biosystematic and molecular phylogenetic studies may complement each other for elucidating the evolution and phylogeny of a group.

Asteraceae↗

Convergent evolution of embryonic growth and development in the eastern fence lizard (Sceloporus undulatus).

Theory predicts that cold environments will select for strategies that enhance the growth of ectotherms, such as early emergence from nests and more efficient use of resources. We used a common garden experiment to detect parallel clines in rates of embryonic growth and development by eastern fence lizards (Sceloporus undulatus). Using realistic thermal conditions, we measured growth efficiencies and incubation periods of lizards from five populations representing two distinct clades. In both clades, embryos from cold environments (Indiana, New Jersey, and Virginia) grew more efficiently and hatched earlier than embryos from warm environments (Florida and South Carolina). Because eggs from cold environments were larger than eggs from warm environments, we experimentally miniaturized eggs from one population (Virginia) to determine whether rapid growth and development were caused by a greater maternal investment. Embryos in miniaturized eggs grew as efficiently and incubated for the same duration as embryos in unmanipulated eggs. Taken together, our results suggest countergradient variation has evolved at least twice in S. undulatus.

Aging↗

[Headache and transformed migraine with medication overuse: what differences between disability, emotional distress and coping?].

LITERATURE FINDINGS: Twelve percent of general population is estimated to suffer from migraine (Henryet al., 2002), which represent in France 6 to 7 millions of individuals. Transformed migraine (TM) with medication overuse is a complication of migraine characterized by an increase of crisis frequency and by a parallel increase of medication intake. French prevalence of TM with analgesic overuse seems to reach up to 3% of general population (Lanteri-Minet, 2003). TM is associated with an increased disability (concerning housework, leisure, job and social activities). Moreover TM is associated with a bad emotional adjustment, which can lead to anxiety and depressive disorders. Those disorders have been founded to be more frequent in TM than in simple migraine (Radatet al., 1999). As a consequence, TM patients's quality of life is severely impaired. The use of dysfunctional coping strategies against pain should explain bad emotional adjustment in those patients. One study have found a statistical relationship between dysfunctional coping strategies such as nd depressive disorders in migraineurs (Materazzo et al., 2000). METHOD: The aim of this study was to compare 30 simple migraineurs (SM) to 32 transformed migraineurs with medication overuse (TM) for impairment, emotional adjustment and coping strategies. Patients have been assessed with Pain Disability Inventory (PDI) (Pollard et al., 1984), Hospital Anxiety Depression scale (HAD) (Zigmond and Snaith, 1983) and Coping Strategies Questionnaire (CSQ) (Rosentiel and Keefe, 1983). RESULTS: Principal Component Analysis (SPSS Software) confirms the good psychometric properties of PDI and HAD in headache patients. Statistical analysis shows higher emotional distress scores (HAD mean score = 32,2 +/- 10,9) in TM than in SM (24, 1 +/- 7,3) (p < 0,001). Both groups didn't use the same coping strategies against pain. TM were characterized by the use of "dramatisation", "distraction" and "pray", which are considered as dysfunctional coping strategies, although SM used "reinterpretation" which is associated with a better adjustment in term of disability and emotional distress (Riley et al., 1999). CONCLUSION: These results suggest that dysfunctional coping strategies in TM should explained the increased prevalence of emotional distress in this population. It should be of an utmost interest to assess temporal evolution of coping strategies after medication withdrawal. Withdrawal is the main therapeutical measure proposed to TM patients. It should also be supposed that behavioural changes related to medication with drawal evolve in parallel with changes in the use of coping strategies against pain.

Adaptation, Psychological↗

Soluble adhesion molecules in acute disseminated encephalomyelitis.

