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Novel pests and diseases are becoming increasingly common, and often cause additional mortality to host species in the newly contacted communities. This can alter the structure of the community up to, and including, the extinction of host species. In the last twenty years, ash dieback disease (ADB) has spread into Europe from East Asia. It has caused substantial mortality in ash tree (Fraxinus excelsior L.) populations. However, a proportion of the individuals in most populations appears to be less susceptible to ADB and resistance seems to have high heritability. These observations have led to suggestions that ash populations may be sustainable after the disease. In order to test this hypothesis, I modified an existing model of UK woodland (parameterised for Wytham Woods, Oxfordshire) to take into account the impact of ADB, and allowed offspring to inherit resistance traits from their parent. The results suggest that ash populations would still exist in 100 years but at lower levels than they are currently. For example, when the initial proportion of resistant individuals is about 10% and heritability of resistance is 0.5, then the population of ash falls to about one third of present levels. The proportion of individuals initially resistant to ADB had a larger effect on population size after 100 years than the heritability of resistance. The fact that the initial size of the resistant population is important to achieving a high population size in the presence of ADB suggests that a selective breeding programme with the intention of augmenting the natural ash populations would be beneficial.
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Birds land on a wide range of complex surfaces, yet it is unclear how they grasp a perch reliably. Here, we show how Pacific parrotlets exhibit stereotyped leg and wing dynamics regardless of perch diameter and texture, but foot, toe, and claw kinematics become surface-specific upon touchdown. A new dynamic grasping model, which integrates our detailed measurements, reveals how birds stabilize their grasp. They combine predictable toe pad friction with probabilistic friction from their claws, which they drag to find surface asperities—dragging further when they can squeeze less. Remarkably, parrotlet claws can undergo superfast movements, within 1–2 ms, on moderately slippery surfaces to find more secure asperities when necessary. With this strategy, they first ramp up safety margins by squeezing before relaxing their grasp. The model further shows it is advantageous to be small for stable perching when high friction relative to normal force is required because claws can find more usable surface, but this trend reverses when required friction shrinks. This explains how many animals and robots may grasp complex surfaces reliably.
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Urine is increasingly being considered as a source of biomarker development in Duchenne Muscular Dystrophy (DMD), a severe, life-limiting disorder that affects approximately 1 in 4500 boys. In this study, we considered the mdx mice—a murine model of DMD—to discover biomarkers of disease, as well as pharmacodynamic biomarkers responsive to prednisolone, a corticosteroid commonly used to treat DMD. Longitudinal urine samples were analyzed from male age-matched mdx and wild-type mice randomized to prednisolone or vehicle control via liquid chromatography tandem mass spectrometry. A large number of metabolites (869 out of 6,334) were found to be significantly different between mdx and wild-type mice at baseline (Bonferroni-adjusted p-value < 0.05), thus being associated with disease status. These included a metabolite with m/z = 357 and creatine, which were also reported in a previous human study looking at serum. Novel observations in this study included peaks identified as biliverdin and hypusine. These four metabolites were significantly higher at baseline in the urine of mdx mice compared to wild-type, and significantly changed their levels over time after baseline. Creatine and biliverdin levels were also different between treated and control groups, but for creatine this may have been driven by an imbalance at baseline. In conclusion, our study reports a number of biomarkers, both known and novel, which may be related to either the mechanisms of muscle injury in DMD or prednisolone treatment.
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Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic ‘landscape’ of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.
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Quantifying mutant or variable allele frequencies (VAFs) of ≤10-3 using next generation sequencing has utility in both clinical and non-clinical settings. Two common approaches for quantifying VAFs using NGS are tagged single strand sequencing and duplex-sequencing. While duplex sequencing is reported to have sensitivity up to 10-8 VAF, it is not a quick, easy, or inexpensive method. We report a method for quantifying VAFs that are ≥ 10-4 that is as easy and quick for processing samples as standard sequencing kits, yet less expensive than the kits. The method was developed using PCR fragment-based VAFs of Kras codon 12 in log10 increments from 10-5 to 10-1, then applied and tested on genomic DNA VAFs. For both sources of DNA there is a proportional increase in the observed VAF to input VAF from 10-4 to 100 (100% mutant) samples. Variability of quantitation error was evaluated within experimental replicates and shown to be consistent across sample preparations. The error at each successive base read was evaluated to determine if there is a limit of read length for quantitation of ≥ 10-4 and was determined that read lengths up to 70 bases are reliable for quantitation. The method described here is adaptable to various oncogene or tumor suppressor gene targets, with potential to implement multiplexing at the initial tagging step. While easy to perform manually, it is also suited for robotic handling and batch processing of samples, facilitating detection and quantitation of genetic carcinogenic biomarkers before tumor formation or in normal appearing tissue.
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Both spatial and temporal cues determine the fate of immature neurons. A major challenge at the interface of developmental and systems neuroscience is to relate this spatiotemporal trajectory of maturation to circuit‐level functional organization. This study examined the development of two extraocular motor nuclei (nIII and nIV), structures in which a motoneuron's identity, or choice of muscle partner, defines its behavioral role. We used retro‐orbital dye fills, in combination with fluorescent markers for motoneuron location and birthdate, to probe spatial and temporal organization of the oculomotor (nIII) and trochlear (nIV) nuclei in the larval zebrafish. We describe a dorsoventral organization of the four nIII motoneuron pools, in which inferior and medial rectus motoneurons occupy dorsal nIII, while inferior oblique and superior rectus motoneurons occupy distinct divisions of ventral nIII. Dorsal nIII motoneurons are, moreover, born before motoneurons of ventral nIII and nIV. The order of neurogenesis can therefore account for the dorsoventral organization of nIII and may play a primary role in determining motoneuron identity. We propose that the temporal development of extraocular motoneurons plays a key role in assembling a functional oculomotor circuit.
