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PubMed1992

Combined inter-observer and inter-method variation in bone histomorphometry.

Manual methods for the measurement of bone biopsies have largely been superseded by semi-automatic computerised techniques. Histomorphometrists often use control data obtained by other observers using different methods, thus combining inter-observer and inter-method variation. We have examined the combined effect of inter-method and inter-observer variation on measurements of bone area, osteoid perimeter, and osteoid width in iliac crest biopsies from healthy subjects, one observer using the manual grid system and the other using a semi-automated technique. Inter-observer and inter-method variation were independently determined, and the proportion of each expressed as a percentage of combined error. Our results indicate that the combination of inter-method and inter-observer variation causes significant differences in the values obtained for osteoid perimeter, whereas inter-method variation is mainly responsible for differences in osteoid width values; differences in bone area are largely due to inherent sampling variation. These variations indicate that caution is required when comparison is made with control data from other sources, especially if different techniques are employed.

Analysis of Variance↗

PubMed2005

An investigation of the origin, location and variations of the renal arteries in human fetuses and their clinical relevance.

We investigated the origin, localizations and anatomic variations of the renal artery (RA) in human fetuses with the aim of determining the distribution of these variations according to lateralization and gender. In total, 90 fetuses of spontaneous abortion (45 males, 45 females) with no congenital malformations were included to the study. The abdominal aorta and its branches were dissected after latex solution colored with red ink had been injected into the vessels from the thoracic aorta. In all, 180 RA dissections were performed bilaterally in 90 cases and the anatomic variations were photographed. Right and left RAs were found to originate from the following levels according to the columna vertebralis, respectively: 3.8% and 1.9% lower T12, 67.3% and 25.0% upper L1, 9.6% and 28.8% mid L1, 15.3% and 40.3 lower L1, 3.8% and 3.8% upper 1/3 part of L2 vertebra. The right RA originated from the lateral part and anterolateral wall of the abdominal aorta in 73.0% and 26.9% of cases while the lateral and anterolateral wall origin percentages of left RA were 90.3% and 9.6%, respectively. The origin site of the right RA from the abdominal aorta was superior to, at the same level with, and inferior to that of the left RA in 53.8%, 34.6% and 11.5% of the cases, respectively. There were no variations in 75% of the cases whereas the remaining 25% had several variation patterns. The presented morphological results are as follows: A single hilar artery in 75% of the cases, double hilar arteries in 11.1%, an inferior polar artery in 10.5%, and a superior polar artery in 3.3% of specimens studied. Anatomical variations were observed more frequently among male fetuses and on the right side. Knowledge of RA variations is important for surgeons in performing many procedures and may help to avoid clinical complications, especially, during radiological examination and/or surgical approaches in the abdominal region.

Abortion, Spontaneous↗

PubMed2006

A multivariate comparison of dental variation in wild and captive populations of baboons (Papio hamadryas).

Phenotypic variation is critical to many aspects of biological research. Use of a captive population to address questions concerning the genetics and evolution of dental variation raises the question of how the pattern of phenotypic variation under study compares with that in a wild population of the same species. Differences in the pattern of variation within wild and captive populations may indicate different genetic and non-genetic factors, and also may have implications for how well the captive group can serve as a model for its wild type relatives. We compared dental size measures from two Papio hamadryas populations, one captive and one wild. Lengths and widths of maxillary and mandibular second molars (M2s) were collected from 630 baboons from a captive pedigreed breeding colony housed at the Southwest National Primate Research Center in San Antonio, Texas, and 125 baboons from a wild population culled from a sisal plantation in Kibweze, Kenya. Although the two populations consistently differed with respect to lengths and widths of the M2s, principal components analyses show that the basic pattern to variation in these molar crown traits is remarkably similar in both populations; and linear functions based on these measures cannot reliably discriminate between the two groups. This similarity in the pattern of variation among these dental crown measures in these two groups suggests that analyses to dissect their genetic architecture in captive populations is likely to be highly relevant to dental variation in wild baboons as well.

Animals↗

PubMed2006

Exploration of methods to identify polymorphisms associated with variation in DNA repair capacity phenotypes.

