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Natural Variation (natural + variation)
Selected AbstractsNATURAL VARIATION FOR A HYBRID INCOMPATIBILITY BETWEEN TWO SPECIES OF MIMULUSEVOLUTION, Issue 1 2007Andrea L. Sweigart Understanding the process by which hybrid incompatibility alleles become established in natural populations remains a major challenge to evolutionary biology. Previously, we discovered a two-locus Dobzhansky,Muller incompatibility that causes severe hybrid male sterility between two inbred lines of the incompletely isolated wildflower species, Mimulus guttatus and M. nasutus. An interspecific cross between these two inbred lines revealed that the M. guttatus (IM62) allele at hybrid male sterility 1 (hms1) acts dominantly in combination with recessive M. nasutus (SF5) alleles at hybrid male sterility 2 (hms2) to cause nearly complete hybrid male sterility. In this report, we extend these genetic analyses to investigate intraspecific variation for the hms1,hms2 incompatibility in natural populations of M. nasutus and M. guttatus, performing a series of interspecific crosses between individuals collected from a variety of geographic locales. Our results suggest that hms2 incompatibility alleles are common and geographically widespread within M. nasutus, but absent or rare in M. guttatus. In contrast, the hms1 locus is polymorphic within M. guttatus and the incompatibility allele appears to be extremely geographically restricted. We found evidence for the presence of the hms1 incompatibility allele in only two M. guttatus populations that exist within a few kilometers of each other. The restricted distribution of the hms1 incompatibility allele might currently limit the potential for the hms1,hms2 incompatibility to act as a species barrier between sympatric populations of M. guttatus and M. nasutus. Extensive sampling within a single M. guttatus population revealed that the hms1 locus is polymorphic and that the incompatibility allele appears to segregate at intermediate frequency, a pattern that is consistent with either genetic drift or natural selection. [source] Natural variation in baseline data: when do we call a new sample ,resistant'?,PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 9 2002Lukas Schaub Abstract Mortality of pear psylla to amitraz was studied by means of bioassays. Variation between samples, temporal variation within the season in one orchard and spatial variation between Swiss regions were considered. Variation between samples was large enough to produce different Probit functions and LC50 values. Temporal and spatial variations were too small to indicate resistance. Prediction intervals of the pooled functions using bootstrapping were calculated to determine if future samples come from a population with decreased sensitivity. Probabilistic criteria on the population level were proposed for resistance. © 2002 Society of Chemical Industry [source] Impact of warming and timing of snow melt on soil microarthropod assemblages associated with Dryas- dominated plant communities on SvalbardECOGRAPHY, Issue 1 2006Rebecca Dollery Open Top Chambers (OTCs) were used to measure impacts of predicted global warming on the structure of the invertebrate community of a Dryas octopetala heath in West Spitsbergen. Results from the OTC experiment were compared with natural variation in invertebrate community structure along a snowmelt transect through similar vegetation up the adjacent hillside. Changes along this transect represent the natural response of the invertebrate community to progressively longer and potentially warmer and drier growing seasons. Using MANOVA, ANOVA, Linear Discriminant Analysis and ,2 tests, significant differences in community composition were found between OTCs and controls and among stations along the transect. Numbers of cryptostigmatic and predatory mites tended to be higher in the warmer OTC treatment but numbers of the aphid Acyrthosiphon svalbardicum, hymenopterous parasitoids, Symphyta larvae, and weevils were higher in control plots. Most Collembola, including Hypogastrura tullbergi, Lepidocyrtus lignorum and Isotoma anglicana, followed a similar trend to the aphid, but Folsomia bisetosa was more abundant in the OTC treatment. Trends along the transect showed clear parallels with the OTC experiment. However, mite species, particularly Diapterobates notatus, tended to increase in numbers under warming, with several species collectively increasing at the earlier exposed transect stations. Overall, the results suggest that the composition and structure of Arctic invertebrate communities associated with Dryas will change significantly under global warming. [source] Parental care in response to natural variation in nest predation pressure in six sunfish (Centrarchidae: Teleostei) speciesECOLOGY OF FRESHWATER FISH, Issue 4 2008S. J. Cooke Abstract,,, Parental care is an important, energetically costly component of the life history of many fishes. Despite this importance, little is known about how different species of fish vary parental care in response to natural nest predator burdens. In this study, underwater videography was used to quantify parental care activity of six species of syntopic nesting male centrarchid fishes in Lake Opinicon, Ontario, in response to natural predators. This approach was used to test the hypothesis that as offspring develop from eggs to wrigglers, parental care activity should decrease or remain static for fish guarding nests with low predator burden and increase for those with high predator burden, reflecting different external risks. Principal components analysis (PCA) was used to derive common aeration and nest defence variables. Aeration and predator defence activity of the fish varied extensively among species. Parental care behaviours indicative of defence and vigilance (e.g., turning, departures, time away from nest, displays) tended to be highest for species that had the most predation attempts, although this was not entirely consistent. There was also a positive relationship between the defence PCA metric and attempted predation. Defence did not vary with stage of offspring development, although interactions between defence and developmental stage were noted for several species. A trade-off between aeration and defence was not observed. In fact, species that provide high levels of aeration also simultaneously provide high levels of defence. Stage-specific patterns of defence in this study were less apparent than those documented by studies using responses to staged predator intrusions making it unclear as to the extent that fish were responding to the level of the risk to offspring than to the value of the brood. Therefore, combined use of observational and experimental assessments of parental care investment may be most appropriate for refining current theoretical paradigms. [source] An application of canonical correspondence analysis for developing ecological quality assessment metrics for river macrophytesFRESHWATER BIOLOGY, Issue 5 2005IAN DODKINS Summary 1. Aquatic macrophyte composition and abundance is required by the European Union's Water Framework Directive for determining ecological status. Five metrics were produced that can be combined to determine the deviation of aquatic macrophytes from reference conditions in Northern Ireland's rivers. 