Equilibrium Expectations Research Articles

A DNA profiling system for conservation management of Kamchatka brown bear (Ursus arctos piscator); population data and system performance from 16 autosomal STRs

Despite the high density of brown bears (Ursus arctos piscator) on the Kamchatka peninsula their genetic variation has not been studied by STR analysis. Our aim was, therefore, to provide population data from the Kamchatka brown bear population applying a validated DNA profiling system. Twelve dinucleotide STRs commonly used in Western-European (WE) populations and four additional ones (G10C, G10J, G10O, G10X), were included. Template input ≥ 0.2 ng was successfully amplified. Measurements of precision, stutter and heterozygous balance showed that markers could be reliably genotyped applying the thresholds used for genotyping WE brown bears. However, locus G10X revealed an ancient allele-specific polymorphism that led to suboptimal amplification of all 174 bp alleles (Kamchatka and WE). Allele frequency estimates and forensic genetic parameters were obtained from 115 individuals successfully identified by genotyping 434 hair samples. All markers met the Hardy-Weinberg and linkage equilibrium expectations, and the power of discrimination ranged from 0.667 to 0.962. The total average probability of identity from the 15 STRs was 1.4 ×10−14 (FST = 0.05) while the total average probability of sibling identity was 6.0 ×10−6. Relationship tests revealed several parent-cub and full sibling pairs demonstrating that the marker set would be valuable for the study of family structures. The population data is the first of its kind from the Kamchatka brown bear population. Population pairwise FST`s revealed moderate genetic differentiation that mirrored the geographic distances to WE populations. The DNA profiling system, providing individual-specific profiles from non-invasive samples, will be useful for future monitoring and conservation purposes

A warm Neptune’s methane reveals core mass and vigorous atmospheric mixing

Observations of transiting gas giant exoplanets have revealed a pervasive depletion of methane1–4, which has only recently been identified atmospherically5,6. The depletion is thought to be maintained by disequilibrium processes such as photochemistry or mixing from a hotter interior7–9. However, the interiors are largely unconstrained along with the vertical mixing strength and only upper limits on the CH4 depletion have been available. The warm Neptune WASP-107b stands out among exoplanets with an unusually low density, reported low core mass10, and temperatures amenable to CH4, though previous observations have yet to find the molecule2,4. Here we present a JWST-NIRSpec transmission spectrum of WASP-107b that shows features from both SO2 and CH4 along with H2O, CO2, and CO. We detect methane with 4.2σ significance at an abundance of 1.0 ± 0.5 ppm, which is depleted by 3 orders of magnitude relative to equilibrium expectations. Our results are highly constraining for the atmosphere and interior, which indicate the envelope has a super-solar metallicity of 43 ± 8 × solar, a hot interior with an intrinsic temperature of Tint = 460 ± 40 K, and vigorous vertical mixing which depletes CH4 with a diffusion coefficient of Kzz = 1011.6±0.1 cm2 s−1. Photochemistry has a negligible effect on the CH4 abundance but is needed to account for the SO2. We infer a core mass of 11.5−3.6+3.0M⊕\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${11.5}_{-3.6}^{+3.0}{M}_{\\oplus }$$\\end{document}, which is much higher than previous upper limits10, releasing a tension with core-accretion models11.

PyPop: a mature open-source software pipeline for population genomics.

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop.

Microsatellite markers for Monitipora digitata designed using restriction-site associated DNA sequencing

Montipora digitata is a species belonging to the Acroporidae. In the Indo-Pacific region, M. digitata is widely distributed and is the dominant species of scleractinian coral in the South China Sea, however, there are currently no molecular markers suitable for assessing the species genetic diversity. Here, restriction-site associated DNA sequencing (RAD-seq) was used to isolate and characterize polymorphic microsatellite loci. A total of 317,361 RAD-tags were obtained using RAD-seq, including 6,778 microsatellite loci. Primer pairs for 106 loci were ordered and twenty-one polymorphic loci, that amplified reliably were identified. The number of alleles per locus were 2-7, observed heterozygosity was 0.111-0.556 with an average value of 0.285, and expected heterozygosity was 0.105- 0.802, with an average value of 0.536. Before Bonferroni correction 13 loci deviated significantly from the expectations of Hardy-Weinberg equilibrium (P < 0.05), after correction, two microsatellite loci deviated significantly (P < 0.0002). The polymorphic information content (PIC) ranged from 0.100-0.778, with 12 loci highly polymorphic (PIC > 0.5), six moderately polymorphic (0.25 < PIC < 0.5), and three loci with low polymorphism (PIC < 0.25). The microsatellite loci developed here will be effective tools for conservation genetic research on M. digitata.

