SEARCH · Search PubMed

Results for “evolutionary genetics”

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.

SourceResearch connectionFrom yearThrough year

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

At least 361 records · Page 20Linked to original sources

PubMed1999

New technologies in medicine: biotechnology and nanotechnology.

In February 1997, researchers created Dolly, a lamb cloned from the DNA of an adult sheep. This was supposed to be impossible (or at least generations away), but suddenly it was here--a clone of a higher mammal. Whatever Dolly's ultimate significance, she conclusively demonstrated the growing power of biotechnology. Many have come to the conclusion that advances in biotechnology will fundamentally transform medicine during the coming decade. Society is in the midst of a technical revolution that will have the same relevance as the development of the printing press, the internal combustion engine, and the microprocessor. Computers have become the key tools in the accelerating progress that is occurring in the field of biotechnology. At the same time, genetic, evolutionary, and other biologic processes are providing new models for the development of computer hardware and software. Today represents the early stages of what has been called the "bionic convergence": the convergence of the biologic revolution with the information revolution, the joining of biology with electronics. Virtually everything that is important to health care practitioners and patients--diagnostic techniques, means of understanding disease causes, methods of treatment, approaches to prevention, health care facility design, medical education, and legal and ethical issues--will be changed by the revolutions currently underway in the fields of biotechnology and genetic medicine. The following monograph includes several forecasts about a range of possible opportunities that may have enormous effects on health care during the next century. These forecasts address the potential impacts of biotechnology on disease detection and diagnosis, treatment, prevention, nanotechnology, and other areas of medical significance. Every area of beneficiary care will be affected as the changes implied by these forecasts begin to develop. Beneficiary care will continue to see the emergence of a "forecast, prevent, and manage" paradigm. The emphasis will be on disease prevention, health promotion, and the creation of healthy communities. New diagnostic and treatment opportunities will be available as a consequence of breakthroughs in genetic medicine. The health care system will view health as a whole, as a person's overall sense of well-being--an entity that encompasses much more than the absence of symptoms.

Biotechnology↗

PubMed2003

Molecular evolution and quantitative variation for chemosensory behaviour in the nematode genus Caenorhabditis.

Caenorhabditis elegans is a model organism in biology, yet despite the tremendous information generated from genetic, genomic and functional analyses, C. elegans has rarely been used to address questions in ecological genetics. Here, we analyse genetic variation for chemosensory behaviour, an ecologically important trait that is also genetically well characterized, at both the phenotypic and molecular levels within three species of the genus Caenorhabditis. We show that the G-protein ODR-3 plays an important role in chemosensory avoidance behaviour and identify orthologues of odr-3 in C. briggsae and C. remanei. Both quantitative genetic analysis of chemosensory behaviour and molecular population genetic analysis of odr-3 show that there is little genetic variation among a worldwide collection of isolates of the primarily selfing C. elegans, whereas there is substantially more variation within a single population of the outcrossing C. remanei. Although there are a large number of substitutions at silent sites within odr-3 among the three species, molecular evolution at the protein level is extremely conserved, suggesting that odr-3 plays an important role in cell signalling during chemosensation and/or neuronal cilia development in C. remanei and in C. briggsae as it does in C. elegans. Our results suggest that C. remanei may be a more suitable subject for ecological and evolutionary genetic studies than C. elegans.

Animals↗

PubMed1997

Genetic variation segregating in natural populations of Tribolium castaneum affecting traits observed in hybrids with T. freemani.

We investigated patterns of within-species genetic variation for traits observed in hybrids (hybrid numbers, hybrid sex ratios, and hybrid male deformities) between two species of flour beetles, Tribolium castaneum and T. freemani. We found genetic variation segregating among four natural populations of T. castaneum as well as within these populations. For some hybrid traits, we observed as much variation among populations 750 km apart as between populations on different continents, suggesting genetic differentiation at a local scale. Within natural populations, the variation segregating among sires is greater than that found in an earlier study for an outbred laboratory population and comparable to that observed between inbred lines derived from the outbred stock by eight generations of brother-sister mating. When sires from T. castaneum are mated to conspecific and heterospecific females, we do not observe a significant correlation at the level of the family mean between the intraspecific and interspecific phenotypes, suggesting the independence of the hybrid traits from comparable traits within species. We discuss our findings in relation to the evolutionary genetics of speciation and the expression of epistatic genetic variance in interspecific crosses.