Elucidating the relationship between polymorphic sequences and risk of common disease is a challenge. For example, although it is clear that variation in DNA repair genes is associated with familial cancer, aging and neurological disease, progress toward identifying polymorphisms associated with elevated risk of sporadic disease has been slow. This is partly due to the complexity of the genetic variation, the existence of large numbers of mostly low frequency variants and the contribution of many genes to variation in susceptibility. There has been limited development of methods to find associations between genotypes having many polymorphisms and pathway function or health outcome. We have explored several statistical methods for identifying polymorphisms associated with variation in DNA repair phenotypes. The model system used was 80 cell lines that had been resequenced to identify variation; 191 single nucleotide substitution polymorphisms (SNPs) are included, of which 172 are in 31 base excision repair pathway genes, 19 in 5 anti-oxidation genes, and DNA repair phenotypes based on single strand breaks measured by the alkaline Comet assay. Univariate analyses were of limited value in identifying SNPs associated with phenotype variation. Of the multivariable model selection methods tested: the easiest that provided reduced error of prediction of phenotype was simple counting of the variant alleles predicted to encode proteins with reduced activity, which led to a genotype including 52 SNPs; the best and most parsimonious model was achieved using a two-step analysis without regard to potential functional relevance: first SNPs were ranked by importance determined by random forests regression (RFR), followed by cross-validation in a second round of RFR modeling that included ever more SNPs in declining order of importance. With this approach six SNPs were found to minimize prediction error. The results should encourage research into utilization of multivariate analytical methods for epidemiological studies of the association of genetic variation in complex genotypes with risk of common diseases.

Cell Line↗

PubMed2003

Interpreting spatial variation in ozone symptoms shown by cutleaf cone flower, Rudbeckia laciniata L.

Visible injury caused by ozone is recorded every year in native plant species growing in Great Smoky Mountains National Park (USA). One of the most sensitive species, cutleaf coneflower (Rudbeckia laciniata L.), shows great variation in symptoms between and within populations but the causes of this variation and its ecological significance are currently unknown. This paper presents data relating to genetic variation, ozone concentrations, stomatal conductance and light (PAR) within populations. The data show that populations differ in genetic diversity, one consisting of only three genets while another was very diverse. In the former population, symptoms varied greatly within a single genet, pointing to a large micro-environmental influence. Measurements of ozone, stomatal conductance and PAR within plant canopies suggest that variation in symptom expression is unlikely to be due to differences in ozone flux and more likely to be due to variation in light. The variation in visible symptoms raises the question of what bioindicators actually indicate, and it suggests that symptoms should be interpreted with great caution until the underlying causes of that variation are fully understood.

Air Pollutants↗

PubMed1997

Influences of ultrasonic machine settings, transducer frequency and placement of region of interest on the measurement of integrated backscatter and cyclic variation.

Integrated backscatter and its cyclic variation are potentially important parameters to discriminate normal from diseased myocardium. Cyclic variation of integrated backscatter is expected to be independent of machine settings. Backscatter images of swine hearts were taken using a two-dimensional backscatter system while acoustic power was varied at different time gain control (TGC) settings. Cyclic variation was measured in vivo with various acoustic power and TGC settings using different transducer frequencies. Three different regions were analyzed. For any given TGC setting, the relationship between acoustic power and integrated backscatter in vitro was linear only over a narrow range. In vivo, cyclic variation was present at all regions studied in both long- and short-axis views. However, lower acoustic power (< 15 dB) and TGC (< 20 dB), or excessive settings of acoustic power (> 35 dB) and TGC (> 50 dB), produced minimal cyclic variation. Appropriate acoustic power (20-35 dB) and TGC (30-50 dB) produced larger and more consistent cyclic, variation at the posterior region of the left ventricle. These data indicate that each region has specific, appropriate machine settings to maximize the magnitude of cyclic variation.

Acoustics↗

PubMed2002

Observer variation in the sonographic measurement of optic nerve sheath diameter in normal adults.

AIM: To quantify the observer variation in the sonographic measurement of optic nerve sheath diameter (ONSD) in normal adults. MATERIALS AND METHODS: Sixty-seven normal adult volunteers underwent ultrasound examination of each eye by three independent observers using a 7 MHz sector probe. Three measurements were made of each eye by each observer and a mean value calculated for each eye. Median and 5th-95th centile values for both intra- and inter-observer variation were calculated for the three observers. RESULTS: The median intra-observer variation was +/-0.1 mm, with 5th-95th centile values of +/-0-0.4 mm. The median inter-observer variation was +/-0.2-0.3 mm, with 5th-95th centile values of +/-0-0.7 mm. Careful review of examination technique by the three observers after the first 17 examinations was shown to reduce both intra- and inter-observer variation. CONCLUSION: The sonographic measurement of ONSD is a readily learned, reproducible technique with low intra- and inter-observer variation. The average inter-observer variation (+/-0.2 mm) is comparable to the inherent variability of the ultrasound machine. The importance of standardisation of examination technique is stressed.

