Pine wilt disease caused by the pinewood nematode (PWN), Bursaphelenchus xylophilus (Steiner et Buhrer) Nickle, has destroyed huge areas of pine forest in East Asia, including Japan, China and Korea. No protection against PWN has been developed, and the responses of pine trees at the molecular level are unrecorded. We isolated and analyzed upregulated or newly induced genes from PWN-inoculated ...

Abstract. Distance energy is a newly introduced molecular graph-based analog of the total π-electron energy, and it is defined as the sum of the absolute eigenvalues of the molecular distance matrix. For trees and unicyclic graphs, distance energy is equal to the doubled value of the distance spectral radius. In this paper, we introduce a general transformation that increases the distance spect...

A great tradition in macroevolution and systematics has been the ritual squabbling between palaeontologists and molecular biologists. But, because both sides were talking past each other, they could never agree. Practitioners in both fields should play to their strengths and work together: palaeontologists can provide minimum constraints on branching points in the Tree of Life with considerable...

Maximum likelihood (ML) is increasingly used as an optimality criterion for selecting evolutionary trees, but finding the global optimum is a hard computational task. Because no general analytic solution is known, numeric techniques such as hill climbing or expectation maximization (EM) are used in order to find optimal parameters for a given tree. So far, analytic solutions were derived only f...

The construction and interpretation of gene trees is fundamental in molecular systematics. If the gene is defined in a historical (coalescent) sense, there can be multiple gene trees within the single contiguous set of nucleotides, and attempts to construct a single tree for such a sequence must deal with homoplasy created by conflict among divergent histories. On a larger scale, incongruence i...