Gene duplication and positive selection can be important determinants of the evolution of venom, a protein-rich secretion used in prey capture and defense. In a typical model of venom evolution, gene ...duplicates switch to venom gland expression and change function under the action of positive selection, which together with further duplication produces large gene families encoding diverse toxins. Although these processes have been demonstrated for individual toxin families, high-throughput multitissue sequencing of closely related venomous species can provide insights into evolutionary dynamics at the scale of the entire venom gland transcriptome. By assembling and analyzing multitissue transcriptomes from the Western black widow spider and two closely related species with distinct venom toxicity phenotypes, we do not find that gene duplication and duplicate retention is greater in gene families with venom gland biased expression in comparison with broadly expressed families. Positive selection has acted on some venom toxin families, but does not appear to be in excess for families with venom gland biased expression. Moreover, we find 309 distinct gene families that have single transcripts with venom gland biased expression, suggesting that the switching of genes to venom gland expression in numerous unrelated gene families has been a dominant mode of evolution. We also find ample variation in protein sequences of venom gland-specific transcripts, lineage-specific family sizes, and ortholog expression among species. This variation might contribute to the variable venom toxicity of these species.
Spiders have evolved two types of sticky capture threads: one with wet adhesive spun by ecribellate orb-weavers and another with dry adhesive spun by cribellate spiders. The evolutionary history of ...cribellate capture threads is especially poorly understood. Here, we use genomic approaches to catalog the spider-specific silk gene family (spidroins) for the cribellate orb-weaver Uloborus diversus. We show that the cribellar spidroin, which forms the puffy fibrils of cribellate threads, has three distinct repeat units, one of which is conserved across cribellate taxa separated by ~ 250 Mya. We also propose candidates for a new silk type, paracribellar spidroins, which connect the puffy fibrils to pseudoflagelliform support lines. Moreover, we describe the complete repeat architecture for the pseudoflagelliform spidroin (Pflag), which contributes to extensibility of pseudoflagelliform axial fibers. Our finding that Pflag is closely related to Flag, supports homology of the support lines of cribellate and ecribellate capture threads. It further suggests an evolutionary phase following gene duplication, in which both Flag and Pflag were incorporated into the axial lines, with subsequent loss of Flag in uloborids, and increase in expression of Flag in ecribellate orb-weavers, explaining the distinct mechanical properties of the axial lines of these two groups.
Orb-web weaving spiders and their relatives use multiple types of task-specific silks. The majority of spider silk studies have focused on the ultra-tough dragline silk synthesized in major ampullate ...glands, but other silk types have impressive material properties. For instance, minor ampullate silks of orb-web weaving spiders are as tough as draglines, due to their higher extensibility despite lower strength. Differences in material properties between silk types result from differences in their component proteins, particularly members of the spidroin (spider fibroin) gene family. However, the extent to which variation in material properties within a single silk type can be explained by variation in spidroin sequences is unknown. Here, we compare the minor ampullate spidroins (MiSp) of orb-weavers and cobweb weavers. Orb-web weavers use minor ampullate silk to form the auxiliary spiral of the orb-web while cobweb weavers use it to wrap prey, suggesting that selection pressures on minor ampullate spidroins (MiSp) may differ between the two groups.
We report complete or nearly complete MiSp sequences from five cobweb weaving spider species and measure material properties of minor ampullate silks in a subset of these species. We also compare MiSp sequences and silk properties of our cobweb weavers to published data for orb-web weavers. We demonstrate that all our cobweb weavers possess multiple MiSp loci and that one locus is more highly expressed in at least two species. We also find that the proportion of β-spiral-forming amino acid motifs in MiSp positively correlates with minor ampullate silk extensibility across orb-web and cobweb weavers.
MiSp sequences vary dramatically within and among spider species, and have likely been subject to multiple rounds of gene duplication and concerted evolution, which have contributed to the diverse material properties of minor ampullate silks. Our sequences also provide templates for recombinant silk proteins with tailored properties.
