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At least 289 records · Page 16Linked to original sources
PubMed2000

Genetic evidence for gonochoristic reproduction in gynogenetic silver crucian carp (Carassius auratus gibelio bloch) as revealed by RAPD assays.

Sex evolution has been a debating focus in evolutionary genetics. In lower vertebrates of reptiles, amphibians, and fish, a species or a bioform reproduces either sexually or asexually but never both. A few species were found to consist of all females in fish. These all-female species can propagate by asexual reproduction modes, such as gynogenesis and hybridogenesis. However, the coexistence of sexuality and asexuality in a single species was recently noted only in a cyprinid fish silver crucian carp, Carassius auratus gibelio. This fish had been demonstrated to be capable of gynogenesis stimulated by sperm from other related species. Surprisingly, natural populations of this fish consist of a minor but significant portion (approx. 20%) of males. As different clones with specific phenotypic and genetic characteristics have been found, and RAPD markers specific to each clone have recently been identified, this fish offers many advantages for analyzing whether or not genetic recombination occurs between different clones. In this study, artificial propagation was performed in clone F and clone D. Ovulated eggs from clone F were divided into two parts and respectively inseminated with sperm from a clone D male and from a red common carp (Cyprinus carpio) male. The control clone D individuals were selected from gynogenetic offspring of clone D activated by sperm of red common carp. The phenotype and sex ratio in the experimental groups were also observed. Using RAPD molecular markers, which allow for reliable discrimination and genetic analysis of different clones, we have revealed direct molecular evidence for gonochoristic reproduction in the gynogenetic silver crucian carp and confirmed a previous hypothesis that the silver crucian carp might reproduce both gynogenetically and gonochoristically. Therefore, we conclude that the silver crucian carp possesses two reproductive modes, i.e., gynogenetic and gonochoristic reproduction. The response mechanism of two reproductive development modes may be the first discovery in vertebrates. Additionally, we discuss the evolutionary implication between gynogenetic and gonochoristic reproduction modes and the contribution of the minor proportion of males to genetic flexibility in the gynogenetic silver crucian carp.

Animals↗
PubMed2000

A genetic linkage map of the baboon (Papio hamadryas) genome based on human microsatellite polymorphisms.

A first-generation genetic linkage map of the baboon (Papio hamadryas) genome was developed for use in biomedical and evolutionary genetics. Pedigreed baboons (n = 694) were selected from the breeding colony maintained by the Southwest Foundation for Biomedical Research. To facilitate comparison with the human genome, the baboon linkage map consists primarily of human microsatellite loci amplified using published human PCR primers. Genotypes for 325 human microsatellites and 6 novel baboon microsatellites were used in linkage analyses performed with the MultiMap expert system. The resulting sex-averaged meiotic recombination map covers all 20 baboon autosomes, with average spacing among loci of 7.2 cM. Direct comparison among homologous (orthologous) loci reveals that, for 7 human autosomes, locus order is conserved between humans and baboons. For the other 15 autosomes, one or more rearrangements distinguish the two genomes. The total centimorgan distances among homologous markers are 28.0% longer in the human genome than in the baboon, suggesting that rates of recombination may be higher in humans. This baboon linkage map is the first reported for any nonhuman primate species and creates opportunities for mapping quantitative trait loci in baboons, as well as for comparative evolutionary analyses of genome structure.

Animals↗
PubMed1999

The genomics of adaptation in yeast.

A recent study has combined methods of experimental evolution and DNA microarray technology to examine evolved changes in gene expression in yeast, providing intriguing insights into the genetics of adaptation and functional genomics, and pointing to future uses of microarray technology in evolutionary genetics.

Adaptation, Physiological↗
PubMed2000

Genetics of alpha-amanitin resistance in a natural population of Drosophila melanogaster.

The genetic basis of variation in resistance to natural toxins is of interest for both ecological and evolutionary genetics. The wide variety of larval resources used by Drosophila, both within and between species, makes flies an excellent system for studying causes and consequences of selection resulting from exposure to natural toxins associated with different resources. In this study we carry out a genetic analysis of alpha-amanitin resistance in a population sample of Drosophila melanogaster. Data from mapping crosses of chromosome III support a role for a naturally occurring polymorphism in a multidrug resistance gene (Mdr65A) in alpha-amanitin resistance. However, there are no amino acid differences between resistant and sensitive chromosomes at Mdr65A. Therefore, if Mdr65A mutants contribute to the difference between alpha-amanitin-resistant and alpha-amanitin-sensitive third chromosome lines, the underlying cause is a gene regulatory mutation.

