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opencc-zeroAug 2022View details →

Low levels of hybridization between domestic and wild Mallards wintering in the Lower Mississippi Flyway

Mallard ducks are a ubiquitous and socio-economically important game bird in North America. Despite their generally abundant midcontinent population, Mallards in eastern North America are declining, which may be partially explained by extensive hybridization with human-released domestically-derived game-farm Mallards. We investigated the genetic composition of Mallards in the middle and lower Mississippi flyway, key wintering regions for the species. We found that nearly 30% of wild Mallards carried mitochondrial haplotypes derived from domestic mallards present in North America, indicating that the individuals had female game-farm Mallard lineage in their past; however nuclear results identified only 4% of the same sample set as putative hybrids. Recovering 30% of samples with OW A mtDNA haplotypes is concordant with general trends across the Mississippi flyway and this percentage was stable across Mallards we sampled a decade apart. The capture and perpetuation of OW A mtDNA haplotypes is likely due to female breeding structure, whereas reversal of the nuclear signal back to wild ancestry is due to sequential backcrossing and lower and/or declining admixture with game-farm Mallards. Future studies of wild ancestry of Mississippi flyway Mallards will benefit from coupling molecular and spatial technology across flyways, seasons, and years to search for potential transitions of Mallard populations with different genetic ancestry, and whether the genetic ancestry is somehow linked to an individual's natal and subsequent breeding location.

opencc-zeroAug 2022View details →

Data from: Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges

The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid-origin lineages to occupy unique environmental space relative to one (or both) parents. We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid-origin individuals display mixed ancestry between the parental taxa – of nearly 7,000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage – approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid-origin lineage, we conducted genotype-environment association analyses on different combinations of loci – with and without excess ancestry – and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.

opencc-by-4.0Apr 2022View details →

Hybrid electro-optical trap for experiments with levitated particles in vacuum

Data for the paper "Hybrid electro-optical trap for experiments with levitated particles in vacuum"

opencc-by-4.0Aug 2022View details →

Multigroup Neutron Transport using a Collision-Based Hybrid Method Dataset

G = 361 Energy Group dataset for the "Multigroup Neutron Transport using a Collision-Based Hybrid Method" paper (under review) by Whewell et al. Included is the total, scattering, and fission cross section matrices for the G = 361 uranium oxide problem and the energy group bounds for G = 361, 300, 240, 180, 150, 120, 90, 60, and 30.

opencc-zeroDec 2021View details →

Population genomics of an emergent tri-species hybrid zone

Isolating barriers that drive speciation are commonly studied in the context of two-species hybrid zones. There is however evidence that more complex introgressive relationships are common in nature. Here, we use field observations and genomic analysis, including the sequencing and assembly of a novel reference genome, to study an emergent hybrid zone involving two colliding hybrid zones of three woodpecker species: red-breasted, red-naped, and yellow-bellied sapsuckers (Sphyrapicus ruber, S. nuchalis, and S. varius). Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of phenotypes and genotypes of mated pairs provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones. However, there is no evidence of a hybrid swarm, and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression likely occurred before the formation of this tri-species hybrid zone and might result from bridge hybridization, vagrancies, or other three-species interactions.

opencc-zeroAug 2022View details →

Introgressive hybridization erodes morphological divergence between lentic and lotic habitats in an endangered minnow

Introgressive hybridization may erode phenotypic divergence along environmental gradients, collapsing locally adapted populations into a hybrid swarm. Alternatively, introgression may promote phenotypic divergence by providing variation on which natural selection can act. In freshwater fishes, water flow often selects for divergent morphological traits in lake versus stream habitats. We tested the effects of introgression on lake-stream morphological divergence in the minnow Owens Tui Chub (Siphateles bicolor snyderi), which has been rendered endangered by introgression from the introduced Lahontan Tui Chub (Siphateles bicolor obesa). Using geometric morphometric analysis of 457 individual Tui Chub from thirteen populations, we found that both the native and introgressing parent taxa exhibited divergent body and caudal fin shapes in lake vs. stream habitats, but their trajectories of divergence were distinct. In contrast, introgressed populations exhibited intermediate body and caudal fin shapes that were not differentiated by habitat type, indicating that introgression has eroded phenotypic divergence along the lentic-lotic gradient throughout the historic range of the Owens Tui Chub. Individuals within hybrid populations were less morphologically variable than those within parent populations, suggesting hybrid adaptation to selective agents other than water flow or loss of variance by drift.

