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At least 379 records · Page 21Linked to original sources
PubMed2006

Functional analysis of gene duplications in Saccharomyces cerevisiae.

Gene duplication can occur on two scales: whole-genome duplications (WGD) and smaller-scale duplications (SSD) involving individual genes or genomic segments. Duplication may result in functionally redundant genes or diverge in function through neofunctionalization or subfunctionalization. The effect of duplication scale on functional evolution has not yet been explored, probably due to the lack of global knowledge of protein function and different times of duplication events. To address this question, we used integrated Bayesian analysis of diverse functional genomic data to accurately evaluate the extent of functional similarity and divergence between paralogs on a global scale. We found that paralogs resulting from the whole-genome duplication are more likely to share interaction partners and biological functions than smaller-scale duplicates, independent of sequence similarity. In addition, WGD paralogs show lower frequency of essential genes and higher synthetic lethality rate, but instead diverge more in expression pattern and upstream regulatory region. Thus, our analysis demonstrates that WGD paralogs generally have similar compensatory functions but diverging expression patterns, suggesting a potential of distinct evolutionary scenarios for paralogs that arose through different duplication mechanisms. Furthermore, by identifying these functional disparities between the two types of duplicates, we reconcile previous disputes on the relationship between sequence divergence and expression divergence or essentiality.

Bayes Theorem↗
PubMed2026

Divergent Biological Consequences of APOE Isoforms Across Industrialized and Non-Industrial Environments.

The apolipoprotein ε4 (APOE ε4) isoform directly alters cholesterol and immune biology and is associated with an increased risk of neurodegenerative and cardiometabolic disease in industrialized settings; nevertheless, APOE ε4-which is ancestral in humans-has persisted over evolutionary time. One potential explanation is that the costs and benefits of APOE ε4 were significantly different in the environments in which humans evolved compared to those we experience today. In support, previous work has suggested that living in a high pathogen environment, engaging in high levels of physical activity, or eating a low fat diet can dampen the detrimental effects of APOE ε4, and has revealed positive effects for fertility. However, direct tests of whether APOE isoforms are associated with different biological outcomes in non-industrial versus industrialized contexts are lacking. Working with the Turkana of Kenya and the Orang Asli of Peninsular Malaysia-two Indigenous groups in which individuals of shared ancestry span a continuum of subsistence, non-industrial to urban, industrialized lifestyles-we investigated how APOE genotypes impact cholesterol, immunological, and reproductive traits and tested for genotype x environment (GxE) interactions. First, we confirmed established genotype effects across lifestyles, showing that more APOE ε4 alleles are associated with higher total cholesterol, higher LDL cholesterol, and lower HDL cholesterol. Second, we tested for lifestyle interactions, finding lifestyle-dependent effects of genotype on innate immune biomarkers in the Orang Asli but not Turkana. Finally, we show that more APOE ε4 alleles are correlated with an extended reproductive lifespan, however this effect is relatively weak, is not consistent across populations, and does not correspond with a higher reproductive output. Together, our study provides evidence that industrialized environments can modify the biology of APOE ε4; however, we find that APOE ε4 is not universally beneficial in non-industrial contexts, highlighting the role of local environmental variation in determining its specific costs and benefits.

Journal Article↗
PubMed2004

The Fusarium oxysporum f. sp. ciceris/Cicer arietinum pathosystem: a case study of the evolution of plant-pathogenic fungi into races and pathotypes.

The use of resistant cultivars is one of the most practical and cost-efficient strategies for managing plant diseases. However, the efficiency of resistant cultivars in disease management is limited by pathogenic variability in pathogen populations. Knowledge of the evolutionary history and potential of the pathogen population may help to optimize the management of disease-resistance genes, irrespective of the breeding strategy used for their development. In this review, we examine the diversity in virulence phenotypes of Fusarium oxysporum f. sp. ciceris, the causal agent of Fusarium wilt of chickpeas, analyze the genetic variability existing within and among those phenotypes, and infer a phylogenetic relationship among the eight known pathogenic races of this fungus. The inferred intraspecific phylogeny shows that each of those races forms a monophyletic lineage. Moreover, virulence of races to resistant chickpea cultivars has been acquired in a simple stepwise pattern, with few parallel gains or losses. Although chickpea cultivars resistant to Fusarium wilt are available, they have not yet been extensively deployed, so that the stepwise acquisition of virulence is still clearly evident.

