Inference of evolutionary jumps in large phylogenies using Lévy processes

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson’s hypothesis

工学部 建築情報処理基礎 1コマコース （平成20年度）

application/pdf54learning objec

無載荷オープンケーソンと周辺砂利層との摩擦抵抗に関する研究

Space System caisson (SS caisson), which is the operation method of constructing caisson foundation, is one of open caisson foundations. The skin friction is reduced by filling space between caisson wall and soil with boulder. Therefore, SS caisson can be sinking by own weight. The skin friction of SS caisson is smaller, but it cannot be quantitatively estimated. So, model tests were carried out to know the tendency of skin friction. In this time, DEM (Distinct Element Method)　analysis was performed to examine legitimacy these experiments.textapplication/pdfdepartmental bulletin pape

Search for matter-dependent atmospheric neutrino oscillations in Super-Kamiokande

We consider ν_μ→ν_τ oscillations in the context of the mass varying neutrino (MaVaN) model, where the neutrino mass can vary depending on the electron density along the flight path of the neutrino. Our analysis assumes a mechanism with dependence only upon the electron density, hence ordinary matter density, of the medium through which the neutrino travels. Fully-contained, partially-contained and upward-going muon atmospheric neutrino data from the Super-Kamiokande detector, taken from the entire SK-I period of 1489 live days, are compared to MaVaN model predictions.We find that, for the case of 2-flavor oscillations, and for the specific models tested, oscillation independent of electron density is favored over density dependence. Assuming maximal mixing, the best-fit case and the densityindependent case do not differ significantly.journal articl

Observation of B+→ΛΛ̅K+

journal articl

Mechanically Manipulating the DNA Threading Intercalation Rate

The dumbbell shaped binuclear ruthenium complex ΔΔ-P requires transiently melted DNA in order to thread through the DNA bases and intercalate DNA. Because such fluctuations are rare at room temperature, the binding rates are extremely low in bulk experiments. Here, single DNA molecule stretching is used to lower the barrier to DNA melting, resulting in direct mechanical manipulation of the barrier to DNA binding by the ligand. The rate of DNA threading depends exponentially on force, consistent with theoretical predictions. From the observed force dependence of the binding rate, we demonstrate that only one base pair must be transiently melted for DNA threading to occur

MOESM4 of Mechanistic differences between HIV-1 and SIV nucleocapsid proteins and cross-species HIV-1 genomic RNA recognition

Additional file 4. Single molecule methods

MOESM10 of Mechanistic differences between HIV-1 and SIV nucleocapsid proteins and cross-species HIV-1 genomic RNA recognition

Additional file 10. SAXS data analysis and results

Structure of MA, CA_ctd and MA/CA_ctd bound state.

A: The entire MA domain is shown in gray. The annotated residues belong to the highly basic region HBR (cyan), the MA-MA trimerization site (yellow) and the newly found, intra-Gag MA/CActd binding site (red). B: the CActd subdomain is shown in tan. Annotated residues belong to the two-fold CActd/CActd (green) and six-fold CActd/CActd (orange) interaction sites in the immature capsid, the inositol hexaphosphate (IP6) binding site (pink asterisks), and the MA/CActd intra-Gag binding site (red). C: The MA/CActd bound state, with participating residues colored by their character: positively charged (blue), negativley charged (red), polar (gold) and nonpolar (violet). D: Snapshot of the MA/CActd bound state from a molecular dynamics simulation of Gag including MA (gray), CAntd (blue), CActd (tan), and SP1 (cyan) in explicit water (not shown).</p