Feasibility of hybrid in-stream generator–photovoltaic systems for Amazonian off-grid communities

While there have been efforts to supply off-grid energy in the Amazon, these attempts have focused on low upfront costs and deployment rates. These "get-energy-quick" methods have almost solely adopted diesel generators, ignoring the environmental and social risks associated with the known noise and pollution of combustion engines. Alternatively, it is recommended, herein, to supply off-grid needs with renewable, distributed microgrids comprised of photovoltaics (PV) and in-stream generators (ISG). Utilization of a hybrid combination of renewable generators can provide an energetically, environmentally, and financially feasible alternative to typical electrification methods, depending on available solar irradiation and riverine characteristics, that with community engagement allows for a participatory codesign process that takes into consideration people's needs. A convergent solution development framework that includes designers—a team of social scientists, engineers, and communication specialists—and communities as well as the local industry is examined here, by which the future negative impacts at the human–machine–environment nexus can be minimized by iterative, continuous interaction between these key actors.

opencc-by-4.0Sep 2022View details →

Degradation of pharmaceuticals using the hybrid ozonation-filtration system

The hybrid ozonation-membrane filtration unit allows the simultaneous treatment of the contaminated water with ozone and micro- and nano-filtration (MF/NF) under controlled conditions using commercial single tubular ceramic membranes with an inside-out operation. In total, four commercial ceramic (CM) membranes with different compositions and pore sizes were selected. The composition of the selected membranes is given below <ul> <li>TiO2/ZrO2 composition of three different pore sizes: 50-, 150-, and 300 kDa MWCO) and</li> <li>TiO2/ TiO2+ZrO2 composition of one pore size (0.200 μm MWCO).</li> </ul> The files contain information on the degradation of the pharmaceuticals using the different membranes under the three surface modifications; CeO2, CeTiOx and CeO2+CeTiOx. Permeability tests have been performed on all four membranes. The filtration unit can operate from 0.3 -1.5 bar pressure with a permeability flow ranging from 200 - 1900 L.m-2.h-1 at 1 bar, starting from the lowest molecular weight cut-off (MWCO) membrane (50 kDa) and moving to the higher (0,200 μm) one.

The diverse effects of phenotypic dominance on hybrid fitness

When divergent populations interbreed, their alleles are brought together in hybrids. In the initial F1 cross, most divergent loci are heterozygous. Therefore, F1 fitness can be influenced by dominance effects that could not have been selected to function well together. We present a systematic study of these F1 dominance effects by introducing variable phenotypic dominance into Fisher's geometric model. We show that dominance often reduces hybrid fitness, which can generate optimal outbreeding followed by a steady decline in F1 fitness, as is often observed. We also show that "lucky" beneficial effects sometimes arise by chance, which might be important when hybrids can access novel environments. We then show that dominance can lead to violations of Haldane's Rule (reduced fitness of the heterogametic F1) but strengthens Darwin's Corollary (F1 fitness differences between cross directions). Taken together, results show that the effects of dominance on hybrid fitness can be surprisingly difficult to isolate because they often resemble the effects of uniparental inheritance or expression. Nevertheless, we identify a pattern of environment-dependent heterosis that only dominance can explain, and for which there is some suggestive evidence. Our results also show how existing data set upper bounds on the size of dominance effects. These bounds could explain why additive models often provide good predictions for later-generation recombinant hybrids, even when dominance qualitatively changes outcomes for the F1.