Animals↗

PubMed2001

Genetic variability of respiratory syncytial virus subgroup B strain isolated during the last 20 years from the same region in Japan: existence of time-dependent linear genetic drifts.

The genetic variability of 32 respiratory syncytial virus (RSV) sub-group B isolates from a single community in Japan during the 20 years from 1980 to 1999 was determined. Two variable regions of the attachment (G) protein gene were amplified by reverse transcriptase-polymerase chain reaction amplification and their products were sequenced directly. Phylogenetic analysis of nucleotide sequences revealed seven distinct branches in which strains isolated during seasons of close proximity were located: however, isolates from the same season were often in plural branches. There was a tendency for recent isolates to lie at the end of each branch and these linear evolutionary changes were typically represented in a branch containing nine strains isolated during 6 seasons from '80 to '86. Three kinds of usages of stop codons were confirmed and isolates located in each branch used the same stop codons. These observations suggest that there are multiple subgroup B lineages co-circulating and that each lineage strain may exhibit linear evolutionary genetic drifts in order to survive over successive epidemics within the same population, although it has a conserved uniform G protein length with the use of the same stop codon.

Amino Acid Sequence↗

PubMed2000

[Selective pressure in host-parasite systems].

Selective pressures in host-parasite systems are the result of a continuous conflict between the divergent interests of each partner, on the long run. Whereas the fitness (lifetime reproductive success) of parasites is usually increased by a higher frequency of encounters with susceptible hosts and a better survival rate after infection, the fitness of hosts is increased by opposite processes, avoidance of encounters with infective stages and destruction of the parasites. These selective processes, often referred to as coevolution or arms races are in agreement with the Red Queen hypothesis of Van Valen, which assumes indefinite adaptive changes in both partners, in order to set up counter-measures against the weapons of "the other". Arms races in host-parasite systems thus suggest a gradualistic evolution, but this does not contradict the present day ideas on the tempo changes in the course of evolution (punctuated equilibria). Numerous factors, either genetic (evolutionary lag...), environmental (nutritional status...) or cultural (prevention, vaccination, therapy...) influence the severity of infections at an individual scale. The "terrain", which is a component of the individual phenotype, is thus at the cross-roads of genes, environment and culture. Humans must count more on their intelligence than on natural selection to prevent and cure infectious and parasitic diseases.

Adaptation, Physiological↗

PubMed2000

Palaeogenetic analysis of (pre)historic artifacts and its significance for anthropology.

The possibility of isolating ancient DNA (aDNA) from all kinds of (pre)historic anthropogenetic artifacts opens new perspectives. This study applies palaeogenetic techniques to three anthropological issues: 1. Palaeodiet. DNA sequences from organic residues in vessels identify Precolumbian Aztec diet. 2. (Pre)historic husbandry and economic structures. aDNA data can reveal the species and the genetic evolutionary stage of animals and plants and show the manner and the extent of their growth, cultivation, or domestication. 3. Production techniques, use, and functionality. Identification of the plant or animal source of an archaeological find can reveal the use or the function of the find. Examples from a Celtic "sausage-end" and an Aztec "eye salve" are given.

Archaeology↗

PubMed2001

Accelerated regulatory gene evolution in an adaptive radiation.

The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3/TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.

Adaptation, Physiological↗

PubMed1995

Genetic and phenotypic heterogeneity of human malignancies: finding order in chaos.

The presence of cellular heterogeneity within human tumors has been recognized for many years. Current concepts regarding the clonal origin of human neoplasms, and recent advances in the study of successive genetic changes that occur during tumor evolution may now make it possible to understand in greater depth the biological and clinical implications of intra-tumor heterogeneity at both the phenotypic and genotypic levels. In order to explore these concepts further, and to better identify the potential contributions that flow and image cytometry can make to our understanding of tumor heterogeneity, a session of the 1994 ISAC Congress was dedicated to plenary presentations on human cancer cell heterogeneity. Here, we provide a brief overview of the genetic evolutionary progression of human cancers, some considerations of clinically important phenotypic and genotypic markers, and an outline that might serve as a basis for framing relevant issues that are ammenable to further study. All Nature is but Art, unknown to thee; All Chance, Direction, which thou canst not see; All Discord, Harmony not understood: All partial Evil, universal Good. (Alexander Pope, Essay on Man, end of Epistle 1).