Biological Evolution↗
PubMed1992

Gene conversion of immunoglobulin variable regions in mutagenesis cassettes by replacement PCR mutagenesis.

A technique, Replacement PCR Mutagenesis, was developed to replace one immunoglobulin variable region (V) in a M13 phage cassette with a different, homologous V. This allows the use of the same mutagenesis and subsequent expression vectors for many V regions or V segments. The method combines PCR of V fragments and in vitro mutagenesis. Primers homologous to 3' and 5' ends of both V regions initiate PCR synthesis of the V DNA fragment (donor) that will replace the V region (recipient) in M13. Donor V PCR DNA may originate from mRNA, cloned V genes or genomic templates. The donor V PCR DNA is denatured and annealed to the M13 cassette containing the recipient V to be supplanted. The second strand is synthesized, transfected into bacteria and mutant plaques selected by hybridization. Since restriction sites in primers are not required, altered primer-encoded amino acids are avoided. Further, the PCR donor piece can be of any length if it shares homology with the recipient gene. This allows construction and expression of complete gene replacements and chimeras. This method is also applicable to V "humanization" and studying sets of homologous genes containing polymorphic or evolutionary disparities. The potential uses of the technique are discussed.

Animals↗
PubMed1986

[Construction of the bacterial genome--the next goal of genetic engineering].

The article deals primarily with literature data on the organization and evolution of bacterial genome. An account of the conception of "current" bacterial evolution consisting of periodical inclusions into a bacterial genome of genes having exogenous origin is given. A hypothesis is proposed that rare inversions going through the oriC or terC chromosomal regions could serve as reparative rearrangements providing balanced distribution of the DNA segments of different origin within the circular genome. It is asserted that the progress in the study of the model microorganism Escherichia coli K-12 as well as in genetical methods give rise to a new experimental challenge--the creation of a "rational" bacterial genome on the basis of E. coli cell. It is proposed that a "rational" bacterial genome could be devoid of many genes which provide the evolutionary formed ecological potential of the species and its capacity for rapid adaptation to new environment.

Biological Evolution↗
PubMedDate not supplied

Detailed staging of inbred C57BL/6 mice between Theiler's [1972] stages 18 and 21 (11-13 days of gestation) based on craniofacial development.

A detailed staging table of inbred C57BL/6 embryonic mice was developed to facilitate a study of the stage-by-stage cellular and molecular mechanisms underlying cranial skeletal development and elucidation of the developmental mechanisms potentially involved in evolutionary changes in cranial skeletal morphology exhibited by different inbred strains of mice. Mice were mated for only 2 hr and embryos were recovered every 2 or 4 hr between 11 and 13 days of gestation. Theiler's [1972] stages 18 through 21 were divided into substages and divisions based on the development of five external structures--the frontonasal area, eyes, auditory meatus, mandibular and hyoid auricular hillocks/pinna, and vibrissae--and three internal histological structures--eyes, tongue, and vibrissae. Each substage and division was designated with a decimal point: e.g., substage 20.1 and division 20.11. Embryos were staged using the staging table and the relationship of the substages and divisions with days of gestation was examined. The results showed considerable intra- and inter-litter variation in stages of embryos, suggesting that days of gestation are not a good indicator for staging embryos. Our staging table offers a more reliable and precise method to standardize embryonic development. Regression analyses of substages on days of gestation showed that the duration of stages increased from stages 18 to 21. Estimated durations were 3.5 hr for stages 18 and 19, 8.8 hr for stage 20, and 38.8 hr for stage 21. Our staging table also provides baseline information on development of the frontonasal area (muzzle) and vibrissae and development and the transformation of the auricular hillocks into the pinna. The developmental sequence of mystacial and labial vibrissae indicated highly regulated differentiation and morphogenesis of vibrissal development at stages 20 and 21. Three hyoid auricular hillocks transiently became four hillocks at stage 19.1 before transforming to the pinna during stage 21. The second and third hyoid auricular hillocks were the major contributor to the pinna before stage 21.2, whereas mandibular auricular hillocks contributed to the pinna from stage 21.32 onward. The staging table has already served to demonstrate stage-specific skeletogenesis of the first arch cartilages in inbred C57BL/6 mice and to reveal differences in the onset of timing of skeletogenesis among inbred C57BL/6, C3H/He and CBA/J mice.