2. Species optima and niche breadths along silt, nitrate, pH, conductivity and dissolved oxygen gradients were generated from aquatic macrophyte and water quality surveys conducted at 273 sites throughout Northern Ireland using Canonical Correspondence Analysis (CCA). Five metric scores based on these environmental gradients were determined at new monitoring sites using the mean optima of the species occurring at the site, weighted by percentage cover and niche breadth of each species. 3. A preliminary reference network of 32 sites of high physico-chemical and hydromorphological quality, and representative of the range of river types in Northern Ireland, enabled reference metric scores to be produced for each river type. Five unimpacted and twenty impacted sites were used for testing the performance of the metrics. By subtracting reference metric scores from metric scores at a monitoring site measures of ecological impact could be determined along five different impact gradients. Metrics were also combined to give a measure of total ecological change. 4. The metrics system distinguished unimpacted from impacted sites and correctly identified 77% of the known impacts. The metrics distinguished different types of impact, e.g. silt and nitrate. 5. Aquatic macrophyte occurrence and abundance has high natural variability at a site, both temporally and spatially. This method was designed to be sensitive to ecological change whilst reducing noise caused by natural variation. [source] Is there a cost of reproduction for Marsh Tits Parus palustris in a primeval forest?IBIS, Issue 1 2006OWSKI TOMASZ We looked for evidence of a cost of reproduction in the Marsh Tit Parus palustris living in the last fragments of primeval temperate forest (Bia,owie,a National Park, eastern Poland). Potential nest-holes were superabundant but the birds had to cope with a diverse set of predators, dangerous both to broods and to parents. Taking advantage of the natural variation in realized reproductive investment that this caused in terms of the loss of nests or mates, we expected to find differences in survival and future fecundity between birds which had lost broods (reduced effort), had reared young (controls) or were either provisioning young single-handed or had laid replacement clutches (increased effort). Despite 13 years of observation, even during seasons with very strenuous conditions, we have failed to demonstrate that the observed range of variation in parental investment caused any demographic cost of reproduction. Incubating females were regularly killed on the nest, which could indicate the existence of a cost operating in the earlier stages of the breeding cycle. Overall, these results suggest that the reproductive rate in Marsh Tits is not controlled proximately by reproductive cost. [source] Beyond taxonomy: a review of macroinvertebrate trait-based community descriptors as tools for freshwater biomonitoringJOURNAL OF APPLIED ECOLOGY, Issue 4 2010Salomé Menezes Summary 1.,Species traits have been frequently used in ecological studies in an attempt to develop a general ecological framework linking biological communities to habitat pressures. The trait approach offers a mechanistic alternative to traditional taxonomy-based descriptors. This review focuses on research employing traits as biomonitoring tools for freshwater ecosystems, although the lessons learned have wider application in the assessment of other ecosystem types. 2.,We review the support from ecological theory to employ species traits for biomonitoring purposes (e.g. the habitat templet concept, landscape filtering hypothesis), and the subsequent studies that test the hypotheses arising from these theories, and apply this knowledge under real freshwater biomonitoring scenarios. We also include studies that deal with more specific issues such as trait trade-offs and trait syndromes. 3.,We highlight the functional trait approach as one of the most promising tools emerging for biomonitoring freshwater ecosystems. Several technical issues are addressed and solutions are proposed. We discuss the need for: a broader unified trait biomonitoring tool; a more accurate understanding of the natural variation of community patterns of trait expression; approaches to diminish the effects of trait trade-offs and trait syndromes; additional life history and ecological requirement studies; and the detection of specific impacts under multiple stressor scenarios. 4.,Synthesis and applications. This review provides biologists with the conceptual underpinning for the use of species traits as community descriptors and for freshwater biomonitoring and management. We expect that the functional trait approach will ultimately improve communication to managers and legislators of the importance of protecting freshwater ecosystem functions. [source] Brood size and environmental conditions sex-specifically affect nestling immune response in the European starling Sturnus vulgarisJOURNAL OF AVIAN BIOLOGY, Issue 6 2005Eunice H. Chin In sexually size-dimorphic species, the larger sex can be more sensitive to stressful environmental conditions, often resulting in reduced growth and elevated mortality rates. Development of the immune system is regarded as highly resource dependent, and recent data suggest that nestling passerines experience a possible resource-based trade-off between growth and immunity. Given the hypothesized importance of maximizing growth for the larger sex, the corresponding immune system may also exhibit similar sensitivity to limited resources. To better understand how natural variation in brood size and resources might differentially affect growth and immune function in nestlings of a sexually size-dimorphic species, we examined the relationship between