Population genomics of the muskox' resilience in the near absence of genetic variation.

Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.

Linear systems characterization of the topographical spatial resolution of optical instruments.

Lateral resolving power is a key performance attribute of Fizeau interferometers, confocal microscopes, interference microscopes, and other instruments measuring surface form and texture. Within a well-defined scope of applicability, limited by surface slope, texture, and continuity, a linear response model provides a starting point for characterizing spatial resolution under ideal conditions. Presently, the instrument transfer function (ITF) is a standardized way to quantify linear response to surface height variations as a function of spatial frequency. In this paper, we build on the ITF idea and introduce terms, mathematical definitions, and appropriate physical units for applying a linear systems model to surface topography measurement. These new terms include topographical equivalents of the point-, line-, and edge-spread functions, as well as a complex-valued transfer function that extends the ITF concept to systems with spatial-frequency-dependent topography distortions. As an example, we consider the experimental determination of lateral resolving power of a coherence scanning interference microscope using a step-height surface feature to measure the ITF directly. The experiment illustrates the proposed mathematical definitions and provides a direct comparison to theoretical calculations performed using a scalar diffraction model.

Surface measuring coherence scanning interferometry beyond the specular reflection limit.

The capability of optical surface topography measurement methods for measurement of steep and tilted surfaces is investigated through modelling of a coherence scanning interferometer. Of particular interest is the effect on the interference signal and measured topography when tilting the object at angles larger than the numerical aperture slope limit (i.e. the specular reflection limit) of the instrument. Here we use theoretical modelling to predict the results across a range of tilt angles for a blazed diffraction grating. The theoretically predicted interference patterns and surface height measurements are then verified directly with experimental measurements. Results illustrate the capabilities, limitations and modelling methods for interferometers to measure beyond the specular reflection limit.

Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus).

Intestinal microbial communities from 362 anadromous Arctic char (Salvelinus alpinus) from the high Arctic Kitikmeot region, Nunavut, Canada, were characterized using high-throughput 16S rRNA gene sequencing. The resulting bacterial communities were compared across four seasonal habitats that correspond to different stages of annual migration. Arctic char intestinal communities differed by sampling site, salinity and stages of freshwater residence. Although microbiota from fish sampled in brackish water were broadly consistent with taxa seen in other anadromous salmonids, they were enriched with putative psychrophiles, including the nonluminous gut symbiont Photobacterium iliopiscarium that was detected in >90% of intestinal samples from these waters. Microbiota from freshwater-associated fish were less consistent with results reported for other salmonids, and highly variable, possibly reflecting winter fasting behaviour of these char. We identified microbiota links to age for those fish sampled during the autumn upriver migration, but little impact of the intestinal content and water microbiota on the intestinal community. The strongest driver of intestinal community composition was seasonal habitat, and this finding combined with identification of psychrophiles suggested that water temperature and migratory behaviour are key to understanding the relationship between Arctic char and their symbionts.

Fourier optics modeling of interference microscopes.

We propose a practical theoretical model of an interference microscope that includes the imaging properties of optical systems with partially coherent illumination. We show that the effects on measured topography of a spatially extended, monochromatic light source at low numerical apertures can be approximated in a simplified model that assumes spatially coherent light and a linear, locally shift-invariant transfer function that accounts for optical aberrations and the attenuation of diffracted plane wave amplitudes with increasing spatial frequencies. Simulation of instrument response using this model agrees with methods using numerical pupil-plane integration and with an experimental measurement of surface topography.

A review of selected topics in interferometric optical metrology.

This review gathers together 15 special topics in modern interferometric metrology representing a sampling of historical, current and future developments. The selected topics cover a wide range of applications, including distance and displacement measurement, the testing of optical components, interference microscopy for surface structure analysis, form and dimensional measurements of industrial parts, and recent applications in semiconductor manufacturing and consumer electronics. Techniques range from laser Fizeau systems to dynamic ellipsometry using polarized heterodyne interferometry.

Clostridium (Clostridioides) difficile shedding by polar bears (Ursus maritimus) in the Canadian Arctic.

