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opencc-by-4.0Jul 2021View details →

Study On Hybrid Model Combining Super Learner And Physics-based Models For SHM In Bridges Using Low-cost BWIM

The main objective of this project is to study and develop hybrid models of BWIM physics-based models incorporates with SHM inspection used by artificial intelligence (AI) techniques to predict structural damage. This study presents a comprehensive assessment of FE simulations leveraging contact method verified by vehicle-bridge interaction(VBI) theory and uses machine learning (ML) techniques to identify and predict structural damages from the structural response automatically. Bridges are a fundamental part of infrastructure management. The main challenge that we face is the aging of these transportation infrastructures without a tool to perform accurate structural assessments in a real-time manner. Unfortunately, this topic is still not completely developed due to the lack of study upon BWIM simulations designed with several different severity damages. The Contact method, a new approach to simulating moving-vehicle motion in BWIM simulation, is to carry out actual structural response verified by the VBI with comprehensive parameter studies. In order to simulation the reality complex condition of the bridge, the FE model is designed by four different classes of damages with three different damage locations applied with two different load conditions (e.g., static load and moving load). The responses collected from FE simulation are used for structural damage prediction leveraging the ML damage prediction model. Among ML methods, the XGBoost with assembly decision tree shows the most reliable results. The results in this project indicate that structural damage prediction can be achieved by using the ML technique and BWIM structural response, which provides high accuracy of damage prediction.

opencc-by-4.0Dec 2021View details →

Fig. 3 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation

Fig. 3. Polyclonal structure of studied Eusomus ovlulum samples inUkraine.

opencc-by-4.0Dec 2021View details →

Fig. 2 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation

Fig. 2. The electrophoretic spectra of the esterases in the Eusomus ovulum specimens.

opencc-by-4.0Dec 2021View details →

Fig. 1 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation

Fig. 1. Geographic localization of Eusomus ovulum samples.

opencc-zeroApr 2022View details →

Profiling, monitoring and conserving caterpillar fungus in the Himalayan region using anchored hybrid enrichment markers

The collection of caterpillar fungus accounts for 50-70% of the household income of thousands of Himalayan communities and has an estimated market value of $5-11 billion across Asia. However, Himalayan collectors are at multiple economic disadvantages compared with collectors on the Tibetan plateau because their product is not legally recognized. Using a customized hybrid-enrichment probe set and market-grade caterpillar fungus (with samples up to 30 years old) from 94 production zones across Asia, we uncovered clear geography-based signatures of historical dispersal and significant isolation-by-distance among caterpillar fungus hosts. This high-throughput approach can readily distinguish samples from major production zones with definitive geographical resolution, especially for samples from the Himalayan region that form monophyletic clades in our analysis. Based on these results, we propose a two-step procedure to help local communities authenticate their produce and improve this multi-national trade route without creating opportunities for illegal exports and other forms of economic exploitation. We argue that policy makers and conservation practitioners must encourage the fair trade of caterpillar fungus in addition to sustainable harvesting to support a transboundary conservation effort that is much needed for this natural commodity in the Himalayan region.

opencc-zeroMay 2022View details →

Data from: Extensive sympatry and frequent hybridization of ecologically divergent aquatic plants on the Qinghai-Tibetan Plateau

Hybridization has fascinated biologists in recent centuries for its evolutionary importance, especially in plants. Hybrid zones are commonly located in regions across environmental gradients due to more opportunities to contact and ecological heterogeneity. For aquatic taxa, intrazonal character makes broad overlapping regions in intermediate environments between related species. However, we have limited information on the hybridization pattern of aquatic taxa in alpines, especially submerged macrophytes. In this study, we aimed to test the hypotheses that niche overlap and hybridization might be extensive in related aquatic plants across an altitudinal gradient. We evaluated the niche overlap in three related species pairs on the Qinghai-Tibetan Plateau and assessed the spatial pattern of hybrid populations. Obvious niche overlap and common hybridization were revealed in all three pairs of related aquatic plants. The plateau edge and river basins were broad areas for the sympatry of divergent taxa, where a large proportion of hybrid populations occurred. Hybrids are also discretely distributed in diverse habitats on the plateau. Differences in the extent of niche overlap, genetic incompatibility and phylogeographic history might lead to variations in hybridization patterns among the three species pairs. Our results suggested that plateau areas are a hotspot for ecologically divergent aquatic species to contact and mate and implied that hybridization may be important for the freshwater biodiversity of highlands.

opencc-by-4.0May 2022View details →

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages.