Biological Evolution↗

PubMed1995

Origins and clinical implications of aneuploidy in early bladder cancer.

Cytogenetic and flow cytometric studies in a variety of human solid tumors have suggested that gross aneuploidy may arise by a process of abrupt chromosome complement doubling followed by gradual chromosome loss. However, this sequence has not been demonstrated directly in serial studies in individual patients in vivo. The purpose of this study was to search for evidence of chromosome complement doubling and subsequent chromosome loss in flow cytometric ploidy patterns in serial bladder washings and/or biopsies from individual patients with early bladder cancer. Fifty-two patients with noninvasive bladder cancer were followed with serial flow cytometric DNA studies for periods ranging from 5.1 to 42.7 months (median 15.1 months). Serial changes in DNA ploidy and S phase fractions were recorded and correlated with histologic and/or cytologic findings, response to treatment and clinical outcome. The data suggest a series of genetic evolutionary changes in early bladder cancer that include the initial development of peridiploid aneuploidy and repeated rounds of DNA content doubling with chromosome loss in patients with progressive disease. It is likely that gross DNA aneuploidy, and more specifically, DNA multiploidy and DNA hypertetraploidy, all arise by this mechanism. The sequence of DNA diploidy, peridiploid aneuploidy, near-tetraploidy, hypotetraploidy and hypertetraploidy is associated with a progressive increase in S phase fraction, and with increasing tumor grade; late steps in this ploidy sequence were often present in tumors that were refractory to local therapeutic measures and tumors that developed deep tumor invasion and/or distant metastases. We conclude that DNA multiploidy and hypertetraploidy are markers of advanced stages of genetic evolution in human bladder cancer.

Adult↗

PubMed2000

Natural variation in phytochrome signaling.

The phytochromes, photoreceptors sensitive to red and far-red light, are critical for sensing foliage shade, canopy breaks, and neighbor proximity. A combination of molecular genetic, evolutionary, and ecological techniques are being used to understand how phytochromes function in the natural environment. We discuss studies on the adaptive value of phytochrome mediated plasticity, as well as the role that variation in phytochrome expression and function might play in allowing plants to adapt to unique light environments. Continued study of phytochrome signaling variation may reveal how natural selection acts at the molecular level.

Adaptation, Physiological↗

PubMed2000

Identification of the human Y-chromosomal microsatellite locus DYS19 from degraded DNA.

STR DYS19 seems to be one of the most useful markers for population genetic, evolutionary, and forensic applications. However, the authors have noticed that the amplification of the DYS19 polymorphism fails when highly degraded DNA is used as a template. The authors designed a new pair of primers that reduce the DYS19 fragment sizes compared with those of the known protocol. Using these primers, an improved success rate can be achieved, particularly when putrefied samples are under investigation.

Alleles↗

PubMed2001

[Studies on genetic diversity in gonochoristic offspring produced from mating between two different gynogenetic clones of silver crucian carp].