ATP Binding Cassette Transporter, Subfamily B↗
PubMed2005

Mapping genome-genome epistasis: a high-dimensional model.

MOTIVATION: The proper development of any organ or tissue requires the coordinated expression of its underlying genes that can be located on different genomes present in an organism. For instance, each step in the development of seed for a higher plant is the consequence of gene interactions from the maternal, embryo and endosperm genomes. RESULTS: We present a multivariate statistical model for mapping quantitative trait loci (QTL) by incorporating two important aspects of seed development in plants-QTL interactions derived from different genomes, the maternal, embryo and endosperm, and genetic correlations among phenotypic traits expressed in different genome-specific tissues. This model, which has a high dimensionality, is constructed within the maximum-likelihood context based on a finite mixture model. The implementation of the expectation-maximization algorithm allows for the efficient estimation of QTL positions, their action and interaction effects and pleiotropic effects. The application of this high-dimensional model to a real rice dataset has validated its usefulness. CONCLUSIONS: Our model was derived for self-pollinated plants, but it can be extended to cross-pollinated plants and to animals. With the burgeoning of genetic and genomic data, this high-dimensional model will have many implications for agricultural and evolutionary genetic research. AVAILABILITY: A package of software will be provided from the corresponding author upon request.

Chromosome Mapping↗
PubMed2003

Population size and identity influence the reaction norm of the rare, endemic plant Cochlearia bavarica across a gradient of environmental stress.

Habitat degradation and loss can result in population decline and genetic erosion, limiting the ability of organisms to cope with environmental change, whether this is through evolutionary genetic response (requiring genetic variation) or through phenotypic plasticity (i.e., the ability of a given genotype to express a variable phenotype across environments). Here we address the question whether plants from small populations are less plastic or more susceptible to environmental stress than plants from large populations. We collected seed families from small (<100) versus large natural populations (>1,000 flowering plants) of the rare, endemic plant Cochlearia bavarica (Brassicaceae). We exposed the seedlings to a range of environments, created by manipulating water supply and light intensity in a 2 x 2 factorial design in the greenhouse. We monitored plant growth and survival for 300 days. Significant effects of offspring environment on offspring characters demonstrated that there is phenotypic plasticity in the responses to environmental stress in this species. Significant effects of population size group, but mainly of population identity within the population size groups, and of maternal plant identity within populations indicated variation due to genetic (plus potentially maternal) variation for offspring traits. The environment x maternal plant identity interaction was rarely significant, providing little evidence for genetically- (plus potentially maternally-) based variation in plasticity within populations. However, significant environment x population-size-group and environment x population-identity interactions suggested that populations differed in the amount of plasticity, the mean amount being smaller in small populations than in large populations. Whereas on day 210 the differences between small and large populations were largest in the environment in which plants grew biggest (i.e., under benign conditions), on day 270 the difference was largest in stressful environments. These results show that population size and population identity can affect growth and survival differently across environmental stress gradients. Moreover, these effects can themselves be modified by time-dependent variation in the interaction between plants and their environment.

Biological Evolution↗
PubMed2025

Genomic-based revelation of genetic structure and adaptive characterization of Schizopygopsis malacanthus in the Jinsha River and Yalong River.

BACKGROUND: As a highly specialized class of schizothoracine fishes, Schizopygopsis malacanthus has attracted much attention due to its widespread distribution. To investigate the impact of the Qinghai&#x2012;Tibet movement on S. malacanthus, we analyzed the genetic evolutionary history of this species. RESULTS: These results showed that there was a high level of genetic differentiation between Jinsha River (JSR) populations and Yalong River (YLR) populations. The genetic diversity of intra-YLR populations was higher than that of the intra-JSR populations. There was gene exchange of the Suwalong population to the Huoqu and Ganzi populations. Furthermore, both of the JSR and YLR populations exhibited a gradual increase in the genetic differentiation index from low to high altitudes, and the effective population of high-elevation populations has gradually expanded. In high-altitude populations, the selected genes were enriched in DNA repair, light transduction, and energy metabolism, reflecting the genetic basis for their migration to higher altitudes. CONCLUSIONS: S. malacanthus populations had the higher genetic differentiation and genetic diversity in the JSR and its main tributary YLR. Therefore, we should preserve high-elevation natural river sections as much as possible and reserve habitats for their migration and diffusion.

Animals↗
PubMed2001

Amantadine-resistant influenza A virus in Taiwan.