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Many species have evolved or currently coexist in sympatry due to differential adaptation in a heterogeneous environment. However, anthropogenic habitat modifications can either disrupt reproductive barriers or obscure environmental conditions which underlie fitness gradients. In this study, we evaluated the potential for an anthropogenically-mediated shift in reproductive boundaries that separate two historically sympatric fish species (Gila cypha and G. robusta) endemic to the Colorado River Basin using ddRAD sequencing of 368 individuals. We first examined the integrity of reproductive isolation while in sympatry and allopatry, then characterized hybrid ancestries using genealogical assignment tests. We tested for localized erosion of reproductive isolation by comparing site-wise genomic clines against global patterns and identified a breakdown in the drainage-wide pattern of selection against interspecific heterozygotes. This, in turn, allowed for the formation of a hybrid swarm in one tributary, and asymmetric introgression where species co-occur. We also detected a weak but significant relationship between genetic purity and degree of consumptive water removal, suggesting a role for anthropogenic habitat modifications in undermining species boundaries or expanding historically limited introgression. In addition, results from basin-wide genomic clines suggested that hybrids and parental forms are adaptively non-equivalent. If so, then a failure to manage for hybridization will exacerbate the long-term extinction risk in parental populations. These results reinforce the role of anthropogenic habitat modification in promoting interspecific introgression in sympatric species by relaxing divergent selection. This, in turn, underscores a broader role for hybridization in decreasing global biodiversity within rapidly deteriorating environments.
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Changes in elements of courtship behaviour can influence sexual isolation between species. Large-scale analyses of changes, including loss and gain of courtship elements, across a relatively complete phylogenetic group are rare but needed to understand the significance of such changes, for example whether the gain and loss of courtship elements are essentially arbitrary or equally reversible. In most species of Drosophila, courtship, including singing, mainly occurs before mounting as pre-mounting courtship. The Drosophila montium species group is unusual because loss of pre-mounting courtship and gain of post-mounting one has been detected in this group. Here we provide an extensive analysis on the courtship repertoire and songs of 42 species in this group. Synchronously captured video and audio recordings were analysed to describe courtship patterns and male courtship songs and changes were analysed in a phylogenetic context. Ancestral state reconstruction suggests that a gain of post-mounting courtship singing at the ancestor of this species group has been accompanied with a concurrent decrease in the incidence of pre-mounting courtship singing and has led to subsequent further decrease and eventually complete loss of pre-mounting courtship song in several lineages. Alongside this evolutionary trend towards post-mounting courtship, sine song and a special type of “high pulse repetition song” have become more widely used for courtship during species diversification in the montium group. It is likely that the elaboration of post-mounting courtship behaviours is associated with changes in the relative importance of pre- and post-mounting components of mating systems, such as sperm competition or cryptic female choice.
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Effects of intraguild predation (IGP) on omnivores and detritivores are relatively understudied when compared to work on predator guilds. Functional genetic work in IGP is even more limited, but its application can help answer a range of questions related to ultimate and proximate causes of this behavior. Here we integrate behavioral assays and transcriptomic analysis of facultative predation in a blow fly (Diptera: Calliphoridae) to evaluate the prevalence, effect, and correlated gene expression of facultative predation by the invasive species Chrysomya rufifacies. Field work observing donated human cadavers indicated facultative predation by C. rufifacies on the native blow fly Cochliomyia macellaria was rare under undisturbed conditions, owing in part to spatial segregation between species. Laboratory assays under conditions of starvation showed predation had a direct fitness benefit (i.e., survival) to the predator. As a genome is not available for C. rufifacies, a de novo transcriptome was developed and annotated using sequence similarity to Drosophila melanogaster. Under a variety of assembly parameters, several genes were identified as being differentially expressed between predators and non-predators of this species, including genes involved in cell-to-cell signaling, osmotic regulation, starvation responses, and dopamine regulation. Results of this work were integrated to develop a model of the processes and genetic regulation controlling facultative predation.
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The dynamic pulsation of the xeniid corals is one of the most fascinating phenomena observed in coral reefs. We quantify for the first time the flow near the tentacles of these soft corals whose active pulsations are thought to enhance their symbionts' photosynthetic rates by up to an order of magnitude. These polyps are about 1 cm in diameter and pulse at frequencies between about 0.5 and 1 Hz. As a result, the frequency based Reynolds number calculated using the tentacle length and pulse frequency is on the order of 10 and rapidly decays as one moves away from the polyp. This introduces the question of how these corals minimize the reversibility of the flow and bring in new volumes of fluid during each pulse. We estimate that the Peclet number of the bulk flow generated by the coral as being on the order of 100-1000 while the flow between the bristles of the tentacles as being on the order of 10. This illustrates the importance of advective transport in removing oxygen waste. Flow measurements using particle image velocimetry reveal that the individual polyps generate a jet of water with positive vertical velocities that do not go below 1 mm/s and with average volumetric flow rates of about 700 cubic mm per second. Our results show that there is nearly continual flow in the radial direction towards the polyp with only about 3.3 percent back flow. 3D numerical simulations uncover a region of slow mixing between the tentacles during expansion. We estimate that the average flow that moves through the bristles of the tentacles are about 0.3 mm/s. The combination of nearly continual flow towards the polyp, slow mixing between the bristles, and the subsequent ejection of this fluid volume into an upward jet ensures the polyp continually samples new water with sufficient time for exchange to occur.
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