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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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Correlative imaging combines information from multiple modalities (physical–chemical–mechanical properties) at various length scales (centimetre to nanometre) to understand the complex biological materials across dimensions (2D–3D). Here, we have used numerous coupled systems: X-ray microscopy (XRM), scanning electron microscopy (SEM), electron backscatter diffraction (EBSD), optical light microscopy (LM) and focused ion beam (FIB-SEM) microscopy to ascertain the microstructural and crystallographic properties of the wall-plate joints in the barnacle Semibalanus balanoides. The exoskeleton is composed of six interlocking wall plates, and the interlocks between neighbouring plates (alae) allow barnacles to expand and grow while remaining sealed and structurally strong. Our results indicate that the ala contain functionally graded orientations and microstructures in their crystallography, which has implications for naturally functioning microstructures, potential natural strengthening and preferred oriented biomineralization. Elongated grains at the outer edge of the ala are oriented perpendicularly to the contact surface, and the c-axis rotates with the radius of the ala. Additionally, we identify for the first time three-dimensional nanoscale ala pore networks revealing that the pores are only visible at the tip of the ala and that pore thickening occurs on the inside (soft bodied) edge of the plates. The pore networks appear to have the same orientation as the oriented crystallography, and we deduce that the pore networks are probably organic channels and pockets, which are involved with the biomineralization process. Understanding these multiscale features contributes towards an understanding of the structural architecture in barnacles, but also their consideration for bioinspiration of human-made materials. The work demonstrates that correlative methods spanning different length scales, dimensions and modes enable the extension of the structure–property relationships in materials to form and function of organisms.
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Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite growing interest in a trait-based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single repository for species traits for deep-sea chemosynthesis-based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global-scale trait database for deep-sea hydrothermal-vent fauna - sFDvent (sDiv-funded trait database for the Functional Diversity of vents). We formed a funded working group to select traits appropriate to: i) capture the performance of vent species and their influence on ecosystem processes, and ii) compare trait-based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal-vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we typify the sFDvent database, describe our approach, and evaluate its scope. Finally, we compare the sFDvent database to similar databases from shallow-marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross-ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique doi. 646 vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided. Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid-ocean ridges and 6 back-arc spreading centres. sFDvent includes information on deep-sea vent species, and associated taxonomic updates, since they were first discovered in 1977. Time is not recorded. The database will be updated every five years. Deep-sea hydrothermal-vent fauna with species-level identification present or in progress. .csv and MS Excel (.xlsx)
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Purpose: Animal studies have demonstrated anti-inflammatory, and anti-nociceptive properties of hyperbaric oxygen therapy (HBOT). However, physiological data are scarce in humans. In a recent experimental study, the authors used the burn injury (BI) model observing a decrease in secondary hyperalgesia area (SHA) in the HBOT-group compared to a control-group.Surprisingly, a long-lasting neuroplasticity effect mitigating the BI-induced SHA-response was seen in the HBOT-preconditioned group. The objective of the present study, therefore, was to confirm our previous findings using an examiner-blinded, block-randomized, controlled, crossover study design. Patients and methods: Nineteen healthy subjects attended two BI-sessions with an inter-session interval of ≥28 days. The BIs were induced on the lower legs by a contact thermode (12.5 cm2, 47C°, 420 s). The subjects were block-randomized to receive HBOT (2.4 ATA, 100% O2, 90 min) or ambient conditions ([AC]; 1 ATA, 21% O2), dividing cohorts equally into two sequence allocations: HBOT-AC or AC-HBOT. All sensory assessments performed during baseline, BI, and post-intervention phases were at homologous time points irrespective of sequence allocation. The primary outcome was SHA, comparing interventions and sequence allocations. Data are mean (95% CI). Results: During HBOT-sessions a mitigating effect on SHAs was demonstrated compared to AC-sessions, ie, 18.8 (10.5–27.0) cm2 vs 32.0 (20.1–43.9) cm2 (P=0.021), respectively. In subjects allocated to the sequence AC-HBOT a significantly larger mean difference in SHA in the AC-session vs the HBOT-session was seen 25.0 (5.4–44.7) cm2 (P=0.019). In subjects allocated to the reverse sequence, HBOT-AC, no difference in SHA between sessions was observed (P=0.55), confirming a preconditioning, long-lasting (≥28 days) effect of HBOT. Conclusion: Our data demonstrate that a single HBOT-session compared to control is associated with both acute and long-lasting mitigating effects on BI-induced SHA, confirming central anti-inflammatory, neuroplasticity effects of hyperbaric oxygen therapy.
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In-silico and in-vitro studies have made progress in understanding protein-protein complexes formation; however, the molecular mechanisms for their dissociation are unclear. Protein-protein complexes, lasting from microseconds to years, often involve induced-fit, challenging computational or kinetic analysis. Charybdotoxin (CTX), a peptide from the Leiurus scorpion venom, blocks voltage-gated K+-channels in a unique example of binding/unbinding simplicity. CTX plugs the external mouth of K+-channels pore, stopping K+-ion conduction, without inducing conformational changes. Conflicting with a tight binding, we show that external permeant ions enhance CTX-dissociation, implying a path connecting the pore, in the toxin-bound channel, with the external solution. This sensitivity is explained if CTX wobbles between several bound conformations, producing transient events that restore the electrical and ionic trans-pore gradients. Wobbling may originate from a network of contacts in the interaction interface that are in dynamic stochastic equilibria. These partially-bound intermediates could lead to distinct, and potentially manipulable, dissociation pathways.