brood size and inter-sexual differences in cell-mediated immunity (CMI) and survival in European starling Sturnus vulgaris nestlings where males are larger in both mass and structural size. We hypothesized that male CMI response should be negatively impacted by increasing sibling competition (brood size), especially during periods of low resource availability. In a year of reduced parental provisioning rates and reduced chick growth rates, male offspring exhibited the predicted negative relationship, whereas female CMI response was unaffected. However, in a year of improved provisioning rates and chick growth, neither sex exhibited a negative relationship between immune response and brood size. Thus, natural variation in brood size can affect sex-specific immunity differently in offspring of a sexually size-dimorphic passerine. However, this relationship appears resource-dependent, suggesting that the hypothesized resource-based trade-off may be compensated for in years of adequate resource abundance. [source] Contribution of the LRP5 Gene to Normal Variation in Peak BMD in Women,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 1 2005Daniel L Koller Abstract The role of the LRP5 gene in rare BMD-related traits has recently been shown. We tested whether variation in this gene might play a role in normal variation in peak BMD. Association between SNPs in LRP5 and hip and spine BMD was measured in 1301 premenopausal women. Only a small proportion of the BMD variation was attributable to LRP5 in our sample. Introduction: Mutations in the low-density lipoprotein receptor-related protein 5 (LRP5) gene have been implicated as the cause of multiple distinct BMD-related rare Mendelian phenotypes. We sought to examine whether the LRP5 gene contributes to the observed variation in peak BMD in the normal population. Materials and Methods: We genotyped 12 single nucleotide polymorphisms (SNPs) in LRP5 using allele-specific PCR and mass spectrometry methods. Linkage disequilibrium between the genotyped LRP5 SNPs was measured. We tested for association between these SNPs and both hip and spine BMD (adjusted for age and body weight) in 1301 healthy premenopausal women who took part in a sibling pair study aimed at identifying the genes underlying peak bone mass. Our study used both population-based (ANOVA) and family-based (quantitative transmission disequilibrium test) association methodology. Results and Conclusions: The linkage disequilibrium pattern and haplotype block structure within the LRP5 gene were consistent with that observed in other studies. Although significant evidence of association was found between LRP5 SNPs and both hip and spine BMD, only a small proportion of the total variation in these phenotypes was accounted for. The genotyped SNPs accounted for ,0.8% of the variation in femoral neck BMD and 1.1% of the variation in spine BMD. Results from our sample suggest that natural variation in and around LRP5 is not a major contributor to the observed variability in peak BMD at either the femoral neck or lumbar spine in white women. [source] Rainfall effects on rare annual plantsJOURNAL OF ECOLOGY, Issue 4 2008Jonathan M. Levine Summary 1Variation in climate is predicted to increase over much of the planet this century. Forecasting species persistence with climate change thus requires understanding of how populations respond to climate variability, and the mechanisms underlying this response. Variable rainfall is well known to drive fluctuations in annual plant populations, yet the degree to which population response is driven by between-year variation in germination cueing, water limitation or competitive suppression is poorly understood. 2We used demographic monitoring and population models to examine how three seed banking, rare annual plants of the California Channel Islands respond to natural variation in precipitation and their competitive environments. Island plants are particularly threatened by climate change because their current ranges are unlikely to overlap regions that are climatically favourable in the future. 3Species showed 9 to 100-fold between-year variation in plant density over the 5,12 years of censusing, including a severe drought and a wet El Niño year. During the drought, population sizes were low for all species. However, even in non-drought years, population sizes and per capita growth rates showed considerable temporal variation, variation that was uncorrelated with total rainfall. These population fluctuations were instead correlated with the temperature after the first major storm event of the season, a germination cue for annual plants. 4Temporal variation in the density of the focal species was uncorrelated with the total vegetative cover in the surrounding community, suggesting that variation in competitive environments does not strongly determine population fluctuations. At the same time, the uncorrelated responses of the focal species and their competitors to environmental variation may favour persistence via the storage effect. 5Population growth rate analyses suggested differential endangerment of the focal annuals. Elasticity analyses and life table response experiments indicated that variation in germination has the same potential as the seeds produced per germinant to drive variation in population growth rates, but only the former was clearly related to rainfall. 6Synthesis. Our work suggests that future changes in the timing and temperatures associated with the first major rains, acting through germination, may more strongly affect population persistence than changes in season-long rainfall. [source] Adaptive evolution of lateral plates in three-spined stickleback Gasterosteus aculeatus: a case study in functional analysis of natural variationJOURNAL OF FISH BIOLOGY, Issue 2 2010R. D. H. Barrett The three-spined stickleback Gasterosteus aculeatus is a model species for studying questions in ecology and evolution. The rapid diversification of G. aculeatus in post-glacial freshwater environments, combined with recently developed molecular tools, provides a unique opportunity to study the functional basis of fitness variation in natural populations. In derived freshwater populations, a number of morphological traits have diverged in parallel from the marine ancestral state, including the number of lateral armour plates. Evolution of reduced armour in freshwater populations is due to positive selection from both abiotic and biotic mechanisms. The major effect gene (ectodysplasin-A or Eda), along with several minor effect genetic