ALBERT

Description: Brachiopods are a lineage of invertebrates well known for the breadth and depth of their fossil record. Although the quality of this fossil record attracts the attention of paleontologists, geochemists, and paleoclimatologists, modern day brachiopods are also of interest to evolutionary biologists due to their potential to address a variety of questions ranging from developmental biology to biomineralization. The brachiopod shell is a composite material primarily composed of either calcite or calcium phosphate in close association with proteins and polysaccharides which give these composite structures their material properties. The information content of these biomolecules, sequestered within the shell during its construction, has the potential to inform hypotheses focused on describing how brachiopod shell formation evolved. Here, using high throughput proteomic approaches and next generation sequencing, we have surveyed and characterized the first shell-proteome and shell-forming transcriptome of any brachiopod, the South American Magellania venosa (Rhynchonelliformea: Terebratulida) . We find that the seven most abundant proteins present in the shell are unique to M. venosa , but that these proteins display biochemical features found in other metazoan biomineralization proteins. We can also detect some M. venosa proteins that display significant sequence similarity to other metazoan biomineralization proteins, suggesting that some elements of the brachiopod shell-forming proteome are deeply evolutionarily conserved. We also employed a variety of preparation methods to isolate shell proteins and find that in comparison to the shells of other spiralian invertebrates (such as mollusks) the shell ultrastructure of M. venosa may explain the effects these preparation strategies have on our results.

Description: We have obtained new results in the statistical analysis of global earthquake catalogues with special attention to the largest earthquakes, and we examined the statistical behaviour of earthquake rate variations. These results can serve as an input for updating our recent earthquake forecast, known as the ‘Global Earthquake Activity Rate 1’ model (GEAR1), which is based on past earthquakes and geodetic strain rates. The GEAR1 forecast is expressed as the rate density of all earthquakes above magnitude 5.8 within 70 km of sea level everywhere on earth at 0.1 x 0.1 degree resolution, and it is currently being tested by the Collaboratory for Study of Earthquake Predictability. The seismic component of the present model is based on a smoothed version of the Global Centroid Moment Tensor (GCMT) catalogue from 1977 through 2013. The tectonic component is based on the Global Strain Rate Map, a ‘General Earthquake Model’ (GEM) product. The forecast was optimized to fit the GCMT data from 2005 through 2012, but it also fit well the earthquake locations from 1918 to 1976 reported in the International Seismological Centre-Global Earthquake Model (ISC-GEM) global catalogue of instrumental and pre-instrumental magnitude determinations. We have improved the recent forecast by optimizing the treatment of larger magnitudes and including a longer duration (1918–2011) ISC-GEM catalogue of large earthquakes to estimate smoothed seismicity. We revised our estimates of upper magnitude limits, described as corner magnitudes, based on the massive earthquakes since 2004 and the seismic moment conservation principle. The new corner magnitude estimates are somewhat larger than but consistent with our previous estimates. For major subduction zones we find the best estimates of corner magnitude to be in the range 8.9 to 9.6 and consistent with a uniform average of 9.35. Statistical estimates tend to grow with time as larger earthquakes occur. However, by using the moment conservation principle that equates the seismic moment rate with the tectonic moment rate inferred from geodesy and geology, we obtain a consistent estimate of the corner moment largely independent of seismic history. These evaluations confirm the above-mentioned corner magnitude value. The new estimates of corner magnitudes are important both for the forecast part based on seismicity as well as the part based on geodetic strain rates. We examine rate variations as expressed by annual earthquake numbers. Earthquakes larger than magnitude 6.5 obey the Poisson distribution. For smaller events the negative-binomial distribution fits much better because it allows for earthquake clustering.

Description: As a consequence of population level constraints in the obligate, host-associated lifestyle, intracellular symbiotic bacteria typically exhibit high rates of molecular sequence evolution and extensive genome degeneration over the course of their host association. While the rationale for genome degeneration is well understood, little is known about the molecular mechanisms driving this change. To understand these mechanisms we compared the genome of Sodalis praecaptivus , a nonhost associated bacterium that is closely related to members of the Sodalis -allied clade of insect endosymbionts, with the very recently derived insect symbiont Candidatus Sodalis pierantonius. The characterization of indel mutations in the genome of Ca . Sodalis pierantonius shows that the replication system in this organism is highly prone to deletions resulting from polymerase slippage events in regions encoding G+C-rich repetitive sequences. This slippage-prone phenotype is mechanistically associated with the loss of certain components of the bacterial DNA recombination machinery at an early stage in symbiotic life and is expected to facilitate rapid adaptation to the novel host environment. This is analogous to the emergence of mutator strains in both natural and laboratory populations of bacteria, which tend to reach high frequencies in clonal populations due to linkage between the mutator allele and the resulting adaptive mutations.

