Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Comparative 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 487 records · Page 27Linked to original sources
PubMed2002

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

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

Animals↗
PubMed1985

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

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

Animals↗
PubMed2001

Chromosome painting in farm, pet and wild animal species.

Among the advanced karyotype analysis approaches embraced by animal cytogenetics during the past decade, chromosome painting has had the greatest impact. Generation of chromosome specific paints is considered pivotal to his development. Additionally, ability to use these paints across species (referred to as Zoo-FISH or comparative painting) is undisputedly the most important breakthrough that has contributed to our ability to compare karyotypes of a wide range of evolutionarily highly diverged chromosome painting, and makes them aware of the tools/resources available to carry out this research in a variety of animal species. An overview of the current status of comparative chromosome painting results across closely as well as distantly related species is presented. Findings from different studies show how some segmental syntenies are more conserved as compared to others. The comparisons provide insight into the likely constitution of a vertebrate/mammalian ancestral karyotype and help understand some of the intricacies about karyotype evolution. Importance of comparative painting in setting the stage for rapid development of gene maps in a number of economically important species is elaborated.

Animals↗
PubMed1997

[Quantification of lamellar bodies in amniotic fluid: a method for the evaluation of fetal pulmonary maturity].

It was tried to know the counting up of lamellar bodies in amniotic fluid, as a test of fetal pulmonary maturity, comparing it with neonatal evolution. 31 samples of amniotic fluid of different ages of gestation, were obtained, lamellar bodies were quantified with a standard equipment of hematic counting, and comparing with neonatal evolution, sensitivity, specificity, positive predictive value, and negative predictive value are established. The established concentration of 30,000/l by comparison with Lecitine/Esfingomieline and with Fosfatidilglycerol was used. From 29 patients with counts greater than 30,000, none presented Respiratory Difficulty syndrome (SDR); and from two patients with lower counts, one presented SDR and one had normal neonatal evolution. Sensitivity was 96%; specificity was 100%; predictive positive value, 50%; and negative predictive value was 100%. Because of this, the test is so useful in practice. Its statistical values, its minimal cost; easiness to do, and equipment availability, justify this test as a first election.

Amniotic Fluid↗
PubMed1994

Comparison and evolution of human immunoglobulin VH segments located in the 3' 0.8-megabase region. Evidence for unidirectional transfer of segmental gene sequences.

Nucleotide sequences of 64 VH segments within the 3' 0.8-megabase region of the human immunoglobulin germ line VH locus were compared with trace evolution of human VH segments. Based on alignment of the deduced amino acid sequences of 37 functional germ line VH segments, a phylogenetic tree was generated using the neighbor-joining method. The phylogenetic tree clearly supports the previous classification of human VH segments into six families, which correlate roughly with mouse VH families with varying conservation. The human VH-III family is most homologous to mouse VH segments, suggesting that members of the VH-III family may be conserved by some functional constraint. The 5'-flanking region of each family has a family-specific structure. The sequenced 64 VH segments include 31 pseudogenes, of which 24 were highly conserved. Unidirectional transfer of segmental sequences was identified within the VH-III and VH-IV families, providing clear examples of germ line gene conversion. Such gene conversion may contribute to conserve structures of pseudo-VH segments. Comparison of the VH-IV family members indicates that recent repeated duplications and frequent gene conversions are responsible for strong conservation of this family, although functional selection is not completely excluded.

Amino Acid Sequence↗
PubMed2025

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.

Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.

Animals↗
PubMed2000

Pinniped diving response mechanism and evolution: a window on the paradigm of comparative biochemistry and physiology.

