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  • Top predators cause avoidance behaviours in competitors and prey, which can lead to niche partitioning and facilitate coexistence. We investigate changes in partitioning of the temporal niche in a mammalian community in response to both the rapid decline in abundance of a top predator and its rapid increase, produced by two concurrent natural experiments: 1) the severe decline of the Tasmanian devil due to a transmissible cancer, and 2) the introduction of Tasmanian devils to an island, with subsequent population increase. We focus on devils, two mesopredators, and three prey species, allowing us to examine niche partitioning in the context of intra- and inter-specific competition, and predator-prey interactions. The most consistent shift in temporal activity occurred in devils themselves, which were active earlier in the night at high densities, presumably because of heightened intraspecific competition. When devils were rare, their closest competitor, the spotted-tailed quoll, increased activity in the early part of the night, resulting in increased overlap with the devil’s temporal niche and suggesting release from interference competition. The invasive feral cat, another mesopredator, did not shift its temporal activity in response to either decreasing or increasing devil densities. Shifts in temporal activity of the major prey species of devils were stronger in response to rising than to falling devil densities. We infer that the costs associated with not avoiding predators when their density is rising (i.e., death) are higher than the costs of continuing to adopt avoidance behaviours as predator densities fall (i.e., loss of foraging opportunity), so rising predator densities may trigger more rapid shifts. The rapid changes in devil abundance provide a unique framework to test how the non-lethal effects of top predators affect community-wide partitioning of temporal niches, revealing that this top-predator has an important but varied influence on the diel activity of other species.
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  • Invasive species may quickly colonize novel environments, which could be attributed to both phenotypic plasticity and an ability to locally adapt. Reproductive traits are expected to be under strong selection when the new environment limits reproductive success of the invading species. This may be especially important for external fertilizers, which release sperm and eggs into the new environment. Despite adult tolerance to high salinity, the invasive fish Neogobius melanostomus (round goby) is absent from fully marine regions of the Baltic Sea, raising the possibility that its distribution is limited by tolerance during earlier life-stages. Here, we investigate the hypothesis that the spread of N. melanostomus is limited by sperm function in novel salinities. We sampled sperm from two invasion fronts with higher and lower salinities in the Baltic Sea and tested them across a range of salinity levels. We found that sperm velocity and percentage of motile sperm declined in salinity levels higher and lower than those currently experienced by the Baltic Sea populations, with different performance curves for the two fronts. Sperm velocity also peaked closer to the home salinity conditions in each respective invasion front, with older localities showing an increased fit to local conditions. By calculating how the sperm velocity has changed over generations, we show this phenotypic shift to be in the range of other fish species under strong selection, indicating on-going local adaptation or epigenetic acclimation to their novel environment. These results show that while immigrant reproductive dysfunction appears to at least partly limit the distribution of invasive N. melanostomus in the Baltic Sea, local adaptation to novel environments could enable future spread beyond their current boundaries.
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  • 1. Plantation silviculture is increasing globally and is particularly intensive in temperate coniferous forests, where densely planting trees requires practices common to non-conifer systems that can alter forest floor microhabitat, and potentially threaten amphibian persistence. Most declining amphibian species depend on specific forest microhabitats as terrestrial refugia, but amphibian extirpation associated with tree harvest alone appears unlikely, suggesting that impacts of planting forests on groundcover might better predict recent declines in amphibian occupancy. 2. We repeatedly sampled larval presence or absence of 10 amphibian species native to temperate coniferous forest in the Southeastern United States for one year at 62 isolated wetlands located in either naturally regenerating or planted forest (plantation) to assess three direct ways that planted forests might reduce amphibian breeding site occupancy by: 1) increasing conifer densities, 2) decreasing groundcover, and 3) an indirect pathway, whereby increased tree densities at plantations might reduce groundcover and thus amphibian site occupancy. 3. After controlling for wetland traits and accounting for differences in detection, breeding site occupancy for 8/10 amphibian species was dependent upon whether forests were planted surrounding wetlands (within 300 m). Herbaceous groundcover, not canopy, most commonly influenced occupancy and increased occupancy for declining surface active or fossorial amphibians. 4. Path analyses showed that, by directly and indirectly reducing groundcover (via conifer densities), plantations had significantly lower occupancy of two declining surface active or fossorial frog species, whereas two common aquatic frog species were tolerant to planting conifers. Among declining species, salamanders showed a greater reduction in occupancy than anurans, likely because of greater vulnerability to the drier forest floor conditions of plantation than naturally regenerating forests. 5. Synthesis and applications: Direct negative impacts of coniferous plantation on amphibians can be addressed by limiting groundcover and soil impacts, including switching from high intensity practices, such as mechanical chopping vegetation or bedding soil, to lower intensity site preparation treatments that are less likely to significantly disturb groundcover. Indirect negative effects of dense canopy cover at planted forests could be lowered by periodically thinning canopies prior to final harvest, thus increasing intact forest groundcover and the conservation of both common and declining amphibians.