Description: The project Seismic Hazard Harmonization in Europe (SHARE), completed in 2013, presents significant improvements over previous regional seismic hazard modeling efforts. The Global Strain Rate Map v2.1, sponsored by the Global Earthquake Model Foundation and built on a large set of self-consistent geodetic GPS velocities, was released in 2014. To check the SHARE seismic source models that were based mainly on historical earthquakes and active fault data, we first evaluate the SHARE historical earthquake catalogues and demonstrate that the earthquake magnitudes are acceptable. Then, we construct an earthquake potential model using the Global Strain Rate Map data. SHARE models provided parameters from which magnitude–frequency distributions can be specified for each of 437 seismic source zones covering most of Europe. Because we are interested in proposed magnitude limits, and the original zones had insufficient data for accurate estimates, we combine zones into five groups according to SHARE's estimates of maximum magnitude. Using the strain rates, we calculate tectonic moment rates for each group. Next, we infer seismicity rates from the tectonic moment rates and compare them with historical and SHARE seismicity rates. For two of the groups, the tectonic moment rates are higher than the seismic moment rates of the SHARE models. Consequently, the rates of large earthquakes forecast by the SHARE models are lower than those inferred from tectonic moment rate. In fact, the SHARE models forecast higher seismicity rates than the historical rates, which indicate that the authors of SHARE were aware of the potentially higher seismic activities in the zones. For one group, the tectonic moment rate is lower than the seismic moment rates forecast by the SHARE models. As a result, the rates of large earthquakes in that group forecast by the SHARE model are higher than those inferred from tectonic moment rate, but lower than what the historical data show. For the other two groups, the seismicity rates from tectonic moment rate, historical data and SHARE models are consistent. For four groups, the maximum magnitudes used by SHARE are fairly consistent with the probable maximum magnitudes inferred from tectonic strain rates. This study demonstrates that: (1) the strain-rate data are useful for constraining seismicity rates and magnitude limits; and (2) SHARE seismic source models and historical earthquake catalogues are satisfactory.

Description: SUMMARY This paper examines the relationship between seismogenic thickness, lithosphere structure and rheology in central and northeastern Asia. We accurately determine earthquake depth distributions which reveal important rheological variations in the lower crust. These variations exert a fundamental control on the active tectonics and the morphological evolution of the continents. We consider 323 earthquakes across the Tibetan Plateau, the Tien Shan and their forelands as well as the Baikal Rift, NE Siberia and the Laptev Sea and present the source parameters of 94 of these here for the first time. These parameters have been determined through body wave inversion, the identification of depth phases or the modelling of regional waveforms. Lower crustal earthquakes are found to be restricted to the forelands in areas undergoing shortening, and to locations where rifting coincides with abrupt changes in lithosphere thickness, such as the NE Baikal Rift and W Laptev Sea. The lower crust in these areas is seismogenic at temperatures that may be as high as 600°C, suggesting that it is anhydrous, and is likely to have great long-term strength. Lower crustal earthquakes are therefore a useful proxy indicating strong lithosphere in places that are too small in areal extent for this to be confirmed independently by estimating effective elastic thickness from gravity–topography relations. The variation in crustal rheology indicated by the distribution of lower-crustal earthquakes has many implications ranging from the support of mountain belts and the formation of steep mountain fronts, to the localization and orientation of rifting. In combination, these processes can also be responsible for the separation of the front of the thin-skinned mountain belts from their hinterlands when continents separate.