Development of twenty-one novel microsatellite loci for Gila topminnow, Poeciliopsis occidentalis occidentalis.

Gila topminnow (Poeciliopsis occidentalis occidentalis) was once highly abundant throughout the Lower Colorado River Basin of the southwestern United States. However, this Sonoran Desert endemic suffered extreme population declines over the past century because of habitat degradation and nonnative species introductions. Much of the prior conservation genetic work conducted on the species relied upon a small number of microsatellite loci; many exhibiting low variability in extant populations. Consequently, there was a need for additional microsatellite loci to provide high-resolution delimitation of populations for conservation purposes. Paired-end Illumina sequencing was utilized to screen the Gila topminnow genome for novel microsatellite loci. We identified 21 novel loci that exhibited no deviations from expectations of genetic equilibrium, and cross-amplified in Yaqui topminnow (P. o. sonoriensis). These loci were amplified from 401 samples representing eight populations of Gila topminnow and Yaqui topminnow. Although diversity was low for all populations (observed heterozygosity = 0.12 to 0.45), these novel markers provided ample power to identify population of origin for each individual in Bayesian assignment tests. This novel set of microsatellite loci provide a useful genetic tool to assess population genetic parameters of the endangered Gila topminnow and delineate populations for identifying conservation priorities. The cross-amplification of these loci in Yaqui topminnow shows promise for application to other Poeciliopsis species of Mexico and Central America.

Tuning nonequilibrium phase transitions with inertia.

In striking contrast to equilibrium systems, inertia can profoundly alter the structure of active systems. Here, we demonstrate that driven systems can exhibit effective equilibrium-like states with increasing particle inertia, despite rigorously violating the fluctuation-dissipation theorem. Increasing inertia progressively eliminates motility-induced phase separation and restores equilibrium crystallization for active Brownian spheres. This effect appears to be general for a wide class of active systems, including those driven by deterministic time-dependent external fields, whose nonequilibrium patterns ultimately disappear with increasing inertia. The path to this effective equilibrium limit can be complex, with finite inertia sometimes acting to accentuate nonequilibrium transitions. The restoration of near equilibrium statistics can be understood through the conversion of active momentum sources to passive-like stresses. Unlike truly equilibrium systems, the effective temperature is now density dependent, the only remnant of the nonequilibrium dynamics. This density-dependent temperature can in principle introduce departures from equilibrium expectations, particularly in response to strong gradients. Our results provide additional insight into the effective temperature ansatz while revealing a mechanism to tune nonequilibrium phase transitions.

Testing of Hardy-Weinberg Equilibrium in Population of Two Nigerian Local Chicken Ecotypes Base on Location

Test of deviation from Hardy-Weinberg equilibrium expectation base on location of the Tiv and Fulani local chicken ecotypes of Nigeria was undertaken using eighty (80) matured birds (40 birds each for Tiv and Fulani ecotypes). Blood samples were collected from five locations each of the ecotype to determine their blood protein. Blood protein loci namely: haemoglobin, albumen, transferrin and carbonic anhydrase were determine using electrophoresis. Data collected were analyzed using popgene version 1.31. The result revealed significant deviations (P<0.05) from Hardy-Weinberg expectations in the two ecotypes except in the Fulani ecotype were haemoglobin did not deviate significantly. Based on location, there were no significant (P>0.05) deviation from Hardy-Weinberg expectations in the Fulani ecotype except in location 4 were Hb, Al and Ca as well as location 5 where Al and Ca were significant. Allelic frequencies of albumin showed significant (P<0.05) deviation from Hardy-Weinberg expectations at locations 1 and 5 while allelic frequencies of transferrin deviated significantly (P<0.05) from the Hardy-Weinberg frequency at location 5. In the Tiv ecotype, albumin showed the highest significant (P<0.05) deviation from the Hardy-Weinberg expectations in all locations. The allelic frequencies of transferrin did not differ significantly (P>0.05) from the Hardy-Weinberg expectations. From the finding of this research, it was concluded that the deviation from Hardy-Weinberg expectations at the four blood proteins loci of the two ecotypes indicated that the Tiv and the Fulani chicken populations are variable in their genome and that there are chances of genetic improvement when crossed between themselves across location or with exotic breeds. Generally, these findings provide the fundamental step in the direction of judicious decision-making before the development of genetic enhancement and preservation programmes without interfering with the uniqueness of the Tiv............