BACKGROUND AND PURPOSE: Amantadine and rimantadine have been used for treatment and prophylaxis of influenza A virus infection. We examined the amantadine susceptibility of field isolates of influenza A virus in Taiwan from 1996 to 1998 to monitor the presence of resistant strains. METHODS: Eighty-four field isolates of influenza A virus were examined for resistance to amantadine by plaque inhibition assay. Virus isolates with amantadine 50% inhibitory concentrations (IC50) greater than 0.9 microgram were chosen for sequence analysis of the M gene that is the molecular target for amantadine/rimantadine. Reverse transcription-polymerase chain reaction (RT-PCR) was used to amplify the viral RNA. RT-PCR products were examined and purified by agarose gel electrophoresis for further sequence analysis. The Genetics Computer Group Sequence Analysis Package and the neighbor-joining method listed in the Molecular Evolutionary Genetic Analysis package were used for phylogenetic analysis. RESULTS: One field strain was amantadine resistant (IC50 > 10 micrograms/mL), with a mutation (position 31, serine to asparagine) in the M2 protein. The resistant virus was isolated from a non-immunocompromised child without a history of amantadine/rimantadine treatment. None of the family members reported previous exposure to amantadine/rimantadine. CONCLUSIONS: In this series, amantadine-resistant influenza A (H1N1) virus was isolated from a non-immunocompromised Taiwanese child without a known history of exposure to this drug. Resistant field isolates were rare. Due to the increasing use of amantadine/rimantadine in Taiwan, continued surveillance for amantadine/rimantadine-resistant influenza A viruses is warranted.

Amantadine↗
PubMed2003

[Microsatellite analysis of genetic diversity and phylogenetic relationship of eight sheep breeds in Xinjiang].

To reveal the genetic diversity and syseighttemic relationship of main sheep breeds in north Xingjiang, the genetic polymorphisms of 10 microsatellites in 8 sheep breeds and one first filial generation (F1) in north Xinjiang were studied by means of PCR, polyacrylamide gel electrophoresis and silver staining. Number of alleles, average effective number of alleles (E) and average rates of homozygote of each breeds were counted. According to allele frequencies of ten microsatellites, polymorphism information content (PIC), mean heterozygosity (h) and genetic distances were calculated for each breeds. By using the Neighbor-joining method of Molecular Evolutionary Genetics Analysis software, a dendrogram was obtained based on genetic distances. Another dendrogram was obtained by Maximum Likelihood method in PHYLIP (3.6) software. The bootstrap values were evaluated for each crunode of the dendrogram by means of bootstrap test. The systemic relationship was analyzed as well. The results showed that 8 of 10 microsatellite loci were highly polymorphic, but BM1824 and MAF65 were low and medium polymorphic respectively, so the 8 microsatellite loci were effective markers for analysis of genetic relationship among sheep breeds. The average PIC (0.5631), h (0.5721) and E(2.9) of the whole population was all lower than those of other sheep breeds reported in the documents, which showed the gene polymorphisms and genetic diversity in these sheep breeds are relative rare. The genetic distances of native Aletai, Kazak and Bashibai sheeps in Xingjiang from foreign sheep breeds and cultivated breeds bearing foreign bloodline are relatively large. Consequently, they clustered in two groups. The phylogenetic relationship between different sheep breeds was in accordance with their resource, breeding history, differentiation and localities.

Algorithms↗
PubMed2002

[Ancient DNA studies: from paleopathology to population genetics].

We discuss the relevance of ancient DNA studies for novel approaches to a variety of fields of scientific inquiry, including population and evolutionary genetics, prehistoric archaeology, paleopathology and history of human diseases. To exemplify the potential of ancient DNA research, we provide accounts of studies currently conducted at our laboratories in four different areas: 1) origins of the dog and phylogeny of prehistoric Italian canids; 2) paleogenetics of ancient Roma; 3) antiquity for variant alleles implicated in disease predisposition; 4) molecular investigation of pathologic lesions in Italian mummies of Renaissance age. The implications of the results obtained are briefly outlined.

DNA↗
PubMed2002

Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench.