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Aim: One aspect that is still poorly explored about the origin and maintenance of Neotropical biodiversity is how the evolutionary dynamics of colonization and differentiation in relation to lowland and highland habitats has impacted lineage formation. Most speciation models for this region have focused on vicariant events, and the need to assess the influence of demographic processes has been recognized only recently. We evaluate if the origin of Andean montane lineages of terciopelo pitvipers is explained by either of two historical processes that represent fundamental phylogeographic mechanisms: differentiation by isolation within the highlands or different dispersal events from the lowlands. Location: Western Ecuador. Taxon: Terciopelo pitvipers (Bothrops asper species complex). Methods: We use genomic data and genetic clustering analyses, evaluation of historical migration between genetic clusters, and demographic model selection to investigate recent diversification events in South America using a vertebrate group rarely explored in phylogeographic studies: tropical Andean snakes. Specifically, the origin of two Ecuadorian montane lineages of terciopelo pitvipers was evaluated given ambiguous phylogenetic relationships with the presumably ancestral Pacific lowland lineage. Results: Discrepancies of evolutionary relationships previously obtained with tree-like methods are resolved through the use of modeling approaches. We found strong support for the independent origin of montane lineages based on topologies inferred by maximum-likelihood trees and modeling approaches that take into account possible gene flow. Main conclusions: Recent large-scale studies have found support for identifying dispersal events as important drivers of diversification in the Neotropical region. We contribute to these ideas by identifying a fine-scale case in a rarely explored group of animals -Andean snakes- in which river valleys acted as an entrance for the upward colonization of montane dry habitats and subsequent ecological diversification.
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Accurate knowledge of skeletal ontogeny in extant organisms is crucial in understanding important morpho-functional systems and in enabling inferences of the ontogenetic stage of fossil specimens. However, detailed knowledge of skeletal ontogeny is lacking for most squamates, including snakes. Very few studies have discussed postnatal development in snakes, with none incorporating data from all three major ontogenetic stages – embryonic, juvenile, and adult. Here, we provide the first analysis encompassing these three ontogenetic stages for any squamate, using the first complete micro-computed tomography (micro-CT)-based segmentations of any non-adult snake, based on fresh specimens of Thamnophis radix. The most significant changes involve the feeding apparatus, with major elongation of the tooth-bearing elements and jaw suspensorium causing a posterior shift in the jaw articulation. This shift enables macrostomy (large-gaped feeding in snakes) and occurs in T. radix via a different developmental trajectory than in most other macrostomatans, indicating that the evolution of macrostomy is more complex than previously thought. The braincase of T. radix is also evolutionarily unique among derived snakes in lacking a crista circumfenestralis, a phenomenon considered herein to represent paedomorphic retention of the embryonic condition. We thus present a number of important challenges to current paradigms regarding snake cranial evolution.
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Humans usually assess things not according to their absolute value, but relative to reference points - a main tenant of Prospect Theory. For example, people rate a new salary relative to previous salaries and salaries of their peers, rather than absolute income. We demonstrate a similar effect in an insect: ants expecting to find low quality food showed higher acceptance of medium quality food than ants expecting medium quality, and vice versa for high expectations. Further experiments demonstrate that these contrast effects arise from cognitive rather than mere sensory or pre-cognitive perceptual causes. Social information gained inside the nest can also serve as a reference point: the quality of food received from other ants affected the perceived value of food found later. Value judgement is a key element in decision making, and thus relative value perception strongly influences which option is chosen and ultimately how all animals make decisions.
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Extant medusozoans (phylum Cnidaria) are dominated by forms showing tetraradial symmetry, but stem-group medusozoans of early Cambrian age collectively exhibit tetra-, bi-, penta-, and hexa-radial symmetry. Moreover, the developmental and evolutionary relationships between four-fold and other types of radial symmetry in medusozoans remain poorly understood. Here we describe a new hexangulaconulariid, Septuconularia yanjiaheensis n. gen. n. sp., from Bed 5 of the Yanjiahe Formation (Cambrian Stage 2) in the Three Gorges area of Hupei Province, China. The laterally compressed, biradially symmetrical periderm of this species possesses 14 gently tapered faces, the most of any hexangulaconulariid described thus far. The faces are bordered by longitudinal ridges and crossed by short, irregularly spaced transverse ribs. Longitudinally, the periderm consists of three regions that probably correspond, respectively, to an embryonic stage, a transient juvenile stage, and a long adult stage. Septuconularia yanjiaheensis n. gen. n. sp. may have been derived from six-faced Hexaconularia (Fortunian Stage), which is morphologically intermediate between Septuconularia yanjiaheensis n. gen. n. sp. and Arthrochites. Furthermore, conulariids sensu stricto, carinachitiids and hexangulaconulariids may constitute a monophyletic group united by possession of an organic or organo-phosphatic periderm exhibiting longitudinal (corner) sulci, a facial midline, and offset of transverse ribs along the facial midline.
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We present an ultra-high resolution magnetic resonance imaging (MRI) dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 µm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of scan time (25 hours per flip angle), allowing derivation of a T1 parameter map and synthesized FLASH volumes. This dataset provides an unprecedented view of the three-dimensional neuroanatomy of the human brain. To optimize the utility of this resource, we warped the dataset into standard stereotactic space. We now distribute the dataset in both native space and stereotactic space to the academic community via multiple platforms. We envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance understanding of human brain anatomy in health and disease.
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