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At least 1,243 records · Page 69Linked to original sources
PubMed2005

Adaptive loss of an old duplicated gene during incipient speciation.

To probe the role of natural selection in species origin, we performed a DNA polymorphism survey of the Drosophila melanogaster desaturase2 (ds2) locus. ds2 is responsible for a cuticular hydrocarbon difference between two behaviorally isolated races--Zimbabwe (Z) and Cosmopolitan (M). The ds2 allele prevalent in the Z populations is functional, while the allele from the M populations harbors a 16-bp deletion upstream of the gene which knocks out its expression. We find a signature of positive selection in the ds2 promoter, but not in the control gene, sas. This signature appears to be confined to the derived M population. We also find that the selection has been recent because the gene retains a signature of a selective sweep evidenced by the departure of Fay and Wu's H test from neutral expectation. We also find that ds2, as well as its duplicate pair ds1, has been maintained in the Drosophila genus for at least 40 Myr without any sign of adaptive change. Taken together with previous molecular genetic evidence, our results suggest that ds2 is one of the genes responsible for adaptive divergence of the Z and M races of D. melanogaster.

Animals↗
PubMed2005

Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations.

Uncertainty about the demographic history of populations can hamper genome-wide scans for selection based on population genetic models. To obtain a portrait of the effects of demographic history on genome variability patterns in Drosophila melanogaster populations, we surveyed noncoding DNA polymorphism at 10 X-linked loci in large samples from three African and two non-African populations. All five populations show significant departures from expectations under the standard neutral model. We detect weak but significant differentiation between East (Kenya and Zimbabwe) and West/Central sub-Saharan (Gabon) African populations. A skew toward high-frequency-derived polymorphisms, elevated levels of linkage disequilibrium (LD) and significant heterogeneity in levels of polymorphism and divergence in the Gabon sample suggest that this population is further from mutation-drift equilibrium than the two Eastern African populations. Both non-African populations harbor significantly higher levels of LD, a large excess of high-frequency-derived mutations and extreme heterogeneity among loci in levels of polymorphism and divergence. Rejections of the neutral model in D. melanogaster populations using these and similar features have been interpreted as evidence for an important role for natural selection in shaping genome variability patterns. Based on simulations, we conclude that simple bottleneck models are sufficient to account for most, if not all, polymorphism features of both African and non-African populations. In contrast, we show that a steady-state recurrent hitchhiking model fails to account for several aspects of the data. Demographic departures from equilibrium expectations in both ancestral and derived populations thus represent a serious challenge to detecting positive selection in genome-wide scans using current methodologies.

Animals↗
PubMed2005

Linkage disequilibrium and selection response in two-stage marker-assisted selection of dairy cattle over several generations.

A stochastic simulation was carried out to investigate the advantage of marker-assisted selection (MAS) in comparison with traditional selection over several generations. The selection goal was a sex-limited trait or a linear combination of traits with a polygenic component, two unlinked additive QTL and a non-genetic component. The simulated QTL were moderate or large and the allele frequencies were varied. Two stages of selection among the male offspring were carried out. In the first stage marker information was used to select among full sibs (MAS) or one full sib was chosen at random. In the second stage young bulls were selected based on a progeny test. The response in total genetic gain was faster with MAS than with traditional selection and persisted over several generations. With a QTL of moderate size and initial allele frequencies of the favourable allele of 0.05 the response with MAS was 6% higher than with traditional selection in the sires selected after progeny test. MAS in a within-family two-stage selection scheme improved the genetic merit of selected bulls even when linkage disequilibrium between QTL and polygenes was initially increased.

Animals↗
PubMedDate not supplied

Investigating the independent evolution of the size of floral organs via G-matrix estimation and artificial selection.