Freezing out fluctuations in Hydro+ near the QCD critical point

We introduce a freeze-out procedure to convert the critical fluctuations in a droplet of quark-gluon plasma (QGP) that has, as it expanded and cooled, passed close to a posited critical point on the phase diagram into cumulants of hadron multiplicities that can subsequently be measured. The procedure connects the out-of-equilibrium critical fluctuations described in concert with the hydrodynamic evolution of the droplet of QGP by extended hydrodynamics, known as Hydro+, with the subsequent kinetic description in terms of observable hadrons. We introduce a critical scalar isoscalar field sigma whose fluctuations cause correlations between observed hadrons due to the couplings of the sigma field to the hadrons via their masses. We match the QGP fluctuations obtained by solving the Hydro+ equations describing the evolution of critical fluctuations before freeze-out to the correlations of the sigma field. In turn, these are imprinted onto correlations and fluctuations in the multiplicity of hadrons, most importantly protons, after freeze-out via the generalization of the familiar half-century-old Cooper-Frye freeze-out prescription which we introduce. The proposed framework allows us to study the effects of critical slowing down and the consequent deviation of the observable predictions from equilibrium expectations quantitatively. We also quantify the suppression of cumulants due to conservation of baryon number. We demonstrate the procedure in practice by freezing out a Hydro+ simulation in an azimuthally symmetric and boost invariant background that includes radial flow discussed in arXiv:1908.08539.

The Three Hundred project: dissecting the Fundamental Plane of galaxy clusters up to z = 1

ABSTRACT We perform a systematic study of the recently discovered Fundamental Plane of galaxy clusters (CFP) using ∼250 simulated clusters from The Three Hundred project, focusing on the stability of the plane against different temperature definitions and its dependence on the dynamical relaxation state of clusters. The CFP is characterized by $T\propto M_\mathrm{s}^\alpha \, r_\mathrm{s}^\beta$, defined with the gas temperature (T) and the characteristic halo scale radius and mass (rs and Ms) assuming a Navarro–Frenk–White halo description. We explore two definitions of weighted temperatures, namely mass-weighted and spectroscopic-like temperatures, in three radial ranges. The Three Hundred project clusters at z = 0 lie on a thin plane whose parameters (α, β) and dispersion (0.015–0.030 dex) depend on the gas temperature definition. The CFP for mass-weighted temperatures is closer to the virial equilibrium expectation (α = 1, β = −1) with a smaller dispersion. For gas temperatures measured within $500\ h^{-1}$ kpc, the resulting CFP deviates the most from the virial expectation and shifts towards the similarity solution for a secondary infall model (α = 1.5, β = −2). Independently of the temperature definition, we find that clusters at z = 1 and relaxed clusters form a CFP similar to the virial expectation, unlike disturbed clusters exhibiting stronger evolution. Only systems formed over the last 4 Gyr present a CFP that is closer to the similarity solution. All these findings are compatible with the CFP obtained for a Cluster Lensing And Supernova survey with Hubble subsample excluding the hottest clusters with TX > 12 keV.

Coupled baryon, electric charge and strangeness fluctuations in heavy-ion collisions

We present for the first time quantitative results for the coupled dynamics of second order fluctuations in the three conserved charges of QCD based on stochastic diffusion equations for a Bjorken-type expanding hadronic medium. We show that the fluctuations deviate from local equilibrium expectations which can result in important phenomenological consequences for the interpretation of experimental data.

Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers.

The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy–Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia.

Genetic polymorphisms of interleukin-6 and interleukin-10 are not associated with new onset atrial fibrillation after coronary artery bypass graft surgery

Abstract Purpose To estimate the association of the genetic polymorphisms of Interleukin-6 (IL-6) and Interleukin-10 (IL-10) with new onset atrial fibrillation (AF) in postoperative period of coronary artery bypass graft (CABG) surgery in patients with coronary artery disease (CAD). Methods Studied were 158 patients who underwent CABG. In all the patients routine laboratory and instrumental tests were performed. Patients also underwent genetic polymorphisms of IL-6 C174G, IL-10 C592A and IL-10 G1082A estimation. All the patients were divided into two groups: 1 group comprised 111 patients without AF (82.0% men, median age 62.0 (56.0; 66.0) years, 2 group - 47 patients with AF development after CABG (84.4% men, median age 65.0 (61.0; 70.0) years). Results During the observation period AF occurred in 29.7% patients, on average 5.2 (2.0; 7.0) days after surgery. Patients of group 2 had longer history of CAD (60.0 (13.5; 138.0) vs. 15.5 (8.0; 72.0) months, p=0.01), had more often NYHA III class (27.7% vs. 9.0%, p=0.002) and larger left atrial (LA) diameter (44.0 (40.5; 46.0) mm vs. 38.0 (36.0; 40.0) mm, p<0.0001) comparing with group 1. Genotype CC IL-6 C174G was found in 19.8% patients of the 1 group and in 25.5% patients of the 2 group (p=0.42), genotype CG - in 56.8% and 53.2% (p=0.68), genotype GG - in 23.4% and 21.3% (p=0.77) respectively. Genotype CC IL-10 C592A was found in 62.2% patients of the 1 group and 46.8% patients of the 2 group (p=0.29), genotype CA - in 37.8% patients of the 1 group and in 53.2% patients of the 2 group (p=0.07) respectively. Genotype GG IL-10 G1082A was found in 25.2% patients of the 1 group and 23.4% patients of the 2 group (p=0.8), genotype GA - in 48.6% patients of the 1 group and in 59.6% patients of the 2 group (p=0.2), genotype AA - in 26.2% patients of the 1 group and in 17.0% patients of the 2 group (p=0.3) respectively. All estimated genotypes fulfilled expectations of Hardy-Weinberg equilibrium. According to the result of multivariate regression analysis the odds ratio for AF development in postoperative period of CABG for history of CAD more than 20 months - 1.1 (95% CI, 1.03–1.2, p=0.04), for LA dimension more than 41 mm - 1.5 (95% CI, 1.28–1.79, p<0.0001). Conclusion Our investigation showed that increased left atrial dimension and the history of coronary artery disease were associated with postoperative atrial fibrillation development in patients who underwent coronary artery bypass graft surgery. However, genetic polymorphisms of IL-6 C174G, IL-10 C592A and IL-10 G1082A were not significantly associated with postoperative atrial fibrillation development. Funding Acknowledgement Type of funding sources: None.

Constant of Motion Identifying Excited-State Quantum Phases.

We propose that a broad class of excited-state quantum phase transitions (ESQPTs) gives rise to two different excited-state quantum phases. These phases are identified by means of an operator C[over ^], which is a constant of motion in only one of them. Hence, the ESQPT critical energy splits the spectrum into one phase where the equilibrium expectation values of physical observables crucially depend on this constant of motion and another phase where the energy is the only relevant thermodynamic magnitude. The trademark feature of this operator is that it has two different eigenvalues ±1, and, therefore, it acts as a discrete symmetry in the first of these two phases. This scenario is observed in systems with and without an additional discrete symmetry; in the first case, C[over ^] explains the change from degenerate doublets to nondegenerate eigenlevels upon crossing the critical line. We present stringent numerical evidence in the Rabi and Dicke models, suggesting that this result is exact in the thermodynamic limit, with finite-size corrections that decrease as a power law.

