ALBERT

Description: Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes.

Description: The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable region of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Together, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.

Description: Among animals, genome sizes range from 20 Mb to 130 Gb, with 380-fold variation across vertebrates. Most of the largest vertebrate genomes are found in salamanders, an amphibian clade of 660 species. Thus, salamanders are an important system for studying causes and consequences of genomic gigantism. Previously, we showed that plethodontid salamander genomes accumulate higher levels of long terminal repeat (LTR) retrotransposons than do other vertebrates, although the evolutionary origins of such sequences remained unexplored. We also showed that some salamanders in the family Plethodontidae have relatively slow rates of DNA loss through small insertions and deletions. Here, we present new data from Cryptobranchus alleganiensis , the hellbender. Cryptobranchus and Plethodontidae span the basal phylogenetic split within salamanders; thus, analyses incorporating these taxa can shed light on the genome of the ancestral crown salamander lineage, which underwent expansion. We show that high levels of LTR retrotransposons likely characterize all crown salamanders, suggesting that disproportionate expansion of this transposable element (TE) class contributed to genomic expansion. Phylogenetic and age distribution analyses of salamander LTR retrotransposons indicate that salamanders’ high TE levels reflect persistence and diversification of ancestral TEs rather than horizontal transfer events. Finally, we show that relatively slow DNA loss rates through small indels likely characterize all crown salamanders, suggesting that a decreased DNA loss rate contributed to genomic expansion at the clade’s base. Our identification of shared genomic features across phylogenetically distant salamanders is a first step toward identifying the evolutionary processes underlying accumulation and persistence of high levels of repetitive sequence in salamander genomes.

Description: Evolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion and deletion mutations (indels) directly impact genome size by adding or removing sequences. Most species lose more DNA through small indels (i.e., ~1–30 bp) than they gain, which can result in genome reduction over time. Because this rate of DNA loss varies across species, small indel dynamics have been suggested to contribute to genome size evolution. Species with extremely large genomes provide interesting test cases for exploring the link between small indels and genome size; however, most large genomes remain relatively unexplored. Here, we examine rates of DNA loss in the tetrapods with the largest genomes—the salamanders. We used low-coverage genomic shotgun sequence data from four salamander species to examine patterns of insertion, deletion, and substitution in neutrally evolving non-long terminal repeat (LTR) retrotransposon sequences. For comparison, we estimated genome-wide DNA loss rates in non-LTR retrotransposon sequences from five other vertebrate genomes: Anolis carolinensis , Danio rerio , Gallus gallus , Homo sapiens , and Xenopus tropicalis . Our results show that salamanders have significantly lower rates of DNA loss than do other vertebrates. More specifically, salamanders experience lower numbers of deletions relative to insertions, and both deletions and insertions are skewed toward smaller sizes. On the basis of these patterns, we conclude that slow DNA loss contributes to genomic gigantism in salamanders. We also identify candidate molecular mechanisms underlying these differences and suggest that natural variation in indel dynamics provides a unique opportunity to study the basis of genome stability.

Description: Sialic acid groups of protein N -glycans are important determinants of biological activity. Exposed at the end of the glycan chain, they are potential targets for glycan remodeling. Sialyltransferases (STs; EC 2.4.99) are the enzymes that catalyze the sialic acid transfer from a CMP-activated donor on to a carbohydrate acceptor in vivo. Recombinant expression of the full-length human β-galactoside α2,6 sialyltransferase I (ST6Gal-I) was hampered and therefore variants with truncated N-termini were investigated. We report on the distinct properties of two N-terminally truncated versions of ST6Gal-I, namely 89ST6Gal-I and 108ST6Gal-I, which were successfully expressed in human embryonic kidney cells. The different properties of these enzymes result most probably from the loss of interactions from helix α1 in the 108ST6Gal-I variant, which plays a role in acceptor substrate binding. The K m for N -acetyl- d -lactosamine was 10-fold increased for 108ST6Gal-I (84 mM) as compared to 89ST6Gal-I (8.3 mM). The two enzyme variants constitute a suitable tool box for the terminal modification of N -glycans. While the enzyme 89ST6Gal-I exhibited both ST (di-sialylation) and sialidase activity on a monoclonal antibody, the enzyme 108ST6Gal-I showed only ST activity with specificity for mono-sialylation.

Description: Although many sources of atmospheric CO2 have been estimated, the major sinks are poorly understood in a deep-time context. Here we combine plate reconstructions, the eruption ages and outlines of Large Igneous Provinces (LIPs), and the atmospheric CO2 proxy record to investigate how their eruptions and weathering within the equatorial humid zone impacted global atmospheric CO2 since 400 Ma. Wavelet analysis reveals significant correlations between the eruption of the Emeishan LIP (259 Ma), the Siberian Traps (251 Ma), the Central Atlantic Magmatic Province (201 Ma), the second pulse of the North Atlantic Igneous Province (55 Ma), the High Arctic LIP (130 Ma), and the Deccan Traps (65 Ma) and perturbations in atmospheric CO2. Our analysis also reveals a clear relationship between the weathering of the Central Atlantic Magmatic Province (~200–100 Ma), the Deccan Traps (50–35 Ma), and the Afar Arabian LIP (30–0 Ma) and a significant atmospheric CO2 drawdown. Our results illustrate the significant role of subaerial LIP emplacement and weathering in modulating atmospheric CO2 and Earth's surface environments. ©2018. American Geophysical Union. All Rights Reserved.