Background. Using multinational collections of methicillin-susceptible Staphylococcus aureus (MSSA) isolates from infective endocarditis (IE) and soft tissue infections (STIs), we sought to (1) ...validate the finding that S. aureus in clonal complex (CC) 30 is associated with hematogenous complications and (2) test the hypothesis that specific genetic characteristics in S. aureus are associated with infection severity. Methods. IE and STI isolates from 2 cohorts were frequency matched by geographic origin. Isolates underwent spa typing to infer CC and multiplex polymerase chain reaction for presence of virulence genes. Results. 114 isolate pairs were genotyped. IE isolates were more likely to be CC30 (19.5% vs 6.2%; P = .005) and to contain 3 adhesins (clfB, cna, map/eap; P < .0001 for all) and 5 enterotoxins (tst, sea, sed, see, and sei; P ≤ .005 for all). CC30 isolates were more likely to contain cna, tst, sea, see, seg, and chp (P <.05 for all). Conclusions. MSSA IE isolates were significantly more likely to be CC30 and to possess a distinct repertoire of virulence genes than MSSA STI isolates from the same region. The genetic basis of this association requires further study.
Live imaging of neuromuscular junctions (NMJs) in situ has been constrained by the suitability of ligands for inert vital staining of motor nerve terminals. Here, we constructed several truncated ...derivatives of the tetanus toxin C-fragment (TetC) fused with Emerald Fluorescent Protein (emGFP). Four constructs, namely full length emGFP-TetC (emGFP-865:TetC) or truncations comprising amino acids 1066-1315 (emGFP-1066:TetC), 1093-1315 (emGFP-1093:TetC) and 1109-1315 (emGFP-1109:TetC), produced selective, high-contrast staining of motor nerve terminals in rodent or human muscle explants. Isometric tension and intracellular recordings of endplate potentials from mouse muscles indicated that neither full-length nor truncated emGFP-TetC constructs significantly impaired NMJ function or transmission. Motor nerve terminals stained with emGFP-TetC constructs were readily visualised in situ or in isolated preparations using fibre-optic confocal endomicroscopy (CEM). emGFP-TetC derivatives and CEM also visualised regenerated NMJs. Dual-waveband CEM imaging of preparations co-stained with fluorescent emGFP-TetC constructs and Alexa647-α-bungarotoxin resolved innervated from denervated NMJs in axotomized
mouse muscle and degenerating NMJs in transgenic SOD1G93A mouse muscle. Our findings highlight the region of the TetC fragment required for selective binding and visualisation of motor nerve terminals and show that fluorescent derivatives of TetC are suitable for in situ morphological and physiological characterisation of healthy, injured and diseased NMJs.
To explore, in a dose-escalation study, the feasibility of hyperbaric oxygen (HBO) treatments immediately before intensity modulated radiation therapy in conjunction with cisplatinum chemotherapy for ...squamous cell carcinoma of the head and neck (SCCHN).
Eligible patients presented with SCCHN (stage III-IV M0), life expectancy >6 months, and Karnofsky performance status ≥70. Enrollees received intensity modulated radiation therapy, 70 Gy in 35 fractions over 7 weeks with weekly cisplatinum. Patients received HBO-100% oxygen, 2.4 atmospheres absolute (ATA) for 30 minutes-twice per week initially. Subsequent patients were escalated to 3 and then 5 times per week. Intensity modulated radiation therapy began within 15 minutes after HBO. Patients were followed for 2 years after RT with quality-of-life questionnaires (Performance Status Scale-Head and Neck Cancer and the Functional Assessment of Cancer Therapy-Head and Neck Cancer) and for 5+ years for local recurrence, distant metastases, disease-specific survival, and overall survival.
Twelve subjects enrolled from 3 centers. Two withdrew during radiation therapy and 1 within 14 weeks after radiation therapy. The remaining 9 had primary oropharyngeal disease and were stage IVA (7) or IVB (2). No dose-limiting toxicities were observed with daily HBO. Two patients (22%) required pressure equalization tubes. The average time between HBO and radiation therapy was 8.5 minutes, with 2 of 231 administrations delivered beyond 15 minutes (0.5%). Per-protocol analysis showed a clinical complete response in 7 and a pathologic complete response without tumor in salvage neck dissections in 2. With minimum follow-up of 61 months, per-protocol 5-year overall survival was 100%, local recurrence 0%, and distant metastases 11%. Patient-reported outcomes for quality of life (Functional Assessment of Cancer Therapy-Head and Neck Cancer) were comparable to published results for chemoradiotherapy without HBO.