Based on the discovery of gonochoristic reproductive mode in silver crucian carp (Carassius auratus gibelio), 18 individuals from the mated offspring between clone F and clone D and their parents were analyzed using 11 RAPD primers. The mated offspring differentiated into three phenotypes. One phenotype is similar to that of clone F (SF). The second is similar to that of clone D (SD). The third shows a novel longer and thinner body type (NL). Electrophoretogram results show abundant polymorhic DNA fragments among individuals in the FD mated offspring. Obviously, the polymorphic DNA fragments originate from the genome recombination owing to the gonochoristic reproductive mode. The FD mated offspring amplify different fingerprints from maternal, and their fingerprints are different from each other. These different DNA fragments can be divided into four groups according to their origin. The average genetic distance among individuals from the FD offspring (0.23 +/- 0.123) is much higher than that of allogynogenetic offspring, which is only about 0.01. Of the three phenotypes in the FD offspring, the average distances among SD is the highest (0.235 +/- 0.097). The next is SF phenotype, in which the average distances is 0.148 +/- 0.073. The average distances among NL is the lowest (0.094 +/- 0.083). The gonochoristic reproductive mode introduces high genotypic variability and underlines genetic diversity. A dendrogram was constructed by NJTREE cluster analysis based on a total of 2320 distinguishable fragments (116 per individual). NL3 and maternal are most closely related, and SD3 and paternal are most closely related. The average genetic distances between SD and SF or NL (> 0.31) is higher than that of between SF and NL (0.124). Consistent with previous study, the genetic distance between maternal and paternal is 0.35. The average genetic distances between FD offspring and parents are both about 0. 32. But the similarities among the three phenotypes in mated group FD offspring and parents are different. The similarity between SF and maternal (71%) is higher than similarities among other phenotypes and maternal. The similarity between SD and paternal (70%) is higher than similarities among other phenotypes and paternal. The results suggest the similarities among three phenotypes in the FD offspring and parents are related with their phenotypes because some DNA fragments specific for phenotypes were amplified in this study. The revelation about reproductive diversity will be able to open the door in which complicated mechanism has been locked in unisexual organisms for long time, and establish the important roles of silver crucian carp in the studies on evolutionary genetics in unisexual or polyploid vertebrates.

Animals↗

PubMed2026

Methicillin-resistant Staphylococcus aureus (MRSA) infection in hospitalized patients is dominated by community-acquired strains: genomic epidemiological evidence.

OBJECTIVE: This study aimed to systematically investigate the molecular epidemiological characteristics of methicillin-resistant Staphylococcus aureus (MRSA) in Ningxia hospitals, to elucidate their genetic evolutionary relationships, and to delineate the genomic and phenotypic profiles of the dominant lineages. METHODS: Clinical isolates of MRSA strains collected between 01/01/2024 and 30/06/2024 were analyzed, employing second-generation gene sequencing technology, combined with MLST and SCCmec typing, along with evaluation of drug resistance and virulence genes. A phylogenetic tree was constructed to analyze strain homology. RESULTS: A total of 74 non-duplicate Staphylococcus aureus strains (67 MRSA and 7 MSSA) were collected. The most common clonal strain was ST59-IVa, accounting for 46.27%. This strain exhibited a high prevalence of resistance genes mecA and blaZ, at 91.04%. All five ST22-IVa strains were found to lack mecA and erm genes but showed β-lactam resistance, while possessing both lukS/F-PV (PVL) and tsst-1 virulence genes, indicating a significant toxicity risk. Genetic evolution analysis revealed that ST3355, ST4513, and ST59 were closely related, all belonging to SCCmec types IVa; the other ST types exhibited mutations at various loci, with ST5 as the central node, resulting in a wider array of ST and SCCmec typing. CONCLUSION: The ST59-IVa clone is the predominant MRSA strain in Ningxia hospitals, exhibiting multidrug resistance and virulence gene profiles consistent with national trends. However, the emergence of hypervirulent ST22-IVa strains with atypical resistance mechanisms warrants increased vigilance. We recommend enhancing the rational use of antibiotics in hospitals and implementing molecular surveillance for these highly virulent strains.

Methicillin-Resistant Staphylococcus aureus↗

PubMed1997

Microsatellites in the HLA region: on overview.

Microsatellites are repeats of a DNA base motif (1-6 bp, mostly CA repeats) up to 100 times; they are distributed regularly all over the genome. Many of them are polymorphic and their high polymorphism is based upon a variable number of repeats. They are widely used for genetic mapping, linkage analysis, population genetics, evolutionary studies and in forensic medicine. Such markers have also been described in the HLA region since 1991, and a growing interest in their potential applications is being expressed. The aims of this review are: 1) to outline the presently available information from literature and molecular databases concerning 53 microsatellites in the HLA region (localization, type of repeat, number of alleles, heterozygosity, primers used for amplification); 2) to address the question of technical pitfalls when using such markers; 3) to discuss specific features such as their mutation rate (10 (-3) to 10 (-6), which is higher than that reported for HLA genes, and their linkage disequilibrium with HLA alleles; 4) to present an integrated map of microsatellites and genes of this region; and 5) to provide a synopsis of their different applications in HLA-related fields (disease studies, population genetics, recombination point studies, HLA region mapping, transplantation) along with perspectives for future use. Although some HLA region microsatellites have already been applied to the analysis of more than 10 diseases, it is now evident that their use in population genetics and the determination of genomic compatibility in bone marrow transplantation represent growing areas of application.