Starting even before the end of World War II, the discipline of comparative physiology and biochemistry experienced a period of unprecedented growth and development that pioneers in this field thought would never end. However, by the mid-1970s many of the major mechanistic problems in the field were pretty well understood in principle, and by the mid-1980s workers in the field widely recognized that the discipline was at the point of diminishing returns. One response to this was disillusionment, which turned out to be premature because the field was already absorbing molecular biology tools which has now caused a kind of renaissance in mechanistic physiology studies. The second major response to the sense of disillusionment led to a search for new approaches, and out of this endeavor the newly rejuvenated field of evolutionary physiology arose, and this research area too is now in a growth phase. These general patterns of growth and development in our discipline as a whole are particularly clearly evident in the field of aquatic mammals and birds. Between the 1930s and the 1970s, studies of diving physiology and biochemistry made great progress in mechanistically explaining the basic diving response of aquatic mammals and birds. Key components of the diving response (apnea, bradycardia, peripheral vasoconstriction, redistribution of cardiac output) were found in essentially all species analyzed and were generally taken to be biological adaptations. By the mid-1970s, this approach to unraveling the diving response had run 'out of steam' and was in conceptual stasis. The breakthrough which gave renewal to the field at this time was the development of microprocessor based monitoring of diving animals in their natural environments, which led to a flurry of studies mostly confirming the essential outlines of the diving response based upon laboratory studies and firmly placing it into a proper biological context, underlining its plasticity and species specificities. Now as we begin a new millenium, despite ever more detailed field monitoring of physiology, behavior and ecology, studies aimed at improving understanding of physiological mechanisms in diving are again approaching a point of diminishing returns. To avoid another conceptual stasis, what seems required are new initiatives which may arise from two differing approaches. The first is purely experimental, relying on magnetic resonance imaging (MRI) and spectroscopy (MRS) to expand the framework of the original 'diving response' concept. The second, evolutionary study of the diving response, is synthetic, linked to both field and laboratory studies. To date the evolution of the diving response has only been analyzed in pinnipeds and from these studies two kinds of patterns have emerged. (1) Some physiological and biochemical characters, required and used in diving animals, are highly conserved not only in pinnipeds but in all vertebrates; these traits are necessarily similar in all pinnipeds and include diving apnea, bradycardia, tissue specific hypoperfusion, and hypometabolism of hypoperfused tissues. (2) Another group of functionally linked characters are more malleable and include (i) spleen mass, (ii) blood volume, and (iii) hemoglobin (Hb) pool size. Increases in any of these traits (or in a morphological character, body size) improve diving capacity. Assuming that conserved physiological function means conserved sequences in specific genes and their products (and that evolving function requires changes in such sequences), it is possible to rationalize both the above trait categories in pinniped phylogeny. However, it is more difficult for molecular evolution theory to explain how complex regulatory systems like those involved in bradycardia and peripheral vasoconstriction remain the same through phylogenetic time than it is to explain physiological change driven by directional natural selection.

Animals↗
PubMed1975

Evolution of mesenchymal cells in fetal rat lung.

The evolution of connective tissue cells in the developing fetal rat lung is studied under the electron microscope from the 15th until the 21st day of gestation and is compared to the evolution of epithelial cells. Three successive types of stem cells ("mesocytoblasts") are present during the first stages of lung development studied (15 to 18 days of gestation). These stem cells appear to be able to differentiate into fibroblasts or into smooth muscle cells, according to their localization along the broncho-alveolar tubule. Myoblasts are situated near the bronchial epithelium, whereas fibroblasts occur under the alveolar epithelium. Epithelo-mesenchymal interactions are assumed to play a role in this differentiation process. Synthesis of both, collagen and elastic fibers and of cytoplasmic filaments by fibroblasts as well as by myoblasts reveal the multiple potentialities of the mesenchymal stem cell and suggest a common origin. The early fibroblast in characterized by long cytoplasmic processes which contain numerous cytofilaments, and by the presence of collagen fibers in the vicinity of the cell. Later on, (20 days of gestation) the mature fibroblast of the lung mesenchyme shows areas of RER, glycogen and lipidic vacuoles in its cytoplasm. Cytofilaments are numerous within very long cytoplasmic processes and elastic and collagen fibers are very frequent beside the cytoplasmic membrane. The earliest fibroblast differentiation occurs under the epithelium of primitive respiratory bronchioles, which indicate the limit between the bronchial and the alveolar territories. Later on, differentiating fibroblasts are found throughout the whole alveolar walls. Connective tissue cells other than mesenchymal stem cells, fibroblasts or myoblasts are observed during lung development. Vacuolar cells, similar to Hofbauer cells, transiently appear on the 16th day of gestation. On the 20th and the 21st day macrophage-like cells are present in the septal space of the alveolar wall. The absence of intermediate stages of differentiation and parallel evolution of blood cells suggest that those connective tissue cells are differentiated elsewhere and have then migrated from blood into lung mesenchyme. No cell death has been observed in the developing lung.

Animals↗
PubMed2003

Very slow EEG responses lateralize temporal lobe seizures: an evaluation of non-invasive DC-EEG.

