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Atrium kidney-shaped (b6); copulatory openings oval (b7) in An of Zelotibia (Araneae, Gnaphosidae), a spider genus with a species swarm in the Albertine Rift

Atrium kidney-shaped (b6); copulatory openings oval (b7)

Epigyne with large hood-shaped atrium anteriorly, lacking a clearly defined scape (a1) in An of Zelotibia (Araneae, Gnaphosidae), a spider genus with a species swarm in the Albertine Rift

Epigyne with large hood-shaped atrium anteriorly, lacking a clearly defined scape (a1)

Spermathecae oval or flask-shaped (d1) in An of Zelotibia (Araneae, Gnaphosidae), a spider genus with a species swarm in the Albertine Rift

Spermathecae oval or flask-shaped (d1)

Embolus blade shaped in ventral view (I2) in An of Zelotibia (Araneae, Gnaphosidae), a spider genus with a species swarm in the Albertine Rift

Embolus blade shaped in ventral view (I2)

Tibial apophysis not scoop-shaped in lateral view and originating midway of tibia (B3) in An of Zelotibia (Araneae, Gnaphosidae), a spider genus with a species swarm in the Albertine Rift

Tibial apophysis not scoop-shaped in lateral view and originating midway of tibia (B3)

Extremity of embolus beak-shaped (G1); median apophysis small (G2) in An of Zelotibia (Araneae, Gnaphosidae), a spider genus with a species swarm in the Albertine Rift

Extremity of embolus beak-shaped (G1); median apophysis small (G2)

copulatory ducts long and s-shaped (9b) in A revision of the African wolf spider genus Amblyothele Simon

copulatory ducts long and s-shaped (9b)

opencc-zeroMay 2020View details →

Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)

As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 SNPs and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and processes shaping them. We found evidence of high (mean FST=0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16, and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium despite no local reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.

opencc-zeroMay 2020View details →

Data from: Ant collective behavior is heritable and shaped by selection

Collective behaviors are widespread in nature and usually assumed to be strongly shaped by natural selection. However, the degree to which variation in collective behavior is heritable and has fitness consequences -- the two prerequisites for evolution by natural selection -- is largely unknown. We used a new pharaoh ant ( Monomorium pharaonis ) mapping population to estimate the heritability, genetic correlations, and fitness consequences of three collective behaviors (foraging, aggression, and exploration) as well as body size, sex ratio, and caste ratio. Heritability estimates for the collective behaviors were moderate, ranging from 0.17 to 0.32, but lower than our estimates for the heritability of caste ratio, sex ratio, and the body size of new workers, queens, and males. Moreover, variation among colonies in collective behaviors was phenotypically correlated, suggesting that selection may shape multiple colony collective behaviors simultaneously. Finally, we found evidence for directional selection that was similar in strength to estimates of selection in natural populations. Altogether, our study begins to elucidate the genetic architecture of collective behavior and is one of the first studies to demonstrate that it is shaped by selection.

opencc-by-4.0Jun 2020View details →

Data, code, and metadata for: Temperature shapes movement and habitat selection by a heat-senstive ungulate

Data, code, and metadata for: Temperature shapes movement and habitat selection by a heat-sensitive ungulate

opencc-by-4.0Dec 2019View details →

Relationship between Epilarynx Tube Shape and the radiated Sound Pressure Level during Phonation is gender specific

There are two types of files: .wav files contain the audio recordings .tif files the mri-data necessary for the study. Please do not use the data without referencing its origin.

HADDOCK shape-based screening against the COVID-19 main protease (Mpro)

The novel coronavirus (SARS-CoV-2) that has emerged from Wuhan, China in December 2019 has spread to almost all countries in the world causing a dramatic number of deaths. The current absence of antiviral treatment against the SARS-CoV-2 urges the scientific community to accelerate the drug discovery research process. One way to identify potential treatments and to be able to administer it swiftly is to focus on drug repurposing studies, i.e. to investigate the SARS-CoV-2 antiviral potential of drugs that have already been approved for human use. Proteins that are crucial for the survival and replication of the virus are the most attractive targets for such studies. Here we have focused on the SARS-CoV-2 main protease (3CLpro) that plays an essential role in the virus replication process by screening ~2000 approved drugs (and 6 experimental ones) against this particular protein using a shape-based assay. This is one part of a multi-target screen emphasising the main protease (Mrpo), the RNA-dependent-RNA-polymerase (RdRp) and human ACE2. The other datasets can found at the following locations: <ul> <li><a href="https://zenodo.org/record/3929446">Mpro: Pharmacophore-based assay</a></li> <li><a href="https://zenodo.org/record/3929463">ACE2</a></li> <li><a href="https://zenodo.org/record/3929449">RdRp</a></li> </ul> More information about this screen along with interactive visualisations of the top compounds can be found on our website <a href="https://bonvinlab.org/covid/">bonvinlab.org</a>.

