Archaic and contemporary topographic diversification of Upper Mississippi River forests

Topographic diversity is an important component of environmental heterogeneity. Topographic diversity within the Upper Mississippi River floodplain has been degraded because of modifications for navigation improvement. Efforts aimed at restoring topographic diversity in the Upper Mississippi River floodplain have been extensive but have not focused on reversing the effects of forest loss and degradation. We investigated habitat features associated with Cerulean Warbler (Setophaga cerulea) locations both within and outside of river floodplains and hypothesized this species would select topographically diverse habitats. Both topographic diversity and the distance to the upland forest/floodplain forest interface were useful predictors of Cerulean Warbler presence. We conclude that incorporation of topographic diversity into floodplain forest restoration planning would likely benefit Cerulean Warblers and the other species with similar habitat requirements. Incorporating topographic diversity into floodplain forest conservation planning will be challenging on major rivers that serve multiple purposes.     

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

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Heterosis is common and inbreeding depression absent in natural populations of Arabidopsis thaliana

The importance of genetic drift in shaping patterns of adaptive genetic variation in nature is poorly known. Genetic drift should drive partially recessive deleterious mutations to high frequency, and inter‐population crosses may therefore exhibit heterosis (increased fitness relative to intra‐population crosses). Low genetic diversity and greater genetic distance between populations should increase the magnitude of heterosis. Moreover, drift and selection should remove strongly deleterious recessive alleles from individual populations, resulting in reduced inbreeding depression. To estimate heterosis, we crossed 90 independent line pairs of Arabidopsis thaliana from 15 pairs of natural populations sampled across Fennoscandia and crossed an additional 41 line pairs from a subset of four of these populations to estimate inbreeding depression. We measured lifetime fitness of crosses relative to parents in a large outdoor common garden (8,448 plants in total) in central Sweden. To examine the effects of genetic diversity and genetic distance on heterosis, we genotyped parental lines for 869 SNPs. Overall, genetic variation within populations was low (median expected heterozygosity = 0.02), and genetic differentiation was high (median F_ST = 0.82). Crosses between 10 of 15 population pairs exhibited significant heterosis, with magnitudes of heterosis as high as 117%. We found no significant inbreeding depression, suggesting that the observed heterosis is due to fixation of mildly deleterious alleles within populations. Widespread and substantial heterosis indicates an important role for drift in shaping genetic variation, but there was no significant relationship between fitness of crosses relative to parents and genetic diversity or genetic distance between populations.     

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Microbiota inhabiting the gastrointestinal (GI) tract of animals has important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut micro‐organismal community, few comparative studies have considered how differences in diet influence community composition across the length of the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's (Sciurus aberti) and fox squirrels (S. niger) living in the same habitat. While fox squirrels are generalist omnivores, the diet of Abert's squirrels is unusually high in plant fiber, particularly in winter when they extensively consume fiber‐rich inner bark of ponderosa pine (Pinus ponderosa). Consistent with previous studies, microbiota of the upper GI tract of both species consisted primarily of facultative anaerobes and was less diverse than that of the lower GI tract, which included mainly obligate anaerobes. While we found relatively little differentiation between the species in the microbiota of the upper GI tract, the community composition of the lower GI tract was clearly delineated. Notably, the Abert's squirrel lower GI community was more stable in composition and enriched for microbes that play a role in the degradation of plant fiber. In contrast, overall microbial diversity was higher in fox squirrels. We hypothesize that these disparities reflect differences in diet quality and diet breadth between the species.     

