Mate choice data for Peromyscus leucopus and P. gossypinus.

Two-way mate choice data for Peromyscus leucopus and P. gossypinus using an electronically-gated choice apparatus. Contains trials where the test mice were raised with their own parents, cross-fostered to parents of the other species, or cross-fostered to unrelated parents of the same species

The fraction of simulated replicates rejecting the neutral model by Sweepfinder and <i>ω_max</i>, with varying population size.

<p>The simulations with demographic models mimic the history of (A) Florida beach mice (<i>N</i>_e = 2500) and (B) Nebraska Sand Hills mice (<i>N</i>_e = 50,000). The time of the bottleneck (<i>t</i>_r = 0.1) and time since fixation (<i>τ</i> = 0.1) are fixed, but selection strength varies from <i>s</i> = 0.001 to 0.1. Ideal performance would be indicated by all replicates showing a significant signal at very small window sizes, suggesting an ability to localize the target.</p

The inferred demographic history of the Florida and Nebraska populations.

<p>Geographic location and photos of the derived light and ancestral dark mouse populations from (A) Florida (photos by J. Miller and S. Carey) and (B) Nebraska (photos by C. Linnen) (top panel). Cartoon representation of the inferred demographic model of the two species (middle panel). Both models include selection acting on the bottlenecked population (with effective population size reduced to <i>fN</i>_e, where <i>N</i>_e is the ancestral population size) immediately after the divergence from the ancestral population at time <i>d</i>, and the selected allele becomes fixed at time <i>τ</i>. Likelihood ratio (LR) profile of Sweepfinder in both populations of light-colored mice (bottom panel), where the horizontal line indicates the significance cutoff. Stars indicate the approximate location of causal mutations conferring light pigmentation. Because there are multiple <i>Agouti</i> alleles, we here polarize (into “light” or “dark” class) based on the SNP mostly strongly associated with pigment variation (as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110579#pone.0110579-Linnen2" target="_blank">[26]</a>).</p

The true positive (TP) and false positive (FP) rates of Sweepfinder and <i>ω_max</i> in Florida and Nebraska population models.

<p>A TP is defined as a significant rejection within 10kb of the true target.</p>a<p>bottleneck severity.</p>b<p>selection coefficient.</p>c<p>timing of fixation of the selected allele.</p><p>The true positive (TP) and false positive (FP) rates of Sweepfinder and <i>ω_max</i> in Florida and Nebraska population models.</p

The fraction of simulated replicates rejecting neutrality by Sweepfinder and <i>ω_max</i>, varying the time since the beneficial fixation.

<p>Simulations with ancestral population size equal to (A) 10⁴, (B) 10⁵ and (C) 10⁶. Selection strength (<i>s</i> = 0.01) and time since bottleneck (<i>t</i>_r = 0.01) are fixed, but the time of selected allele fixation (<i>τ</i>) varied from 0.01 to 0.3.</p

Comparison of demographic parameters in Florida mice and Nebraska mice.

a<p>pairwise nucleotide diversity per site.</p>b<p>ratio of bottleneck population size to ancient population size.</p>c<p>ratio of contemporary to ancient population size.</p><p>Comparison of demographic parameters in Florida mice and Nebraska mice.</p

The fraction of simulated replicates rejecting neutrality by Sweepfinder and <i>ω</i><i>_max</i>, with varying bottleneck severity.

<p>Simulations with ancestral population size equal to (A) 10⁴, (B) 10⁵ and (C) 10⁶. Selection strength (<i>s</i> = 0.01), time since fixation (<i>τ</i> = 0.1), and time since bottleneck (<i>t</i>_r = 0.1) are fixed, but bottleneck severity (<i>f</i>) varied from 0.01 to 0.5.</p

Copes et al. Dryad submission

The zipped folder contains the original Excel spreadsheet with 3D digitized points from ~400 non-human primate skulls. It also contains "cleaned up" versions of the points split into separate files by infraorder (strepsirrhines, catarrhines, platyrrines) and R code for importing the files. Many thanks to Randi Griffin for her assistance in reformatting the original data to make it more useful/accessible for analysis

Double digest RAD sequencing provides flexibility in the number of homologous fragments recovered.

<p>Changing the restriction enzyme (RE) or size-selection regime modifies the fraction of genome recovered. <b>Simulation 1</b> (blue lines, shading): the expected fragment size distribution for a RE digest with NlaIII and MluCI (CATG and AATT) in the <i>Mus musculus</i> genome is shown (solid blue line). “Broad” size selection (300 bp±50 bp) is modeled by a normal sampling distribution (mean = 300 bp, SD = 25 bp). Under this sampling distribution, 4,900,000 sequence reads (dashed blue line) are expected to cover ∼119,000 regions at 7× or greater (blue area). <b>Simulation 2</b> (red lines, shading): the expected fragment size distribution for a digest with EcoRI and MspI (GAATTC and CCGG) is shown (solid red line). “Narrow” size selection (300 bp±24 bp; see text) is modeled by a normal sampling distribution (mean = 300 bp, SD = 11 bp; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037135#pone.0037135.s003" target="_blank">Analysis S1</a> Supporting <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037135#pone-0037135-g001" target="_blank">Figure 1</a>). Under this sampling distribution, an investment of 315,000 sequence reads (dashed red line) is sufficient to recover ∼17,000 regions at 7× or greater (red area).</p

Double digest RAD sequencing improves efficiency and robustness while minimizing cost.

<p>(<b>A</b>) Traditional Restriction-Site Associated DNA sequencing (RADseq) uses a single restriction enzyme (RE) digest coupled with secondary random fragmentation and broad size selection to generate reduced representation libraries consisting of all genomic regions adjacent to the RE cut site (red segments). (<b>B</b>) Double digest RAD sequencing (ddRADseq), by contrast, uses a two enzyme double digest followed by precise size selection that excludes regions flanked by either [a] very close or [b] very distant RE recognition sites, recovering a library consisting of only fragments close to the target size (red segments). Representation in this library is expected to be inversely proportional to deviation from the size-selection target, thus read counts across regions are expected to be correlated between individuals (yellow and green bars).</p