Multidimensional scaling of Nei's genetic distances.

<p>Genetic data from Highton and MacGregor (1983). Populations numbers match <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.g001" target="_blank">Fig 1</a>.</p

Bayesian maximum clade credibility tree.

<p>As with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.g003" target="_blank">Fig 3</a>, but showing relationships within Clades B-D.</p

bGMYC analyses.

<p>To the left is the maximum clade credibility tree from BEAST 2 (Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.g003" target="_blank">3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.g004" target="_blank">4</a>). The table is a sequence-by-sequence matrix, with cells colored by the posterior probability that the corresponding sequences are conspecific. Off-diagonal colors indicate uncertainty due to uncertainty in topology.</p

Geneland results, with grouping inferred from nuclear loci.

<p>The three colors correspond to the three groups inferred by Geneland. The dots are the collecting localities (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.g001" target="_blank">Fig 1</a>), and are colored by clade: white = Clade A; blue = Clade B; red = Clade C; black = Clade D. The histogram shows the log of the ratio of the estimates rates of coalescence and the estimated Yule rates. Values above zero indicate the estimated rate of coalescence is higher.</p

Sampling, genetic diversity, and models of evolution.

<p>For the models of evolution, "All data" refers to the inclusion of every DNA sequence, whereas the “Complete data set" refers to the data set with no missing data (68 individuals). Numbers in parentheses refer to codon positions.</p

Design and analysis of control systems: case studies

This book provides methods to unify different approaches to tackle stability theory problems. In particular, it presents a methodology to blend approaches obtained from measure theory with methods obtained from Lyapunov’s stability theory. The author summarizes recent works on how different analysis/design methods can be unified and employed for systems that do not belong to either of domains of validity

Map of the range of <i>Plethodon kentucki</i>.

<p>Sample localities are numbered, and match <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.g003" target="_blank">Fig 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.s001" target="_blank">S1 Appendix</a>. Symbols identify the mtDNA clade of individuals in that population (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.g003" target="_blank">Fig 3</a>).</p

Estimates of median rates of evolution.

<p>Three estimates of the age of the crown group of plethodontids were used [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.ref071" target="_blank">71</a>]. 95% confidence intervals are in parentheses. For clarity, all values are multiplied by 100, and thus are the estimated percentage change per million years.</p

Maximum clade credibility trees from *BEAST 2, with species delimitations from BPP.

<p>Numbers at tree nodes are posterior probabilities; numbers <0.95 have been omitted. Bars at nodes represent the 95% highest posterior density for the inferred ages of nodes. To the right, bars connect putative species that were combined in the BPP analyses. (A) 16 species as delimited by bGMYC, using mtDNA data; (B) 3 species as delimited by Geneland, using the nuclear data; (4) 2 species as delimited by bGMYC, using mtDNA data. See also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150022#pone.0150022.g003" target="_blank">Fig 3</a> for species delimitations.</p

BOTTLENECK results by sampling locality and STRUCTURE cluster.

<p>Shown are <i>P</i>-values for a genetic bottleneck under the SMM and TPM. An “L-Shaped” distribution under a Mode-Shift test indicates a bottleneck was not detected.</p