Cryptic divergences and repeated hybridizations within the endangered "living fossil" dove tree (Davidia involucrata) revealed by whole genome resequencing.

The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a "living fossil" dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.

Prenatal exposure to per-and polyfluoroalkyl substances and child executive function: Evidence from the Shanghai birth cohort study.

BACKGROUND: Per-and polyfluoroalkyl substances (PFAS) are ubiquitous in the environment and accumulate in humans. Toxicological studies have indicated the potential neurotoxicity of PFAS during the fetal development. However, in epidemiological studies, the association between prenatal exposure to PFAS and executive function in offspring remains unclear. OBJECTIVES: To investigate the association between prenatal exposure to PFAS and executive function in offspring. METHOD: This study included 1765 mother-child pairs in the Shanghai Birth Cohort, a prospective birth cohort enrolled during 2013-2016. The levels of 10 PFAS were measured in maternal plasma samples collected during early gestation. Child executive function was assessed at 4 years of age using the parent-reported Behavior Rating Inventory of Executive Function-Preschool version (BRIEF-P), which provided 4 composite measures: Inhibitory Self-Control Index, Flexibility Index, Emergent Metacognition Index, and Global Executive Composite. We used multivariable linear regression to examine the associations between individual PFAS and BRIEF-P scores. Bayesian kernel machine regression (BKMR) was employed to evaluate the joint effects. We also investigated whether these associations were modified by sex. RESULT: We found no significant associations between prenatal PFAS exposure and BRIEF-P scores when the child was 4 years old. BKMR analysis showed no joint effect of the PFAS mixture on child executive function. RCS analysis indicated that the majority of relationships between PFAS and BRIEF-P did not deviate from the linear relationship, even though there was a nonlinear association between PFUA and EMI. Additionally, the associations were not modified by sex. CONCLUSION: Overall, our findings showed that there were no associations between prenatal exposure to PFAS and child executive function at 4 years of age.

Prenatal exposure to perfluoroalkyl substances and child intelligence quotient: Evidence from the Shanghai birth cohort.

BACKGROUND AND AIM: Epidemiological evidence on the association between prenatal exposure to Perfluoroalkyl substances (PFAS) and child cognition remains unclear. Thus, we aimed to investigate whether prenatal exposure to PFAS is associated with intelligence quotient (IQ) in offspring. METHOD: This study population included 2031 mother-child pairs in the Shanghai Birth Cohort (SBC) enrolled during 2013-2016. Ten PFAS were measured by high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS-MS) in maternal plasma samples collected in early gestation between 9 and 16 weeks of gestation. Child IQ was assessed using the Wechsler Preschool and Primary Scales of Intelligence-Fourth Edition (WPPSI-IV) at 4 years of age. Multivariable linear regression models were used to estimate the associations between individual PFAS concentrations (as a continuous variable or categorized into tertiles) and child IQ. A quantile g-computation approach was used to evaluate the joint and independent effects of PFAS on IQ. We also examined whether the associations varied by child sex. RESULTS: We found no significant associations between ln-transformed nine individual PFAS and child full scale IQ (FSIQ) or subscale IQ after adjusting for potential confounders. The observed associations were not modified by child sex. PFAS in tertiles showed the same pattern. Results from quantile g-computation showed that PFAS mixture was not associated with child IQ; perfluorobutane sulfonate was negatively associated with FSIQ (ß, -0.81; 95 % CI: -1.55, -0.07), and perfluorooctane sulfonate was also associated with lower fluid reasoning index scores (ß, -1.61; 95 % CI: -3.07, -0.16) while adjusting for the other PFAS. CONCLUSION: PFAS mixture during early pregnancy was not associated with child IQ. For certain individual PFAS, there were inverse associations with FSIQ or subscale IQ. Considering the evidence is still inconsistent, further research is needed to confirm or refute these results in other populations and to elucidate the potential neurotoxicology of PFAS.

Chiral Excitonics in Monolayer Semiconductors on Patterned Dielectrics.

