Shifts in diversification rate with the origin of angiosperms

The evolutionary success of flowering plants has been attributed to key innovations that originated at the base of that clade. Maximum likelihood methods were used to assess whether branching rate increases were correlated with the origin of these traits. Four hypotheses for the basal relationships of angiosperms were examined by methods that are robust to uncertainty about the timing of internal branch points. Recent hypotheses based on molecular evidence, or on a combination of molecular and morphological characters, imply that large increases in branching rate did not occur until after the putative key innovations of angiosperms had evolved.     

Phylogenetic signal in the eukaryotic tree of life

Molecular sequence data have been sampled from 10% of all species known to science. Although it is not yet feasible to assemble these data into a single phylogenetic tree of life, it is possible to quantify how much phylogenetic signal is present. Analysis of 14,289 phylogenies built from 2.6 million sequences in GenBank suggests that signal is strong in vertebrates and specific groups of nonvertebrate model organisms. Across eukaryotes, however, although phylogenetic evidence is very broadly distributed, for the average species in the database it is equivalent to less than one well-supported gene tree. This analysis shows that a stronger sampling effort aimed at genomic depth, in addition to taxonomic breadth, will be required to build high-resolution phylogenetic trees at this scale.     

Observations of energetic ions from comet giacobini-zinner

During the encounter with comet Giacobini-Zinner, the energetic particle anisotropy spectrometer on the International Cometary Explorer spacecraft observed large fluxes of energetic ions, believed to result principally from ionization of the cometary atmosphere followed by pickup and acceleration by the ambient flow of the solar wind. These heavy cometary ions were observed from approximately 1 day before closest approach to about 2(1/2) days afterward. Three regimes of differing ion characteristics have been identified. An outer region with a scale of approximately 10(6) kilometers contains variable fluxes of antisolar-streaming pick-up ions in the undisturbed solar wind. In the middle region, of approximately 10(5) kilometers, fluxes have less large-scale variability and broader angular and energy distributions. This region is separated from the outer zone by a sharp transition. The inner region has a scale of approximately 10(4) kilometers and is characterized by reduced fluxes and complex angular distributions.     

Terraces in phylogenetic tree space

A key step in assembling the tree of life is the construction of species-rich phylogenies from multilocus--but often incomplete--sequence data sets. We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces" of trees with identical quality, arranged on islands of phylogenetically similar trees. Phylogenetic ambiguity within a terrace can be characterized efficiently and then ameliorated by new algorithms for obtaining a terrace's maximum-agreement subtree or by identifying the smallest set of new targets for additional sequencing. Algorithms to find optimal trees or estimate Bayesian posterior tree distributions may need to navigate strategically in the neighborhood of large terraces in tree space.