Residual Tau-Fluvalinate in Honey Bee Colonies Is Coupled with Evidence for Selection for Varroa destructor Resistance to Pyrethroids.

Simple SummaryVarroa destructor is one of the most prevalent honey bee (Apis mellifera) pathogens worldwide. Nowadays, the main method to control this parasite involves the application of different acaricidal treatments, among which the pyrethroid tau-fluvalinate is one of the most widely used. However, the intensive and repetitive application of these chemicals generates a selective pressure that, when maintained over time, contributes to the emergence of resistant mites in the honey bee colonies. Here we analysed the presence of residual tau-fluvalinate and the patterns of genetic resistance to this acaricide in Varroa mites collected from tau-fluvalinate untreated honey bee colonies. Our results show the widespread and persistent pyrethroid contamination of beeswax and beebread in the hives, along with an excess of pyrethroid-resistant genotypes and an overall increase in the frequency of the pyrethroid-resistant allele in the mite population over time. Persistent contamination of the hives likely compromises the efficacy of tau-fluvalinate treatments and, therefore, may have serious long-term consequences for the control of varroosis.Varroa destructor is considered one of the most devastating parasites of the honey bee, Apis mellifera, and a major problem for the beekeeping industry. Currently, the main method to control Varroa mites is the application of drugs that contain different acaricides as active ingredients. The pyrethroid tau-fluvalinate is one of the acaricides most widely used in beekeeping due to its efficacy and low toxicity to bees. However, the intensive and repetitive application of this compound produces a selective pressure that, when maintained over time, contributes to the emergence of resistant mites in the honey bee colonies, compromising the acaricidal treatments efficacy. Here we studied the presence of tau-fluvalinate residues in hives and the evolution of genetic resistance to this acaricide in Varroa mites from honey bee colonies that received no pyrethroid treatment in the previous four years. Our data revealed the widespread and persistent tau-fluvalinate contamination of beeswax and beebread in hives, an overall increase of the pyrethroid resistance allele frequency and a generalized excess of resistant mites relative to Hardy–Weinberg equilibrium expectations. These results suggest that tau-fluvalinate contamination in the hives may seriously compromise the efficacy of pyrethroid-based mite control methods.

Genetic diversity and genetic structures of original plants of Viticis Fructus:an SSR markers-based analysis

The present study aimed to provide the protection strategies for wild germplasm resources of original plants of Viticis Fructus and a theoretical basis for the sustainable use of Viticis Fructus. The genetic diversity and genetic structures of the 232 indivi-duals in 19 populations of Vitex rotundifolia and V. trifolia were analyzed by eight SSR markers with tools such as Popgene32, GenAlex 6.502, and STRUCTURE. Bottleneck effect was detected for the population with more than 10 individuals. The results indicated that 42 and 26 alleles were detected from the populations of V. rotundifolia and V. trifolia, respectively, with average expected heterozygo-sities of 0.448 6 and 0.583 9, which are indicative of low genetic diversity. AMOVA revealed the obvious genetic variation of V. rotundifolia and V. trifolia within population(84.43%, P<0.01; 60.37%, P<0.01). Furthermore, in eight SSR loci, six from V. rotundifolia populations and two from V. trifolia populations failed to meet Hardy-Weinberg equilibrium expectations(P<0.05), which confirmed that the populations experienced bottleneck effect. As assessed by Mantel test, geographical distance posed slight impacts on the genetic variation between the populations of V. rotundifolia and V. trifolia. Principal component analysis(PCA) and STRUCTURE analysis demonstrated evident introgression of genes among various populations. The original plants of Viticis Fructus were confirmed low in genetic diversity and genetic differentiation level. Therefore, the protection of wild resources of original plants of Viticis Fructus should be strengthened to ensure its sustainable use.