Monolayer transition metal dichalcogenides feature tightly bound bright excitons at the degenerate valleys, where electron-hole Coulomb exchange interaction strongly couples the valley pseudospin to the momentum of the exciton. Placed on a periodically structured dielectric substrate, the spatial modulation of the Coulomb interaction leads to the formation of exciton Bloch states with real-space valley pseudospin texture displayed in a mesoscopic supercell. We find this spatial valley texture in the exciton Bloch function is pattern locked to the propagation direction, enabling nano-optical excitation of directional exciton flow through the valley selection rule. The left-right directionality of the injected exciton current is controlled by the circular polarization of excitation, while the angular directionality is controlled by the excitation location, exhibiting a vortex pattern in a supercell. The phenomenon is reminiscent of the chiral light-matter interaction in nanophotonics structures, with the role of the guided electromagnetic wave now replaced by the valley-orbit coupled exciton Bloch wave in a uniform monolayer, which points to new excitonic devices with nonreciprocal functionalities.

Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.

Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs-paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.].

A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis.

Camptothecin and its derivatives are widely used for treating malignant tumors. Previous studies revealed only a limited number of candidate genes for camptothecin biosynthesis in Camptotheca acuminata, and it is still poorly understood how its biosynthesis of camptothecin has evolved. Here, we report a high-quality, chromosome-level C. acuminata genome assembly. We find that C. acuminata experiences an independent whole-genome duplication and numerous genes derive from it are related to camptothecin biosynthesis. Comparing with Catharanthus roseus, the loganic acid O-methyltransferase (LAMT) in C. acuminata fails to convert loganic acid into loganin. Instead, two secologanic acid synthases (SLASs) convert loganic acid to secologanic acid. The functional divergence of the LAMT gene and positive evolution of two SLAS genes, therefore, both contribute greatly to the camptothecin biosynthesis in C. acuminata. Our results emphasize the importance of high-quality genome assembly in identifying genetic changes in the evolutionary origin of a secondary metabolite.

Excitons in strain-induced one-dimensional moiré potentials at transition metal dichalcogenide heterojunctions.

The possibility of confining interlayer excitons in interfacial moiré patterns has recently gained attention as a strategy to form ordered arrays of zero-dimensional quantum emitters and topological superlattices in transition metal dichalcogenide heterostructures. Strain is expected to play an important role in the modulation of the moiré potential landscape, tuning the array of quantum dot-like zero-dimensional traps into parallel stripes of one-dimensional quantum wires. Here, we present real-space imaging of unstrained zero-dimensional and strain-induced one-dimensional moiré patterns along with photoluminescence measurements of the corresponding excitonic emission from WSe2/MoSe2 heterobilayers. Whereas excitons in zero-dimensional moiré traps display quantum emitter-like sharp photoluminescence peaks with circular polarization, the photoluminescence emission from excitons in one-dimensional moiré potentials shows linear polarization and two orders of magnitude higher intensity. These results establish strain engineering as an effective method to tailor moiré potentials and their optoelectronic response on demand.

Author Correction: Excitons in strain-induced one-dimensional moiré potentials at transition metal dichalcogenide heterojunctions.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis.

The deciduous Chinese tupelo (Nyssa sinensis Oliv.) is a popular ornamental tree for the spectacular autumn leaf color. Here, using single-molecule sequencing and chromosome conformation capture data, we report a high-quality, chromosome-level genome assembly of N. sinensis. PacBio long reads were de novo assembled into 647 polished contigs with a total length of 1,001.42 megabases (Mb) and an N50 size of 3.62 Mb, which is in line with genome sizes estimated using flow cytometry and the k-mer analysis. These contigs were further clustered and ordered into 22 pseudo-chromosomes based on Hi-C data, matching the chromosome counts in Nyssa obtained from previous cytological studies. In addition, a total of 664.91 Mb of repetitive elements were identified and a total of 37,884 protein-coding genes were predicted in the genome of N. sinensis. All data were deposited in publicly available repositories, and should be a valuable resource for genomics, evolution, and conservation biology.

Composting swine carcasses with nitrogen transformation microbial strains: Succession of microbial community and nitrogen functional genes.

In this study, nitrogen transformation strains, including three ammonium transformation strains, one nitrite strain and one nitrogen fixer, were inoculated at different swine carcass composting stages to regulate the nitrogen transformation and control the nitrogen loss. The final total nitrogen content was significantly increased (p < 0.01). The bacterial communities were assessed by amplicon sequencing and association analysis. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were the four most dominant phyla.,Brevibacterium, Streptomyces and Ochrobactrum had a significant (p < 0.05) and positive correlation with total nitrogen and ammonium nitrogen content in both groups. The quantitative results of nitrogen transformation genes showed that ammonification, nitrification, denitrification and nitrogen fixation were simultaneously present in the composting process of swine carcasses, with the latter two accounting for a higher proportion. The ammonium transformation strains significantly (p < 0.05) strengthened nitrogen fixation and remarkably (p < 0.01) weakened nitrification and denitrification, which, however, were notably (p < 0.05) enhanced by the nitrite strain and nitrogen fixer. In this research, the inoculated strains changed the bacterial structure by regulating the abundance and activity of the highly connected taxa, which facilitated the growth of nitrogen transformation bacteria and regulated the balance/symbiosis of nitrogen transformation processes to accelerate the accumulation of nitrogen.