opencc-by-4.0Sep 2022View details →

IROS 22 - A Hybrid Primitive-Based Navigation Planner for the Wheeled-Legged Robot CENTAURO (Extended)

IROS 22 - A Hybrid Primitive-Based Navigation Planner for the Wheeled-Legged Robot CENTAURO - Extended Version A. De Luca, L. Muratore and N. Tsagarakis. Italian institute of Technology, IIT.   Hybrid Primitive Based planner executed on the real CENTAURO robot. The planner searches for a plan to reach the goal assigned with the available primitives. In this experiment, the primitives are: whole robot driving, and single wheel action. The latter can be divided into single-wheel driving and stepping, based on the elevation difference during the trajectory of the wheel. In addition, single-wheel driving can be merged to obtain the Macro "Reshape", speeding up the execution.

opencc-by-4.0Sep 2022View details →

IROS 22 - A Hybrid Primitive-Based Navigation Planner for the Wheeled-Legged Robot CENTAURO

IROS 22 - A Hybrid Primitive-Based Navigation Planner for the Wheeled-Legged Robot CENTAURO A. De Luca, L. Muratore and N. Tsagarakis. Italian institute of Technology, IIT.   Hybrid Primitive Based planner executed on the real CENTAURO robot. The planner searches for a plan to reach the goal assigned with the available primitives. In this experiment, the primitives are: whole robot driving, and single wheel action. The latter can be divided into single-wheel driving and stepping, based on the elevation difference during the trajectory of the wheel. In addition, single-wheel driving can be merged to obtain the Macro "Reshape", speeding up the execution.

The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela)

Discrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and the key to understanding their true evolutionary process. The genetic differentiation of the northern and southern Izu lineages of the Japanese newt Cynops pyrrhogaster was investigated through their single nucleotide polymorphism variations by multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto, and S-Kanto) those not detected by mtDNA in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The western populations of N-Kanto are close to S-Kanto, whereas the eastern populations of N-Kanto are close to Tohoku. Tohoku, N-Kanto, and S-Kanto are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history by the Approximate Bayesian Computation approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of the climatic oscillation in the Pleistocene. We concluded that the mitochondrial genome of S-Kanto was captured into Tohoku and the past original mitochondrial genome of Tohoku was entirely swept out from Tohoku through the hybridization.

Testing hypotheses of hybrid taxon formation in the shrubby beardtongues (Penstemon subgenus Dasanthera)

Premise Hybridization is increasingly being identified in the genomes of species across the tree of life. This has led to a general recognition that hybridization plays an important role in the generation of species diversity. While hybridization may increase species diversity directly via the formation of new taxa through hybrid speciation, it may also act indirectly via the exchange of phenotypic and genetic variance between species, which may in turn stimulate future speciation events. Methods Using high-throughput sequence data, we resolve phylogenetic relationships and investigate the role of hybridization as a diversification mechanism in the shrubby beardtongues (Penstemon subgenus Dasanthera), a group of North American wildflowers that has undergone a recent and rapid adaptive radiation. Specifically, we test four hypotheses of hybrid taxon formation resulting from hybridization between P. davidsonii and P. fruticosus. Key Results Species tree inference supports the monophyly of subgenus Dasanthera and elucidates relationships between taxa distributed in the Cascades and Sierra Nevada Mountains. Results also provide evidence of gene flow between P. davidsonii and P. fruticosus and support at least one hybrid origin hypothesis (P. davidsonii var. menziesii) in a region of contemporary distributional overlap. Hybridization may have also been facilitated by historical overlap in geographic distribution caused by species' responses to climatic changes during the Pleistocene. Conclusions Our results support a history of hybridization between focal taxa in a rapidly radiating clade of plants and more broadly contribute to our growing understanding of the role of hybridization as a diversification mechanism in plants.