Clostridium (Clostridioides) difficile has been identified in humans and a wide range of animal species, but there has been little study of remote animal populations with limited human contact. The objective of this study was to determine the prevalence and types of C. difficile in wild and captive polar bears (Ursus maritimus). Fecal samples were collected from two populations of wild polar bears in Nunavut Canada; M'Clintock Channel and Hudson Strait (Davis Strait or Foxe Basin), as well as from a facility (PBJ) in Churchill, Manitoba that temporarily houses nuisance polar bears and from captive bears in a zoological park. Enrichment culture was performed and isolates were characterized by ribotyping and toxinotyping. Clostridium difficile was isolated from 24/143 (16.8%) of samples; 18/120 (15%) wild bear samples, 4/7 (57%) from the PBJ and 2/16 (13%) samples from three zoo bears. The prevalence of C. difficile was significantly higher in bears that were housed at the PBJ vs wild bears (P = 0.0042), but there was no difference between wild bears from M'Clintock Channel (14/100, 14%) and those from Hudson Strait (4/20, 20%) (P = 0.50). Fourteen of the 24 (58%) isolates were toxigenic; 13/18 (72%) wild bear isolates, 0/4 PBJ isolate and 1/2 zoo isolates. Four toxigenic ribotypes were identified, with one that possessed tcdB and cdtA predominating. None of the toxigenic isolates were ribotypes that have been identified previously by the authors. There was no overlap in toxigenic ribotypes between the different populations. Clostridium difficile was not uncommonly identified in polar bears, with differences in type distribution amongst the different regions. The presence of strains that have not been identified in humans or domestic animals suggests that polar bears may be a natural reservoir of unique strains of this important bacterium.

Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis).

The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed 2 sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, though an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore 2 overriding priorities for the species: 1) translocation of wild rhinos to ex situ facilities, and 2) collection and storage of gametes and cell lines from every surviving captive and wild individual.

Solanum lycopersicum AUXIN RESPONSE FACTOR 9 regulates cell division activity during early tomato fruit development.

The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early fruit development in tomato is Solanum lycopersicum AUXIN RESPONSE FACTOR 9 (SlARF9). Here, the functional analysis of this ARF is described. SlARF9 expression was found to be auxin-responsive and SlARF9 mRNA levels were high in the ovules, placenta, and pericarp of pollinated ovaries, but also in other plant tissues with high cell division activity, such as the axillary meristems and root meristems. Transgenic plants with increased SlARF9 mRNA levels formed fruits that were smaller than wild-type fruits because of reduced cell division activity, whereas transgenic lines in which SlARF9 mRNA levels were reduced showed the opposite phenotype. The expression analysis, together with the phenotype of the transgenic lines, suggests that, in tomato, ARF9 negatively controls cell division during early fruit development.

"Bareback" pornography consumption and safe-sex intentions of men having sex with men.

Men having sex with men (MSM) commonly consume "bareback" pornography, which includes scenes of unprotected anal intercourse. Prior research on human imitative behavior suggests that these media might counteract efforts to promote safe-sex behaviors. To date, no studies have demonstrated a causal link between bareback pornography consumption and reduced safe-sex intentions. Study 1 utilized a correlational design conducted as an online survey. Study 2 was set in an actual MSM sex club, using a 2 × 2 mixed-factorial design to compare type of pornography (unprotected vs. protected anal intercourse) and age of actors (younger vs. older). As the main dependent variable in both studies, participants self-reported their inclinations toward unprotected versus protected intercourse, using a 100-point sliding scale (1 = unprotected, 100 = protected). In Study 1, more attention to unprotected sex acts on actual DVD film covers predicted lower safe-sex intentions, as compared to other elements of the film cover. In Study 2, safe-sex intentions after viewing unprotected-sex films were lower than after viewing protected-sex films. The results provide novel and ecologically valid evidence that "bareback" pornography consumption impacts viewer's inclinations toward sexual risk-taking by lowering their intentions to use protected sex measures. Suggestions are given as to how these findings can be utilized for purposes of intervention and prevention of STI and HIV infections.

Correlated errors in phase-shifting laser Fizeau interferometry.