In this study, we collected and analyzed DNA sequence data for 789 previously mapped RFLP probes from Sorghum bicolor (L.) Moench. DNA sequences, comprising 894 non-redundant contigs and end sequences, were searched against three GenBank databases, nucleotide (nt), protein (nr) and EST (dbEST), using BLAST algorithms. Matching ESTs were also searched against nt and nr. Translated DNA sequences were then searched against the conserved domain database (CDD) to determine if functional domains/motifs were congruent with the proteins identified in previous searches. More than half (500/894 or 56%) of the query sequences had significant matches in at least one of the GenBank searches. Overall, proteins identified for 148 sequences (17%) were consistent among all searches, of which 66 sequences (7%) contained congruent coding domains. The RFLP probe sequences were also evaluated for the presence of simple sequence repeats (SSRs) and 60 SSRs were developed and assayed in an array of sorghum germplasm comprising inbreds, landraces and wild relatives. Overall, these SSR loci had lower levels of polymorphism ( D = 0.46, averaged over 51 polymorphic loci) compared with sorghum SSRs that were isolated by library hybridization screens ( D = 0.69, averaged over 38 polymorphic loci). This result was probably due to the relatively small proportion of di-nucleotide repeat-containing markers (42% of the total SSR loci) obtained from the DNA sequence data. These di-nucleotide markers also contained shorter repeat motifs than those isolated from genomic libraries. Based on BLAST results, 24 SSRs (40%) were located within, or near, previously annotated or hypothetical genes. We determined the location of 19 of these SSRs relative to putative coding regions. In general, SSRs located in coding regions were less polymorphic ( D = 0.07, averaged over three loci) than those from gene flanking regions, UTRs and introns ( D = 0.49, averaged over 16 loci). The sequence information and SSR loci generated through this study will be valuable for application to sorghum genetics and improvement, including gene discovery, marker-assisted selection, diversity and pedigree analyses, comparative mapping and evolutionary genetic studies.

Journal Article↗
PubMed1997

Isoenzyme diversity in Pneumocystis carinii from rats, mice, and rabbits.

Pneumocystis carinii is an opportunistic pathogen that causes pneumonia in immunocompromised patients. To investigate the genetic diversity of P. carinii populations, multilocus enzyme electrophoresis was used to analyze five enzyme systems (malate dehydrogenase, glucose phosphate isomerase, leucine aminopeptidase, malic enzyme, and 6-phosphogluconate dehydrogenase). Only five different multilocus associations (zymodemes) were recorded for the 70 isolates studied. While only one multilocus combination was found in mice and rabbits, three different multilocus associations were recorded in rats. Population genetic tests and phylogenetic analysis strongly suggest that P. carinii genotypes are host-specific, in agreement with molecular study results, and that no genetic exchange occurs between genotypes from different host species. This hypothesis could be verified only by the evolutionary genetic approach, which relies here on multilocus analysis.

Animals↗
PubMed2004

Fitness costs and benefits of novel herbicide tolerance in a noxious weed.

Glyphosate, the active ingredient in the herbicide RoundUp, has increased dramatically in use over the past decade and constitutes a potent anthropogenic source of selection. In the southeastern United States, weedy morning glories have begun to develop tolerance to glyphosate, representing a unique opportunity to examine the evolutionary genetics of a novel trait. We found genetic variation for tolerance, indicating the potential for the population to respond to selection by glyphosate. However, the following significant evolutionary constraint exists: in the absence of glyphosate, tolerant genotypes produced fewer seeds than susceptible genotypes. The combination of strong positive directional selection in the presence of glyphosate and strong negative directional selection in its absence may indicate that the selective landscape of land use could drive the evolutionary trajectory of glyphosate tolerance. Understanding these evolutionary forces is imperative for devising comprehensive management strategies to help slow the rate of the evolution of tolerance.

Biological Evolution↗
PubMed1995

Physiological genetics of the response to a high-sucrose diet by Drosophila melanogaster.

A diet medium containing 10% (w/v) sucrose can be inferred to be stressful to Drosophila melanogaster from the increased developmental time and reduced size and fecundity of emerging flies. The metabolic basis for this stress and the genetic response to it are of interest from the point of view of both metabolic regulation and the evolutionary genetics of adaptation to stress. Here the effects of a high-sucrose diet on live weight, total protein, stored lipid and glycogen, and crude activities of 12 enzymes involved in energy metabolism were quantified. Assays were done on a large population of Drosophila that had been acclimated to the laboratory. A collection of eggs was divided to produce two replicate populations maintained on standard medium and two replicates maintained on high-sucrose medium for 133 generations. At the end of this period, both control and sucrose-selected populations were tested on standard and on high-sucrose medium. Results showed that the immediate effect of the high-sucrose diet (compared to standard medium) for both populations was a reduction in live weight and total protein, and activities of many of the enzymes were also reduced by the sucrose treatment, even after adjusting for the weight effect. Selection resulted in several changes on both the standard and the sucrose medium, but the direction of change was not always the same as the acute effect. In no case was there a significant medium by selection-treatment interaction. The pattern of phenotypic correlations did not resolve the reasons for the direction of the genetic responses. Correlations were generally stable across diets and after selection, but there were notable exceptions.

Adaptation, Physiological↗
PubMed2005

Rapid evolutionary escape by large populations from local fitness peaks is likely in nature.