The attractiveness of a plant to pollinators is dependent on both the number of flowers produced and the size of the petals. However, limiting resources often result in a size/number trade-off, whereby the plant can make either more flowers or larger flowers, but not both. If developmental genes underlying sepal and petal identity (some of which overlap) also influence size, then this shared genetic basis could constrain the independent evolution of floral size and attractiveness. Here, we determined whether the size of sepals and petals in the dioecious perennial, Silene latifolia, are developmentally independent by performing two experiments: a genetic variance-covariance experiment to estimate genetic correlations between calyx width, petal-limb length, flower mass, and number and a four-bout artificial-selection experiment to alter calyx width and estimate the correlated response in petal-limb length. In addition, we determined whether variation in petal-limb length is the result of cell expansion or cell proliferation. The first experiment revealed that petal-limb length is not genetically correlated with calyx width, and the second experiment confirmed this; selection on calyx width did not result in a predictable or significant change in petal-limb length. Flower number was negatively correlated with all the floral traits measured, indicating a flower size/number trade-off. Cell number, but not size, explained a significant amount of the variation in petal-limb length. We conclude that the size of the two outer floral organs can evolve independently. This species can therefore increase the number of flowers produced by decreasing investment in the calyx without simultaneously decreasing petal size and the attractiveness of each individual flower to pollinators.

Biological Evolution↗
PubMedDate not supplied

Response to mass selection when the genotype by environment interaction is modelled as a linear reaction norm.

A breeding goal accounting for the effects of genotype by environment interaction (G x E) has to define not only traits but also the environment in which those traits are to be improved. The aim of this study was to predict the selection response in the coefficients of a linear reaction norm, and response in average phenotypic value in any environment, when mass selection is applied to a trait where G x E is modelled as a linear reaction norm. The optimum environment in which to test the selection candidates for a given breeding objective was derived. Optimisation of the selection environment can be used as a means to either maximise genetic progress in a certain response environment, to keep the change in environmental sensitivity at a desired rate, or to reduce the proportion of animals performing below an acceptance level. The results showed that the optimum selection environment is not always equal to the environment in which the response is to be realised, but depends on the degree of G x E (determined by the ratio of variances in slope and level of a linear reaction norm), the correlation between level and slope, and the heritability of the trait.

Animals↗
PubMed2006

Two- and three-locus tests for linkage analysis using recombinant inbred lines.

We consider fixed recombinant inbred lines (RILs) derived either by selfing or by full-sib mating; when applicable, we also consider intermated recombinant inbreds (IRIs). First, we show that the usual estimate of recombination fraction based on RIL data is biased, and we provide an estimate where the major part of that bias is removed. Second, we derive simple formulas to compute the frequencies of genotypes at three loci in RILs. We describe the nonindependence of multiple recombinations arising in RIL recombination data even though there may be no interference in each meiosis. Finally, we give formulas for interference tests, gene mapping, or QTL detection in RIL populations.

Chromosome Mapping↗
PubMed2006

Signatures of demographic history and natural selection in the human major histocompatibility complex Loci.

Many lines of evidence show that several HLA loci have experienced balancing selection. However, distinguishing among demographic and selective explanations for patterns of variation observed with HLA genes remains a challenge. In this study we address this issue using data from a diverse set of human populations at six classical HLA loci and, employing a comparative genomics approach, contrast results for HLA loci to those for non-HLA markers. Using a variety of analytic methods, we confirm and extend evidence for selection acting on several HLA loci. We find that allele frequency distributions for four of the six HLA loci deviate from neutral expectations and show that this is unlikely to be explained solely by demographic factors. Other features of HLA variation are explained in part by demographic history, including decreased heterozygosity and increased LD for populations at greater distances from Africa and a similar apportionment of genetic variation for HLA loci compared to putatively neutral non-HLA loci. On the basis of contrasts among different HLA loci and between HLA and non-HLA loci, we conclude that HLA loci bear detectable signatures of both natural selection and demographic history.

Evolution, Molecular↗
PubMed2006

A Bayesian heterogeneous analysis of variance approach to inferring recent selective sweeps.

The distribution of microsatellite allele sizes in populations aids in understanding the genetic diversity of species and the evolutionary history of recent selective sweeps. We propose a heterogeneous Bayesian analysis of variance model for inferring loci involved in recent selective sweeps by analyzing the distribution of allele sizes at multiple loci in multiple populations. Our model is shown to be consistent with a multilocus test statistic, ln RV, proposed for identifying microsatellite loci involved in recent selective sweeps. Our methodology differs in that it accepts original allele size data rather than summary statistics and allows the incorporation of prior knowledge about allele frequencies using a hierarchical prior distribution consisting of log normal and gamma probability distributions. Interesting features of the model are its ability to simultaneously analyze allele size data for any number of populations and to cope with the presence of any number of selected loci. The utility of the method is illustrated by application to two sets of microsatellite allele size data for a group of West African Anopheles gambiae populations. The results are consistent with the suppressed-recombination model of speciation, and additional candidate loci on chromosomes 2 (079 and 175) and 3 (088) are discovered that escaped former analysis.