High-performance data processing algorithms for phase-shifting interferometry accommodate adjustment errors in the phase shift increment as well as harmonic distortions in the interference signal. However, a widely overlooked error source is the combination of these two imperfections. Phase shift tuning errors increase the sensitivity of phase estimation algorithms to second-order and higher harmonics present in Fizeau interference signals. I derive an analytical formula for evaluating these errors more realistically, in part to identify the characteristics of the optimal PSI algorithm. Even for advanced algorithms, it is found that multiple reflections increase the error contribution of detuning by orders of magnitude compared with the two-beam calculation and impose a practical limit of 30% in tuning error for sub-nm metrology in a 4%-4% Fizeau cavity. Consequently, a preferred approach for high precision spherical cavities is to use either wavelength tuning in place of mechanical phase shifting or an iterative solver that accommodates unknown phase shifts as a function of field position.

Large-aperture, equal-path interferometer for precision measurements of flat transparent surfaces.

The measurement of flat optical components often presents difficulties because the presence of parallel surfaces generates multiple reflections that confuse conventional laser-based interferometers. These same parts have increasingly demanding surface finish tolerances as technologies improve over time, further complicating the metrology task. Here we describe an interferometric optical system for high-accuracy noncontact evaluation of the form and texture of precision flat surfaces based on an equal-optical-path geometry that uses extended, broadband illumination to reduce the influence of speckle noise, multiple reflections, and coherent artifacts by a factor of 10 when compared to laser-based systems. Combined with a low-distortion, fixed-focus imaging system and 4-Mpixel camera, the 100 mm aperture instrument offers surface height resolutions of 0.1 nm over lateral spatial frequencies extending from 0.01 to 10 cycles/mm. The instrument is vibration resistant for production-line testing of flat optics such as glass hard disks for the data-storage industry and flat-panel-display substrates.

Non-invasive biomonitoring of polar bear feces can be used to estimate concentrations of metals of concern in traditional food.

The Arctic faces increasing exposure to environmental chemicals such as metals, posing health risks to humans and wildlife. Biomonitoring of polar bears (Ursus maritimus) can be used to quantify chemicals in the environment and in traditional foods consumed by the Inuit. However, typically, these samples are collected through invasive or terminal methods. The biomonitoring of feces could be a useful alternative to the current metal monitoring method within the Arctic. Here, we aim to 1) quantify the relationship between concentrations of metals in the feces and tissues (muscle, liver, and fat) of polar bears using predictive modeling, 2) develop an easy-to-use conversion tool for use in community-based monitoring programs to non-invasively estimate contaminant concentrations in polar bears tissues and 3) demonstrate the application of these models by examining potential exposure risk for humans from consumption of polar bear muscle. Fecal, muscle, liver, and fat samples were harvested from 49 polar bears through a community-based monitoring program. The samples were analyzed for 32 metals. Exploratory analysis indicated that mean metal concentrations generally did not vary by age or sex, and many of the metals measured in feces were positively correlated with the internal tissue concentration. We developed predictive linear regression models between internal (muscle, liver, fat) and external (feces) metal concentrations and further explored the mercury and methylmercury relationships for utility risk screening. Using the cross-validated regression coefficients, we developed a conversion tool that contributes to the One Health approach by understanding the interrelated health of humans, wildlife, and the environment in the Arctic. The findings support using feces as a biomonitoring tool for assessing contaminants in polar bears. Further research is needed to validate the developed models for other regions in the Arctic and assess the impact of environmental weathering on fecal metal concentrations.

The geographic distribution, and the biotic and abiotic predictors of select zoonotic pathogen detections in Canadian polar bears.