Animals↗
PubMed1997

Neural crest potential for tooth development in a urodele amphibian: developmental and evolutionary significance.

Tooth development in urodele amphibians occurs from a restricted region of anterior cranial neural crest. An in vitro culture system was used to test the odontogenic potential of more caudal regions of neural crest, including an "intermediate region" of neural folds which has never previously been tested for either fate or potential. Explants of different axial levels of neural crest with stomodaeal ectoderm and endoderm demonstrated that odontogenic potential extends not only further caudally than the axial level fated to produce teeth, but also beyond that with potential to produce cartilage. Our results show that chondrogenic potential is found only within the most rostral portion of the intermediate region, but that odontogenic potential extends to its most caudal limit. This separation of skeletogenic cell lineages in the neural crest necessitates a reevaluation of the designations of "cranial" and "trunk" and a reconsideration of the evolutionary implications of developmentally distinct crest-derived mesenchyme populations. The proposal that odontogenic potential extends into the trunk neural crest may be explained as conserved from a phylogenetically older, more extensive skeletogenic ability which produced the exoskeleton of more basal vertebrates.

Ambystoma mexicanum↗
PubMed1992

Evolution of developmental decisions and morphogenesis: the view from two camps.

Modern developmental biology largely ignores evolution and instead focuses on use of standard model organisms to reveal general mechanisms of development. Evolutionary biologists more widely hold developmental biology to be of major consequence in providing potential insights into evolution. Evolutionary insights can enlighten our views of developmental mechanisms as much as developmental data offer clearer views of mechanisms which underlie evolutionary change. However, insights have been limited by the long-term disengagement of the two fields dating to the rise of experimental embryology in the 1890s. Molecular genetics now provides a powerful tool to probe both gene function and evolutionary relationships, and a greater connection has become possible. The expansion of experimental organisms beyond the standard model animals used in most studies of development allows us to ask deeper questions about the interaction of development and evolution. This paper presents an analysis of the complementary uses of the resulting data in the two fields as they grope for accommodation. Analysis of the radical changes in early development seen in closely related sea urchins with alternate modes of development illustrate the complementarity of developmental and evolutionary data. These studies show that what have been thought to be constrained mechanisms of axial determination, cell lineage patterning, and gastrulation in fact evolve readily and provide the means for the rapid evolution of development.

Animals↗
PubMed2003

Erotomanic stalking in evolutionary perspective.

Erotomania, the delusion of being loved by another person, comprises marked sex differences concerning prevalence rates and behavior. Whereas traditional psychiatry has considered erotomania to be almost entirely restricted to women, recent studies have revealed that criminal offenses associated with the condition occur much more frequently in men. The main hypothesis of this article is that these findings may be explained in terms of evolutionary theory. Erotomania, accordingly, may be viewed as a pathological variant of a specific sexual strategy that evolved under selection pressures of the human environment of evolutionary adaptedness. The overt behavior is related to the pursuit of long-term mating, its potentially beneficial effect on inclusive fitness of the individual, and disparate strategies of the sexes to ensure sexual fidelity of the potential partner. Therefore, the evolutionary approach provides a plausible explanation as to why forensically relevant erotomania prevails in men. The pathological process of delusional misinterpretation of perceived signals from the social environment itself may result from poor reality testing due to a failure of social meta-cognition. The evolutionary perspective may provide additional insights into the nature of sex-specific behaviors and may improve our understanding of forensically relevant behaviors.