Fitness interactions between loci in the genome, or epistasis, can result in mutations that are individually deleterious but jointly beneficial. Such epistasis gives rise to multiple peaks on the genotypic fitness landscape. The problem of evolutionary escape from such local peaks has been a central problem of evolutionary genetics for at least 75 years. Much attention has focused on models of small populations, in which the sequential fixation of valley genotypes carrying individually deleterious mutations operates most quickly owing to genetic drift. However, valley genotypes can also be subject to mutation while transiently segregating, giving rise to copies of the high fitness escape genotype carrying the jointly beneficial mutations. In the absence of genetic recombination, these mutations may then fix simultaneously. The time for this process declines sharply with increasing population size, and it eventually comes to dominate evolutionary behavior. Here we develop an analytic expression for N(crit), the critical population size that defines the boundary between these regimes, which shows that both are likely to operate in nature. Frequent recombination may disrupt high-fitness escape genotypes produced in populations larger than N(crit) before they reach fixation, defining a third regime whose rate again slows with increasing population size. We develop a novel expression for this critical recombination rate, which shows that in large populations the simultaneous fixation of mutations that are beneficial only jointly is unlikely to be disrupted by genetic recombination if their map distance is on the order of the size of single genes. Thus, counterintuitively, mass selection alone offers a biologically realistic resolution to the problem of evolutionary escape from local fitness peaks in natural populations.

Biological Evolution↗
PubMed1986

Genetics of Aedes albopictus.

Aedes albopictus is an important vector of dengue fever and dengue hemorrhagic fever in Southeast Asia. Its distribution extends from Madagascar to Hawaii and is currently expanding. From its proposed origin in Southeast Asia, Ae. albopictus has migrated as far as Mauritius and Madagascar to the west and Korea, Japan, Guam, Hawaii and other Pacific Islands to the east. In the continental United States, it was originally reported in the Texas area in August 1985 and is now well established in several states. This paper reviews information on distribution, cytology and genetics of Aedes albopictus. In addition, it includes comments on its competitive interaction with several other species. Relevant information on evolutionary genetics of certain other related sibling species is also included for comparative purposes.

Aedes↗
PubMed2000

How genomic and developmental dynamics affect evolutionary processes.

Evolutionary genetics is concerned with natural selection and neutral drift, to the virtual exclusion of almost everything else. In its current focus on DNA variation, it reduces phenotypes to symbols. Varying phenotypes, however, are the units of evolution, and, if we want a comprehensive theory of evolution, we need to consider both the internal and external evolutionary forces that shape the development of phenotypes. Genetic systems are redundant, modular and subject to a variety of genomic mechanisms of "turnover" (transposition, gene conversion, unequal crossingover, slippage and so on). As such the construction and spread of novel combinations of modules by turnover, in particular within gene promoters, contributes significantly to the evolution of phenotypes. Furthermore, redundancy, turnover and modularity lead to ever more complex networks of genetic interactions and ever more functions for a given module. The significant interaction between genomic turnover and natural selection leads to a molecular coevolution between interacting modules and hence facilitates the establishment of biological novelties.

Animals↗
PubMed1993

The comparative imperative: genetics and ontogeny of chemoreceptive prey responses in natricine snakes.

Reptiles offer a rich diversity for the study of chemoreception, and snakes are a particularly appropriate group for comparative, evolutionary, genetic, developmental, and mechanistic studies. A long-term program of research is described that attempts to integrate these approaches, focusing on the widespread North American genus Thamnophis (Natricinae). Prior to their first meal, neonatal snakes respond to aqueous surface substances from species-typical prey with increased tongue-flicking and open-mouth attacks; these responses are mediated by the vomeronasal organ. Such responses predict what prey snakes will eat and can also predict relative prey preference. Species, population, litter, and individual differences exists and are important at different levels of analysis. Chemoreceptive responses are heritable, although they may show different developmental trends. Some species respond to prey types they do not eat in nature. In the earthworm specialist, T. butleri, response to fish chemicals can be interpreted as a chemoreceptive response inertially inherited from ancestral species, decoupled from prey capture techniques, and in the process of being lost. Ontogeny and experience can modify behavior of the neonate in various ways. Feeding experience can alter response to some prey more than others, and ambient prey odor may shift prey preference. Psychophysical studies show that prey preference and threshold sensitivity to prey chemicals can be independent and differ between closely related species, indicating that neural tissue is devoted to recognition of specific types of prey. In site choice tests, garter snakes can also discriminate between feces derived from conspecific snakes fed similar or different diets.(ABSTRACT TRUNCATED AT 250 WORDS)

Age Factors↗