Soluble adhesion molecules are overexpressed in neuroinflammatory disorders. Their synthesis parallels that of their membrane-bound counterparts, which modulate lymphocyte transmigration through the blood-brain barrier. Blood-brain barrier cellular migration may be essential in the evolution of postinfectious inflammatory central nervous system disease. The serum levels of soluble intercellular adhesion molecule-1, soluble vascular adhesion molecule-1, and soluble E-selectin were measured in 12 children with acute disseminated encephalomyelitis and in two control groups (35 healthy and 35 affected by noninflammatory neurologic diseases) of similar age. In patients with acute disseminated encephalomyelitis, soluble E-selectin serum levels were significantly higher (median 113 ng/mL, range 54-144) than in both control groups (median 44, range 31-63, and median 58, range 43-89, respectively; one-way analysis of variance, P < 0.0001); a statistical trend for higher levels of soluble intercellular adhesion molecule-1 was observed in acute disseminated encephalomyelitis subjects, whereas soluble vascular adhesion molecule-1 titers did not differ between the three groups. The specific role played by each of these molecules in lymphocyte extravasation and the differential cytokine modulation of their expression might explain the result. Further larger studies are required including serial measurements and cerebrospinal fluid analysis.

Adolescent↗

Bursting, beating, and chaos in an excitable membrane model.

We have studied periodic as well as aperiodic behavior in the self-sustained oscillations exhibited by the Hodgkin-Huxley type model of Chay, T. R., and J. Keizer (Biophys. J., 1983, 42:181-190) for the pancreatic beta-cell. Numerical solutions reveal a variety of patterns as the glucose-dependent parameter kCa is varied. These include regimes of periodic beating (continuous spiking) and bursting modes and, in the transition between these modes, aperiodic responses. Such aperiodic behavior for a nonrandom system has been called deterministic chaos and is characterized by distinguishing features found in previous studies of chaos in nonbiophysical systems and here identified for an (endogenously active) excitable membrane model. To parallel the successful analysis of chaos in other physical/chemical contexts we introduce a simplified, but quantitative, one-variable, discrete-time representation of the dynamics. It describes the evolution of intracellular calcium (which activates a potassium conductance) from one spike upstroke to the next and exhibits the various modes of behavior.

Animals↗

An old epithelial cell never dies, it just agonesces away.

The behavior of mammary epithelial cells during aging is dynamic and is likely to have significant implications in the pathogenesis of human breast cancer. The growth of epithelial cells over time was thought to parallel that of their underlying stroma, sequentially undergoing a defined period of growth, followed by senescence and, ultimately, cell crisis or rarely immortalization. Recent findings, however, suggest that the evolution of mammary epithelium at the proliferative and chromosomal levels is distinct from that of stroma, contributing to the neoplastic susceptibilities of epithelial cells.

Breast Neoplasms↗

Alteration of testicular response to long photoperiod by transient exposure to short photoperiod in collared lemmings (Dicrostonyx groenlandicus).

The reproductive response of collared lemmings (Dicrostonyx groenlandicus) to photoperiod is unique for rodents. Whereas most reproductively photoresponsive rodents show maximal gonadal growth when exposed to long photoperiod (long day), collared lemmings show delayed maturation when born and maintained under this condition. However, transfer of lemmings from short photoperiod (short day) to long day results in maximal gonadal growth, indicating that the response to long day depends upon photoperiod history. We hypothesized that the slowing of maturation observed in animals born and maintained on long day reflects an inability to respond fully to long day, resulting from the absence of previous exposure to short day. To determine whether young lemmings born in long day are capable of being stimulated by long day, we exposed them at weaning (19 days of age) to 1, 6 or 10 weeks of short day, and then challenged them with a second exposure to long day. Relative to animals transferred permanently to short day at weaning, lemmings exposed to 6 weeks of short day showed accelerated gonadal growth after both 5 and 10 weeks of subsequent exposure to long day, and those exposed to 10 weeks of short day had larger testes after 6 weeks of long day. Thus, during transient exposure to short day, the animals acquired sensitivity to the stimulatory effects of long day. The responses of body mass, bifid claw width and pelage colour to the photoperiod manipulations did not parallel that of the gonads, indicating independent regulation of somatic and reproductive parameters. The unique way in which the reproductive system of collared lemmings responds to photoperiod may reflect evolution in an environment where the production of offspring during periods of unchanging long day (for example, the Arctic summer) is not selectively advantageous.