Delusions↗
PubMed2001

Phenotypic plasticity in the interactions and evolution of species.

When individuals of two species interact, they can adjust their phenotypes in response to their respective partner, be they antagonists or mutualists. The reciprocal phenotypic change between individuals of interacting species can reflect an evolutionary response to spatial and temporal variation in species interactions and ecologically result in the structuring of food chains. The evolution of adaptive phenotypic plasticity has led to the success of organisms in novel habitats, and potentially contributes to genetic differentiation and speciation. Taken together, phenotypic responses in species interactions represent modifications that can lead to reciprocal change in ecological time, altered community patterns, and expanded evolutionary potential of species.

Animals↗
PubMed1996

Stem-loop potential in MHC genes: a new way of evaluating positive Darwinian selection?

The domains of polymorphic major histocompatibility complex (MHC) proteins which interact with peptides and T-cell receptors are considered to have been under positive evolutionary selection pressure. Evidence for this is a high ratio of non-synonymous to synonymous mutations in the corresponding genomic domains. By this criterion snake venom phospholipase A2 genes have also been under positive selection pressure. Recent studies of the latter genes indicate that positive selection has overridden an evolutionary pressure on base order which normally promotes the potential to extrude single-strand stem-loops from supercoiled duplex DNA ( fold pressure ). This has resulted in base order-dependent stem-loop potential being shifted to introns, which are highly conserved between species. It is now shown that, like snake venom phospholipase A2 genes, the domains of polymorphic MHC genes which appear to have responded to positive selection pressure have decreased base order-dependent stem-loop potential. The evolutionary pressure to generate stem-loop potential (believed to be important for recombination) has been overridden less in exons under negative purifying selection than in exons under positive Darwinian selection. Thus, base order-dependent stem-loop potential shows promise as an independent indicator of positive selection.

Animals↗
PubMed1998

Evolutionary conservation and tissue-specific processing of Hoxa 11 antisense transcripts.

We previously described the existence of abundant, processed, polyadenylated murine Hoxa 11 antisense transcripts. Of particular interest, in the developing limbs the antisense transcripts were observed to be present in a pattern complementary to that of the sense transcripts, suggesting a possible regulatory function (Hsieh-Li et al. 1995). We have analyzed the human HOXA 11 genomic locus, showing strong evolutionary conservation of regions potentially encoding antisense transcripts. Human HOXA 11 fetal kidney antisense cDNAs were identified and sequenced, demonstrating the evolutionary conservation of Hoxa 11 antisense transcription. As for the mouse, the human antisense RNAs were polyadenylated and showed several alternative processing patterns, but shared the sequences of a common 3' exon. The evolutionary conservation of the opposite strand transcripts strongly suggests function. A significantly long open reading frame was observed, but mouse-human comparisons argued against true coding function. Murine kidney Hoxa 11 antisense transcription and processing was also examined, revealing tissue-specific differences between limb and kidney. A novel procedure, designated Race in Circles, was devised and used to define mouse limb antisense transcription start sites. Furthermore, comparisons of human, mouse, and chicken sense transcript Hoxa 11 homeobox nucleotide sequences and their respective encoded homeodomains indicate a very strong selective pressure in vertebrates against mutations that result in coding changes. Given the significant differences in amino acid sequences of the homeodomains of different Hox genes, this observation argues for individual homeodomain functional specificity.

5' Untranslated Regions↗
PubMed1974

The importance of gene rearrangement in evolution: evidence from studies on rates of chromosomal, protein, and anatomical evolution.

We have compared the relative rates of protein evolution and chromosomal evolution in frogs and mammals. The average rate of change in chromosome number has been about 20 times faster in mammals than in frogs. Whereas it takes only 3.5 million years, on the average, for a pair of mammal species to develop a difference in chromosome number, the corresponding period for frogs is 70 million years. In contrast, the rate of protein evolution in mammals has been roughly equal to that in frogs. The rapid rate of gene rearrangement in mammals parallels both their rapid anatomical evolution and their rapid evolutionary loss of the potential for interspecific hybridization. Thus, gene rearrangements may be more important than point mutations as sources for evolutionary changes in anatomy and way of life.