BACKGROUND: This study tested the idea that very slow EEG responses (direct current [DC] potential shifts) could be detected noninvasively during temporal lobe (TL) seizures, and that these shifts give lateralizing information consistent with that obtained by other methods. METHODS: Seven patients with TL epilepsy (TLE) were recorded with scalp DC-EEG technique at bedside. All recordings were performed simultaneously with conventional EEG (scalp in five, and intracranially in two; two patients with scalp recordings were recorded intracranially later). Seizures in five patients originated in the mesial TL. Ictal DC shifts were evaluated by comparing them to the temporal evolution of ictal discharges, and by comparing the laterality of these shifts to the side of seizure onset defined by routine EEG and other presurgical diagnostic tests. RESULTS: All seizures (35/35) were associated with negative DC shifts at temporal derivations (30 to 150 micro V relative to vertex), beginning at the electrical seizure onset, and lasting for the whole seizure. In eight seizures (five patients) with documented mesial TL onset, the polarity of the DC shift was initially positive followed by a negative one after lateral spread of seizure activity. In all cases, the side of the EEG shift agreed with other diagnostic tests, and, at times, was more clearly lateralized than the conventional scalp EEG. CONCLUSIONS: DC-EEG recordings are practical and achievable at the bedside. Ictal DC shifts are consistently observed in scalp recordings in TL seizures, and reliably lateralize them. This method may hold promise in reducing the need for invasive monitoring in patients with TLE where other noninvasive tests are equivocal.

Adult↗
PubMed2001

Different patterns in molecular evolution of the Triticeae.

A huge part of the genomes of most Triticeae species is formed by different families of repetitive DNA sequences. In this paper the phylogenetic distribution of two major classes of the repeats, retrotransposons and tandemly organized DNA sequences, are considered and compared with the evolution of gene-rich regions and generally accepted Triticeae phylogenetic relationships. In Hordeum, LTR-containing retrotransposons are dispersed along the chromosomes and are consistent with the existing picture of the phylogeny of Hordeum. Another retrotransposon class, LINEs, have evolved independently from LTR-retrotransposons. Different retrotransposon classes appear to have competed for genome space during the evolution of Hordeum. Another class of repeats, tandemly organized DNA sequences, tends to cluster at the functionally important regions of chromosomes, centromeres and telomeres. The distribution of a number of tandem DNA families in Triticeae is not congruent with generally accepted phylogenetic relationships. While natural selection is the dominant factor determining the structure of genic regions we suggest that the contribution of random events is important in the evolution of repetitive DNA sequences. The interplay of stochastic processes, molecular drive, and selection determines the structure of chromosomal regions, notably at centromeres and telomeres, stabilizing and differentiating species-specific karyotypes. Thus, the evolution of these regions may occur largely independently of the evolution of gene-rich regions.

Blotting, Southern↗
PubMed1976

Functional aspects of hemoglobin evolution in the mammals.

Comparative studies of red cells 2, 3 Diphosphoglycerate (DPG) and its effect on hemoglobin oxygen affinity from a taxonomically diverse set of mammals indicate two anomalous groups: members of the superfamilies Bovoidea (Actiodactyla) and Feloidea (Carnivora). In both taxa all of the individuals assayed had very low or unmeasurable quantities of DPG and red cell lysates with little, if any, DPG effect as measured by the change in oxygen affinity in the absence and presence of the phosphate. However, in both groups compensatory changes have occurred in hemoglobin structure and function so as to reduce the native oxygen affinity and thus cause them to resemble the hemoglobins of DPG-utilizing mammals as they occur in the setting of the red cell. We conclude that this parallelism of function is the result of convergent evolution.

Amino Acid Sequence↗
PubMed1994

Clinical aspects of incomplete septal cirrhosis in comparison with macronodular cirrhosis.

BACKGROUND/AIMS: Incomplete septal cirrhosis (ISC) is a form of macronodular cirrhosis characterized by slender, incomplete septa that demarcate inconspicuous nodules. Its clinical features have not been investigated in a large series. The aims of this study were to review the clinical symptoms and evolution of ISC in 42 patients. METHODS: Forty-two patients with at least one liver biopsy strongly suggestive of ISC were selected for the study covering a period between 1968 and 1987. Data for these patients were compared with the evolution of 49 patients with classical macronodular cirrhosis after chronic active hepatitis type B or C. RESULTS: Possible etiological factors for ISC were alcohol abuse, arsenic treatment, and hepatitis B infection. In three cases, a genetic factor could not be excluded. Patients with ISC had significantly lower serum concentrations of transaminases and bilirubin at diagnosis. Compared with macronodular cirrhosis, bleeding varices were more frequent (57% vs. 22%) in ISC. Ten-year survivals in the ISC and the macronodular cirrhosis groups were 54% and 57%, respectively. CONCLUSIONS: ISC represents a relatively stable burnt-out form of macronodular cirrhosis with an unusually high incidence of variceal bleeding. This could be explained by a superimposed insufficiency of the portal vascular supply.