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  • Visually hunting predators must overcome the challenges that prey groups present. One such challenge is the confusion effect where an overburdened visual system means predators are unable to successfully target prey. A strategy to overcome confusion is the targeting of distinct, or odd, individuals (the oddity effect). In live prey experiments, manipulation of group member phenotypes can be challenging and prey may differ on more than the single feature one intends to define as odd. The use of highly controllable computerized stimuli to study predator-prey interactions is increasingly popular in the field of behavioral ecology. However, to our knowledge, the validity of computerized stimuli to study the oddity effect has not been established. Predator choice experiments were conducted using naive stickleback predators to ascertain whether the oddity effect could be demonstrated in the absence of live prey. We found evidence for both the oddity effect and preferential targeting of group edges and low density regions, as would be predicted if predators targeted prey individuals to minimize confusion. The oddity effect was evident at a low threshold, above which dots were no longer perceived as odd, and no longer attacked more often than expected by chance. We conclude that computerized stimuli are an improved, practical method for studying oddity effects while further validating the use of similar methods for studying other aspects of visual predation. In addition to higher control of ‘prey’ appearance, the replacement of live prey animals with digital stimuli is ethically beneficial and reusing code improves experimental efficiency.
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  • Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification, conditioned on the true genotype, which we call Expected Genotype Quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) compared with 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in Variant Call Format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa (syn. Brachiaria). When reads were aligned to a mock reference genome created from GBS data of the U. brizantha cultivar ‘Marandu’, 25,678 bi-allelic SNPs were discovered, compared to approximately 3000 SNPs when aligning to the closest true reference genomes, Setaria viridis and S. italica. Cross-validation revealed that missing genotypes were imputed by the Random Forest method with a median accuracy of 0.85, regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on GQ creates genotype bias; a depth threshold based on EGQ is also needed, regardless of whether genotypes are called using a diploidized or allele dosage model.
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  • C. elegans is an animal with few cells, but a striking diversity of cell types. Here, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and pre-terminal cell types, mapping most single cell transcriptomes to their exact position in C. elegans’ invariant lineage. Using these annotations, we find that: 1) the correlation between a cell’s lineage and its transcriptome increases from mid to late gastrulation, then falls dramatically as cells in the nervous system and pharynx adopt their terminal fates; 2) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and 3) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state.
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  • The airway epithelium is critical for maintaining innate and adaptive immune responses, and occupational exposures that disrupt its immune homeostasis may initiate and amplify airway inflammation. In our previous study, we demonstrated that silver nanoparticles (AgNP), which are engineered nanomaterials used in multiple applications but primarily in the manufacturing of many antimicrobial products, induce toxicity in organotypic cultures derived from murine tracheal epithelial cells (MTEC), and those differentiated toward a “Type 2 [T2]-Skewed” phenotype experienced an increased sensitivity to AgNP toxicity, suggesting that asthmatics could be a sensitive population to AgNP exposures in occupational settings. However, the mechanistic basis for this genotype × phenotype interaction (G×P) has yet to be defined. In the present study, we conducted transcriptional profiling using RNA-sequencing (RNA-seq) to predict the enrichment of specific canonical pathways and upstream transcriptional regulators to assist in defining a mechanistic basis for G×P effects on AgNP toxicity. Organotypic cultures were derived from MTEC across two genetically inbred mouse strains (A/J and C57BL/6J mice), two phenotypes (“Normal” and “T2-Skewed”), and one AgNP exposure (an acute 24 h exposure) to characterize G×P effects on transcriptional response to AgNP toxicity. The “T2-Skewed” phenotype was marked by increased pro-inflammatory T17 responses to AgNP toxicity, which are significant predictors of neutrophilic/difficult-to-control asthma and suggests that asthmatics could be a sensitive population to AgNP exposures in occupational settings. This study highlights the importance of considering G×P effects when identifying these sensitive populations, whose underlying genetics or diseases could directly modify their response to AgNP exposures.