Data from: Phenological synchrony shapes pathology in host–parasite systems

A key challenge surrounding ongoing climate shifts is to identify how they alter species interactions, including those between hosts and parasites. Because transmission often occurs during critical time windows, shifts in the phenology of either taxa can alter the likelihood of interaction or the resulting pathology. We quantified how phenological synchrony between vulnerable stages of an amphibian host (Pseudacris regilla) and infection by a pathogenic trematode (Ribeiroia ondatrae), determined infection prevalence, parasite load, and host pathology. By tracking hosts and parasite infection throughout development between low- and high-elevation regions (San Francisco Bay Area and the Southern Cascades [Mt. Lassen]), we found that when phenological synchrony was high (Bay Area), each established parasite incurred a 33% higher probability of causing severe limb malformations relative to areas with less synchrony (Mt. Lassen). As a result, hosts in the Bay Area had up to a 50% higher risk of pathology even while controlling for mean infection load. Our results indicate that host-parasite interactions and the resulting pathology were the joint product of infection load and phenological synchrony, highlighting the sensitivity of disease outcomes to forecasted shifts in climate.

Data from: Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees

Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species' present-day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present-day gene flow dynamics in determining the genetic diversity and structure of the newt Calotriton asper (Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a clear phylogeographic pattern and presented low levels of variation. In contrast, microsatellites revealed five major genetic lineages with admixture patterns at their boundaries. Approximate Bayesian computation analyses and linear models indicated that the five lineages likely underwent separate evolutionary histories and can be tracked back to distinct glacial refugia. Lineage differentiation started around the Last Glacial Maximum at three focal areas (western, central and eastern Pyrenees) and extended through the end of the Last Glacial Period in the central Pyrenees, where it led to the formation of two more lineages. Our data revealed no evidence of recent dispersal between lineages, whereas borders likely represent zones of secondary contact following expansion from multiple refugia. Finally, we did not find genetic evidence of sex-biased dispersal. This work highlights the importance of integrating past evolutionary processes and present-day gene flow and dispersal dynamics, together with multilocus approaches, to gain insights into what shaped the current genetic attributes of amphibians living in montane habitats.

Data from: Does local adaptation along a latitudinal cline shape plastic responses to combined thermal and nutritional stress?

Thermal and nutritional stress are commonly experienced by animals. This will become increasingly so with climate change. Whether populations can plastically respond to such changes will determine their survival. Plasticity can vary among populations depending on the extent of environmental heterogeneity. However, theory conflicts as to whether environmental heterogeneity should increase or decrease plasticity. Using three locally-adapted populations of Drosophila melanogaster sampled from a latitudinal gradient, we investigated whether plastic responses to combinations of nutrition and temperature increase or decrease with latitude for four traits: egg-adult viability, egg-adult development time, and two body size traits. Employing nutritional geometry, we reared larvae on 25 diets varying in protein and carbohydrate content at two temperatures: 18ºC and 25ºC. Plasticity varied among traits and across the three populations. Viability was highly canalized in all three populations. The tropical population showed the least plasticity for development time, the sub-tropical showed the highest plasticity for wing area, and the temperate population showed the highest plasticity for femur length. We found no evidence of latitudinal plasticity gradients in either direction. Our data highlight that differences in thermal variation and resource predictability experienced by populations along a latitudinal cline are not sufficient to predict their plasticity.

Adaptive zones shape the magnitude of premating reproductive isolation in Timema stick insects

Simpson's fossil-record inspired model of 'adaptive zones' proposes that evolution is dominated by small fluctuations within adaptive zones, occasionally punctuated by larger shifts between zones. This model can help explain why the process of population divergence often results in weak or moderate reproductive isolation (RI), rather than strong RI and distinct species. Applied to the speciation process, the adaptive zones hypothesis makes two inter-related predictions: (i) large shifts between zones are relatively rare, (ii) when large shifts do occur they generate stronger RI than shifts within zones. Here we use ecological, phylogenetic, and behavioural data to test these predictions in Timema stick insects. We show that host use in Timema is dominated by moderate shifts within the systematic divisions of flowering plants and conifers, with only a few extreme shifts between these divisions. However, when extreme shifts occur they generate greater RI than do more moderate shifts. Our results support the adaptive zones model, and suggest that the net contribution of ecological shifts to diversification is dependent on both their magnitude and frequency. We discuss the generality of our findings in light of emerging evidence from diverse taxa that the evolution of RI is not always the only factor determining the origin of species diversity