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages. preprint, bioRxiv, 2022. DOI: 10.1101/2022.05.06.490883 Each zip file contains the raw computational data (as a gzip compressed tarball), YAML input files, as well as Python plotting scripts. The Python plotting scripts have dependencies on the packages: tarfile, multiprocessing, numpy, scipy, and matplotlib. Note that the Python plotting scripts plot directly from the gzip compressed tarballs. The corresponding code can be found on GitHub: https://github.com/Ruth-Bowness-Group/CAModel

opencc-zeroMay 2022View details →

Data from: Convergent evolution of disordered lipidic structural color in the fruits of Lantana strigocamara (syn. L. camara hybrid cultivar)

Research conducted: The majority of plant colors are produced by anthocyanin and carotenoid pigments, but coloration obtained by nanostructured materials (i.e., structural colors) is increasingly reported in plants. Here, we identify a multilayer photonic structure in the fruits of Lantana strigocamara and compare it to a previously described origin in Viburnum tinus. Methods: We used a combination of transmission electron microscopy, serial EM tomography, scanning force microscopy, and optical simulations to characterize the photonic structure in L. strigocamara. We also examine the development of the structure during maturation. Key results: We find that the structural color derives from a disordered, multilayered reflector consisting of lipid droplets of ~105 nm that form a plate-like structure in 3D. This structure begins to form early in development and reflects blue wavelengths of light with increasing intensity over time as the structure develops. The lipids used are likely polymers of lipid monomers. Main conclusions: Lantana strigocamara is the second origin of a lipid-based photonic structure, convergently evolved with the structure in Viburnum tinus. Chemical differences between the lipids in L. strigocamara and those of V. tinus suggest a distinct evolutionary trajectory with implications for the signaling function of structural colors in fruits.

opencc-by-4.0Aug 2021View details →

Data release: Genomic evidence of contemporary hybridization between Schistosoma species

This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see https://www.sanger.ac.uk/about/who-we-are/research-policies/open-access-science/ Please contact Duncan Berger (db22@sanger.ac.uk) with questions regarding pre-publication use of this dataset.  SchCurr1.primary.fa - Schistosoma curassoni primary genome assembly  SchCurr1.haplotypes.fa - Haplotype variants (unphased from SchCurr1.primary.fa) SchCurr1.primary.fa.tbl - RepeatMasker2 output (run on the primary assembly). allchrs.vcf.gz - All variants called on chromosomes 1-7+Z (Post quality control, with the exception that variants found within repetitive regions are included) MITO.vcf.gz - All mitochondrial variants.   SchCurr1.genomethreader.gff3 - Genomethreader based gene structure predictions (based on spliced alignments of S. mansoni (v9) transcript and protein sequences).

opencc-zeroJun 2022View details →

Morphometric data of two tree frog species and their hybrids from a hybrid zone in Poland

Under incomplete reproductive isolation, secondary contact of diverged allopatric lineages may form hybrid zones that allow to study recombinants over several generations as excellent systems of genomic interactions, resulting from the evolutionary forces, acting on certain genes and phenotypes. Hybrid phenotypes are expected to either exhibit intermediacy or, alternatively, transgressive traits, which exceed the extremes of their parents due to epistasis and segregation of complementary alleles. While transgressive morphotypes have been examined in fish, reptiles, birds, and mammals, studies in amphibians are rare. Here, we associate microsatellite-based genotypes and morphometrics-based morphotypes of two European tree frog species of the Hyla arborea group, sampled across a hybrid zone in Poland, to understand whether the genetically differentiated parental species also differ in morphology between each other and their hybrids, and whether secondary contact leads to the evolution of intermediate or transgressive morphotypes. Using univariate approaches, explorative multivariate methods (Principal Component Analyses) as well as techniques with prior grouping (Discriminant Function Analyses), we find that morphotypes of both parental species and hybrids differ from each other. Importantly, hybrid morphotypes are neither intermediate nor transgressive but found to be more similar to H. orientalis than to H. arborea. Our study presents one of the rare datasets, in which genotypes along with morphotypes examined the occurrence or absence of transgressive morphologies in wild amphibians.

opencc-by-4.0Jun 2022View details →

Business load profiles used in "Maximising the benefits of renewable energy infrastructure in displacement settings: Optimising the operation of a solar-hybrid mini-grid for institutional and business users in Mahama Refugee Camp, Rwanda"

Version used in the submission of "Maximising the benefits of renewable energy infrastructure in displacement settings: Optimising the operation of a solar-hybrid mini-grid for institutional and business users in Mahama Refugee Camp, Rwanda" by Hamish Beath, Javier Baranda Alonso, Richard Mori, Ajay Gambhir, Jenny Nelson and Philip Sandwell.

