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

Analyse av ein konveksjonskanal og rekonstruksjon av den ionosfæriske storskalakonveksjonen observert med EISCAT

Denne oppgåva studerer ein smal (100-200 km) konveksjonskanal observert med EISCAT Svalbard Radar (ESR) den 20. desember 2001. Oppgåva har to mål. Det eine er å forklara den observerte konveksjonskanalen og fastslå kva for ein mekanisme som skapar han. Det andre er å kombinera målingar frå EISCAT Tromsø (TOS) og ESR og konstruera konveksjonsvektorar. Oppgåva er i stor grad ei programmeringsoppgåve. Algoritmar for å identifisera og klassifisera dei ulike radarpeikeretningane i datasettet vert presenterte. Når datasettet er ordna, vert kvar databoks (range gate) spora langs magnetfeltet frå si faktiske høgde til ei referansehøgde på 250 km. Dette gjer det mogleg å finna volum i ulike høgder som deler feltlinje, og som dermed har same E x B-drift. Når målingane gjort med TOS er kopla mot ESR-målingane slik, er det mogleg å konstruera konveksjonsvektorar. Ein algoritme for dette formålet vert presentert og diskutert. Datasettet er henta frå 20. desember 2001 frå klokka 10 til 11 UT. IMF Bz er i hovudsak negativ, og IMF By er positiv heile tida. MSP og himmelkamera ser ein sekvens av PMAF-ar. Ein austleg retta konveksjonskanal startar samtidig med at ein stor PMAF bryt ut av nordlysbogen. Samtidig skjer ei kraftig intensivering av nordlysbogen, som også vandar eit stykke mot ekvator. Radaren ser ut til å observera utviklinga av konveksjonskanalen heilt frå han startar til han døyr ut. Kanalen er mellom 150 og 190 km brei når konveksjonen er sterkast. Konveksjonskanalen er synleg i synsfeltet i over 12 minutt, mykje lenger enn den observerte PMAF-en. Det oppstår heller ikkje nokon nye PMAF-ar så lenge konveksjonskanalen er aktiv. Konveksjonskanalen døyr ut om lag samtidig som at nordlysbogen går nordover att. Konveksjonskanalen er austleg. Det er i utgangspunktet uventa sidan Svalgard-Mansurov-effekten spår at impulsen som vert overført til ionosfæren ved magnetisk fluksomkopling (reconnection) skal vera vestleg retta når IMF By > 0. Det vert observert at bakrgrunnsnordlyset er lokalisert på sørgrensa av konveksjonskanalen, og at kanalen held denne posisjonen så lenge han er synleg i radarsveipa. Det vert vist at konveksjonskanalen ikkje kan vera ein returkonveksjon i eit FTE-fotpunkt av Southwood-typen. Argumentet er at i så fall må den observerte PMAF-en vera kopla til den andre returkonveksjonen. Men levetida til denne PMAF-en er for kort til at han kan vera ein del av eit Southwood-fluksrøyr som skal produsera den observerte konveksjonskanalen. Hadde det vore tilfelle, måtte PMAF-en hatt same levetid som konveksjonskanalen. Ein hypotese om at konveksjonskanalen er eit resultat av elektrisk polarisering vert lagt fram. Dersom ein utgåande birkelandstraum i nordlysbogen fører til opphoping av negativ ladning i ionosfæren, vil eit elektrisk felt konvergera på nordlysbogen. Det vil gje opphav til ei E x B-drift som svarar til observasjonane. Potensialfallet over kanalen vert estimert til rundt 7 kV. Ein mindre konveksjonskanal som oppstår seinare i sekvensen vert også diskutert, og dei same argumenta held for denne kanalen. Her er potensialfallet om lag 2 kV. Det ser ut til at vektoralgoritmen fungerer godt sør for nordlysbogen. Nord for nordlysbogen er det ikkje data, og i nordlysbogen er plasmaet for uroleg og tidsoppløysinga til TOS for grov til å få meinigsfulle vektordata. Her er det truleg også ioneoppstrøyming, og dette vil øydeleggja utrekninga av vektorane, sidan denne krev at konveksjonen i ionosfæren ikkje har nokon loddrett komponent

Integrated field-aligned radar data and analysis results

<p>Dataset used in a study of cusp temperatures and densities. In review, J. Geophys. Res. 2017. Will be made available when paper is published.</p

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

On the relationship between flux transfer events, temperature enhancements, and ion upflow events in the cusp ionosphere

[1] A transit of the dayside aurora across the field-of-view of the EISCAT Svalbard Radar occurred on 20 December 1998. This offered an excellent opportunity to study the spatial structure of the cusp/cleft aurora using meridian scanning photometer and incoherent scatter radar. We were able to identify distinct regions of upflow driven by ion heating (type 1) and upflow driven by electron heating (type 2) around poleward moving auroral forms, a transient auroral feature tied to flux transfer events. A quiet period before the auroral transit allowed us to estimate a neutral temperature profile, which enabled calculation of the ion-neutral relative wind. We found evidence for purely ion heating-driven upflow equatorward of the cusp auroral boundary, and for electron heating-driven upflow near the equatorward auroral boundary. The greatest upflow occurred near the center of the cusp aurora when both ion and electron temperatures were enhanced. The observed upflows were greater than expected from ambipolar diffusion alone, suggesting that ion-neutral frictional heating did contribute to upflow events in most cases. The great variability observed in ion temperature indicates that the ion flow was greatly structured within the aurora. Type 1–2 upflows may be considered as spatial structures of active cusp. Upflows are observed at various times in their evolution, and one upflow event, estimated to be 5–10 minutes old, showed a lifting of the F region of some 100 km, indicating a hybrid of type 1 and type 2

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

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

Background. Large 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. Results Here 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-Appender, AIR-Identifier, and AIR-Remover (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. Conclusion The 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.Botany, Department ofScience, Faculty ofNon UBCReviewedFacult

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