Adult↗

PubMed1999

Biomechanical effects of intraspecimen variations in trabecular architecture: a three-dimensional finite element study.

Trabecular architecture is considered important in osteoporosis and has been quantified by a variety of mean parameters characteristic of a whole specimen. Variations within a specimen, however, have been mostly ignored. In this study, the theoretical effects of these intraspecimen variations in architecture on predicted mechanical properties were investigated through a three-dimensional finite element parameter study that simulated variations in trabecular thickness in a controlled manner. An irregularly spaced lattice of different sized rods was used to simulate trabecular bone in three distinct volume fraction ranges, representing young, middle-aged, and elderly vertebral bone. Beta distributions (a type of non-normal distribution) of trabecular thickness with coefficients of variation of either 25%, 40%, or 55% were applied to the rods in each model, and 225 simulations of uniaxial compression tests were performed to obtain modulus values. Percent modulus reductions of 22% and 43% were predicted when the intraspecimen coefficient of variation in trabecular thickness was increased from 25% to 40% and from 25% to 55%, respectively, for models of equal volume fraction. Furthermore, this trend was predicted to be independent of volume fraction. We conclude, therefore, that consideration of the intraspecimen trabecular thickness variation in conjunction with volume fraction may improve the ability to predict trabecular modulus compared with use of volume fraction alone. Further, the model suggests that if age, disease, or drug treatments increase trabecular thickness variation, this may be detrimental to mechanical properties.

Adult↗

PubMed1991

Population genetics of the Y chromosome of Drosophila melanogaster: rDNA variation and phenotypic correlates.

One means of examining the evolutionary significance of molecular variation on the Y chromosome is to identify phenotypes specifically affected by Y-linked genes, and to quantify the phenotypic variation and its correlation to the molecular variation. The functional importance of the Y-linked array of rRNA genes is demonstrated by the ability of Y chromosome to rescue X-linked bobbed lethal alleles, whose lethality is seen in homozygous females. Because low numbers of X-linked rDNA gene copies result in increased developmental time and shortened bristles, and because there is considerable natural variation in Y-linked copy number, a careful examination of Y-linked variation in these two traits may uncover a mode of selection acting on the multigene family. In this study, 36 Y-chromosome replacement lines were tested to detect subtle variation in bristle phenotypes and developmental rates. Correlations among these traits, rDNA gene copy number, and intergenic sequence length were quantified. The absence of significant correlations between phenotypic characters and rDNA copy number of intergenic sequence length suggests that the extant molecular variation in Y-linked rDNA can have at most very small selective effects.

Animals↗

PubMed2001

August Weismann on germ-plasm variation.

August Weismann is famous for having argued against the inheritance of acquired characters. However, an analysis of his work indicates that Weismann always held that changes in external conditions, acting during development, were the necessary causes of variation in the hereditary material. For much of his career he held that acquired germ-plasm variation was inherited. An irony, which is in tension with much of the standard twentieth-century history of biology, thus exists - Weismann was not a Weismannian. I distinguish three claims regarding the germ-plasm: (1) its continuity, (2) its morphological sequestration, and (3) its variational sequestration. With respect to changes in Weismann's views on the cause of variation, I divide his career into four stages. For each stage I analyze his beliefs on the relative importance of changes in external conditions and sexual reproduction as causes of variation in the hereditary material. Weissmann believed, and Weismannism denies, that variation, heredity, and development were deeply intertwined processes. This article is part of a larger project comparing commitments regarding variation during the latter half of the nineteenth century.

Biological Evolution↗

PubMed2002

Variation and inter-relationships of quantitative traits in tef (Eragrostis tef (Zucc.) Trotter) germplasm from western and southern Ethiopia.