Alleles↗
PubMed2006

Population models of genomic imprinting. II. Maternal and fertility selection.

Under several hypotheses for the evolutionary origin of imprinting, genes with maternal and reproductive effects are more likely to be imprinted. We thus investigate the effect of genomic imprinting in single-locus diallelic models of maternal and fertility selection. First, the model proposed by Gavrilets for maternal selection is expanded to include the effects of genomic imprinting. This augmented model exhibits novel behavior for a single-locus model: long-period cycling between a pair of Hopf bifurcations, as well as two-cycling between conjoined pitchfork bifurcations. We also examine several special cases: complete inactivation of one allele and when the maternal and viability selection parameters are independent. Second, we extend the standard model of fertility selection to include the effects of imprinting. Imprinting destroys the "sex-symmetry" property of the standard model, dramatically increasing the number of degrees of freedom of the selection parameter set. Cycling in all these models is rare in parameter space.

Alleles↗
PubMed2006

Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize.

A new genetic map of maize, ISU-IBM Map4, that integrates 2029 existing markers with 1329 new indel polymorphism (IDP) markers has been developed using intermated recombinant inbred lines (IRILs) from the intermated B73xMo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences from which IDP primers were designed, optimized marker-specific PCR conditions, and polymorphism data for all IDP markers. This new gene-based genetic map will facilitate a wide variety of genetic and genomic research projects, including map-based genome sequencing and gene cloning. The mosaic structures of the genomes of 91 IRILs, an important resource for identifying and mapping QTL and eQTL, were defined. Analyses of segregation data associated with markers genotyped in three B73/Mo17-derived mapping populations (F2, Syn5, and IBM) demonstrate that allele frequencies were significantly altered during the development of the IBM IRILs. The observations that two segregation distortion regions overlap with maize flowering-time QTL suggest that the altered allele frequencies were a consequence of inadvertent selection. Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs.

Alleles↗
PubMed2003

Improved strain distribution patterns of SMXA recombinant inbred strains by microsatellite markers.

To develop SMXA recombinant inbred (RI) strains as more valuable genetic resources, 302 microsatellite (Mit) loci were added to the strain distribution patterns (SDP) reported previously. The improved SDP were constructed in a total of 1085 loci containing 484 Mit markers, 571 restriction landmark genomic scanning (RLGS) spot markers and 30 others. This substantially improved SDP can be freely accessed on our homepage (http://www.med.nagoya-u.ac.jp/sisetu/SDP.htm).

Animals↗
PubMed1994

Quantitative- and molecular-genetic effects on animal well-being: adaptive mechanisms.

Domestic farm animals play an important role in meeting some basic needs of humankind, especially food and clothing. The aspects of genetic improvement programs in livestock production pertinent to animal welfare and animal well-being are reviewed. A link is made between the evolutionary processes of adaptation and domestication and animal well-being. Animal behavior is a component of all these. Thus, the genetics of behavior may provide clues to the well-being of farm animal populations, and it will also be of relevance to public opinion issues of animal welfare. Many expressions of behavior by domestic livestock may be influenced by those processes that change gene as well as genotypic frequencies such as inbreeding, drift, and artificial selection. The environment in which the individual lives will also play a role, along with the interaction between genotype and environment. Selection for or against such behaviors as aggressiveness, docility, response to stress, and certain sexual behaviors in some livestock species has often been successful. This points to the existence of additive genetic variation for behavior, and scope for the inclusion of behavioral traits into selection programs, if these measures are shown to be related to welfare. Negative relationships between behaviors associated with well-being and traits of economic importance have been reported in most livestock species. However, estimates of genetic parameters, especially genetic correlations between objective measures of well-being and production traits, are scarce. There have been no comprehensive studies of the welfare of transgenic animals reported in the scientific literature. Increased use of biotechnology in animal agriculture, coupled with greater public scrutiny of livestock industries, may precipitate decisions concerning the interface of behavior and genetics that need to be addressed before scientists can conduct appropriate experimental evaluations.

Adaptation, Physiological↗
PubMed2004

Number of calves born, number of calves weaned, and cumulative weaning weight as measures of lifetime production for Hereford cows.