Description: The pyBacktrack software package allows the backtracking of the paleo-water depth of ocean drill sites, providing a framework for reconstructing the accumulation history of sediment components through time. The software incorporates the effects of decompaction of common marine lithologies and allows backtracking of sites on both oceanic and continental crust. Backtracking on ocean crust is based on a user-selected lithospheric age-depth model and the present-day unloaded basement depth. Backtracking on continental crust is based on syn-rift and post-rift subsidence that is modeled using the total sediment thickness at the site and the timing of the transition from rifting to thermal subsidence. On sites that did not penetrate basement, the age-coded stratigraphy is supplemented with a synthetic stratigraphic section that represents the undrilled section, whose thickness is estimated using a global sediment thickness map. This is essential for estimating the decompacted thickness of the total sedimentary section, and thus bathymetry, through time. PyBacktrack further allows the consideration of the effects of mantle-convection driven dynamic topography on paleo-water depth. The user can select one of the dynamic topography models bundled with pyBacktrack or add other models. PyBacktrack runs on all platforms with a Python 2.7 and a pyGPlates installation and is available via Github. © 2018. American Geophysical Union. All Rights Reserved.

Description: GPlates is an open-source, cross-platform plate tectonic geographic information system, enabling the interactive manipulation of plate-tectonic reconstructions and the visualization of geodata through geological time. GPlates allows the building of topological plate models representing the mosaic of evolving plate boundary networks through time, useful for computing plate velocity fields as surface boundary conditions for mantle convection models and for investigating physical and chemical exchanges of material between the surface and the deep Earth along tectonic plate boundaries. The ability of GPlates to visualize subsurface 3-D scalar fields together with traditional geological surface data enables researchers to analyze their relationships through geological time in a common plate tectonic reference frame. To achieve this, a hierarchical cube map framework is used for rendering reconstructed surface raster data to support the rendering of subsurface 3-D scalar fields using graphics-hardware-accelerated ray-tracing techniques. GPlates enables the construction of plate deformation zones—regions combining extension, compression, and shearing that accommodate the relative motion between rigid blocks. Users can explore how strain rates, stretching/shortening factors, and crustal thickness evolve through space and time and interactively update the kinematics associated with deformation. Where data sets described by geometries (points, lines, or polygons) fall within deformation regions, the deformation can be applied to these geometries. Together, these tools allow users to build virtual Earth models that quantitatively describe continental assembly, fragmentation and dispersal and are interoperable with many other mapping and modeling tools, enabling applications in tectonics, geodynamics, basin evolution, orogenesis, deep Earth resource exploration, paleobiology, paleoceanography, and paleoclimate. ©2018. American Geophysical Union. All Rights Reserved.

Description: A recent hypothesis contends that abyssal hill topography is linked to sea level periodicities expressed by Milankovitch cycles, predicting that abyssal hill elevation is correlated to crustal age. We test this prediction by stacking (averaging) bathymetry as a function of age to enhance age-dependent signal while suppressing random (primarily faulted) components. Stacking is applied to bathymetry data flanking intermediate, fast, and superfast spreading ridges. Revised digital crustal age models were generated in these regions using a recent compilation of reliable magnetic anomaly identifications, with inferred temporal uncertainty of ~0.01 my. We utilize statistical properties of abyssal hills to predict the variability of the age-stack under the null hypothesis that abyssal hills are random with respect to crustal age; the age-stacked profile is significantly different from zero only if it exceeds this expected variability by a large margin. Our results do not support the presence of Milankovitch-driven signals in abyssal hill topography. ©2018. American Geophysical Union. All Rights Reserved.

Description: Mantle convection shapes Earth's surface by generating dynamic topography. Observational constraints and regional convection models suggest that surface topography could be sensitive to mantle flow for wavelengths as short as 1,000 and 250 km, respectively. At these spatial scales, surface processes including sedimentation and relative sea-level change occur on million-year timescales. However, time-dependent global mantle flow models do not predict small-scale dynamic topography yet. Here we present 2-D spherical annulus numerical models of mantle convection with large radial and lateral viscosity contrasts. We first identify the range of Rayleigh number, internal heat production rate and yield stress for which models generate plate-like behavior, surface heat flow, surface velocities, and topography distribution comparable to Earth's. These models produce both whole-mantle convection and small-scale convection in the upper mantle, which results in small-scale (〈500 km) to large-scale (〉104 km) dynamic topography, with a spectral power for intermediate scales (500 to 104 km) comparable to estimates of present-day residual topography. Timescales of convection and the associated dynamic topography vary from five to several hundreds of millions of years. For a Rayleigh number of 107, we investigate how lithosphere yield stress variations (10–50 MPa) and the presence of deep thermochemical heterogeneities favor small-scale (200–500 km) and intermediate-scale (500–104 km) dynamic topography by controlling the formation of small-scale convection and the number and distribution of subduction zones, respectively. The interplay between mantle convection and lithosphere dynamics generates a complex spatial and temporal pattern of dynamic topography consistent with constraints for Earth. ©2018. American Geophysical Union. All Rights Reserved.