Sliding-window plots of <i>d̂</i><i>_S</i>, <i>d̂</i><i>_N</i> and <i>ω̂</i> = <i>d̂</i><i>_N</i>/<i>d̂</i><i>_S</i> in pairwise comparisons of the BRCA1 genes from mammalian species.

<p>The window size is 100 codons, and the offset between windows is one codon.</p

Log-likelihood values and parameter estimates under site models for the nine mammalian BRCA1 genes.

<p>Note.— <i>p</i>: Number of parameters including 15 branch lengths in the tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003746#pone-0003746-g004" target="_blank">Figure 4</a>). Estimates of <i>κ</i> range from 3.4 to 3.6 among models. Sites potentially under positive selection are listed for different models, with the human sequence used as reference. The posterior probability <i>P</i> that a site is from the positive-selection class is calculated using BEB <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003746#pone.0003746-Yang4" target="_blank">[17]</a>.</p

Sliding window plots of <i>d̂</i><i>_S</i>, <i>d̂</i><i>_N</i> and <i>ω̂</i> = <i>d̂</i><i>_N</i>/<i>d̂</i><i>_S</i> from two simulated data sets, generated under model M0 (one-ratio) using parameter estimates obtained from the comparison of the mouse and rat BRCA1 genes.

<p>The window size is 100 codons, and the offset between windows is one codon.</p

The phylogeny for nine mammalian species.

<p>The branch lengths, in the expected number of nucleotide substitutions per codon, are estimated under the free-ratios model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003746#pone.0003746-Yang5" target="_blank">[18]</a> from analysis of the BRCA1 genes, while the estimated <i>ω</i> ratios for branches are shown along the branches.</p

Test of sites under positive selection by the sliding-windows analysis and by the LRT.

a<p>The test statistic in the sliding window analysis is the number of windows in which <i>ω̂</i>>1. The window size is 100 codons, and the offset is 10 codons. In the LRTs, the test statistic 2Δℓ is the log likelihood difference between the null and alternative models.</p>*<p>: significance with <i>p</i><5%.</p>**<p>: significance with <i>p</i><1%.</p

Raw data and scripts

Raw data and script

Uncovering Genes and Ploidy Involved in the High Diversity in Root Hair Density, Length and Response to Local Scarce Phosphate in <i>Arabidopsis thaliana</i>

<div><p>Plant root hairs increase the root surface to enhance the uptake of sparingly soluble and immobile nutrients, such as the essential nutrient phosphorus, from the soil. Here, root hair traits and the response to scarce local phosphorus concentration were studied in 166 accessions of <i>Arabidopsis thaliana</i> using split plates. Root hair density and length were correlated, but highly variable among accessions. Surprisingly, the well-known increase in root hair density under low phosphorus was mostly restricted to genotypes that had less and shorter root hairs under P sufficient conditions. By contrast, several accessions with dense and long root hairs even had lower hair density or shorter hairs in local scarce phosphorus. Furthermore, accessions with whole-genome duplications developed more dense but phosphorus-insensitive root hairs. The impact of genome duplication on root hair density was confirmed by comparing tetraploid accessions with their diploid ancestors. Genome-wide association mapping identified candidate genes potentially involved in root hair responses tp scarce local phosphate. K<i>nock-</i>out mutants in identified candidate genes (<i>CYR1</i>, <i>At1g32360</i> and <i>RLP48</i>) were isolated and differences in root hair traits in the mutants were confirmed. The large diversity in root hair traits among accessions and the diverse response when local phosphorus is scarce is a rich resource for further functional analyses.</p></div

Root hair length and density in <i>loss of function</i> mutants of candidate genes.

<p>(A) Root hair density of wild type (Col-0), <i>rlp48–1</i>, <i>aox1d-1</i>, <i>at1g32360–1</i>, <i>cyr1</i> (all mutants in the Col-0 background). Black bars: with P, grey bars: without P. (B) Root hair length of wild type (Col-0), <i>rlp48–1</i>, <i>aox1d-1</i>, <i>at1g32360–1</i>, <i>cyr1</i>. Black bars: control with P, grey bars: without P, error bars indicate standard error. Statistically significant data points compared to diploid individuals under the same conditions are given as ‘*’ (p<0.05).</p

Natural variation in root hair traits of 166 <i>Arabidopsis thaliana</i> accessions.

<p>(A) Root hair density, (B) length, (C) surface under control (white bars) and scarce local phosphorus (blue bars). Error bars indicate standard error.</p

Dependence of root hair density change with—P on root hair density under control conditions.

<p>Weak negative correlation (R = -0.27, red line) and 95% confidence interval (grey lines) of root hair density response and density under control conditions.</p