Increasing Arctic temperatures are facilitating the northward expansion of more southerly hosts, vectors, and pathogens, exposing naïve populations to pathogens not typical at northern latitudes. To understand such rapidly changing host-pathogen dynamics, we need sensitive and robust surveillance tools. Here, we use a novel multiplexed magnetic-capture and droplet digital PCR (ddPCR) tool to assess a sentinel Arctic species, the polar bear (Ursus maritimus; n = 68), for the presence of five zoonotic pathogens (Erysipelothrix rhusiopathiae, Francisella tularensis, Mycobacterium tuberculosis complex, Toxoplasma gondii and Trichinella spp.), and observe associations between pathogen presence and biotic and abiotic predictors. We made two novel detections: the first detection of a Mycobacterium tuberculosis complex member in Arctic wildlife and the first of E. rhusiopathiae in a polar bear. We found a prevalence of 37% for E. rhusiopathiae, 16% for F. tularensis, 29% for Mycobacterium tuberculosis complex, 18% for T. gondii, and 75% for Trichinella spp. We also identify associations with bear age (Trichinella spp.), harvest season (F. tularensis and MTBC), and human settlements (E. rhusiopathiae, F. tularensis, MTBC, and Trichinella spp.). We demonstrate that monitoring a sentinel species, the polar bear, could be a powerful tool in disease surveillance and highlight the need to better characterize pathogen distributions and diversity in the Arctic.

Magnetic control of a meta-molecule.

Metamaterials offer the prospect of new science and applications. They have been designed by shaping or changing the material of the individual meta-molecules to achieve properties not naturally attainable. Composite meta-molecules incorporating a magnetic component offer new opportunities. In this work we report on the interaction between a non-magnetic split ring resonator (SRR) and a thin film of yttrium iron garnet (YIG). Strong hybridized resonances are observed. While the SRR is characterized by a magnetic and electric resonance, in practice, it is found that the YIG couples strongly to this symmetric (electric) mode of the SRR. It is also demonstrated that the anti-crossing region provides fertile ground for the creation of elementary excitations such as backward volume magnetostatic waves.

Lack of fidelity revealed in an insect-fungal mutualism after invasion.

Symbiont fidelity is an important mechanism in the evolution and stability of mutualisms. Strict fidelity has been assumed for the obligate mutualism between Sirex woodwasps and their mutualistic Amylostereum fungi. This assumption has been challenged in North America where the European woodwasp, Sirex noctilio, and its fungal mutualist, Amylostereum areolatum, have recently been introduced. We investigate the specificity of the mutualism between Sirex and Amylostereum species in Canada, where S. noctilio co-infests Pinus with native Sirex nigricornis and its mutualist, Amylostereum chailletii. Using phylogenetic and culture methods, we show that extensive, reciprocal exchange of fungal species and strains is occurring, with 75.3 per cent of S. nigricornis carrying A. areolatum and 3.5 per cent of S. noctilio carrying A. chailletii. These findings show that the apparent specificity of the mutualism between Sirex spp. and their associated Amylostereum spp. is not the result of specific biological mechanisms that maintain symbiont fidelity. Rather, partner switching may be common when shifting geographical distributions driven by ecological or anthropogenic forces bring host and mutualist pairs into sympatry. Such novel associations have potentially profound consequences for fitness and virulence. Symbiont sharing, if it occurs commonly, may represent an important but overlooked mechanism of community change linked to biological invasions.

A new multiplexed magnetic capture-Droplet digital PCR tool for monitoring wildlife population health and pathogen surveillance.

Anthropogenic stressors are exacerbating the emergence and spread of pathogens worldwide. In regions like the Arctic, where ecosystems are particularly susceptible, marked changes are predicted in regional diversity, intensity, and patterns of infectious diseases. To understand such rapidly changing host-pathogen dynamics and mitigate the impacts of novel pathogens, we need sensitive disease surveillance tools. We developed and validated a novel multiplexed, magnetic capture, and ddPCR tool for the surveillance of multiple pathogens in polar bears, a sentinel species that is considered susceptible to climate change and other stressors with a pan-Arctic distribution. Through sequence-specific magnetic capture, we concentrated five target template sequences from three zoonotic bacteria (Erysipelothrix rhusiopathiae, Francisella tularensis, and Mycobacterium tuberculosis complex) and two parasitic (Toxoplasma gondii and Trichinella spp.) pathogens from large quantities (<100 g) of host tissue. We then designed and validated two multiplexed probe-based ddPCR assays for the amplification and detection of the low-concentration target DNA. Validations used 48 polar bear tissues (muscle and liver). We detected 14, 1, 3, 4, and 22 tissue positives for E. rhusiopathiae, F. tularensis, M. tuberculosis complex, T. gondii, and Trichinella spp., respectively. These multiplexed assays offer a rapid, specific tool for quantifying and monitoring the changing geographical and host distributions of pathogens relevant to human and animal health.