Animals↗

[Functional neuroimaging of emotions and bipolar disorder].

In this review we comment the results of functional neuroimaging works of emotions on normal population and some parallelisms with the emotional changes of bipolar disorder correlated with their functional neuroimaging. Initially we refer the emotional ontogenetical development of human brain based on regional cerebral sanguineous flow evolution (FSC). Secondly we describe the differences of FSC between the externally generated emotions versus internally; between positive versus negative emotions and the correlation between FSC and some facial expressions. When FSC of bipolar disorder is compared with normal emotions on general population, we observe that temporal cortex, the prefrontal medial and insular anterior cortex, change their perfusion with the switch or the change of emotional expression. It is possible to determine if the findings obtained in samples of healthy subjects and bipolar patients converge in a dimensional model, or if on the contrary they support the categorical hypotheses, moving the emotional aspects to a second term on bipolar disorder.

Bipolar Disorder↗

Evolution of serum amylase, lipase and immunoreactive trypsin during pancreatitis attacks.

The characteristics of the blood curves of alpha-amylase (SA), pancreatic lipase (SL) and immunoreactive trypsin (SIT) have been analyzed in a series of patients daily explored throughout the evolution of pancreatitis attacks; urines were also collected to estimate the amylase-creatinine clearance ratio (ACCR). The following results were obtained. a). The 3 enzymes profiles ran roughly parallel during an acute attack. b). SL rose far higher than SA at the onset of the attack but its decay displayed a shorter half-life than the latter; these features resulted in an absence of systematic difference between their times of return to normal levels at the end of the attack. c). SIT more closely correlated with SL than with SA. d). In common hospital practice, simultaneous SA and SL determinations were proving a more reliable help to diagnose pancreatitis attack than ACCR.

Acute Disease↗

Intraventricular pressure monitoring in patients with thalamic and ganglionic hemorrhages.

In the present study, we have evaluated the use of intraventricular pressure catheters in thalamic and ganglionic hemorrhages. Ten patients admitted in our Emergency Department in Glasgow Coma Scale (GCS) equal or below 13 enrolled the study (at least one point should have been lost in the eye opening score to exclude purely aphasic patients that were fully alert). After a complete clinical and neurological evaluation, computed tomography scans were obtained and the volume of the hematomas, as well as presence or absence of hydrocephalus, were considered. Intraventricular pressure catheters connected in parallel to external derivation systems were implanted and patients were thereafter sent to the ICU. Patients that presented mass effect lesions with sustained increased ICP levels or clinical and neurological deterioration were submitted in addition, to the surgical evacuation of the hematomas. Clinical evolution, complications and the rehabilitation of the patients were recorded. Clinical outcome was assessed with the Glasgow Outcome Score. In all but three patients the initial intracranial pressure levels were bellow 20 mmHg (mean for all patients was 14.1 +/- 6.5 mmHg). Notwithstanding, these three patients were extremely difficult to treat. For this group of patients mortality was 100%. Among the patients that presented ICP levels bellow 20 mmHg, 04 developed hydrocephalus and 03 did not display ventricular dilation. As expected, the major benefits concerning the intraventricular pressure catheters connected in parallel with external derivation systems were observed in the group of patients that presented ICP levels bellow 20 mmHg and had hydrocephalus. Mild non-statistically significant correlations for all the three groups were achieved either when the initial GCS and ICP levels (r=-0.28, p=0.43) or when ICP levels and the volumes of the hematomas were compared (r=0.38, p=0.28). In addition, no significant correlations were observed concerning the final outcome of the patients and the variables previously evaluated.

Adult↗

Analysis of the human Alu Ye lineage.