opencc-zeroOct 2022View details →

Reference genes for quantitative Arabidopsis single molecule RNA fluorescence in situ hybridization

Abstract Subcellular mRNA quantities and spatial distributions are fundamental for driving gene regulatory programmes. Single molecule RNA fluorescence in situ hybridization (smFISH) uses fluorescent probes to label individual mRNA molecules, thereby facilitating both localization and quantitative studies. Validated reference mRNAs function as positive controls and are required for calibration. Here we present selection criteria for the first set of Arabidopsis smFISH reference genes. Following sequence and transcript data assessments, four mRNA probe sets were selected for imaging. Transcript counts per cell, correlations with cell size, and corrected fluorescence intensities were all calculated for comparison. In addition to validating reference probe sets, we present sample preparation steps that can retain green fluorescent protein fluorescence, thereby providing a method for simultaneous RNA and protein detection. In summary, our reference gene analyses, modified protocol, and simplified quantification method together provide a firm foundation for future quantitative single molecule RNA studies in Arabidopsis root apical meristem cells.

opencc-by-4.0Oct 2017View details →

Figure 6 in Evaluation of geostatistical method and hybrid Artificial Neural Network with imperialist competitive algorithm for predicting distribution pattern of Tetranychus urticae (Acari: Tetranychidae) in cucumber field of Behbahan, Iran

Figure 6. Motion of colonies toward their relevant imperialist (AtashpazGargari 2009).

opencc-by-4.0Oct 2017View details →

Figure 4 in Evaluation of geostatistical method and hybrid Artificial Neural Network with imperialist competitive algorithm for predicting distribution pattern of Tetranychus urticae (Acari: Tetranychidae) in cucumber field of Behbahan, Iran

Figure 4. Flowchart of Imperialist Competitive Algorithm (AtashpazGargari 2009).

opencc-by-4.0Oct 2017View details →

Figure 7 in Evaluation of geostatistical method and hybrid Artificial Neural Network with imperialist competitive algorithm for predicting distribution pattern of Tetranychus urticae (Acari: Tetranychidae) in cucumber field of Behbahan, Iran

Figure 7. Distribution of T. urticae in different stages of sampling.

opencc-zeroOct 2022View details →

SNP amplicons results of 50 hybrid Chinook-Coho salmon

These SNP panel results confirm the hybrid origin in 50 Chinook-Coho Salmon individuals. The SNP panel is composed of two amplicons and five diagnostic SNPs. DNA amplicons OkiOts_120255 and Oki_RAD41030 have SNP sites fixed for alternate base pairs in Chinook and Coho salmon (Beacham and Wallace 2019). The panel examined genotypes at one diagnostic position in OkiOts_120255 SNP: 113 (Reference=A, Variant=C) and four positions in Oki_RAD41030: 45 (TC), 51(CG), 195 (GA), and 198 (TG) called via Proton software Variant Caller®. The hybrid salmon were heterozygous for a Chinook and Coho haplotype at both SNP loci, confirming these as the parental species involved in the hybridization and consistent with all being F1 or higher order (F2 or back-cross) hybrid individuals. Beacham, T. D. & Wallace, C. G. (2019). Salmon species identification via direct DNA sequencing of single amplicons. Conservation Genetics Resources, 1-7. <a href="https://doi.org/10.1007/s12686-o19-01102-1">https://doi.org/10.1007/s12686-o19-01102-1</a>.

opencc-by-4.0Oct 2022View details →

Supporting Data of Bonadonna et al. "Physical Characterization of Long-Lasting Hybrid Eruptions: the Tajogaite Eruption of Cumbre Vieja (La Palma, Canary Islands)"

Data on plume height, volcanic tremor, deposit thinning and lava emissions of Bonadonna et al. "Physical Characterization of Long-Lasting Hybrid Eruptions: the Tajogaite Eruption of Cumbre Vieja (La Palma, Canary Islands)"