Three thousand tef (Eragrostis tef (Zucc.) Trotter) lines representing 60 germplasm populations from western and southern Ethiopia were sown on pellic Vertisols at Debre Zeit Agricultural Research Center during the 1999/2000 main season. The objectives were to assess the variation with respect to regions and altitude zones of origin and to study the inter-relationships of 17 pheno-morphic and agronomic traits. The populations showed significant (p < or = 0.05) regional variation in 10 (59%) of the quantitative traits, but clinal variation among altitude zones was significant (p < or = 0.05) only for six (35%) of the traits. On the other hand, the populations revealed consistent variation (p < or = 0.05) within both regions and altitude zones in all the traits evaluated. Likewise, the variation among lines within populations of both regions and altitude zones was significant (p < or = 0.05) in most of the traits. The number of characters showing substantial correlation depicted regional and clinal variation mainly depending on the number of populations. Based on the mean of the populations, grain yield panicle and shoot phytomass plant showed negative correlation with harvest index, and positive correlation with most of the remaining traits. Individual plant grain yield was positively correlated with all the other traits except harvest index, days to maturity, grain filling period and number of primary panicle branches. Overall, the tef germplasm populations showed substantial phenotypic variation which can be utilized in the genetic improvement of the crop.

Edible Grain↗

PubMed2004

Genetic variation increases during biological invasion by a Cuban lizard.

A genetic paradox exists in invasion biology: how do introduced populations, whose genetic variation has probably been depleted by population bottlenecks, persist and adapt to new conditions? Lessons from conservation genetics show that reduced genetic variation due to genetic drift and founder effects limits the ability of a population to adapt, and small population size increases the risk of extinction. Nonetheless, many introduced species experiencing these same conditions during initial introductions persist, expand their ranges, evolve rapidly and become invasive. To address this issue, we studied the brown anole, a worldwide invasive lizard. Genetic analyses indicate that at least eight introductions have occurred in Florida from across this lizard's native range, blending genetic variation from different geographic source populations and producing populations that contain substantially more, not less, genetic variation than native populations. Moreover, recently introduced brown anole populations around the world originate from Florida, and some have maintained these elevated levels of genetic variation. Here we show that one key to invasion success may be the occurrence of multiple introductions that transform among-population variation in native ranges to within-population variation in introduced areas. Furthermore, these genetically variable populations may be particularly potent sources for introductions elsewhere. The growing problem of invasive species introductions brings considerable economic and biological costs. If these costs are to be mitigated, a greater understanding of the causes, progression and consequences of biological invasions is needed.

Animal Migration↗

PubMed2003

Natural variation in human gene expression assessed in lymphoblastoid cells.

The sequencing of the human genome has resulted in greater attention to genetic variation among individuals, and variation at the DNA sequence level is now being extensively studied. At the same time, it has become possible to study variation at the level of gene expression by various methods. At present, it is largely unknown how widespread this variation in transcript levels is over the entire genome and to what extent individual differences in expression level are genetically determined. In the present study, we used lymphoblastoid cells to examine variation in gene expression and identified genes whose transcript levels differed greatly among unrelated individuals. We also found evidence for familial aggregation of expression phenotype by comparing variation among unrelated individuals, among siblings within families and between monozygotic twins. These observations suggest that there is a genetic contribution to polymorphic variation in the level of gene expression.

Female↗

PubMed2005

Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes.

To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r=0.33, P=0.001) and no correlation between genetic and geographic distances (r=-0.08, P>0.10). In contrast, mtDNA variation is weakly correlated with both language (r=0.16, P=0.046) and geography (r=0.17, P=0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (Phi(CT)=0.21) than by geography (Phi(CT)=0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (Phi(CT)=0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.

Africa↗

PubMed2002

Effect of low stressful temperature on genetic variation of five quantitative traits in Drosophila melanogaster.

A half-sib analysis was used to investigate genetic variation for three morphological traits (thorax length, wing length and sternopleural bristle number) and two life-history traits (developmental time and larva-to-adult viability) in Drosophila melanogaster reared at a standard (25 degrees C) and a low stressful (13 degrees C) temperature. Both phenotypic and environmental variation showed a significant increase under stressful conditions in all traits. For estimates of genetic variation, no statistically significant differences were found between the two environments. Narrow heritabilities tended to be higher at 13 degrees C for sternopleural bristle number and viability and at 25 degrees C for wing length and developmental time, whereas thorax length did not show any trend. However, the pattern of genetic variances and evolvability indices (coefficient of genetic variation and evolvability), considered in the context of literature evidence, indicated the possibility of an increase in additive genetic variation for the morphological traits and viability and in nonadditive genetic variation for developmental time. The data suggest that the effect of stressful temperature may be trait-specific and this warns against generalizations about the behaviour of genetic variation under extreme conditions.

