Galactic Phylogenetics

Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our intention for this approach to be employed in the analysis of Galactic history. In Galactic archaeology the shared environment is the interstellar medium in which stars form and provides the basis for tree-building as a methodological tool. Using elemental abundances of solar-type stars as a proxy for DNA, we built in Jofre et al 2017 such an evolutionary tree to study the chemical evolution of the solar neighbourhood. In this proceeding we summarise these results and discuss future prospects.Comment: Contribution to IAU Symposium No. 334: Rediscovering our Galax

Additional file 1: Table S1. of Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis

Primer sequences for detecting RNA editing sites. (DOC 140 kb

Additional file 2: Table S2. of Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis

RNA editing sites of Ginkgo biloba chloroplast protein-coding genes. (XLSX 26 kb

Additional file 6: Figure S2. of The PIN gene family in cotton (Gossypium hirsutum): genome-wide identification and gene expression analyses during root development and abiotic stress responses

Measurements of lateral root number of three-week-old G. hirsutum and G. arboreum seedlings. (PDF 100 kb

Additional file 2: Table S1. of The PIN gene family in cotton (Gossypium hirsutum): genome-wide identification and gene expression analyses during root development and abiotic stress responses

Analysis of G. hirsutum PIN genes and their corresponding orthologues in the AA and DD genomes. (PDF 16 kb

Additional file 4: Figure S1. of The PIN gene family in cotton (Gossypium hirsutum): genome-wide identification and gene expression analyses during root development and abiotic stress responses

Multiple sequence alignment of the deduced amino acid sequences of predicted PINs from G. hirsutum. (PDF 2431 kb

Summary of experimental results in the object-localization task [37].

<p><b>(a)</b> Top, schematic illustrates measurement of whisker position (azimuthal angle <i>θ</i>), instances of touch and an example trace of whisker position. Protraction corresponds to positive changes in <i>θ</i>. <b>(b)</b> Schematics of the thalamocortical circuit and relevant cell-types. <b>(c)</b> Spike rate aligned to transitions from non-whisking to whisking (adapted from panel 5e in [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref037" target="_blank">37</a>]). <b>(d)</b> Average spike rate as a function of whisking amplitude. <b>(e)</b> Average population response aligned to touch (adapted from panel 5c in [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref037" target="_blank">37</a>]). Data and figures corresponding to previously reported datasets [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref036" target="_blank">36</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref037" target="_blank">37</a>].</p

Simulated light activation of halorhodopsin expressed in L4I-Hr⁺ neurons.

<p>Simulations with <i>f</i>_halo = 0.5 reveals a reduction in the whisking suppression and an enhancement of touch responses by L4E neurons. <b>(a)</b> Halorhodopsin activation in L4I-Hr⁺ causes an average increase in response of L4E during whisking and no touch, with a wide distribution of halorhodopsin—induced modifications. <b>(b)</b> Most L4I-Hr⁺ neurons reduce their activity during whisking while L4I-Hr^- neurons increase it. <b>(c)</b> Increase in the touch responses in L4E neurons during suppression of L4I-Hr⁺. <b>(d)</b> Increase in the touch responses in L4I neurons. The increase in touch responses is only seen in Hr⁺ cells. <b>(e</b>,<b>f)</b> Population PSTH of L4E (<b>e</b>) and L4I (<b>f</b>) neurons with and without L4I-Hr⁺ activity suppression. <b>(g)</b> Reduction of L4I-Hr⁺ activity diminishes the whisking suppression effect in L4E neurons. Black line: T neurons; solid grey line: L4E neurons without halorhodopsin activation; dashed grey line: L4E neurons during halorhodopsin activation. <b>(h)</b> Reduction of L4I-Hr⁺ activity diminishes the whisking response in L4I-Hr⁺ neurons. Solid red line: L4I-Hr⁺ neurons without halorhodopsin activation; dashed red line: L4I-Hr⁺ neurons during halorhodopsin activation. Dashed blue line: L4I-Hr^- neurons during halorhodopsin activation.</p

Network parameters in the reference parameter set: - synaptic delay, <i>K</i>_<i>αβ</i>—average number of presynaptic inputs, <i>g</i>_<i>αβ</i>—synaptic conductance, <i>V</i>_extr—the extremal value of the unitary synaptic membrane potential change.

<p>The corresponding experimental values for <i>K</i>_<i>αβ</i> and <i>V</i>_extr are written in the two right columns. Those values are taken from the following references: a—[<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref053" target="_blank">53</a>], b—[<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref056" target="_blank">56</a>], c—[<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref034" target="_blank">34</a>], d- [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref028" target="_blank">28</a>], e–[<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref057" target="_blank">57</a>], f—[<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.ref027" target="_blank">27</a>].</p

Neural network model of L4.

<p><b>(a)</b> Diagram of the recurrent model of L4 network. <b>(b)</b> Spike shape of VPM (schematic), L4E and L4I neurons. <b>(c)</b> Temporal dynamics of individual EPSPs for the different synaptic connections (T = VPM; I = L4 FS; E = L4E). The convention is that that the first letter corresponds to the post-synaptic neuron and the second letter to the presynaptic neuron. <b>(d)</b> Thalamic generating function <i>F</i>_T (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005576#pcbi.1005576.e003" target="_blank">Eq 1</a>). The panels on the right show the same figure in a magnified scale. For simplicity, we assume that all T neurons have the same preferred phase.</p