BACKGROUND: Alu elements are short (approximately 300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition. The expansion of these elements has had a significant impact on the structure and function of primate genomes. Approximately 10 % of the mass of the human genome is comprised of Alu elements, making them the most abundant short interspersed element (SINE) in our genome. The majority of Alu amplification occurred early in primate evolution, and the current rate of Alu retroposition is at least 100 fold slower than the peak of amplification that occurred 30-50 million years ago. Alu elements are therefore a rich source of inter- and intra-species primate genomic variation. RESULTS: A total of 153 Alu elements from the Ye subfamily were extracted from the draft sequence of the human genome. Analysis of these elements resulted in the discovery of two new Alu subfamilies, Ye4 and Ye6, complementing the previously described Ye5 subfamily. DNA sequence analysis of each of the Alu Ye subfamilies yielded average age estimates of approximately 14, approximately 13 and approximately 9.5 million years old for the Alu Ye4, Ye5 and Ye6 subfamilies, respectively. In addition, 120 Alu Ye4, Ye5 and Ye6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and levels of human genomic diversity. CONCLUSION: The Alu Ye lineage appears to have started amplifying relatively early in primate evolution and continued propagating at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Detailed sequence analysis of several Alu pre-integration sites indicated that multiple types of events had occurred, including gene conversions, near-parallel independent insertions of different Alu elements and Alu-mediated genomic deletions. A potential hotspot for Alu insertion in the Fer1L3 gene on chromosome 10 was also identified.

Alu Elements↗

On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled.

Using analytical methods, we show that under a variety of model misspecifications, Neighbor-Joining, minimum evolution, and least squares estimation procedures are statistically inconsistent. Failure to correctly account for differing rates-across-sites processes, failure to correctly model rate matrix parameters, and failure to adjust for parallel rates-across-sites changes (a rates-across-subtrees process) are all shown to lead to a "long branch attraction" form of inconsistency. In addition, failure to account for rates-across-sites processes is also shown to result in underestimation of evolutionary distances for a wide variety of substitution models, generalizing an earlier analytical result for the Jukes-Cantor model reported in Golding and a similar bias result for the GTR or REV model in Kelly and Rice (1996). Although standard rates-across-sites models can be employed in many of these cases to restore consistency, current models cannot account for other kinds of misspecification. We examine an idealized but biologically relevant case, where parallel changes in rates at sites across subtrees is shown to give rise to inconsistency. This changing rates-across-subtrees type model misspecification cannot be adjusted for with conventional methods or without carefully considering the rate variation in the larger tree. The results are presented for four-taxon trees, but the expectation is that they have implications for larger trees as well. To illustrate this, a simulated 42-taxon example is given in which the microsporidia, an enigmatic group of eukaryotes, are incorrectly placed at the archaebacteria-eukaryotes split because of incorrectly specified pairwise distances. The analytical nature of the results lend insight into the reasons that long branch attraction tends to be a common form of inconsistency and reasons that other forms of inconsistency like "long branches repel" can arise in some settings. In many of the cases of inconsistency presented, a particular incorrect topology is estimated with probability converging to one, the implication being that measures of uncertainty like bootstrap support will be unable to detect that there is a problem with the estimation. The focus is on distance methods, but previous simulation results suggest that the zones of inconsistency for distance methods contain the zones of inconsistency for maximum likelihood methods as well.

Archaea↗

Chicken genome: current status and future opportunities.

The chicken genome sequence is important for several reasons. First, the chicken shared a common ancestor with mammals approximately 310 million years ago (Mya) at a phylogenetic distance not previously covered by other genome sequences. It therefore fills a gap in our knowledge and understanding of the evolution and conservation of genes, regulatory sequences, genomes, and karyotypes. The chicken is also a major source of protein in the world, with billions of birds used in meat and egg production each year. It is the first livestock species to be sequenced and so leads the way for others. The sequence and the 2.8 million genetic polymorphisms defined in a parallel project are expected to benefit agriculture and cast new light on animal domestication. Also, as the first bird to be sequenced, it is a model for the 9600 avian species thought to exist today. Many of the features of the chicken genome and its biology make it an ideal organism for studies in development and evolution, along with applications in agriculture and medicine.

Animals↗