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  • Our understanding of the ecology and phylogenetic relationships of Pachycormiformes, a group of Mesozoic stem teleosts including the iconic Leedsichthys, has often been hindered by a lack of comprehensive morphological information. Micro‐CT scanning of an articulated, although flattened, cranium of the edentulous Martillichthys renwickae from the Middle Jurassic (Callovian) Oxford Clay of the UK reveals previously unknown internal details of the most complete suspension‐feeding pachycormiform skull known, including the palate, braincase and branchial skeleton. The latter preserves gill rakers with elongate, pointed projections similar to those of Asthenocormus, in contrast to the finer fimbriations associated with Leedsichthys. We also reinterpret some previously described features, including dermal bone patterns of the snout, skull roof and lower jaw, and the morphology of the ventral hyoid arch. These new anatomical data reinforce the phylogenetic placement of Martillichthys as part of the Jurassic clade of edentulous pachycormiforms. The elongate skull geometry of these Jurassic taxa is strikingly similar to that of Ohmdenia, the sister taxon to edentulous pachycormiforms, but contrasts sharply with the morphology of the Late Cretaceous edentulous pachycormiform Bonnerichthys, raising questions over the phylogenetic relationships among these taxa. Most significantly, Martillichthys shows specialized characters with a restricted phylogenetic distribution among suspension‐feeding pachycormiforms, including the distinctive gill rakers and a greatly extended occipital stalk. Our analysis of Martillichthys supports past interpretations of a close relationship with Asthenocormus, and provides a model for interpreting the less complete remains of other members of this enigmatic group of fishes.
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  • Analysing genomic variation within and between sister species is a first step towards understanding species boundaries. We focused on two sister species of cold-resistant leaf beetles, Gonioctena quinquepunctata and G. intermedia, whose ranges overlap in the Alps. A previous study of DNA sequence variation had revealed multiple instances of mitochondrial genome introgression in this region, suggesting recent hybridizations between the two species. To evaluate the extent of gene exchange resulting from these hybridization events, we sampled individuals of both species inside and outside the hybrid zone and analysed genomic variation among them using RAD-seq markers. Individual levels of introgression in the nuclear genome were estimated first by defining species-specific SNPs (displaying a fixed difference between species) a priori, and second by using model-based methods. Both types of analyses indicated little gene exchange, if any, between species at the level of the nuclear genome. While the first method suggested slightly more gene flow, we argue that it has likely overestimated introgression in the phylogeographic context of this study. We conclude that strong intrinsic barriers prevent genetic exchange at the level of the nuclear genome between the two species. The apparent discrepancy observed between introgression occurring in the nuclear and mitochondrial genomes could be explained by selection acting in favour of the latter. Also, these results have consequences for the phylogeographic study of each species, since we can assume that genetic diversity in the overlapping portion of their ranges is not the product of introgression.
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  • Idelalisib is a phosphatidylinositol 3-kinase inhibitor highly selective for the delta isoform that has shown good efficacy in treating chronic lymphocytic leukemia and follicular lymphoma. In clinical trials, however, idelalisib was associated with rare, but potentially serious liver and lung toxicities. In this study, we used the Collaborative Cross (CC) mouse population to identify genetic factors associated with the drug response that may inform risk management strategies for idelalisib in humans. Eight (8) male mice (4 matched pairs) from 50 CC lines were treated once daily for 14 days by oral gavage with either vehicle or idelalisib at a dose selected to achieve clinically-relevant peak plasma concentrations (150 mg/kg/day). The drug was well tolerated across all CC lines, and there were no observations of overt liver injury. Differences across CC lines were seen in drug concentration in plasma samples collected at the approximate Tmax on study Days 1, 7, and 14. There were also small but statistically significant treatment-induced alterations in plasma total bile acids and microRNA-122, and these may indicate early hepatocellular stress required for immune-mediated hepatotoxicity in humans. Idelalisib treatment further induced significant elevations in the total cell count of terminal bronchoalveolar lavage fluid, which may be analogous to pneumonitis observed in the clinic. Genetic mapping identified loci associated with interim plasma idelalisib concentration and the other three treatment-related endpoints. Thirteen (13) priority candidate quantitative trait genes identified in CC mice may now guide interrogation of risk factors for adverse drug responses associated with idelalisib in humans.
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