regions, has recently been shown to control lateral plate variation. Field experiments have further determined the fitness consequences of allelic variation at the major effect locus. This work helps elucidate the mechanisms connecting genetic variation with phenotypic variation and fitness in the wild, a synthesis that should be applicable to many other phenotypic traits and species of fishes. [source] A reliable externally fixated murine femoral fracture model that accounts for variation in movement between animalsJOURNAL OF ORTHOPAEDIC RESEARCH, Issue 5 2003Chris K. Connolly Abstract Fifty-two CFLP mice had an open femoral diaphyseal osteotomy held in compression by a four-pin external fixator. The movement of 34 of the mice in their cages was quantified before and after operation, until sacrifice at 4, 8, 16 or 24 days. Thirty-three specimens underwent histomorphometric analysis and 19 specimens underwent torsional stiffness measurement. The expected combination of intramembranous and endochondral bone formation was observed, and the model was shown to be reliable in that variation in the histological parameters of healing was small between animals at the same time point, compared to the variation between time-points. There was surprisingly large individual variation in the amount of animal movement about the cage, which correlated with both histomorphometric and mechanical measures of healing. Animals that moved more had larger external calluses containing more cartilage and demonstrated lower torsional stiffness at the same time point. Assuming that movement of the whole animal predicts, at least to some extent, movement at the fracture site, this correlation is what would be expected in a model that involves similar processes to those in human fracture healing. Models such as this, employed to determine the effect of experimental interventions, will yield more information if the natural variation in animal motion is measured and included in the analysis. © 2003 Orthopaedic Research Society. Published by Elsevier Science Ltd. All rights reserved. [source] Dopamine D2 Receptor Binding, Drd2 Expression and the Number of Dopamine Neurons in the BXD Recombinant Inbred Series: Genetic Relationships to Alcohol and Other Drug Associated PhenotypesALCOHOLISM, Issue 1 2003Robert Hitzemann Background: It has not been established to what extent the natural variation in dopamine systems contribute to the variation in ethanol response. The current study addresses this issue by measuring D2 dopamine (DA) receptor binding, the expression of Drd2, the number of midbrain DA neurons in the BXD recombinant inbred (RI) series and then compares these strain means with those previously reported for a variety of ethanol and other drug-related phenotypes. Methods: Data were collected for 21 to 23 of the BXD RI strains and the parental strains. D2 DA receptor autoradiography was performed using 125I-epidepride as the ligand [Kanes S, Dains K, Cipp L, Gatley J, Hitzemann B, Rasmussen E, Sanderson S, Silverman S, Hitzemann R (1996) Mapping the genes for haloperidol-induced catalepsy. J Pharmacol Exp Ther 277:1016,1025]. Drd2 expression was measured using the Affymetrix oligoarray system. Immunocytochemical techniques were used to determine the number of midbrain DA neurons [Hitzemann B, Dains K, Hitzemann R (1994) Further studies on the relationship between dopamine cell density and haloperidol response. J Pharmacol Exp Ther 271:969,976]. Results and Conclusions: The range of difference in receptor binding for the RI strains was approximately 2-fold in all regions examined, the core, the shell of the nucleus accumbens (NAc) and the dorsomedial caudate-putamen (CPu); heritability in all regions was moderate,(h 2,0.35). Drd2 expression in forebrain samples from the RI and parental strains ranged 1.5- to 2-fold and h2 was moderate,0.47. Variation in the number of tyrosine hydroxylase (TH) positive neurons was moderate, 41% and 26% and h2 was low,0.19 and 0.15 for the ventral tegmental area (VTA) and substantia nigra compacta (SNc), respectively. Significant correlations were found between D2 DA receptor binding and the low dose (1.33 g/kg) ethanol stimulant response. (p < 0.002) and between Drd2 expression and conditioned place preference (CPP) (p < 0.0005). No significant correlations were detected between ethanol preference and either receptor binding or Drd2 expression; however, a significant correlation was found between preference and Ncam expression. Ncam is approximately 0.2 Mb from Drd2. Overall, the data suggest ethanol preference and CPP are associated with the expression of Drd2 or closely linked genetic loci. [source] Variable but predictable prey availability affects predator breeding success: natural versus experimental evidenceJOURNAL OF ZOOLOGY, Issue 4 2008A. Millon Abstract Food supply is a major source of variation in breeding success for predators, and to what extent individuals are able to cope with temporal variability in food availability remains an outstanding question in life-history studies. We confronted the natural variation in clutch size and breeding success with results from a food supplementation experiment during egg formation, conducted over several contrasted years of natural food supply in an avian specialist predator, the Montagu's harrier Circus pygargus. This raptor mainly preys on common vole Microtus arvalis a cyclic microtine under temperate latitudes. Vole abundance together with timing of breeding accounted for most of the variance in clutch size and number of fledglings. Results from empirical and experimental data were overall in agreement. Fed pairs consistently increased clutch size compared with controls in all experimental years, whereas no effect of food supplementation on egg volume was detected. Supplemented pairs, however, did not fledge significantly more chicks than controls. The costs entailed by the increase in clutch size appear nevertheless to be limited compared with previous studies. Food supply seemed therefore to display sufficient predictability throughout a breeding season to afford individuals the opportunity to adjust their breeding effort to an optimal number of offspring, in agreement with Lack's anticipation hypothesis. [source] Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppiesMOLECULAR ECOLOGY, Issue 5 2010EVA-MARIA WILLING Abstract Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise FST values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. FST outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations [source] Heat shock protein 101 effects in A. thaliana: genetic variation, fitness and pleiotropy in controlled temperature conditionsMOLECULAR ECOLOGY, Issue 6 2008S. J. TONSOR Abstract The Hsp100/ClpB heat shock protein family is ancient and required for high temperature survival, but natural variation in expression and its phenotypic effects is unexplored in plants. In controlled environment experiments, we examined the effects of variation in the Arabidopsis cytosolic AtHsp101 (hereafter Hsp101). Ten wild-collected ecotypes differed in Hsp101 expression responses across a 22 to 40 °C gradient. Genotypes from low latitudes expressed the least Hsp101. We tested fitness and pleiotropic consequences of varying Hsp101 expression in ,control' vs. mild thermal stress treatments (15/25 °C D/N vs. 15/25° D/N plus 3 h at 35 °C 3 days/week). Comparing wild type and null mutants, wt Columbia (Col) produced ~33% more fruits compared to its Hsp101 homozygous null mutant. There was no difference between Landsberg erecta null mutant NIL (Ler) and wt Ler; wt Ler showed very low Hsp101 expression. In an assay of six genotypes, fecundity was a saturating function of Hsp101 content, in both experimental treatments. Thus, in addition to its essential role in acquired thermal tolerance, Hsp101 provides a substantial fitness benefit under normal growth conditions. Knocking out Hsp101 decreased fruit production, days to germination and days to bolting, total dry mass, and number of inflorescences; it increased transpiration rate and allocation to root mass. Root : total mass ratio decayed exponentially with Hsp101 content. This study shows that Hsp101 expression is evolvable in natural populations. Our results further suggest that Hsp101 is primarily an emergency high-temperature tolerance mechanism, since expression levels are lower in low-latitude populations from warmer climates. Hsp101 expression appears to carry an important trade-off in reduced root growth. This trade-off may select for suppressed expression under chronically high temperatures. [source] Sequence diversity and haplotype associations with phenotypic responses to crowding: GIGANTEA affects fruit set in Arabidopsis thalianaMOLECULAR ECOLOGY, Issue 14 2007MARCUS T. BROCK Abstract Identifying the molecular genetic basis of intraspecific variation in quantitative traits promises to provide novel insight into their evolutionary history as well as genetic mechanisms of adaptation. In an attempt to identify genes responsible for natural variation in competitive responses in Arabidopsis thaliana, we examined DNA sequence diversity at seven loci previously identified as members of the phytochrome B signalling network. For one gene, GIGANTEA (GI), we detected significant haplotype structure. To test for GI haplogroup,phenotype associations, we genotyped 161 A. thaliana accessions at GI and censused the same accessions for total fruit set and the expression of three phenotypic traits (days to flowering, petiole length, and inflorescence height) in a greenhouse experiment where plants were grown in crowded and uncrowded environments. We detected a significant association between GI and total fruit set that resulted in a 14% difference in average fruit set among GI haplogroups. Given that fruit set is an important component of fitness in this species and given the magnitude of the effect, the question arises as to how variation at this locus is maintained. Our observation of frequent and significant epistasis between GI and background single nucleotide polymorphisms (SNP), where the fitness ranking of the GI allele either reverses or does not differ depending on the allele at the interacting SNP, suggests that epistatic selection may actively maintain or at least slow the loss of variation at GI. This result is particularly noteworthy in the light of the ongoing debate regarding the genetic underpinnings of phenotypic evolution and recent observations that epistasis for phenotypic traits and components of fitness is common in A. thaliana. [source] Placebo-associated improvements in motor function: Comparison of subjective and objective sections of the UPDRS in early Parkinson's disease,MOVEMENT DISORDERS, Issue 2 2002Christopher G. Goetz MD Abstract The Unified Parkinson's Disease Rating Scale (UPDRS) is primarily composed of an investigator-derived objective rating of motor function and a patient-derived assessment of activities of daily living (ADL). Using a stringent definition of placebo effect, we examined the frequency, temporal development, and stability of improvements during placebo treatment over 6 months in a large placebo-controlled trial of deprenyl and tocopherol in early Parkinson's disease (DATATOP). One hundred ninety-nine subjects received placebo treatment in the randomized, multicenter, placebo-controlled DATATOP study. We compared the baseline UPDRS motor section scores with follow-up scores at 4, 13, and 26 weeks. Placebo-associated improvement was defined as an improvement over baseline score in motor UPDRS of at least 50% or a change in at least two motor items at any one visit by two or more points. Seventeen percent of the 185 subjects who qualified for analysis met the placebo response criteria. The group prevalence of response was steady (7% to 10%) at any one visit without a marked predominance of an early study effect. Older subjects with more motor impairment at baseline were most likely to show a placebo-associated improvement. ADL scores were low throughout the study, and ADL improvements did not identify the subjects with objectively defined placebo-associated improvement. Prominent improvements in investigator-derived objective measures of Parkinson's disease motor impairment occur during clinical trials, including one that was not aimed at showing improved short-term efficacy. Although the notion of placebo effect often implies patient-based perceptions, we found subjective changes to be infrequent in placebo-treated patients, suggesting that either: (1) the placebo effect was rater-driven; (2) the ADL questionnaire is insensitive to transient but objectively demonstrable motor changes; or (3) that the objective changes, albeit major, are within the realm of natural variation in the UPDRS motor scale from visit to visit. © 2002 Movement Disorder Society. [source] Natural genetic resources of Arabidopsis thaliana reveal a high prevalence and unexpected phenotypic plasticity of RPW8- mediated powdery mildew resistanceNEW PHYTOLOGIST, Issue 3 2008Katharina Göllner Summary ,,Here, an approach based on natural