Contents and colophon : Philological Studies of the Ainu Language 2

Alignment results of 5S gene NTS sequences from all kinds of groupers. a: The 266 bp NTS sequences of E. coioides, diploid hybrid and triploid hybrid; b: The 272 bp NTS sequences of E. coioides, diploid hybrid and triploid hybrid; c: The 275 bp NTS sequences of E. lanceolatus, diploid hybrid and triploid hybrid; d: The 284 bp NTS sequences of E. lanceolatus, diploid hybrid and triploid hybrid. The TATA sequences were framed in boxes. Dots indicated the identical nucleotides. In bold letters were shown the nucleotide substitutions. (TIF 2265 kb

Least squares regression interpretation of .

<p>Grey circles indicate the genotypic value of each genotype, which is coded as 0, 2, 2 for aa, Aa, and AA respectively. A regression line (red line) is fitted to the data, on which the fitted values are indicated by white circles. The fitted line must pass through the center of the data, as indicated by the cross. The fitted line must also pass through the circle (half grey and half white to indicate the overlap of the genotypic and fitted values) denoting genotype aa. The fitted values are equivalent to dominance values as defined in this parameterization. The arrows between the dominance values and the genotypic values are the residuals of the regression, which we define as “additive deviation”, therefore the residual variance is . Note that the data points are weighted by their frequencies in the population. An additive model is used so that the additive deviation can be illustrated.</p

Conventional and alternative parameterizations capture the majority of polygenic genetic variance.

<p>Simulation is used to generate data sets with the additive (A), dominant (D), and additive by additive (AxA) genetic models and <i>V</i>_<i>A</i>, and are estimated using linear mixed models. The results are presented as the proportion of heritability explained by the genetic variance component; corresponds to <i>V</i>_<i>A</i> (<b>a</b>), to (<b>b</b>), and to (<b>c</b>).</p

Additive genetic variance <i>V</i>_<i>A</i> is a major determinant of total genetic variance.

<p>Under additive (<b>a</b>), dominant (<b>b</b>), or additive by additive (<b>c, d</b>) models, the proportion of total genetic variance explained by the additive genetic variance <i>V</i>_<i>A</i> and dominance genetic variance <i>V</i>_<i>D</i> are estimated either analytically (<b>a, b</b>) or numerically by simulation (<b>d</b>).</p

Alternative parameterizations capture the majority of genetic variance.

<p>Using an alternative parameterization that emphasizes dominant gene action, a newly defined dominance variance and additive deviation variance are estimated analytically under dominant (<b>a</b>) and additive (<b>b</b>) models. Using an alternative parameterization that emphasizes additive by additive gene action, a newly defined interaction variance is estimated numerically under additive by additive (<b>c</b>) and additive (<b>d</b>) models.</p

Variance component analyses of human height data.

<p>Phenotypic variation of height (in cm) observed in the GENEVA study is partitioned into genetic variance components as indicated (color-coded bars) and environmental variance (<i>V</i>_<i>e</i>, grey bar). The colors of bars correspond to the colors of the text indicating the variance components. Error bars indicate standard errors of the variance component estimates provided by GCTA. Proportions of the components are also indicated.</p

Least squares regression interpretation of <i>V</i>_<i>A</i>.

<p>This representation is adapted from Fig. 7.2 of Reference [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006421#pgen.1006421.ref002" target="_blank">2</a>]. Grey circles indicate the genotypic value of each genotype, which is coded as 0, 1, 2 for aa, Aa, and AA respectively. A regression line (red line) is fitted to the data, on which the fitted values are indicated by white circles. The fitted line must pass through the center of the data, as indicated by the cross. The fitted values are equivalent to breeding values. The arrows between the breeding values and the genotypic values are the dominance deviations, which are the same as residuals of the regression. Note that the data points are weighted by their frequencies in the population. A dominance model is used so that the dominance deviation can be illustrated.</p

Notations and definitions of variance components in this study.

<p>Notations and definitions of variance components in this study.</p

Relationship between gene actions and variance components.

<p>(<b>a</b>) Ideally, the variance generated by each type of gene actions is mutually exclusive therefore variance components provide a measure of relative importance of gene actions. (<b>b</b>) In the classical <i>V</i>_<i>A</i> + <i>V</i>_<i>D</i> + <i>V</i>_<i>I</i> variance partition, additive genetic variance <i>V</i>_<i>A</i> has contribution from all of additive, dominant, and epistatic gene actions in most circumstances. With the alternative parameterizations, all types of gene actions contribute to (<b>c</b>) and (<b>d</b>) in most circumstances.</p

Additional file 1: of Visualizing phylogenetic tree landscapes

Appendix. Detailed description of the intrinsic dimensionality measures, nonlinear dimensionality reduction methods, and the goodness of fit measures [45–49]. (PDF 195 kb