Effects of exogenous microbial inoculum on the structure and dynamics of bacterial communities in swine carcass composting.

Composting is a widely accepted method for the disposal of deceased livestock. It is a biological self-heating process during which animal carcasses are converted to fertilizer products. Additional inoculants can facilitate the composting progress. This study investigated how the addition of microbial inoculants could improve the composting effectiveness and could change the structure and dynamics of bacterial communities in the carcass composting process. Four strains of Bacillus were inoculated into the swine carcass composting piles. The groups with the additional inoculants showed a higher temperature in the thermophilic phase and higher germination indices in the composted products. The sequencing results showed that the dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria, and the dominant classified genera were Brevibacterium and Bacillus. Canonical correlation analysis showed that temperature and moisture exerted a stronger influence on the bacterial community diversity. The interaction network of dominant genera and the abundance variation of the bacterial community demonstrated that the inoculated bacterial agent changed the structure of bacterial communities and enriched the diversity of the species due to antagonism and symbiosis among the dominant bacterial communities.

Randomized Benchmarking of Barrier versus Tilt Control of a Singlet-Triplet Qubit.

Decoherence due to charge noise is one of the central challenges in using spin qubits in semiconductor quantum dots as a platform for quantum information processing. Recently, it has been experimentally demonstrated in both Si and GaAs singlet-triplet qubits that the effects of charge noise can be suppressed if qubit operations are implemented using symmetric barrier control instead of the standard tilt control. Here, we investigate the key issue of whether the benefits of barrier control persist over the entire set of single-qubit gates by performing randomized benchmarking simulations. We find the surprising result that the improvement afforded by barrier control depends sensitively on the amount of spin noise: for the minimal nuclear spin noise levels present in Si, the coherence time improves by more than 2 orders of magnitude whereas in GaAs, by contrast the coherence time is essentially the same for barrier and tilt control. However, we establish that barrier control becomes beneficial if qubit operations are performed using a new family of composite pulses that reduce gate times by up to 90%. With these optimized pulses, barrier control is the best way to achieve high-fidelity quantum gates in singlet-triplet qubits.

Noise filtering of composite pulses for singlet-triplet qubits.

Semiconductor quantum dot spin qubits are promising candidates for quantum computing. In these systems, the dynamically corrected gates offer considerable reduction of gate errors and are therefore of great interest both theoretically and experimentally. They are, however, designed under the static-noise model and may be considered as low-frequency filters. In this work, we perform a comprehensive theoretical study of the response of a type of dynamically corrected gates, namely the supcode for singlet-triplet qubits, to realistic 1/f noises with frequency spectra 1/ω(α). Through randomized benchmarking, we have found that supcode offers improvement of the gate fidelity for α 1 and the improvement becomes exponentially more pronounced with the increase of the noise exponent in the range 1 α ≤ 3 studied. On the other hand, for small α, supcode will not offer any improvement. The δJ-supcode, specifically designed for systems where the nuclear noise is absent, is found to offer additional error reduction than the full supcode for charge noises. The computed filter transfer functions of the supcode gates are also presented.

Controllable high-fidelity quantum state transfer and entanglement generation in circuit QED.

We propose a scheme to realize controllable quantum state transfer and entanglement generation among transmon qubits in the typical circuit QED setup based on adiabatic passage. Through designing the time-dependent driven pulses applied on the transmon qubits, we find that fast quantum sate transfer can be achieved between arbitrary two qubits and quantum entanglement among the qubits also can also be engineered. Furthermore, we numerically analyzed the influence of the decoherence on our scheme with the current experimental accessible systematical parameters. The result shows that our scheme is very robust against both the cavity decay and qubit relaxation, the fidelities of the state transfer and entanglement preparation process could be very high. In addition, our scheme is also shown to be insensitive to the inhomogeneous of qubit-resonator coupling strengths.