Animals↗

PubMedDate not supplied

Genomic distribution of P elements in Drosophila willistoni and a search for their relationship with chromosomal inversions.

According to the recent-invasion hypothesis, Drosophila melanogaster may have acquired its P elements in a fairly recent process of horizontal transmission between species. Drosophila willistoni has been identified as the potential donor species in that transfer process. A most remarkable feature of D. willistoni is its extensive chromosomal polymorphism due to inversions-the adaptiveness of which has been the subject of many classical studies on evolutionary genetics. In this article, we further extend the study of P elements in D. willistoni, focusing on the possible role they may play in the generation of chromosomal inversions. Our results may be summarized as follows. P-homologous sequences were detected in South American populations of D. willistoni. In two of them, a recently collected wild population and an old laboratory stock, the P insertion sites were located in the polytene chromosomes. Several hybridization sites were mapped in all major chromosome arms of the natural population, which was also chromosomally polymorphic; in the laboratory population, nearly devoid of inversions, hybridization sites were found to be confined to the chromocenter. In the wild population, 10 of the 24 P hybridized sites coincided with several inversions break points and another five sites located themselves very close to those points. The results are discussed within the context of evolutionary hypotheses.

Animals↗

PubMed2005

Role of selection in fixation of gene duplications.

New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10(-9)-10(-10) per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication.

Animals↗

PubMed1998

Study of the relatedness of isolates of Shigella flexneri and Shigella sonnei obtained in 1986 and 1987 and in 1994 and 1995 from Hong Kong.

We used pulsed-field gel electrophoresis (PFGE) to study the genetic relatedness of 235 isolates of Shigella flexneri and Shigella sonnei collected in Hong Kong (97 isolates from 1986 and 1987 and 138 isolates from 1994 and 1995). Altogether, 13 gels were run with bacteriophage lambda ladder DNA (Pharmacia) as an external reference in every sixth lane, standardized reagents and methods, and isolates randomized for species and years. For quantitative illustration of the relationships within a large body of isolates, computer-generated dendrograms were used to determine the number of isolates in pulsotypes at Dice coefficients of similarity of 75% (PT75) and 50% (PT50). For S. flexneri, there was a significant difference in the distribution of isolates collected during the two periods in both PT75 and PT50, with 68% of isolates collected in 1994 and 1995 sharing a coefficient of similarity of >/=68%. For S. sonnei, a significant difference was observed in PT50 only. We also used Upholt's formula for an approximation of the fraction of nucleotide difference between isolates and Molecular Evolutionary Genetics Analysis to determine relative genetic distances. For both species, the relative genetic distances between isolates of the earlier collection period were significantly greater (P < 0.0001), i. e., they were further apart and therefore more diverse than those of the later period. We conclude that it is possible for a typical clinical laboratory to analyze a large amount of PFGE information on Shigella isolates obtained under controlled conditions. Such data analysis should enhance surveillance capabilities and give indications of further work to be done on various aspects of bacterial pathogenicity of the species.

Bacteriophage lambda↗

PubMed2007

Improved evolutionary optimization from genetically adaptive multimethod search.

In the last few decades, evolutionary algorithms have emerged as a revolutionary approach for solving search and optimization problems involving multiple conflicting objectives. Beyond their ability to search intractably large spaces for multiple solutions, these algorithms are able to maintain a diverse population of solutions and exploit similarities of solutions by recombination. However, existing theory and numerical experiments have demonstrated that it is impossible to develop a single algorithm for population evolution that is always efficient for a diverse set of optimization problems. Here we show that significant improvements in the efficiency of evolutionary search can be achieved by running multiple optimization algorithms simultaneously using new concepts of global information sharing and genetically adaptive offspring creation. We call this approach a multialgorithm, genetically adaptive multiobjective, or AMALGAM, method, to evoke the image of a procedure that merges the strengths of different optimization algorithms. Benchmark results using a set of well known multiobjective test problems show that AMALGAM approaches a factor of 10 improvement over current optimization algorithms for the more complex, higher dimensional problems. The AMALGAM method provides new opportunities for solving previously intractable optimization problems.

Algorithms↗