Adolescent↗
PubMed2000

"Alien" wasps and evolution of development.

A comparative analysis of early developmental programs in a group of parasitic wasps reveals that closely related species can undergo dramatic evolutionary shifts in their patterns of embryogenesis. Developmental changes detected include alterations in early cleavage divisions, the establishment of embryonic anteroposterior polarity and modifications of the segmentation gene hierarchy described from Drosophila. These changes appear to be adaptations to parasitic development, taking place within the body of the host. Wasps illustrate a surprising plasticity in their early development and embryogenesis. The alterations associated with different parasitic strategies suggest that ecological adaptations may have profound influences on developmental processes in animals.

Animals↗
PubMed2002

A deer (subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes.

Comparative maps between ruminant species and humans are increasingly important tools for the discovery of genes underlying economically important traits. In this article we present a primary linkage map of the deer genome derived from an interspecies hybrid between red deer (Cervus elaphus) and Père David's deer (Elaphurus davidianus). The map is approximately 2500 cM long and contains >600 markers including both evolutionary conserved type I markers and highly polymorphic type II markers (microsatellites). Comparative mapping by annotation and sequence similarity (COMPASS) was demonstrated to be a useful tool for mapping bovine and ovine ESTs in deer. Using marker order as a phylogenetic character and comparative map information from human, mouse, deer, cattle, and sheep, we reconstructed the karyotype of the ancestral Pecoran mammal and identified the chromosome rearrangements that have occurred in the sheep, cattle, and deer lineages. The deer map and interspecies hybrid pedigrees described here are a valuable resource for (1) predicting the location of orthologs to human genes in ruminants, (2) mapping QTL in farmed and wild deer populations, and (3) ruminant phylogenetic studies.

Animals↗
PubMed2000

Protein surface similarities: a survey of methods to describe and compare protein surfaces.

Many methods have been developed to analyse protein sequences and structures, although less work has been undertaken describing and comparing protein surfaces. Evolution can lead sequences to diverge or structures to change topology; nevertheless, surface determinants that are essential to protein function itself may be mantained. Moreover, different molecules could converge to similar functions by gaining specific surface determinants. In such cases, sequence or structure comparisons are likely to be inadequate in describing or identifying protein functions and evolutionary relationships among proteins. Surface analysis can identify function determinants that are independent of sequence or secondary structure and can therefore be a powerful tool to highlight cases of possible convergent or divergent evolution. This kind of approach can be useful for a better understanding of protein molecular and biochemical mechanisms of catalysis or interaction with a ligand, which are usually surface dependent. Protein surface comparison, when compared to sequence or structure comparison methods, is a hard computational challenge and evaluated methods allowing the comparison of protein surfaces are difficult to find. In this review, we will survey the current knowledge about protein surface similarity and the techniques to detect it.

Algorithms↗
PubMed2001

Quartet-mapping, a generalization of the likelihood-mapping procedure.

Likelihood-mapping (LM) was suggested as a method of displaying the phylogenetic content of an alignment. However, statistical properties of the method have not been studied. Here we analyze the special case of a four-species tree generated under a range of evolution models and compare the results with those of a natural extension of the likelihood-mapping approach, geometry-mapping (GM), which is based on the method of statistical geometry in sequence space. The methods are compared in their abilities to indicate the correct topology. The performance of both methods in detecting the star topology is especially explored. Our results show that LM tends to reject a star tree more often than GM. When assumptions about the evolutionary model of the maximum-likelihood reconstruction are not matched by the true process of evolution, then LM shows a tendency to favor one tree, whereas GM correctly detects the star tree except for very short outer branch lengths with a statistical significance of >0.95 for all models. LM, on the other hand, reconstructs the correct bifurcating tree with a probability of >0.95 for most branch length combinations even under models with varying substitution rates. The parameter domain for which GM recovers the true tree is much smaller. When the exterior branch lengths are larger than a (analytically derived) threshold value depending on the tree shape (rather than the evolutionary model), GM reconstructs a star tree rather than the true tree. We suggest a combined approach of LM and GM for the evaluation of starlike trees. This approach offers the possibility of testing for significant positive interior branch lengths without extensive statistical and computational efforts.

Computer Simulation↗