Data from: Quantifying shape and ecology in avian pedal claws: the relationship between the bony core and keratinous sheath

Terrestrial tetrapods use their claws to interact with their environments in a plethora of ways. Birds in particular have developed a diversity of claw shapes since they are often not bound to terrestrial locomotion and have heterogeneous body masses ranging several orders of magnitude. Numerous previous studies have hypothesized a connection between pedal claw shape and ecological mode in birds, yet have generated conflicting results, spanning from clear ecological groupings based on claw shape to a complete overlap of ecological modes. The majority of these studies have relied on traditional morphometric arc measurements of keratinous sheaths and have variably accounted for likely confounding factors such as body mass and phylogenetic relatedness. To better address the hypothesized relationship between ecology and claw shape in birds, we collected 580 radiographs allowing visualization of the bony core and keratinous sheath shape in 21 avian orders. Geometric morphometrics was used to quantify bony core and keratinous sheath shape and was compared to results using traditional arc measurements. Neither approach significantly separates bird claws into coarse ecological categories after integrating body size and phylogenetic relatedness; however, some separation between ecological groups is evident and we find a gradual shift from the claw shape of ground-dwelling birds to those of predatory birds. Further, the bony claw core and keratinous sheath are significantly correlated, and the degree of functional integration does not differ across ecological groups. Therefore, it is likely possible to compare fossil bony cores with extant keratinous sheaths after applying corrections. Finally, traditional metrics and geometric morphometric shape are significantly, yet loosely correlated. Based on these results, future workers are encouraged to use geometric morphometric approaches to study claw geometry and account for confounding factors such as body size, phylogeny, and individual variation prior to predicting ecology in fossil taxa.

opencc-zeroJun 2020View details →

Data from: Hurricanes overcome migration lag and shape intraspecific genetic variation beyond a poleward mangrove range limit

Expansion of many tree species lags behind climate-change projections. Extreme storms can rapidly overcome this lag, especially for coastal species, but how will storm-driven expansion shape intraspecific genetic variation? Do storms provide recruits only from the nearest sources, or from more distant sources? Answers to these questions have ecological and evolutionary implications, but empirical evidence is absent from the literature. Hurricane Irma provided an opportunity to address this knowledge gap at the northern range limit of the neotropical black mangrove (Avicennia germinans) on the Atlantic coast of Florida, USA. We observed massive post-hurricane increases in beach-stranded A. germinans propagules at, and past, this species' present-day range margin when compared to a previously-surveyed, non-hurricane year. Yet, propagule dispersal does not guarantee subsequent establishment and reproductive success (i.e., effective dispersal). We also evaluated prior effective dispersal along this coastline with isolated A. germinans trees identified beyond the most northern established population. We used 12 nuclear microsatellite loci to genotype hurricane-driven drift propagules from nine sites (n = 896 propagules) and isolated trees from four sites (n = 10 trees), determined their sources of origin, and estimated dispersal distances. Almost all drift propagules and all isolated trees came from the nearest sources. This research suggests that hurricanes are a prerequisite for poleward range expansion of a coastal tree species and that storms can shape the expanding gene pool by providing almost exclusively range-margin genotypes. These insights and empirical estimates of hurricane-driven dispersal distances should improve our ability to forecast distributional shifts of coastal species.

opencc-zeroAug 2020View details →

MVCNN++: CAD model shape classification and retrieval using multi-view convolutional neural networks

Deep neural networks have shown promising success towards the classification and retrieval tasks for images and text data. While there have been several implementations of deep networks in the area of computer graphics, these algorithms do not translate easily across different datasets, especially for shapes used in product design and manufacturing domain. Unlike datasets used in the 3D shape classification and retrieval in the computer graphics domain, engineering level description of 3D models do not yield themselves to neat distinct classes. The current study looks at an improved form of the 3D shape deep learning algorithm for classification and retrieval through the use of techniques such as relaxed classification, use of prime angled camera angles for capturing feature detail and transfer learning for reducing the amount of data and processing time needed to train shape recognition algorithms. The proposed algorithm (MVCNN++) builds on top of multi-view convolutional neural network (MVCNN) algorithm, improving its efficacy for manufacturing part classification by enabling use of part metadata, yielding an improvement of almost 6% over the original version. With the explosive growth of 3D product models available in publicly available repositories, search and discovery of relevant models is critical to democratizing access to design models.