BackgroundResolving 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 FindingsHere, 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.ConclusionsThis 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.

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.

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.

[1] This first-principles examination of physics driving the cusp/polar upper thermosphere response to significant input energy impulses discloses previously unappreciated factors essential to thermospheric input-response relationships. The physics essential to coupling of cusp input-response processes is detailed, to make previously unexplained up-to-doubling of air density and drag near 400 km not only understandable but expected, if not inevitable. Presented as a common natural consequence of magnetic reconnection near the magnetopause, this energy-coupling from sun to upper atmosphere is through familiar processes, but by inadequately appreciated linkages. The underlying physics applies more broadly than this. We trace a logic path that should clarify the inputresponse, and lay out a path which if followed should enable most existing time-dependent 3-D global thermospheric models to significantly improve the realism of their representation and prediction of cusp/polar thermosphere disturbances to transient energy sources. We illustrate the concept with a sample model-run incorporating representative data. Citation:

[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.Citation: Skjaeveland, Å., J. Moen, and H. C. Carlson (2011), On the relationship between flux transfer events, temperature enhancements, and ion upflow events in the cusp ionosphere,