genetic variation was adopted to analyse powdery mildew resistance in Arabidopsis thaliana. ,,Accessions resistant to multiple powdery mildew species were crossed with the susceptible Col-0 ecotype and inheritance of resistance was analysed. Histochemical staining was used to visualize archetypal plant defence responses such as callose deposition, hydrogen peroxide accumulation and host cell death in a subset of these ecotypes. ,,In six accessions, resistance was likely of polygenic origin while 10 accessions exhibited evidence for a single recessively or semi-dominantly inherited resistance locus. Resistance in the latter accessions was mainly manifested at the terminal stage of the fungal life cycle by a failure of abundant conidiophore production. The resistance locus of several of these ecotypes was mapped to a genomic region containing the previously analysed atypical RPW8 powdery mildew resistance genes. Gene silencing revealed that members of the RPW8 locus were responsible for resistance to Golovinomyces orontii in seven accessions. ,,These results suggest that broad-spectrum powdery mildew resistance in A. thaliana is predominantly of polygenic origin or based on RPW8 function. The findings shed new light on the natural variation of inheritance, phenotypic expression and pathogen range of RPW8 -conditioned powdery mildew resistance. [source] Evaluation of a Non-Targeted "Omic" Approach in the Safety Assessment of Genetically Modified PlantsPLANT BIOLOGY, Issue 5 2006S. B. Metzdorff Abstract: Genetically modified plants must be approved before release in the European Union, and the approval is generally based upon a comparison of various characteristics between the transgenic plant and a conventional counterpart. As a case study, focusing on safety assessment of genetically modified plants, we here report the development and characterisation of six independently transformed Arabidopsis thaliana lines modified in the flavonoid biosynthesis. Analyses of integration events and comparative analysis for characterisation of the intended effects were performed by PCR, quantitative Real-time PCR, and High Performance Liquid Chromatography. Analysis by cDNA microarray was used as a non-targeted approach for the identification of potential unintended effects caused by the transformation. The results revealed that, although the transgenic lines possessed different types of integration events, no unintended effects were identified. However, we found that the majority of genes showing differential expression were identified as stress-related genes and that environmental conditions had a large impact on the expression of several genes, proteins, and metabolites. We suggest that the microarray approach has the potential to become a useful tool for screening of unintended effects, but state that it is crucial to have substantial information on the natural variation in traditional crops in order to be able to interpret "omics" data correctly within the framework of food safety assessment strategies of novel plant varieties, including genetically modified plant varieties. [source] Relation among plant growth, carbohydrates and flowering time in the Arabidopsis Landsberg erecta × Kondara recombinant inbred line populationPLANT CELL & ENVIRONMENT, Issue 8 2010MOHAMED E. EL-LITHY ABSTRACT Arabidopsis thaliana natural variation was used to study plant performance viewed as the accumulation of photo-assimilates, their allocation and storage, in relation to other growth-related features and flowering-related traits. Quantitative trait locus (QTL) analysis using recombinant inbred lines derived from the cross between Landsberg erecta (originating from Poland) and Kondara (originating from Tajikistan) grown on hydroponics, revealed QTLs for the different aspects of plant growth-related traits, sugar and starch contents and flowering-related traits. Co-locations of QTLs for these different aspects were detected at different regions, mainly at the ER locus; the top of chromosomes 3, 4 and 5; and the bottom of chromosome 5. Increased plant growth was associated with early flowering and leaf transitory starch, and correlated negatively with the levels of soluble sugar at early phases of development. From the significant correlations and the co-locations of the QTLs for these aspects, we conclude that there is a complex relationship between plant growth-related traits, carbohydrate content and flowering-related traits. [source] Gene function beyond the single trait: natural variation, gene effects, and evolutionary ecology in Arabidopsis thalianaPLANT CELL & ENVIRONMENT, Issue 1 2005S. J. TONSOR ABSTRACT The purpose of plant functional genomics is to describe the patterns of gene expression and internal plant function underlying the ecological functions that sustain plant growth and reproduction. Plants function as integrated systems in which metabolic and developmental pathways draw on common resource pools and respond to a relatively small number of signal/response systems. Plants are also integrated with their environment, exchanging energy and matter with their surroundings and are consequently sensitive to changes in energy and resource fluxes. These two levels of integration complicate the description of gene function. Internal integration results in single genes often affecting multiple characteristics (pleiotropy) and interacting with multiple other genes (epistasis). Integration with the external environment leads to gene expression and the genes' phenotypic effects varying across environmental backgrounds (gene,environment interaction). An accurate description of the function of all genes requires an augmentation, already underway, of the study of isolated developmental and metabolic pathways to a more integrated approach involving the study of genetic effects across scales of variation usually regarded as the purview of ecological and evolutionary research. Since the evolution of gene function also depends on this complex of gene effects, progress in evolutionary genetics will also require understanding the nature of gene interactions and pleiotropy and the constraints and patterns they impose on adaptive evolution. Studying gene function in the context of the integrated organism is a major challenge, best met by developing co-ordinated research efforts in model systems. This review highlights natural variation in A. thaliana as a system for understanding integrated gene function in an ecological and evolutionary context. The current state of this research integration in A. thaliana