Description: Symbiotic associations between animals and microbes are ubiquitous in nature, with an estimated 15% of all insect species harboring intracellular bacterial symbionts. Most bacterial symbionts share many genomic features including small genomes, nucleotide composition bias, high coding density, and a paucity of mobile DNA, consistent with long-term host association. In this study, we focus on the early stages of genome degeneration in a recently derived insect-bacterial mutualistic intracellular association. We present the complete genome sequence and annotation of Sitophilus oryzae primary endosymbiont (SOPE). We also present the finished genome sequence and annotation of strain HS, a close free-living relative of SOPE and other insect symbionts of the Sodalis -allied clade, whose gene inventory is expected to closely resemble the putative ancestor of this group. Structural, functional, and evolutionary analyses indicate that SOPE has undergone extensive adaptation toward an insect-associated lifestyle in a very short time period. The genome of SOPE is large in size when compared with many ancient bacterial symbionts; however, almost half of the protein-coding genes in SOPE are pseudogenes. There is also evidence for relaxed selection on the remaining intact protein-coding genes. Comparative analyses of the whole-genome sequence of strain HS and SOPE highlight numerous genomic rearrangements, duplications, and deletions facilitated by a recent expansion of insertions sequence elements, some of which appear to have catalyzed adaptive changes. Functional metabolic predictions suggest that SOPE has lost the ability to synthesize several essential amino acids and vitamins. Analyses of the bacterial cell envelope and genes encoding secretion systems suggest that these structures and elements have become simplified in the transition to a mutualistic association.

Description: In our paper published earlier we discussed forecasts of earthquake focal mechanism and ways to test the forecast efficiency. Several verification methods were proposed, but they were based on ad hoc, empirical assumptions, thus their performance is questionable. We apply a conventional likelihood method to measure the skill of earthquake focal mechanism orientation forecasts. The advantage of such an approach is that earthquake rate prediction can be adequately combined with focal mechanism forecast, if both are based on the likelihood scores, resulting in a general forecast optimization. We measure the difference between two double-couple sources as the minimum rotation angle that transforms one into the other. We measure the uncertainty of a focal mechanism forecast (the variability), and the difference between observed and forecasted orientations (the prediction error), in terms of these minimum rotation angles. To calculate the likelihood score we need to compare actual forecasts or occurrences of predicted events with the null hypothesis that the mechanism's 3-D orientation is random (or equally probable). For 3-D rotation the random rotation angle distribution is not uniform. To better understand the resulting complexities, we calculate the information (likelihood) score for two theoretical rotational distributions (Cauchy and von Mises-Fisher), which are used to approximate earthquake source orientation pattern. We then calculate the likelihood score for earthquake source forecasts and for their validation by future seismicity data. Several issues need to be explored when analyzing observational results: their dependence on forecast and data resolution, internal dependence of scores on forecasted angle and random variability of likelihood scores. Here, we propose a simple tentative solution but extensive theoretical and statistical analysis is needed.

Description: Forecasts of the focal mechanisms of future shallow (depth 0–70 km) earthquakes are important for seismic hazard estimates and Coulomb stress, and other models of earthquake occurrence. Here we report on a high-resolution global forecast of earthquake rate density as a function of location, magnitude and focal mechanism. In previous publications we reported forecasts of 0.5° spatial resolution, covering the latitude range from –75° to +75°, based on the Global Central Moment Tensor earthquake catalogue. In the new forecasts we have improved the spatial resolution to 0.1° and the latitude range from pole to pole. Our focal mechanism estimates require distance-weighted combinations of observed focal mechanisms within 1000 km of each gridpoint. Simultaneously, we calculate an average rotation angle between the forecasted mechanism and all the surrounding mechanisms, using the method of Kagan & Jackson proposed in 1994. This average angle reveals the level of tectonic complexity of a region and indicates the accuracy of the prediction. The procedure becomes problematical where longitude lines are not approximately parallel, and where shallow earthquakes are so sparse that an adequate sample spans very large distances. North or south of 75°, the azimuths of points 1000 km away may vary by about 35°. We solved this problem by calculating focal mechanisms on a plane tangent to the Earth's surface at each forecast point, correcting for the rotation of the longitude lines at the locations of earthquakes included in the averaging. The corrections are negligible between –30° and +30° latitude, but outside that band uncorrected rotations can be significantly off. Improved forecasts at 0.5° and 0.1° resolution are posted at http://eq.ess.ucla.edu/kagan/glob_gcmt_index.html .