Panmixia in the American eel extends to its tropical range of distribution: Biological implications and policymaking challenges.

The American eel (Anguilla rostrata) has long been regarded as a panmictic fish and has been confirmed as such in the northern part of its range. In this paper, we tested for the first time whether panmixia extends to the tropical range of the species. To do so, we first assembled a reference genome (975 Mbp, 19 chromosomes) combining long (PacBio and Nanopore and short (Illumina paired-end) reads technologies to support both this study and future research. To test for population structure, we estimated genotype likelihoods from low-coverage whole-genome sequencing of 460 American eels, collected at 21 sampling sites (in seven geographic regions) ranging from Canada to Trinidad and Tobago. We estimated genetic distance between regions, performed ADMIXTURE-like clustering analysis and multivariate analysis, and found no evidence of population structure, thus confirming that panmixia extends to the tropical range of the species. In addition, two genomic regions with putative inversions were observed, both geographically widespread and present at similar frequencies in all regions. We discuss the implications of lack of genetic population structure for the species. Our results are key for the future genomic research in the American eel and the implementation of conservation measures throughout its geographic range. Additionally, our results can be applied to fisheries management and aquaculture of the species.

Design and validation of a high-density single nucleotide polymorphism array for the Eastern oyster (Crassostrea virginica).

Dense single nucleotide polymorphism (SNP) arrays are essential tools for rapid high-throughput genotyping for many genetic analyses, including genomic selection and high-resolution population genomic assessments. We present a high-density (200 K) SNP array developed for the Eastern oyster (Crassostrea virginica), which is a species of significant aquaculture production and restoration efforts throughout its native range. SNP discovery was performed using low-coverage whole-genome sequencing of 435 F1 oysters from families from 11 founder populations in New Brunswick, Canada. An Affymetrix Axiom Custom array was created with 219,447 SNPs meeting stringent selection criteria and validated by genotyping more than 4,000 oysters across 2 generations. In total, 144,570 SNPs had a call rate >90%, most of which (96%) were polymorphic and were distributed across the Eastern oyster reference genome, with similar levels of genetic diversity observed in both generations. Linkage disequilibrium was low (maximum r2 ∼0.32) and decayed moderately with increasing distance between SNP pairs. Taking advantage of our intergenerational data set, we quantified Mendelian inheritance errors to validate SNP selection. Although most of SNPs exhibited low Mendelian inheritance error rates overall, with 72% of called SNPs having an error rate of <1%, many loci had elevated Mendelian inheritance error rates, potentially indicating the presence of null alleles. This SNP panel provides a necessary tool to enable routine application of genomic approaches, including genomic selection, in C. virginica selective breeding programs. As demand for production increases, this resource will be essential for accelerating production and sustaining the Canadian oyster aquaculture industry.

Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides).

Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1594 scaffolds (scaffold N50 = 25 Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.

Fabrication and nanophotonic waveguide integration of silicon carbide colour centres with preserved spin-optical coherence.

Optically addressable spin defects in silicon carbide (SiC) are an emerging platform for quantum information processing compatible with nanofabrication processes and device control used by the semiconductor industry. System scalability towards large-scale quantum networks demands integration into nanophotonic structures with efficient spin-photon interfaces. However, degradation of the spin-optical coherence after integration in nanophotonic structures has hindered the potential of most colour centre platforms. Here, we demonstrate the implantation of silicon vacancy centres (VSi) in SiC without deterioration of their intrinsic spin-optical properties. In particular, we show nearly lifetime-limited photon emission and high spin-coherence times for single defects implanted in bulk as well as in nanophotonic waveguides created by reactive ion etching. Furthermore, we take advantage of the high spin-optical coherences of VSi centres in waveguides to demonstrate controlled operations on nearby nuclear spin qubits, which is a crucial step towards fault-tolerant quantum information distribution based on cavity quantum electrodynamics.

Spin-controlled generation of indistinguishable and distinguishable photons from silicon vacancy centres in silicon carbide.

Quantum systems combining indistinguishable photon generation and spin-based quantum information processing are essential for remote quantum applications and networking. However, identification of suitable systems in scalable platforms remains a challenge. Here, we investigate the silicon vacancy centre in silicon carbide and demonstrate controlled emission of indistinguishable and distinguishable photons via coherent spin manipulation. Using strong off-resonant excitation and collecting zero-phonon line photons, we show a two-photon interference contrast close to 90% in Hong-Ou-Mandel type experiments. Further, we exploit the system's intimate spin-photon relation to spin-control the colour and indistinguishability of consecutively emitted photons. Our results provide a deep insight into the system's spin-phonon-photon physics and underline the potential of the industrially compatible silicon carbide platform for measurement-based entanglement distribution and photonic cluster state generation. Additional coupling to quantum registers based on individual nuclear spins would further allow for high-level network-relevant quantum information processing, such as error correction and entanglement purification.

