The inference of gene trees with species trees

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can co-exist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice-versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. In this article we review the various models that have been used to describe the relationship between gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a better basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.Comment: Review article in relation to the "Mathematical and Computational Evolutionary Biology" conference, Montpellier, 201

Distribution System Outage Detection using Consumer Load and Line Flow Measurements

An outage detection framework for power distribution networks is proposed. Given the tree structure of the distribution system, a method is developed combining the use of real-time power flow measurements on edges of the tree with load forecasts at the nodes of the tree. A maximum a posteriori detector {\color{black} (MAP)} is formulated for arbitrary number and location of outages on trees which is shown to have an efficient detector. A framework relying on the maximum missed detection probability is used for optimal sensor placement and is solved for tree networks. Finally, a set of case studies is considered using feeder data from the Pacific Northwest National Laboratories. We show that a 10\% loss in mean detection reliability network wide reduces the required sensor density by 60 \% for a typical feeder if efficient use of measurements is performed.Comment: Complete rework of result