Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

We present an evolutionary placement algorithm (EPA) and a Web server for the rapid assignment of sequence fragments (short reads) to edges of a given phylogenetic tree under the maximum-likelihood model. The accuracy of the algorithm is evaluated on several real-world data sets and compared with placement by pair-wise sequence comparison, using edit distances and BLAST. We introduce a slow and accurate as well as a fast and less accurate placement algorithm. For the slow algorithm, we develop additional heuristic techniques that yield almost the same run times as the fast version with only a small loss of accuracy. When those additional heuristics are employed, the run time of the more accurate algorithm is comparable with that of a simple BLAST search for data sets with a high number of short query sequences. Moreover, the accuracy of the EPA is significantly higher, in particular when the sample of taxa in the reference topology is sparse or inadequate. Our algorithm, which has been integrated into RAxML, therefore provides an equally fast but more accurate alternative to BLAST for tree-based inference of the evolutionary origin and composition of short sequence reads. We are also actively developing a Web server that offers a freely available service for computing read placements on trees using the EPA.

To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

The geometric aspects of quantum mechanics are underlined most prominently by the concept of geometric phases, which are acquired whenever a quantum system evolves along a closed path in Hilbert space. The geometric phase is determined only by the shape of this path [1][2][3][4] and is -in its simplest form -a real number. However, if the system contains degenerate energy levels, matrix-valued geometric phases, termed non-abelian holonomies, can emerge 5 . They play an important role for the creation of synthetic gauge fields in cold atomic gases 6 and the description of non-abelian anyon statistics 7 . Moreover, it has been proposed to exploit non-abelian holonomic gates for robust quantum computation [8][9][10] . In contrast to abelian geometric phases 11 , nonabelian ones have been observed only in nuclear quadrupole resonance experiments with a large number of spins and without fully characterizing the geometric process and its non-commutative nature 12,13 . Here, we realize non-abelian holonomic quantum operations 14,15 on a single superconducting artificial three-level atom 16 by applying a well controlled two-tone microwave drive. Using quantum process tomography, we determine fidelities of the resulting non-commuting gates exceeding 95%. We show that a sequence of two paths in Hilbert space traversed in different order yields inequivalent transformations, which is an evidence for the non-abelian character of the implemented holonomic quantum gates. In combination with two-qubit operations, they form a universal set of gates for holonomic quantum computation.A cyclic evolution of a non-degenerate quantum system is in general accompanied by a phase change of its wave function. The acquired abelian phase can be divided into two parts: The dynamical phase which is proportional to the evolution time and the energy of the system, and the geometric phase which depends only on the path of the system in Hilbert space. This characteristic feature leads to a resilience of the geometric phase to certain fluctuations during the evolution 17-19 , a property which has attracted particular attention in the field of quantum information processing 20 . However, universal quantum computation cannot be based on simple phase gates, which modify only the relative phase of a superposition state, unless they act on specific basis states 21 . Furthermore, geometric operations acting on degenerate subspaces have * abdumalikov@phys.ethz.ch † Now at Institute for Quantum Information and Matter, California Institute of Technology, Pasadena, CA 91125, USA been proposed for holonomic quantum computation fully based on geometric concepts 8 . In this scheme, quantum bits are encoded in a doubly degenerate eigenspace of the system hamiltonian h( λ). The parameters λ are varied to induce a cyclic evolution of the system. When the system returns back to its initial state, it can acquire not only a simple geometric phase factor, but also undergoes a path-dependent unitary transformation, a non-abelian holonomy, which causes a transition bet...

http://www.exelixis-lab.org/software.html