Genetic parameters for lifetime production for cows with the opportunity to produce from 2 through 7 yr of age, as measured by the number of calves born (NB2, ..., NB7), the number of calves weaned (NW2, ..., NW7), and cumulative weaning weight (CW2, ..., CW7), were estimated using data from 3,064 Hereford cows from a selection experiment with a control line (CTL) and three lines selected for weaning weight (WWL), yearling weight (YWL), and an index of yearling weight and muscle score (IXL). Weaning weights were adjusted to 200 d of age and for sex and age of dam. Estimates of heritability and genetic and environmental correlations were obtained by restricted maximum likelihood with bivariate animal models, with year of birth of the cow as a fixed effect and direct genetic and residual as random effects. Genetic trends were estimated by regressing means of estimated breeding values by year of birth and line on birth year. Estimates of heritability (SE) for opportunity groups of 2 to 7 yr of age ranged from 0.08 (0.03) to 0.16 (0.05) for NB; from 0.05 (0.02) to 0.16 (0.05) for NW; and from 0.06 (0.02) to 0.16 (0.05) for CW. Estimates of genetic correlations (SE) among NB traits ranged from 0.60 (0.14) to 1.00 (0.00), and estimates of environmental correlations (SE) ranged from 0.67 (0.02) to 0.99 (0.00). For NW, estimates of genetic and environmental correlations ranged from 0.98 (0.11) to 1.00 (0.00) and from 0.65 (0.02) to 0.99 (0.00), respectively. Estimates of genetic correlations (SE) among CW traits ranged from 0.94 (0.08) to 1.00 (0.00). Estimates of environmental correlations (SE) ranged from 0.66 (0.02) to 0.99 (0.00). Estimates of genetic correlations for NB2 with all definitions of NW ranged from 0.47 (0.18) to 0.71 (0.12), and with all definitions of CW ranged from 0.55 (0.16) to 0.80 (0.11). Estimates of genetic correlations between NW2 and all definitions for CW ranged from 0.95 (0.02) to 0.99 (0.06). Estimates of annual genetic (SE) change were negligible for NB2, NB6, NW2, and NW6 for all lines. Estimates of annual genetic (SE) change for CW2 were 0.85 (0.11), 0.79 (0.14), 0.51 (0.10), and 0.52 (0.18) kg/yr, and for CW6 were 5.01 (1.25), 2.64 (1.75), 3.67 (1.16), and 3.33 (2.37) kg/yr for WWL, YWL, IXL, and CTL, respectively. Selection for lifetime production as measured by NB, NW, or CW could be effective but would be relatively slow due to low estimates of heritability and to increased generation intervals.

Animals↗
PubMed2005

[Laboratory performance study of the quantitative detection method for genetically modified soybeans (roundup ready soybeans 40-3-2)].

To investigate important factors affecting the analytical results, a laboratory-performance study was attempted for the Japanese official methods to detect genetically modified (GM) soybeans (40-3-2). Test samples containing 0, 1 and 5% GM soya powder in non-GM soya powder was prepared. A set of 3 test samples was sent to the participating laboratories along with the protocol. The data were collected from all laboratories and statistically analyzed. In the real-time PCR detection method, the average values of the GM 1% and 5% samples were both much lower than the spiked value because the laboratories using a silica-membrane DNA extraction method underestimated the GM value. On the other hand, the laboratories using other extraction methods, such as the CTAB method obtained values close to the spiked value. These results suggest that use of the silica-membrane DNA extraction method may result in underestimation of the GM content in the real-time PCR method. In the ELISA method, the average value of 5% spiked samples appears to be slightly higher than the fortified value. But, overall, it was considered that reported values were close to the spiked level.

DNA, Plant↗
PubMed1999

[The association of genetic markers in two related swine breeds].

The combinations of genetic markers (allotypes, blood-group systems, and polymorphic proteins) were analyzed in pigs of two phylogenetically related Siberian populations: the newly selected Siberian specialized meat breed SM-1 (daughter breed) and the reproductive core of the Kemerovo breed (maternal breed). Statistically significant interlocus associations were found between the genetic markers that are known not to be linked, being assigned to different linkage groups, and the main selected meat-productivity traits. Some of these associations were shared by both breeds; others were found to be specific to either maternal or daughter populations. Possible genetic mechanisms underlying these associations and their significance are discussed.

Animals↗