Analysis of Variance↗

PubMed2004

Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster.

Drosophila melanogaster originated in Africa, spread to Europe and Asia, and is believed to have colonized the New World in the past few hundred years. Levels of genetic variation are typically reduced in New World populations, consistent with a founder event following range expansion out of Africa and the Old World. We describe the patterns of mtDNA length variation within and among several populations of Drosophila melanogaster from the Old and New World. MtDNA length variation is due to insertion and deletion of tandem repeats in the control region (D-loop) of D. melanogaster mitochondrial genome. The distinct mutational dynamics of this system provide an opportunity to compare the patterns of variation in this marker to those of other markers with different mutational pressures and linkage relationships. The data show significantly more length variation in African and Asian samples than in New World samples. New World samples also show more pronounced skew of the length distribution. Our results are distinct from an earlier study that showed significantly higher levels of length variation and heteroplasmy. The level of heteroplasmy is highly correlated with the number of years that samples have been maintained in laboratory culture, suggesting that relaxed selection in small populations permits the accumulation of mtDNA length variation and heteroplasmy. Together, the data indicate that mtDNA length variants retain a signature of founder events and selection, and suggest that further investigation into the mutation-selection dynamics of the D-loop region of mtDNA would provide a distinct and informative marker for analysis of the recent history of populations.

Animals↗

PubMed2001

Comparison of genetic variation in growth performance on normal and novel host plants in a local population of a herbivorous ladybird beetle, Epilachna vigintioctomaculata.

Local populations of herbivore species that display variation in host plant use are subject to natural selection for improved ability to use their own host species. Since natural selection changes the frequency of alleles that control host use, genetic variation in growth performance on host plants may change with each generation of selection. Therefore, within-population variations in the ability to use different hosts may reflect past selective forces. The present study reports the genetic variation in growth performance in a population of the herbivorous ladybird beetle, Epilachna vigintioctomaculata Motschulsky (Coccinellidae, Epilachninae) on both the normal host and a novel host. The present study found higher heritabilities for growth performance on the novel host than the normal host. The difference in heritabilities was caused by smaller among-family variance components on the normal host compared to those on the novel host. The results are compatible with the view that natural selection, which improved the ability of the population to use a particular host plant, has reduced genetic variation within that population in the ability to use that host plant. The pattern of reduced genetic variation in a population reared on the normal host observed in the present study is compared with that in another population, which showed local adaptation in the use of its own host plant. The effect of natural selection on differing host plant use on within-population genetic variation is discussed.

Adaptation, Physiological↗

PubMed1999

Extensive intraspecific chloroplast DNA (cpDNA) variation in the alpine Draba aizoides L. (Brassicaceae): haplotype relationships and population structure.

Chloroplast DNA (cpDNA) sequence variation is currently the most widely used tool for the inference of phylogenetic relationships among plants at all taxonomic levels. Generally, noncoding regions tend to evolve faster than coding sequences and have recently been applied to the study of phylogenetic relationships among closely related taxa. An implicit assumption of many of these studies is that intraspecific cpDNA variation is either absent or low and therefore will not interfere with the reconstruction of interspecific relationships. A survey of cpDNA sequence variation in the common alpine plant species Draba aizoides L. was undertaken to assess levels of intraspecific cpDNA sequence variation. These levels were compared to levels of interspecific sequence divergence between D. aizoides and related alpine Draba species. Intraspecific cpDNA sequence divergence was extensive in D. aizoides, and intraspecific differences were often larger than interspecific differences. cpDNA haplotype relationships were explored using a maximum parsimony approach and minimum-spanning networks. Results from both methods were largely congruent but comparisons provided interesting insights into the presumed evolutionary history of cpDNA haplotypes. A combined effect of cpDNA introgression and complex lineage sorting was inferred to explain the pattern of cpDNA variation found in D. aizoides. Our results suggest that intraspecific cpDNA variation can be extensive and that intraspecific variation needs to be taken into account when inferring phylogenetic relationships among closely related taxa.

Brassicaceae↗