ALBERT

Description: ABSTRACT The ridgelines of mountain ranges are a source of geomorphic information unadulterated by the arrival of sediment from upslope. Studies along ridgecrests, therefore, can help identify and isolate the controls on important regolith properties such as thickness and texture. A 1.5-km section of ridgeline in the Sierra Nevada (CA) with a tenfold decrease in erosion rate (inferred from ridgetop convexity) provided an opportunity to conduct a high-resolution survey of regolith properties and investigate their controls. We found that regolith along the most quickly eroding section of the ridge was the rockiest and had the lowest clay concentrations. Furthermore, a general increase in regolith thickness with a slowing of erosion rate was accompanied by an increase in biomass, changes in vegetation community, broader ridgeline profiles, and an apparent increase in total available moisture. The greatest source of variation in regolith thickness at the 10–100-m scale, however, was the local topography along the ridgeline, with the deepest regolith in the saddles and the thinnest on the knobs. Because regolith in the saddles had higher surface soil moisture than the knobs, we conclude that the hydrological conditions primarily driven by local topography (i.e., rapid vs. slow drainage and water-storage potential) provide the fundamental controls on regolith thickness through feedbacks incorporating physical weathering by the biota and chemical weathering. Moreover, because the ridgeline saddles are the uppermost extensions of 1 st -order valleys, we propose that the fluvial network affects regolith properties in the furthest reaches of the watershed. This article is protected by copyright. All rights reserved.

Description: When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (〈100 kb) but extends much further. Sex-specific expression change is also genomically clustered. As genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking.

Description: The nearly neutral theory predicts that small effective population size provides the conditions for weakened selection. This is postulated to explain why our genome is more "bloated" than that of, for example, yeast, ours having large introns and large intergene spacer. If a bloated genome is also an error prone genome might it, however, be the case that selection for error-mitigating properties is stronger in our genome? We examine this notion using splicing as an exemplar, not least because large introns can predispose to noisy splicing. We thus ask whether, owing to genomic decay, selection for splice error-control mechanisms is stronger, not weaker, in species with large introns and small populations. In humans much information defining splice sites is in cis- exonic motifs, most notably exonic splice enhancers (ESEs). These act as splice-error control elements. Here then we ask whether within and between-species intron size is a predictor of the commonality of exonic cis- splicing motifs. We show that, as predicted, the proportion of synonymous sites that are ESE-associated and under selection in humans is weakly positively correlated with the size of the flanking intron. In a phylogenetically controlled framework, we observe, also as expected, that mean intron size is both predicted by N e .μ and is a good predictor of cis- motif usage across species, this usage coevolving with splice site definition. Unexpectedly, however, across taxa intron density is a better predictor of cis -motif usage than intron size. We propose that selection for splice-related motifs is driven by a need to avoid decoy splice sites that will be more common in genes with many and large introns. That intron number and density predict ESE usage within human genes is consistent with this, as is the finding of intragenic heterogeneity in ESE density. As intronic content and splice site usage across species is also well predicted by N e .μ , the result also suggests an unusual circumstance in which selection (for cis- modifiers of splicing) might be stronger when population sizes are smaller, as here splicing is noisier, resulting in a greater need to control error-prone splicing.

Description: Where in genes do pathogenic mutations tend to occur and does this provide clues as to the possible underlying mechanisms by which single nucleotide polymorphisms (SNPs) cause disease? As splice-disrupting mutations tend to occur predominantly at exon ends, known also to be hot spots of cis -exonic splice control elements, we examine the relationship between the relative density of such exonic cis -motifs and pathogenic SNPs. In particular, we focus on the intragene distribution of exonic splicing enhancers (ESE) and the covariance between them and disease-associated SNPs. In addition to showing that disease-causing genes tend to be genes with a high intron density, consistent with missplicing, five factors established as trends in ESE usage, are considered: relative position in exons, relative position in genes, flanking intron size, splice sites usage, and phase. We find that more than 76% of pathogenic SNPs are within 3–69 bp of exon ends where ESEs generally reside, this being 13% more than expected. Overall from enrichment of pathogenic SNPs at exon ends, we estimate that approximately 20–45% of SNPs affect splicing. Importantly, we find that within genes pathogenic SNPs tend to occur in splicing-relevant regions with low ESE density: they are found to occur preferentially in the terminal half of genes, in exons flanked by short introns and at the ends of phase (0,0) exons with 3' non-"AGgt" splice site. We suggest the concept of the "fragile" exon, one home to pathogenic SNPs owing to its vulnerability to splice disruption owing to low ESE density.

