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Premise of the research. The disjunct distribution of plant genera between eastern Asia (EA) and eastern North America (ENA) has long attracted the attention of biologists and biogeographers. For most genera that have been studied, there are more species in EA than ENA and the diversity anomaly may have resulted from the greater physiographical heterogeneity in conjunction with climate and sea level changes in EA than in ENA. However, few empirical studies have explicitly tested the association between species diversity and allopatric speciation events. The genus Stewartia (Theaceae) displays this diversity anomaly with two species in ENA and 21 species in EA, but the phylogeny of this group has not been resolved due to insufficient data. Methodology. Here, we sampled 15 species of Stewartia (65%) and generated data from over 500 nuclear loci using the anchored phylogenomic approach to produce a robust phylogeny of Stewartia. In addition, biogeographical analyses were performed to elucidate the natural history of Stewartia including estimated times of divergence, ancestral areas, and speciation patterns. Pivotal results. Our parsimony, Bayesian, and species tree analyses produced congruent phylogenies with high resolution of the interspecific relationships within Stewartia. Speciation in Asia was mostly allopatric between the Japanese islands and the Asian continent during the Miocene and early Pliocene, while the two ENA species represent lineages from different times with S. malacodendron being the first lineage to split off from the remaining species and S. ovata coming later sister to the deciduous species of Asian Stewartia. Conclusions. The results provide direct evidence for the importance of allopatry in the differential diversity between EA and ENA.
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The Chihuahuan Desert includes many endemic angiosperm species, some having very restricted geographic ranges. One of these species is Oreocarya crassipes (I. M. Johnst.) Hasenstab & M. G. Simpson, an endangered distylous gypsophile from the Trans-Pecos region in southern Brewster County, Texas, USA. The species is known from 10 populations, and this small number of populations, human development in the area, a distylous breeding system, and edaphic requirements threaten the long-term viability of the species. Using both hundreds of single nucleotide polymorphisms identified via tunable genotyping-by-sequencing (tGBS) and 10 microsatellite loci, patterns of genetic diversity, demography, selection, and migration were examined for 192 individuals from four populations of O. crassipes. From the sampled individuals, two populations (clusters) were identified via multiple methodologies and with both types of data. With SNP data, population substructure was further resolved among one of these populations to identify two distinct groups of individuals. Multiple individuals recognized as having mixed ancestry, along with Fst values and AMOVA results, provide evidence of genetic exchange among populations, which is less common for gypsophiles than non-gypsophiles, and the rate of migration among populations has been increasing recently. The Fst values for O. crassipes are more similar to those of other rare species than to other gypsophiles. Additionally, while distyly specifically does not necessarily impact the population genetics of the species, allogamy, which is facilitated by distyly, seems to have played a role in the genetic structure of O. crassipes.
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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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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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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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Nitrogen mustard (NM) is a vesicant known to target the lung, causing acute injury which progresses to fibrosis. Evidence suggests that activated macrophages contribute to the pathologic response to NM. In these studies, we analyzed the role of lung lipids generated following NM exposure on macrophage activation and phenotype. Treatment of rats with NM (0.125 mg/kg, i.t.) resulted in a time-related increase in enlarged vacuolated macrophages in the lung. At 28 d post exposure, macrophages stained positively for Oil Red O, a marker of neutral lipids. This was correlated with an accumulation of oxidized phospholipids in lung macrophages and epithelial cells, and increases in bronchoalveolar lavage fluid (BAL) phospholipids and cholesterol. RNA-sequencing and immunohistochemical analysis revealed that lipid handling pathways under the control of the transcription factors LXR, FXR, PPAR-ɣ and SREBP were significantly altered following NM exposure. Whereas at 1-3 d post NM, FXR and the downstream oxidized low density lipoprotein receptor, Cd36, were increased, Lxr and the lipid efflux transporters, Abca1 and Abcg1, were reduced. Treatment of naïve lung macrophages with phospholipid and cholesterol enriched large aggregate fractions of BAL prepared 3 d after NM exposure resulted in upregulation of Nos2 and Ptgs2, markers of pro-inflammatory activation, while large aggregate fractions prepared 28 d post NM upregulated expression of the anti-inflammatory markers, Il10, Cd163, and Cx3cr1, and induced the formation of lipid-laden foamy macrophages. These data suggest that NM-induced alterations in lipid handling and metabolism drive macrophage foam cell formation, potentially contributing to the development of pulmonary fibrosis.
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Identifying correlates of extinction risk is important for understanding the underlying mechanisms driving differential rates of extinction and variability in the temporal durations of taxa. Increasingly, it is recognized that the effects of multiple, potentially interacting variables and phylogenetic relationships should be incorporated when studying extinction selectivity to account for covariation of traits and shared evolutionary history. Here, I explore a variety of biological and ecological controls on genus longevity in the global fossil record of diplobathrid crinoids by analyzing the combined effects of species richness, habitat preference, body size, filtration fan density, and food size selectivity. I employ a suite of taxic and phylogenetic approaches to (1) quantitatively compare and rank the relative effects of multiple factors on taxonomic longevity, and (2) determine how phylogenetic comparative approaches alter interpretations of extinction selectivity. I find controls on diplobathrid genus duration are hierarchically structured, where species richness is the primary predictor of duration, habitat is the secondary predictor, and a combination of ecological and biological traits are tertiary controls. Ecology plays an important but complex role in the generation of crinoid macroevolutionary patterns. Notably, tolerance of environmental heterogeneity promotes increased genus duration across diplobathrid crinoids, and the effects of traits related to feeding ecology vary depending on habitat lithology. Finally, I find accounting for phylogeny does not consistently decrease the significance of correlations between traits and genus duration, as is commonly expected. Instead, the strength of relationships between traits and duration may increase, decrease, or remain statistically similar, and both the magnitude and direction of these shifts are generally unpredictable. However, traits with strong correlations and/or moderately large effect sizes (Cohen’s f2 > 0.15) under taxic approaches tend to remain qualitatively unchanged under phylogenetic approaches.
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Quantifying patterns of variation and coordination of plant functional traits can help to understand the mechanisms underlying both invasiveness and adaptation of plants. Little is known about the coordinated variations of performance and functional traits of different organs in invasive plants, especially in response to their adaptation to environmental stressors. To identify the responses of the invasive species Solidago canadensis to drought, 180 individuals were randomly collected from 15 populations and 212 ramets were replanted in a greenhouse to investigate both the response and coordination between root and leaf functional traits. Drought significantly decreased plant growth and most of the root and leaf functional traits, i.e. root length, surface area, volume and leaf size, number, and mass fraction, except for the root length ratio and root mass fraction. Phenotypic plasticity was higher in root traits than in leaf traits in response to drought, and populations did not differ significantly. The plasticity of most root functional traits, i.e., root length (RL), root surface area (RSA), root volume (RV), and root mass fraction (RMF), were significantly positively correlated with biomass between control and drought. However, the opposite was found for leaf functional traits, i.e. specific leaf area (SLA), leaf area ratio (LAR), and leaf mass fraction (LMF). Drought enhanced the relationship between root and leaf, i.e., 26 pairwise root-leaf traits were significantly correlated under drought, while only 15 pairwise root-leaf traits were significantly correlated under control conditions. Significant correlations were found between biomass and all measured functional traits except for leaf size. RV, root length ratio, RMF, total area of leaves, and LMF responded differently to water availability. These responses enable S. canadensis to cope with drought conditions and may help to explain the reason of the vast ecological amplitude of this species.
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