A distance–performance trade‐off in the phenotypic basis of dispersal

Across taxa, individuals vary in how far they disperse, with most individuals staying close to their origin and fewer dispersing long distances. Costs associated with dispersal (e.g., energy, risk) are widely believed to trade off with benefits (e.g., reduced competition, increased reproductive success) to influence dispersal propensity. However, this framework has not been applied to understand variation in dispersal distance, which is instead generally attributed to extrinsic environmental factors. We alternatively hypothesized that variation in dispersal distances results from trade‐offs associated with other aspects of locomotor performance. We tested this hypothesis in the stream salamander Gyrinophilus porphyriticus and found that salamanders that dispersed farther in the field had longer forelimbs but swam at slower velocities under experimental conditions. The reduced swimming performance of long‐distance dispersers likely results from drag imposed by longer forelimbs. Longer forelimbs may facilitate moving longer distances, but the proximate costs associated with reduced swimming performance may help to explain the rarity of long‐distance dispersal. The historical focus on environmental drivers of dispersal distances misses the importance of individual traits and associated trade‐offs among traits affecting locomotion.     

Mapping quantitative trait Loci underlying fitness-related traits in a free-living sheep population

We searched for quantitative trait loci (QTL) underlying fitness-related traits in a free-living pedigree of 588 Soay sheep in which a genetic map using 251 markers with an average spacing of 15 cM had been established previously. Traits examined included birth date and weight, considered both as maternal and offspring traits, foreleg length, hindleg length, and body weight measured on animals in August and jaw length and metacarpal length measured on cleaned skeletal material. In some cases the data were split to consider different age classes separately, yielding a total of 15 traits studied. Genetic and environmental components of phenotypic variance were estimated for each trait and, for those traits showing nonzero heritability (N= 12), a QTL search was conducted by comparing a polygenic model with a model including a putative QTL. Support for a QTL at genome-wide significance was found on chromosome 11 for jaw length; suggestive QTL were found on chromosomes 2 and 5 (for birth date as a trait of the lamb), 8 (birth weight as a trait of the lamb), and 15 (adult hindleg length). We discuss the prospects for refining estimates of QTL position and effect size in the study population, and for QTL searches in free-living pedigrees in general.     

Enhancing the latent nucleotide triphosphate flexibility of the glucose-1-phosphate thymidylyltransferase RmlA

Nucleotidyltransferases are central to nearly all glycosylation-dependent processes and have been used extensively for the chemoenzymatic synthesis of sugar nucleotides. The determination of the NTP specificity of the model thymidylyltransferase RmlA revealed RmlA to utilize all eight naturally occurring NTPs with varying levels of catalytic efficiency, even in the presence of nonnative sugar-1-phosphates. Guided by structural models, active site engineering of RmlA led to alterations of the inherent pyrimidine/purine bias by up to three orders of magnitude. This study sets the stage for engineering single universal nucleotidyltransferases and also provides new catalysts for the synthesis of novel nucleotide diphosphosugars.     

Glutamate regulates neurite outgrowth of cultured descending brain neurons from larval lamprey

In larval lamprey, descending brain neurons, which regenerate their axons following spinal cord injury, were isolated and examined in cell culture to identify some of the factors that regulate neurite outgrowth. Focal application of 5 mM or 25 mM L-glutamate to single growth cones inhibited outgrowth of the treated neurite, but other neurites from the same neuron were not inhibited, an effect that has not been well studied for neurons in other systems. Glutamate-induced inhibition of neurite outgrowth was abolished by 10 mM kynurenic acid. Application of high potassium media to growth cones inhibited neurite outgrowth, an effect that was blocked by 2 mM cobalt or 100 microM cadmium, suggesting that calcium influx via voltage-gated channels contributes to glutamate-induced regulation of neurite outgrowth. Application of glutamate to growth cones in the presence of 2 microM omega-conotoxin MVIIC (CTX) still inhibited neurite outgrowth, while CTX blocked high potassium-induced inhibition of neurite outgrowth. Thus, CTX blocked virtually all of the calcium influx resulting from depolarization. To our knowledge, this is the first direct demonstration that calcium influx via ligand-gated ion channels can contribute to regulation of neurite outgrowth. Finally, focal application of glutamate to the cell bodies of descending brain neurons inhibited outgrowth of multiple neurites from the same neuron, and this is the first demonstration that multiple neurites can be regulated in this fashion. Signaling mechanisms involving intracellular calcium, similar to those shown here, may be important for regulating axonal regeneration following spinal cord injury in the lamprey.