Laser Writing of Scalable Single Color Centers in Silicon Carbide.

Single photon emitters in silicon carbide (SiC) are attracting attention as quantum photonic systems ( Awschalom et al. Nat. Photonics 2018 , 12 , 516 - 527 ; Atatüre et al. Nat. Rev. Mater. 2018 , 3 , 38 - 51 ). However, to achieve scalable devices, it is essential to generate single photon emitters at desired locations on demand. Here we report the controlled creation of single silicon vacancy (VSi) centers in 4H-SiC using laser writing without any postannealing process. Due to the aberration correction in the writing apparatus and the nonannealing process, we generate single VSi centers with yields up to 30%, located within about 80 nm of the desired position in the transverse plane. We also investigated the photophysics of the laser writing VSi centers and concluded that there are about 16 photons involved in the laser writing VSi center process. Our results represent a powerful tool in the fabrication of single VSi centers in SiC for quantum technologies and provide further insights into laser writing defects in dielectric materials.

Intercontinental karyotype-environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly.

Large chromosomal rearrangements are thought to facilitate adaptation to heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in adaptation along environmental clines and in ecotype specialization. Here, we combine classical ecological studies and population genetics to investigate an inversion polymorphism previously documented in Europe among natural populations of the seaweed fly Coelopa frigida along a latitudinal cline in North America. We test if the inversion is present in North America and polymorphic, assess which environmental conditions modulate the inversion karyotype frequencies, and document the relationship between inversion karyotype and adult size. We sampled nearly 2000 flies from 20 populations along several environmental gradients to quantify associations of inversion frequencies to heterogeneous environmental variables. Genotyping and phenotyping showed a widespread and conserved inversion polymorphism between Europe and America. Variation in inversion frequency was significantly associated with environmental factors, with parallel patterns between continents, indicating that the inversion may play a role in local adaptation. The three karyotypes of the inversion are differently favoured across micro-habitats and represent life-history strategies likely to be maintained by the collective action of several mechanisms of balancing selection. Our study adds to the mounting evidence that inversions are facilitators of adaptation and enhance within-species diversity.

Quantum enhancement of accuracy and precision in optical interferometry.

White-light interferometry is one of today's most precise tools for determining the properties of optical materials. Its achievable precision and accuracy are typically limited by systematic errors due to a high number of interdependent data-fitting parameters. Here, we introduce spectrally resolved quantum white-light interferometry as a novel tool for optical property measurements, notably, chromatic dispersion in optical fibres. By exploiting both spectral and photon-number correlations of energy-time entangled photon pairs, the number of fitting parameters is significantly reduced, which eliminates systematic errors and leads to an absolute determination of the material parameter. By comparing the quantum method to state-of-the-art approaches, we demonstrate the quantum advantage of 2.4 times better measurement precision, despite requiring 62 times fewer photons. The improved results are due to conceptual advantages enabled by quantum optics, which are likely to define new standards in experimental methods for characterising optical materials.

RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata).

The American Eel (Anguilla rostrata) has an exceptional life cycle characterized by panmictic reproduction at the species scale, random dispersal, and selection in a highly heterogeneous habitat extending from subtropical to subarctic latitudes. The genetic consequences of spatially-varying selection in this species have been investigated for decades, revealing subtle clines in allele frequency at a few loci that contrast with complete panmixia on the vast majority of the genome. Because reproduction homogenizes allele frequencies every generation, sampling size, and genomic coverage are critical to reach sufficient power to detect selected loci in this context. Here, we used a total of 710 individuals from 12 sites and 12,098 high-quality single nucleotide polymorphisms to re-evaluate the extent to which local selection affects the spatial distribution of genetic diversity in this species. We used environmental association methods to identify markers under spatially-varying selection, which indicated that selection affects ∼1.5% of the genome. We then evaluated the extent to which candidate markers collectively vary with environmental factors using additive polygenic scores. We found significant correlations between polygenic scores and latitude, longitude and temperature which are consistent with polygenic selection acting against maladapted genotypes in different habitats occupied by eels throughout their range of distribution. Gene functions associated with outlier markers were significantly enriched for the insulin signaling pathway, indicating that the trade-offs inherent to occupying such a large distribution range involve the regulation of metabolism. Overall, this study highlights the potential of the additive polygenic scores approach in detecting selective effects in a complex environment.