Åsmund Skjæveland

Phylogenomics Reshuffles the Eukaryotic Supergroups

Background Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial. Methodology/Principle Findings Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history. Conclusions This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name ‘SAR’ (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes.

AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

BackgroundLarge multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites.ResultsHere we present a batch-oriented web-based program package, named AIR that allows 1) transformation of several single genes to one multigene alignment, 2) identification of evolutionary rates in multigene alignments and 3) removal of fast evolving sites. These three processes can be done with the programs AIR-A ppender, AIR-I dentifier, and AIR-R emover (AIR), which can be used independently or in a semi-automated pipeline. AIR produces user-friendly output files with filtered and non-filtered alignments where residues are colored according to their evolutionary rates. Other bioinformatics applications linked to the AIR package are available at the Bioportal http://www.bioportal.uio.no, University of Oslo; together these greatly improve the flexibility, efficiency and quality of phylogenomic analyses.ConclusionThe AIR program package allows for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes.

Evolutionary position of breviate amoebae and the primary eukaryote divergence

Integration of ultrastructural and molecular sequence data has revealed six supergroups of eukaryote organisms (excavates, Rhizaria, chromalveolates, Plantae, Amoebozoa and opisthokonts), and the root of the eukaryote evolutionary tree is suggested to lie between unikonts (Amoebozoa, opisthokonts) and bikonts (the other supergroups). However, some smaller lineages remain of uncertain affinity. One of these unassigned taxa is the anaerobic, free-living, amoeboid flagellate Breviata anathema, which is of key significance as it is unclear whether it is a unikont (i.e. possibly the deepest branching amoebozoan) or a bikont. To establish its evolutionary position, we sequenced thousands of Breviata genes and calculated trees using 78 protein sequences. Our trees and specific substitutions in the 18S RNA sequence indicate that Breviata is related to other Amoebozoa, thereby significantly increasing the cellular diversity of this phylum and establishing Breviata as a deep-branching unikont. We discuss the implications of these results for the ancestral state of Amoebozoa and eukaryotes generally, demonstrating that phylogenomics of phylogenetically ‘nomadic’ species can elucidate key questions in eukaryote evolution. Furthermore, mitochondrial genes among the Breviata ESTs demonstrate that Breviata probably contains a modified anaerobic mitochondrion. With these findings, remnants of mitochondria have been detected in all putatively deep-branching amitochondriate organisms.

Which cusp upflow events can possibly turn into outflows

Two sequences, before and after magnetic noon, respectively, of poleward moving auroral forms with associated upflows situated above the European Incoherent Scatter Svalbard Radar allowed close study of ion upflow dynamics. We find that flux intensity is correlated with plasma temperature and that upflowing plasma undergoes acceleration proportional to the slope of the velocity profile and to the velocity at each altitude. The potential for upflows to lift thermal plasma to regions where broadband extremely low frequency electric field activity can cause nonthermal acceleration leading to outflow is examined. Equations for estimating the travel time of upflowing plasma are presented. We find that around 40% of the observed upflow profiles with a unit number flux greater than 1 × 1013 m−2 s−1 can transport plasma from 500 to 800 km altitude in less than 10 min, approximately the typical lifetime of pulsed upflow events. Almost all such profiles can transport plasma from 600 to 800 km in the same time span. Typical transport times for other altitude ranges are also presented. Post magnetic noon the background electron density was somewhat higher than prenoon due to transport of EUV-enhanced plasma, and the postnoon ion flux was somewhat weaker than prenoon.

Interplanetary magnetic field and solar cycle dependence of Northern Hemisphere F region joule heating

Joule heating in the ionosphere takes place through collisions between ions and neutrals. Statistical maps of F region Joule heating in the Northern Hemisphere polar ionosphere are derived from satellite measurements of thermospheric wind and radar measurements of ionospheric ion convection. Persistent mesoscale heating is observed near postnoon and postmidnight magnetic local time and centered around 70° magnetic latitude in regions of strong relative ion and neutral drift. The magnitude of the Joule heating is found to be largest during solar maximum and for a southeast oriented interplanetary magnetic field. These conditions are consistent with stronger ion convection producing a larger relative flow between ions and neutrals. The global-scale Joule heating maps quantify persistent (in location) regions of heating that may be used to provide a broader context compared to small-scale studies of the coupling between the thermosphere and ionosphere.

A statistical survey of heat input parameters into the cusp thermosphere

Based on three winters of observational data, we present those ionosphere parameters deemed most critical to realistic space weather ionosphere and thermosphere representation and prediction, in regions impacted by variability in the cusp. The CHAMP spacecraft revealed large variability in cusp thermosphere densities, measuring frequent satellite drag enhancements, up to doublings. The community recognizes a clear need for more realistic representation of plasma flows and electron densities near the cusp. Existing average value models produce order of magnitude errors in these parameters, resulting in large underestimations of predicted drag. We fill this knowledge gap with statistics-based specification of these key parameters over their range of observed values. The European Incoherent Scatter Svalbard Radar tracks plasma flow Vi , electron density Ne, and electron, ion temperatures Te, Ti , with consecutive 2–3 min windshield wipe scans of 1000 × 500 km areas. This allows mapping the maximum Ti of a large area within or near the cusp with high temporal resolution. In magnetic field-aligned mode the radar can measure high-resolution profiles of these plasma parameters. By deriving statistics for Ne and Ti , we enable derivation of thermosphere heating deposition under background and frictional drag-dominated magnetic reconnection conditions. We separate our Ne and Ti profiles into quiescent and enhanced states, which are not closely correlated due to the spatial structure of the reconnection foot point. Use of our data-based parameter inputs can make order of magnitude corrections to input data driving thermosphere models, enabling removal of previous twofold drag errors. Plain Language Summary Input of energy into the polar ionosphere from the solar wind causes local heating and upwelling of air in the region known as the “cusp.” This upwelling in turn dramatically changes the density of the atmosphere as it rises, which has consequences for atmospheric composition and transport as well as for spacecraft that experience increased drag and possibly shortened lifetimes. We show that because of the highly dynamic nature of the cusp, long-term averages and models will not accurately reproduce the energy input to the cusp and the consequent upwelling of the air. We use empirical data to show that the energy input is highly dynamic and that it is necessary to separate active and quiet periods when modeling heating and upwelling in the cusp, as well as to detect or predict accurately where the cusp is located. We present statistical models of the active and quiescent cusp ionization density and temperature of the ionized gas. Occurrence rates of heating events in and near the cusp are estimated by using rapid radar scans covering a large area.