opencc-zeroJun 2022View details →

Data from: Species recognition limits mating between hybridizing ant species

Identifying mechanisms limiting hybridization is a central goal of speciation research. Here, we studied pre-mating and post-mating barriers to hybridization between two ant species, Formica selysi and Formica cinerea. These species hybridize in the Rhône valley in Switzerland, where they form a mosaic hybrid zone, with limited introgression from F. selysi into F. cinerea. There was no sign of temporal isolation between the two species in the production of queens and males. With choice experiments, we showed that queens and males strongly prefer to mate with conspecifics. Yet we did not detect post-mating barriers caused by genetic incompatibilities. Specifically, hybrids of all sexes and castes were found in the field and F1 hybrid workers did not show reduced viability compared to non-hybrid workers. To gain insights into the cues involved in species recognition, we analyzed the cuticular hydrocarbons of queens, males and workers and staged dyadic encounters between workers. Cuticular hydrocarbon profiles differed markedly between species, but were similar in F. cinerea and hybrids. Accordingly, workers also discriminated species, but they did not discriminate F. cinerea and hybrids. We discuss how the CHC-based recognition system of ants may facilitate the establishment of pre-mating barriers to hybridization, independent of hybridization costs.

opencc-zeroDec 2021View details →

Site impacts nutrient translocation efficiency in intra- and interspecies miscanthus hybrids on marginal lands

Miscanthus, a C4 perennial rhizomatous grass, is capable of growing in varied climates and soil types in Europe, including on marginal lands. It can produce high yields with low nutrient inputs when harvested after complete senescence. Senescence induction and rate depend on complex genetic, environmental, and management interactions. To explore these interactions, we analysed four miscanthus hybrids (two novel seed-based hybrids, GRC 3 (M. sinensis × sinensis) and GRC 14 (M. sacchariflorus × sinensis); GRC 15, a novel M. sacchariflorus × sinensis clone; and GRC 9, a standard M. × giganteus clone) in Italy, Croatia, Germany and the UK. Over all trial locations and hybrids, the average aboveground biomass of the three-year-old stands in August 2020 was 15 t DM ha-1 with nutrient contents of 7.6 mg N g-1 and 14.6 mg K g-1. As expected, delaying the harvest until spring reduced overall yield and nutrient contents (12 t DM ha-1, 3.3 mg N g-1 and 5.5 mg K g-1). At lower latitudes, the late-ripening M. sacchariflorus × sinensis GRC 14 and GRC 15 combined high yields with low nutrient contents. At the most elevated latitude location (UK), the early-ripening M. sinensis × sinensis combined high biomass yields with low nutrient offtakes. The clonal M. × giganteus with intermediate flowering and senescence attained similar low nutrient contents by spring harvest at all four locations. Seasonal changes in yield and nutrient levels analysed in this study provide: 1) a first step towards recommending hybrids for specific locations and end uses in Europe; 2) crucial data for determination of harvest time and practical steps in the valorisation of biomass; and 3) key sustainability data for life cycle assessments. Identification of trade-offs resulting from genetic × environment × management interactions are critical for increasing sustainable biomass supply from miscanthus grown on marginal lands.

Abiotic niche divergence of hybrid species from their progenitors

Although more frequently discussed recently than previously, the role of ecology in homoploid hybrid and allopolyploid speciation has not been subjected to comparative analysis. We examined abiotic niche divergence of 22 assumed homoploid hybrid species and 60 allopolyploid species from those of their progenitors. Ecological niche modeling (ENM) was employed in an analysis of each species' fundamental niche, and ordination methods were used in an analysis of realized niches. Both analyses utilized 100, 000 georeferenced records. From estimates of niche overlap and niche breadth, we identified for both types of hybrid species four niche divergence patterns: niche novelty, niche contraction, niche intermediacy and niche expansion. Niche shifts involving niche novelty were common and considered likely to play an important role in the establishment of both types of hybrid species, although more so for homoploid hybrid species than allopolyploid species. Approximately 70% of homoploid hybrid species versus 37% allopolyploid species showed shifts in fundamental niche from their parents, and ~86% versus ~52%, respectively, exhibited shifts in realized niche. Climate was shown to contribute more than soil and landform to niche shifts in both types of hybrid species. Overall, our results highlight the significance of abiotic niche divergence for hybrid speciation, especially without genome duplication.

Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation

Estimating the complex relationship between fitness and genotype or phenotype (i.e. the adaptive landscape) is one of the central goals of evolutionary biology. However, adaptive walks connecting genotypes to organismal fitness, speciation, and novel ecological niches are still poorly understood and processes for surmounting fitness valleys remain controversial. One outstanding system for addressing these connections is a recent adaptive radiation of ecologically and morphologically novel pupfishes (a generalist, molluscivore, and scale-eater) endemic to San Salvador Island, Bahamas. We leveraged whole-genome sequencing of 139 hybrids from two independent field fitness experiments to identify the genomic basis of fitness, estimate genotypic fitness networks, and measure the accessibility of adaptive walks on the fitness landscape. We identified 132 SNPs that were significantly associated with fitness in field enclosures. Six out of the 13 regions most strongly associated with fitness contained differentially expressed genes and fixed SNPs between trophic specialists; one gene (mettl21e) was also misexpressed in lab-reared hybrids, suggesting a potential intrinsic genetic incompatibility. We then constructed genotypic fitness networks from adaptive alleles and show that scale-eating specialists are the most isolated of the three species on these networks. Intriguingly, introgressed and de novo variants reduced fitness landscape ruggedness as compared to standing variation, increasing the accessibility of genotypic fitness paths from generalist to specialists. Our results suggest that adaptive introgression and de novo mutations alter the shape of the fitness landscape, providing key connections in adaptive walks circumventing fitness valleys and triggering the evolution of novelty during adaptive radiation.