Description: ABSTRACT Hillslope length is a fundamental attribute of landscapes, intrinsically linked to drainage density, landslide hazard, biogeochemical cycling and hillslope sediment transport. Existing methods to estimate catchment average hillslope lengths include inversion of drainage density or identification of a break in slope-area scaling, where the hillslope domain transitions into the fluvial domain. Here we implement a technique which models flow from point sources on hilltops across pixels in a digital elevation model (DEM), based on flow directions calculated using pixel aspect, until reaching the channel network, defined using recently developed channel extraction algorithms. Through comparisons between these measurement techniques, we show that estimating hillslope length from plots of topographic slope versus drainage area, or by inverting measures of drainage density, systematically underestimates hillslope length. In addition, hillslope lengths estimated by slope-area scaling breaks show large variations between catchments of similar morphology and area. We then use hillslope length – relief structure of landscapes to explore nature of sediment flux operating on a landscape. Distinct topographic forms are predicted for end-member sediment flux laws which constrain sediment transport on hillslopes as being linearly or nonlinearly dependent on hillslope gradient. Because our method extracts hillslope profiles originating from every ridgetop pixel in a DEM, we show that the resulting population of hillslope length – relief measurements can be used to differentiate between linear and nonlinear sediment transport laws in soil mantled landscapes. We find that across a broad range of sites across the continental United States, topography is consistent with a sediment flux law in which transport is nonlinearly proportional to topographic gradient. This article is protected by copyright. All rights reserved.

Description: Exonic splice enhancers (ESEs) are short nucleotide motifs, enriched near exon ends, that enhance the recognition of the splice site and thus promote splicing. Are intronless genes under selection to avoid these motifs so as not to attract the splicing machinery to an mRNA that should not be spliced, thereby preventing the production of an aberrant transcript? Consistent with this possibility, we find that ESEs in putative recent retrocopies are at a higher density and evolving faster than those in other intronless genes, suggesting that they are being lost. Moreover, intronless genes are less dense in putative ESEs than intron-containing ones. However, this latter difference is likely due to the skewed base composition of intronless sequences, a skew that is in line with the general GC richness of few exon genes. Indeed, after controlling for such biases, we find that both intronless and intron-containing genes are denser in ESEs than expected by chance. Importantly, nucleotide-controlled analysis of evolutionary rates at synonymous sites in ESEs indicates that the ESEs in intronless genes are under purifying selection in both human and mouse. We conclude that on the loss of introns, some but not all, ESE motifs are lost, the remainder having functions beyond a role in splice promotion. These results have implications for the design of intronless transgenes and for understanding the causes of selection on synonymous sites.

Description: Accurate knowledge of the mutation rate provides a base line for inferring expected rates of evolution, for testing evolutionary hypotheses and for estimation of key parameters. Advances in sequencing technology now permit direct estimates of the mutation rate from sequencing of close relatives. Within insects there have been three prior such estimates, two in nonsocial insects ( Drosophila : 2.8 x 10 – 9 per bp per haploid genome per generation; Heliconius : 2.9 x 10 – 9 ) and one in a social species, the honeybee (3.4 x 10 – 9 ). Might the honeybee’s rate be ~20% higher because it has an exceptionally high recombination rate and recombination may be directly or indirectly mutagenic? To address this possibility, we provide a direct estimate of the mutation rate in the bumblebee ( Bombus terrestris ), this being a close relative of the honeybee but with a much lower recombination rate. We confirm that the crossover rate of the bumblebee is indeed much lower than honeybees (8.7 cM/Mb vs. 37 cM/Mb). Importantly, we find no significant difference in the mutation rates: we estimate for bumblebees a rate of 3.6 x 10 – 9 per haploid genome per generation (95% confidence intervals 2.38 x 10 – 9 and 5.37 x 10 – 9 ) which is just 5% higher than the estimate that of honeybees. Both genomes have approximately one new mutation per haploid genome per generation. While we find evidence for a direct coupling between recombination and mutation (also seen in honeybees), the effect is so weak as to leave almost no footprint on any between-species differences. The similarity in mutation rates suggests an approximate constancy of the mutation rate in insects.