Long-Term Mild Heat Causes Post-Mitotic Pollen Abortion Through a Local Effect on Flowers.

Crop reproductive success is significantly challenged by heatwaves, which are increasing in frequency and severity globally. Heat-induced male sterility is mainly due to aborted pollen development, but it is not clear whether this is through direct or systemic effects. Here, long-term mild heat (LTMH) treatment, mimicking a heatwave, was applied locally to tomato flowers or whole plants and followed up by cytological, transcriptomic, and biochemical analyses. By analyzing pollen viability, LTMH was shown to act directly on the flowers and not via effects on other plant tissue. The meiosis to early microspore stage of pollen development was the most sensitive to LTMH and 3 days of exposure around this period was sufficient to significantly reduce pollen viability at the flower anthesis stage. Extensive cytological analysis showed that abnormalities in pollen development could first be observed after pollen mitosis I, while no deviations in tapetum development were observed. Transcriptomic and biochemical analyses suggested that pollen development suffered from tapetal ER stress and that there was a limited role for oxidative stress. Our results provide the first evidence that heat acts directly on flowers to induce pollen sterility, and that the molecular-physiological responses of developing anthers to the LTMH are different from those to severe heat shock.

Genotyping-in-thousands by sequencing (GT-seq) of noninvasive faecal and degraded samples: A new panel to enable ongoing monitoring of Canadian polar bear populations.

Genetic monitoring using noninvasive samples provides a complement or alternative to traditional population monitoring methods. However, next-generation sequencing approaches to monitoring typically require high quality DNA and the use of noninvasive samples (e.g., scat) is often challenged by poor DNA quality and contamination by nontarget species. One promising solution is a highly multiplexed sequencing approach called genotyping-in-thousands by sequencing (GT-seq), which can enable cost-efficient genomics-based monitoring for populations based on noninvasively collected samples. Here, we develop and validate a GT-seq panel of 324 single nucleotide polymorphisms (SNPs) optimized for genotyping of polar bears based on DNA from noninvasively collected faecal samples. We demonstrate (1) successful GT-seq genotyping of DNA from a range of sample sources, including successful genotyping (>50% loci) of 62.9% of noninvasively collected faecal samples determined to contain polar bear DNA; and (2) that we can reliably differentiate individuals, ascertain sex, assess relatedness, and resolve population structure of Canadian polar bear subpopulations based on a GT-seq panel of 324 SNPs. Our GT-seq data reveal spatial-genetic patterns similar to previous polar bear studies but at lesser cost per sample and through use of noninvasively collected samples, indicating the potential of this approach for population monitoring. This GT-seq panel provides the foundation for a noninvasive toolkit for polar bear monitoring and can contribute to community-based programmes - a framework which may serve as a model for wildlife conservation and management for species worldwide.

Overexpression of PhEXPA1 increases cell size, modifies cell wall polymer composition and affects the timing of axillary meristem development in Petunia hybrida.

• Expansins are cell wall proteins required for cell enlargement and cell wall loosening during many developmental processes. The involvement of the Petunia hybrida expansin A1 (PhEXPA1) gene in cell expansion, the control of organ size and cell wall polysaccharide composition was investigated by overexpressing PhEXPA1 in petunia plants. • PhEXPA1 promoter activity was evaluated using a promoter-GUS assay and the protein's subcellular localization was established by expressing a PhEXPA1-GFP fusion protein. PhEXPA1 was overexpressed in transgenic plants using the cauliflower mosaic virus (CaMV) 35S promoter. Fourier transform infrared (FTIR) and chemical analysis were used for the quantitative analysis of cell wall polymers. • The GUS and GFP assays demonstrated that PhEXPA1 is present in the cell walls of expanding tissues. The constitutive overexpression of PhEXPA1 significantly affected expansin activity and organ size, leading to changes in the architecture of petunia plants by initiating premature axillary meristem outgrowth. Moreover, a significant change in cell wall polymer composition in the petal limbs of transgenic plants was observed. • These results support a role for expansins in the determination of organ shape, in lateral branching, and in the variation of cell wall polymer composition, probably reflecting a complex role in cell wall metabolism.