Resolving higher-level phylogenetic networks with repeated hybridization in a complex of polytypic salamanders (Plethodontidae: Desmognathus)

Repeated hybridization between incipient lineages is a common feature of ecological speciation and ecomorphological diversification. However, computational constraints currently limit our ability to reconstruct network radiations from gene-tree data. Available methods are limited to level-1 networks wherein reticulations do not share edges, and higher-level networks may be non-identifiable in many cases. We present a heuristic method to recover information from higher-level networks across a range of potentially identifiable empirical scenarios, supported by a theorem and success in simulated data. When extrinsic information indicating the location and direction of recent or ancestral hybridization events is available, our method can yield successful estimates of non-level-1 networks, or at least a reduced possible set thereof. We apply this technique to the Pisgah clade of Desmognathus salamanders, which contains four to seven species exhibiting two discrete phenotypes, aquatic "shovel-nosed" and semi-aquatic "black-bellied" forms in the southern Appalachian Mountains of the eastern United States. Phylogenomic data strongly support a single backbone topology with up to five overlapping hybrid edges. These results suggest an unusual mechanism of ecomorphological hybrid speciation, wherein a binary threshold trait causes hybrids to shift between two microhabitat niches, promoting ecological divergence between sympatric hybrids and parentals. This contrasts with other well-known systems in which hybrids exhibit intermediate, novel, or transgressive phenotypes. Geographically proximate populations of both phenotypes exhibit admixture, and at least two black-bellied lineages have been produced via reticulations between shovel-nosed parentals, suggesting complex transmission dynamics. The genetic basis of these phenotypes is unclear and further data are needed to clarify the nature of selection and speciation in the group.

Data from: First evidence of WW superfemale for hybrid sturgeon, the bester (Huso huso × A. ruthenus)

Sturgeons possess ZZ/ZW genetic sex determination system and are popular aquaculture target for high-priced black caviar originated from female roe. Therefore, the production of all-female seedling is highly desired, but this has not yet been achieved to date. In this study, we identified a short nucleotide sequence specific to putative Z and W scaffolds of Acipenser ruthenus genome and developed the PCR to discriminate Z and W alleles. Using this PCR, A. ruthenus (N = 1,280), A. baerii baerii (N = 66), and F2 of the bester hybrid (Huso huso × A. ruthenus: N = 31) were genotyped. Of those, the gonadal sexes were identified for 145 individuals, and all were concordant with their genetic sex. Additionally, we applied the Z/W-discriminative PCR for gynogenetic population of F3 bester and identified 25 out of 112 individuals (22.3%) showing only W amplicon, indicating that they are WW superfemales.

Demographic history shapes genomic ancestry in hybrid zones

Demographic factors such as migration rate and population size can impede or facilitate speciation. In hybrid zones, reproductive boundaries between species are tested and demography mediates the opportunity for admixture between lineages that are partially isolated. Genomic ancestry is a powerful tool for revealing the history of admixed populations, but models and methods based on local ancestry are rarely applied to structured hybrid zones. To understand the effects of demography on ancestry in hybrids zones, we performed individual-based simulations under a stepping-stone model, treating migration rate, deme size, and hybrid zone age as parameters. We find that the number of ancestry junctions (the transition points between genomic regions with different ancestries), as well as heterogenicity (the genomic proportion heterozygous for ancestry), are often closely connected to demographic history. Reducing deme size reduces junction number and heterogenicity. Elevating migration increases heterogenicity, but migration affects junction number in more complex ways. We highlight the junction frequency spectrum as a novel and informative summary of ancestry that responds to demographic history. A substantial proportion of junctions are expected to fix when migration is limited or deme size is small, changing the shape of the spectrum. Our findings suggest that genomic patterns of ancestry could be used to infer demographic history in hybrid zones.

opencc-by-3.0-atAug 2022View details →

Dataset for the structural investigation of hybrid SLS joints

The dataset contains raw data of structural tests performed on pinned hybrid titanium-composite joints. Geometry is similar to ASTM D5868. For further context, the creators refer to the research conducted at the Institute of Structural Lightweight Design, Johannes Kepler University, Linz, Austria. This research was conducted within the SUSTAINair project. This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 101006952.