is described by summarizing relevant approaches, current knowledge, and some potentially fruitful future studies. By introducing some of the fundamental questions of ecological and evolutionary research, experimental approaches and systems that can reveal new facets of gene function and gene effect are also described. A glossary is included in the Appendix. [source] Stable isotope variation in wool as a means to establish Turkish carpet provenance,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2005Robert E. M. Hedges The problem of establishing the provenance of carpets of artistic and historical importance is well known. We have addressed this by investigating whether there is sufficient geographical variation in the stable isotopes in wool (namely C, N and S) between key areas of Turkey to be able to recognize the different regions where carpets were made. Here we report results from modern wool samples taken from the winter growth of sheep in 2003/2004 from 13 carpet-producing sites. Although each site has a characteristic composition, most sites cannot be distinguished from each other, and the overall isotopic pattern is unexpectedly complicated. Thus in Western Turkey there is no sign of sea-spray effects in the ,34S values for sites close (10,km) to the sea, while, in the Konya Basin (Central Turkey), the ,34S values vary significantly between nearby sites. Two ,urban' settlements where sheep are now raised have dramatically higher ,15N values. It is nevertheless possible that certain production centers may have distinct signatures, and further work will compare carpets from known sources with the currently produced wool values. The results also provide additional insight into the natural variation found in archaeological faunal isotopic values, e.g. in bone collagen. Copyright © 2005 John Wiley & Sons, Ltd. [source] Ossification of the mouse metatarsal: Differentiation and proliferation in the presence/absence of a defined growth plateTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 1 2006Philip L. Reno Abstract There is significant diversity in growth plate behavior among sites within an individual skeleton and between skeletons of different species. This variation within wild-type animals is an underutilized resource for studying skeletal development. One bone that potentially exhibits the most diverse behavior is the metatarsal. While one end forms a growth plate with an epiphyseal secondary center of ossification as in other long bones, the opposite end undergoes direct ossification in a manner more similar to short bones. Although descriptions of human metatarsal/metacarpal ossification are available, a detailed comparative analysis has yet to be conducted in an animal model amenable to biomolecular analysis. Here we report an analysis of proximal and distal ossification in an age series of mouse metatarsals. Safranin O staining was used for qualitative and quantitative histology, and chondrocyte differentiation and proliferation were analyzed using immunohistochemistry for type X collagen and proliferative cell nuclear antigen expression. We establish that, as in the human, both growth plate formation and direct ossification occur in the mouse metatarsal, with chondrocyte populations showing distinct differentiation patterns at opposite ends of the bone. In addition, growth plate formation is characterized by a peak of proliferation in reserve zone chondrocytes that distinguishes it from both established growth plates and direct ossification. Our analysis demonstrates that the mouse metatarsal is a productive model for investigating natural variation in ossification that can further understanding of vertebrate skeletal development and evolution. © 2005 Wiley-Liss, Inc. [source] Minimax weights for generalised M-estimation in biased regression modelsTHE CANADIAN JOURNAL OF STATISTICS, Issue 3 2002Sanjoy Sinha Abstract The authors consider the construction of weights for Generalised M-estimation. Such weights, when combined with appropriate score functions, afford protection from biases arising through incorrectly specified response functions, as well as from natural variation. The authors obtain minimax fixed weights of the Mallows type under the assumption that the density of the independent variables is correctly specified, and they obtain adaptive weights when this assumption is relaxed. A simulation study indicates that one can expect appreciable gains in precision when the latter weights are used and the various sources of model uncertainty are present. Poids minimax pour la M-estimation généralisée dans le cadre de modéles de régression biaisés Les auteurs s' interessent à la construction de poids pour la M-estimation généralisée. Combinés à des fonctions scores judicieusement choisies, de tels poids fournissent une protection non seulement contre la variation naturelle, mais aussi contre les biais émanant de fonctions de réponse incorrectement spécifiées. Les auteurs présentent des poids fixes minimax du type Mallows pour le cas où la densité des variables exogènes est bien spécifiée et ils proposent des poids adaptatifs qui restent valables autrement. Ils montrent par voie de simulation que l' emploi de poids adaptatifs conduit généralement à des gains de précision appréciables en présence de nombreuses sources d' incertitude concernant le modèle. [source] Lactational programming? mother's milk energy predicts infant behavior and temperament in rhesus macaques (Macaca mulatta)AMERICAN JOURNAL OF PRIMATOLOGY, Issue 6 2010Katie Hinde Abstract There are many aspects of "mothering" that may provide information to the mammalian infant about environmental conditions during critical periods of development. One essential element of mothering involves the quantity and quality of milk that mothers provide for their infants, but little is known about the consequences of variation in milk production. Mother's milk may affect infant behavior by contributing to brain development and to the development of behavioral dispositions. Here we present the first evidence for any mammal that natural variation in available milk energy (AME) from the mother is associated with later variation in infant behavior and temperament in rhesus macaques (Macaca mulatta, N=59). In the early postnatal period, heavier mothers with more reproductive experience produced greater AME, which is the product of milk energy density (kcal/g) and milk yield (g). Moreover, infants whose mothers produced greater AME in the early postnatal period showed higher activity levels and greater confidence in a stressful setting later in infancy. Our results suggest that the milk energy available soon after birth may be a nutritional cue that calibrates the infant's behavior to environmental or maternal conditions. These data provide new insight into potential mechanisms for the development of behavior and temperament and illuminate new directions for investigating maternal effects, nutritional programming, and developmental plasticity. Am. J. Primatol. 