While acknowledging the study's small size and early attrition of 3 patients, our in-depth review of the acquired data indicates the feasibility of combining HBO with chemoradiation.
Modern, tide‐dominated and tide‐influenced coastlines are characterized by a range of environments, including deltas, estuaries and lagoons. However, some tide‐dominated basins and related ...sedimentary units in the rock record, such as the semi‐enclosed, shallow, Utah–Idaho Trough foreland basin of the Jurassic Curtis Sea, do not correspond to any of these modern systems. Persistent aridity caused the characteristic severe starvation of perennial fluvial input throughout this basin, in which the informal lower, middle and upper Curtis, as well as the underlying Entrada Sandstone, and the overlying Summerville Formation were deposited. Wave energy was efficiently dissipated by the shallow basin's elongated morphology (approximately 800 × 150 km), as its semi‐enclosed morphology further protected the system from significant wave impact. Consequently, the semi‐enclosed, shallow‐marine system was dominated by amplified tidal forces, resulting in a complex distribution of heterolithic deposits. Allocyclic forcing strongly impacted upon the system's intrinsic autocyclic processes as the lower Curtis was deposited. Short‐lived relative sea‐level variations, along with uplift and deformation episodes, resulted in the accumulation of three parasequences, each separated by traceable flooding and ravinement surfaces. The subsequent transgression, which defines the base of the middle Curtis, allowed for the shallow‐marine part of the system to enter into tidal resonance as a consequence of the flooded basin reaching the optimal configuration of approximately 800 km in length, corresponding to an odd multiple of the quarter of the tidal wavelength given an average minimum water depth of 20–25 m. This resonant system overprinted the effects of allocyclic forcing and related traceable stratigraphic surfaces. However, the contemporaneous and neighbouring coastal dune field sedimentary rocks of the Moab Member of the Curtis Formation, characterized by five stacked aeolian sequences, as well as the supratidal deposits of the Summerville Formation, lingered to record allocyclic signals, as the Curtis Sea regressed. This study shows that a tide‐dominated basin can enter into tidal resonance as it reaches its optimal morphological configuration, leading to the overprinting of otherwise dominant allocyclic processes by autocyclic behaviour. It is only by considering the sedimentological relationships of neighbouring and contemporaneous depositional systems that a full understanding of the dynamic stratigraphic history of a basin alternatively dominated by autocyclic and allocyclic processes can be achieved.
This study shows that (a) a tide‐dominated basin can enter into tidal resonance as it reaches its optimal morphological configuration, leading to the overprinting of otherwise dominant allocyclic processes by autocyclic behaviour. (b) It is therefore required to extend the research focus to neighbouring and contemporaneous depositional systems in order to fully understand the dynamic stratigraphic history of a basin alternatively dominated by auto‐ and allocyclic processes.
