Principal components analysis in the space of phylogenetic trees

Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary trees on a fixed set of taxa is not a vector space. This paper describes a novel geometrical approach to PCA in tree-space that constructs the first principal path in an analogous way to standard linear Euclidean PCA. Given a data set of phylogenetic trees, a geodesic principal path is sought that maximizes the variance of the data under a form of projection onto the path. Due to the high dimensionality of tree-space and the nonlinear nature of this problem, the computational complexity is potentially very high, so approximate optimization algorithms are used to search for the optimal path. Principal paths identified in this way reveal and quantify the main sources of variation in the original collection of trees in terms of both topology and branch lengths. The approach is illustrated by application to simulated sets of trees and to a set of gene trees from metazoan (animal) species.Comment: Published in at http://dx.doi.org/10.1214/11-AOS915 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Osculating orbits in Schwarzschild spacetime, with an application to extreme mass-ratio inspirals

We present a method to integrate the equations of motion that govern bound, accelerated orbits in Schwarzschild spacetime. At each instant the true worldline is assumed to lie tangent to a reference geodesic, called an osculating orbit, such that the worldline evolves smoothly from one such geodesic to the next. Because a geodesic is uniquely identified by a set of constant orbital elements, the transition between osculating orbits corresponds to an evolution of the elements. In this paper we derive the evolution equations for a convenient set of orbital elements, assuming that the force acts only within the orbital plane; this is the only restriction that we impose on the formalism, and we do not assume that the force must be small. As an application of our method, we analyze the relative motion of two massive bodies, assuming that one body is much smaller than the other. Using the hybrid Schwarzschild/post-Newtonian equations of motion formulated by Kidder, Will, and Wiseman, we treat the unperturbed motion as geodesic in a Schwarzschild spacetime whose mass parameter is equal to the system's total mass. The force then consists of terms that depend on the system's reduced mass. We highlight the importance of conservative terms in this force, which cause significant long-term changes in the time-dependence and phase of the relative orbit. From our results we infer some general limitations of the radiative approximation to the gravitational self-force, which uses only the dissipative terms in the force.Comment: 18 pages, 6 figures, final version to be published in Physical Review

Geodesic Equations on Diffeomorphism Groups

We bring together those systems of hydrodynamical type that can be written as geodesic equations on diffeomorphism groups or on extensions of diffeomorphism groups with right invariant $L^2$ or $H^1$ metrics. We present their formal derivation starting from Euler's equation, the first order equation satisfied by the right logarithmic derivative of a geodesic in Lie groups with right invariant metrics.Comment: This is a contribution to the Proc. of the Seventh International Conference ''Symmetry in Nonlinear Mathematical Physics'' (June 24-30, 2007, Kyiv, Ukraine), published in SIGMA (Symmetry, Integrability and Geometry: Methods and Applications) at http://www.emis.de/journals/SIGMA