72:522,529, 2010. © 2010 Wiley-Liss, Inc. [source] Arabidopsis proteins important for modulating defense responses to Pseudomonas syringae that secrete HopW1-1THE PLANT JOURNAL, Issue 3 2008Min Woo Lee Summary Plant infection responses result from the interaction of pathogen-derived molecules with host components. For the bacterial pathogen Pseudomonas syringae, these molecules are often effector proteins (Hops) that are injected into plant cells. P. syringae carrying hopW1-1 have restricted host range on some Arabidopsis thaliana accessions. At least two Arabidopsis genomic regions are important for the natural variation that conditions resistance to P. syringae/hopW1-1. HopW1-1 elicits a resistance response, and consequently the accumulation of the signal molecule salicylic acid (SA) and transcripts of HWI1 (HopW1-1-Induced Gene1). This work identified three HopW1-1-interacting (WIN) plant proteins: a putative acetylornithine transaminase (WIN1), a protein phosphatase (WIN2) and a firefly luciferase superfamily protein (WIN3). Importantly, WIN2 and WIN3 are partially required for HopW1-1-induced disease resistance, SA production and HWI1 expression. The requirement for WIN2 is specific for HopW1-1-induced resistance, whereas WIN3 is important for responses to several effectors. Overexpression of WIN2 or WIN3 confers resistance to virulent P. syringae, which is consistent with these proteins being defense components. Several known genes important for SA production or signaling are also partially (EDS1, NIM1/NPR1, ACD6 and ALD1) or strongly (PAD4) required for the robust resistance induced by HopW1-1, suggesting a key role for SA in the HopW1-1-induced resistance response. Finally, WIN1 is an essential protein, the overexpression of which over-rides the resistance response to HopW1-1 (and several other defense-inducing effectors), and delays SA and HWI1 induction. Thus, the WIN proteins have different roles in modulating plant defense. [source] Nested core collections maximizing genetic diversity in Arabidopsis thalianaTHE PLANT JOURNAL, Issue 1 2004Heather I. McKhann Summary The successful exploitation of natural genetic diversity requires a basic knowledge of the extent of the variation present in a species. To study natural variation in Arabidopsis thaliana, we defined nested core collections maximizing the diversity present among a worldwide set of 265 accessions. The core collections were generated based on DNA sequence data from a limited number of fragments evenly distributed in the genome and were shown to successfully capture the molecular diversity in other loci as well as the morphological diversity. The core collections are available to the scientific community and thus provide an important resource for the study of genetic variation and its functional consequences in Arabidopsis. Moreover, this strategy can be used in other species to provide a rational framework for undertaking diversity surveys, including single nucleotide polymorphism (SNP) discovery and phenotyping, allowing the utilization of genetic variation for the study of complex traits. [source] Craniological differentiation amongst wild-living cats in Britain and southern Africa: natural variation or the effects of hybridisation?ANIMAL CONSERVATION, Issue 4 2004Nobuyuki Yamaguchi The natural morphological variation in the wildcat, Felis silvestris, and morphological changes possibly caused by introgressive hybridisation with the domestic cat, F. catus, were examined, based on up to 39 variables concerning cranial morphology. The samples of wild-living cats originated from Scotland and southern Africa and consisted of both classical wildcat and other pelage types. Principal component and cluster analyses suggested that introgressive hybridisation occurred in both areas, with the consequence that the characteristics of local wildcat populations had been altered in terms of the frequencies of occurrence of certain characters, especially those concerning cranial capacity. In both regions the clustering patterns of wild-living cats can be interpreted as containing four main groups. One of these consisted mainly of ,non-wildcats' and groups furthest from the ,non-wild' cluster consisted of the highest proportion of ,wildcats' (c. 80%). We propose that where a population is heavily introgressed, the only feasible way to define a wildcat is on the basis of inter-correlated features and conservationists must take a population-based approach to assess the extent of introgression. This approach may provide an operational standard for assessing the impact of hybridisation between wildcats and domestic cats throughout the species' range; it suggests that the Scottish wildcats may be critically endangered. [source] Migratory behaviour affects the trade-off between feather growth rate and feather quality in a passerine birdBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009IVÁN DE LA HERA Migratory birds have less time for moulting than sedentary birds, which may force them to produce their feathers faster at the expense of reducing feather quality. However, the effects of migration on the trade-off between moult speed and plumage quality remain to be studied in natural populations. We analysed the relationship between growth rate and quality of individual feathers, taking advantage of natural variation between migratory and sedentary populations of blackcaps Sylvia atricapilla. As predicted by life-history theory, individual blackcaps showed variable individual quality, which was revealed by positive correlations between feather growth rate and feather mass within populations. However, migrants grew up their feathers faster, producing lighter feathers than sedentary blackcaps. These results support the idea that feather growth rate and feather quality are traded against each other in blackcaps. Such a trade-off is apparently caused by different selection associated to migratory and sedentary life styles, which opens new insights into the diversification of moult patterns in birds. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 98,105. [source] |