Adaptation, Biological↗
PubMedDate not supplied

Evolutionary approaches to psychiatry and problems of method.

Evolutionary hypotheses have been used widely to interpret enigmatic psychiatric phenomena. In applying evolutionary theory, three common methodological errors occur: imprecise and inappropriate use of evidence and theoretical concepts; incorrect assessment of the level at which evolutionary processes occur; and potential misinterpretation of observations due to a confusion of proximate and ultimate causation. Guidelines and criteria for developing meaningful evolutionary hypotheses and rigorous research strategies are described. It is hoped that these efforts will enhance the contribution evolutionary theory may have as it is applied to psychiatric observations in the future.

Adaptation, Psychological↗
PubMed2005

The proper place of hopeful monsters in evolutionary biology.

Hopeful monsters are organisms with a profound mutant phenotype that have the potential to establish a new evolutionary lineage. The Synthetic Theory of evolutionary biology has rejected the evolutionary relevance of hopeful monsters, but could not fully explain the mechanism and mode of macroevolution. On the other hand, several lines of evidence suggest that hopeful monsters played an important role during the origin of key innovations and novel body plans by saltational rather than gradual evolution. Homeotic mutants are identified as an especially promising class of hopeful monsters. Examples for animal and plant lineages that may have originated as hopeful monsters are given. Nevertheless, a brief review of the history of the concept of hopeful monsters reveals that it needs refinements and empirical tests if it is to be a useful addition to evolutionary biology. While evolutionary biology is traditionally zoocentric, hopeful monsters might be more relevant for plant than for animal evolution. Even though during recent years developmental genetics has provided detailed knowledge about how hopeful monsters can originate in the first place, we know almost nothing about their performance in natural populations and thus the ultimate difference between hopeful and hopeless. Studying the fitness of candidate hopeful monsters (suitable mutants with profound phenotype) in natural habitats thus remains a considerable challenge for the future.

Animals↗
PubMed2002

Phylogenetic relationships and morphological diversity in Darwin's finches and their relatives.

Despite the importance of Darwin's finches to the development of evolutionary theory, the origin of the group has only recently been examined using a rigorous, phylogenetic methodology that includes many potential outgroups. Knowing the evolutionary relationships of Darwin's finches to other birds is important for understanding the context from which this adaptive radiation arose. Here we show that analysis of mitochondrial DNA sequence data from the cytochrome b gene confirm that Darwin's finches are monophyletic. In addition, many taxa previously proposed as the sister taxon to Darwin's finches can be excluded as their closest living relative. Darwin's finches are part of a well-supported monophyletic group of species, all of which build a domed nest. All but two of the non-Darwin's finches included in this clade occur on Caribbean islands and most are Caribbean endemics. These close relatives of Darwin's finches show a diversity of bill types and feeding behaviors similar to that observed among Darwin's finches themselves. Recent studies have shown that adaptive evolution in Darwin's finches occurred relatively quickly. Our data show that among the relatives of Darwin's finches, the evolution of bill diversity was also rapid and extensive.

Animals↗
PubMed1977

Neuroticism, extraversion and slow brain potentials.

Peak amplitude and area under the curve of average vertex slow potentials recorded during the foreperiod of a reaction time task were found to discriminate between high- and low-neuroticism subjects, defined according to the Eysenck Personality Inventory. High-neuroticism subjects developed smaller peak amplitude, greater area and longer reaction times, presenting a high extinction rate when the imperative stimulus was omitted. Differences between extraverts and introverts were found within the low-neuroticism group and for area values, extraverts exhibiting larger area. A significant interaction effect of extraversion and neuroticism on slow-potential parameters was evidenced. Results are interpreted in terms of heightened arousal and disrupted focused attention in high-neuroticism subjects. Although evolutionary indexes of slow potentials could differentiate between extraverts and introverts, further work using inhibition indicators is needed to further clarify the differences between them. The data reported also suggest that different aspects of overt behavior would be associated diversely with slow-potential parameters.

Arousal↗