Hybrid event beds are texturally and compositionally‐diverse deposits preserved within deepwater settings. They are deposited by flows exhibiting ‘mixed behaviour’, forming complex successions of ...sandstone and mudstone, which are often challenging to predict. Hybrid event beds are documented in deep‐marine settings, where they have been thoroughly characterized, and are well‐known as effective fluid transmissibility barriers and baffles in reservoirs. By comparison, there are far‐fewer studies of hybrid event beds from deep‐lacustrine settings, where their character and distribution remains relatively under‐explored. In order to provide insights into these deposits, this study presents the detailed analysis of three‐dimensional seismic data, wireline logs and core from a series of ancient deep‐lacustrine fan systems in the North Falkland Basin. Results confirm that deep‐lacustrine hybrid event beds comprise the same idealized sequence of the ‘H1–H5’ divisions. However, in this study H3 ‘debrite’ units can be sub‐divided into ‘H3a–H3c’, based on: sharp or erosional intra‐H3 contacts, bulk lithology, mud‐content and discrete sedimentary textures. This study interprets the H3a–H3c sub‐units as the products of multiple flow components formed through significant rearward longitudinal flow transformation processes, during the emplacement of a single hybrid event bed. Hybrid event beds are observed within lobe fringes, where flow types, energies and transport mechanisms diversify as a result of flow transformation. The temporal context of hybrid event bed occurrences is considered in relation to stages of fan evolution, including: the Initiation; Growth (I); Growth (II); By‐pass; Abandonment; and Termination phases. Hybrid event beds are mainly found in either the initiation phase where flow interaction and erosion of initial substrates promoted mixed flow behaviour, or in the abandonment phase as facies belts retreated landward. The results of this study have important implications in terms of flow processes of hybrid event bed emplacement, in particular sub‐division of the H3 unit, as well as the prediction of hybrid event bed occurrence and character within ancient deep‐lacustrine fan settings, in general.
1. Species richness is a state variable of some interest in monitoring programmes but raw species counts are often biased due to imperfect species detectability. Therefore, monitoring programmes ...should quantify detectability for target taxa to assess whether it varies over temporal or spatial scales. We assessed the potential for tropical bat monitoring programmes to reliably estimate trends in species richness. 2. Using data from 25 bat assemblages from the Old and New World tropics, we estimated detectability for all species in an assemblage (mean proportion of species detected per sampling plot) and for individual species (species-specific detectability). We further assessed how these estimates of detectability were affected by external sources of variation relating to time, space, survey effort and biological traits. 3. The mean proportion of species detected across 96 sampling plots was estimated at 0·76 (range 0·57—1·00) and was significantly greater for phytophagous than for animalivorous species. Species-averaged detectability for phytophagous species was influenced by the number of surveys and season, whereas the number of surveys and sampling methods ground- or canopy-level mist nets, harp traps and acoustic sampling (AS) most strongly affected estimates of detectability for animalivorous bats. Species-specific detectability averaged 0·4 and was highly heterogeneous across 232 species, with estimates ranging from 0·03 to 0·84. Species-level detectability was influenced by a range of external factors such as location, season, or sampling method, suggesting that raw species counts may sometimes be strongly biased. 4. Synthesis and applications. Due to generally high species-specific detection probabilities, Neotropical aerial insectivorous bats proved to be well suited for monitoring using AS. However, for species with low detectability, such as most gleaning animalivores or nectarivores, count data obtained in bat monitoring surveys must be corrected for detection bias. Our results indicate that species-averaged detection probabilities will rarely approach 1 unless many surveys are conducted. Consequently, long-term bat monitoring programmes need to adopt an estimation scheme that corrects for variation in detectability when comparing species richness over time and when making regional comparisons. Similar corrections will be needed for other species-rich tropical taxa.
Trait Evolution in Adaptive Radiations Clarke, Magnus; Thomas, Gavin H.; Freckleton, Robert P.
The American naturalist,
02/2017, Volume:
189, Issue:
2
Journal Article
Peer reviewed
Open access
The incorporation of ecological processes into models of trait evolution is important for understanding past drivers of evolutionary change. Species interactions have long been thought to be key ...drivers of trait evolution. However, models for comparative data that account for interactions between species are lacking. One of the challenges is that such models are intractable and difficult to express analytically. Here we present phylogenetic models of trait evolution that include interspecific competition among chosen species. Competition is modeled as a tendency of sympatric species to evolve toward difference from one another, producing trait overdispersion and high phylogenetic signal. The model predicts elevated trait variance across species and a slowdown in evolutionary rate both across the clade and within each branch. The model also predicts a reduction in correlation between otherwise correlated traits. We use an approximate Bayesian computation approach to estimate model parameters. We find reasonable power to detect competition in sufficiently large (20+ species) trees compared with Brownian trait evolution and with Ornstein-Uhlenbeck and early burst models. We apply the model to examine the evolution of bill morphology of Darwin’s finches and find evidence that competition affects the evolution of bill length.
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