Stochastic recruitment alters the frequencies of alternative life histories in age‐structured populations

AbstractAlternative reproductive tactics, where members of a population exhibit divergent mating approaches, are widespread in fishes. The maintenance of such polymorphisms is often explained using game‐theoretic concepts such as frequency‐dependent selection, which typically assume populations are at equilibrium. However, fish populations exhibit stochastic variability that is inconsistent with the assumption of equilibrium dynamics. We explored how stochastic population dynamics interact with sexual and harvest‐induced selection to shape the frequencies of alternative male phenotypes in Pacific salmon (Oncorhynchus spp., Salmonidae). Males of several salmon species are composed of typical “hooknoses” that compete on the spawning grounds for mating opportunities, and rarer “jacks” that mature younger and at smaller sizes to attempt reproduction by “sneaking.” Using stochastic simulations, we found that realistic levels of recruitment variation could increase the prevalence of jacks relative to equilibrium expectations. This result is attributable to the “cohort mismatch” phenomenon, whereby differences in age at maturity between male phenotypes cause jacks from strong recruitments to spawn in the same year as hooknoses from weaker cohorts, elevating the proportion of jacks among spawners. Simulations were supported by data from major populations of sockeye salmon (O. nerka, Salmonidae) throughout their North American range, which indicated a positive association between recruitment variability and jack prevalence in some regions. Moreover, we found that frequency‐dependent mating dampened population responses to fisheries‐induced selection. Our findings emphasize that stochastic ecological processes are important to the maintenance of alternative life histories and interact with selection to produce emergent dynamics that have not previously been recognized.

Quantum adiabatic cycles and their breakdown

The assumption that quasi-static transformations do not quantitatively alter the equilibrium expectation of observables is at the heart of thermodynamics and, in the quantum realm, its validity may be confirmed by the application of adiabatic perturbation theory. Yet, this scenario does not straightforwardly apply to Bosonic systems whose excitation energy is slowly driven through the zero. Here, we prove that the universal slow dynamics of such systems is always non-adiabatic and the quantum corrections to the equilibrium observables become rate independent for any dynamical protocol in the slow drive limit. These findings overturn the common expectation for quasi-static processes as they demonstrate that a system as simple and general as the quantum harmonic oscillator, does not allow for a slow-drive limit, but it always displays sudden quench dynamics.

Allelic losses and gains during translocations of a high conservation value fish, Coregonus lavaretus

Abstract The use of translocations to establish new or ‘refuge’ populations for species with high conservation value is controversial but widely used in conservation management. One of the risks of this approach is that an establishing population does not adequately capture the genetic diversity of the donor gene pool. This effect, rarely examined, is tested here. In this study the genetic consequences of two conservation translocations after five generations (16 years) of the European whitefish, Coregonus lavaretus, were quantified. Both translocations were made using almost the same genetic groups and thus represent a partly replicated natural study. Analysis of 12 informative microsatellites showed that expected heterozygosity, the mean number of alleles per locus and allelic richness did not differ between donor and translocated populations. There was also no loss of heterozygosity in the translocated populations, nor deviations from Hardy–Weinberg equilibrium expectations, nor signs of linkage disequilibrium. All populations were genetically differentiated but pairwise FST values were low, indicating that the magnitude of divergence was small. There was no evidence of inbreeding but there were significant differences in private allelic richness between donor and translocated populations. Of 50 alleles found in the donor population, 16% of the rarer alleles were lost in one translocated population and 8% in the other. Allele loss without a reduction in heterozygosity strongly points to stochastic drift effects having occurred following translocation. The evidence indicates that alleles that were not detected in the donor population have arisen de novo in the translocated populations. It is concluded that conservation translocations comprising even a modest number of propagules can successfully capture a high proportion of genetic variation of the host population, and that reduced genetic variation in the translocated population may be mitigated by the emergence of new variation over short time periods.

Male-biased effective sex ratio across populations of the threatened Zamia boliviana (Zamiaceae)

Populations of dioecious plants commonly exhibit dissimilarities to the equilibrium expectation of a 1:1 sex ratio. Differential expenditure for reproduction between genders is cited as the primary mechanism responsible for a male-biased sex ratio, with increased effects on long-living species, but these mechanisms are still poorly understood. We explore the sex ratio in the endemic gymnosperm Zamia boliviana (Zamiaceae) populations from the Brazilian savanna (the Cerrado). We aim to investigate what the Z. boliviana sex ratio is, and whether population density and ecological correlates lead to variation in the sex proportion among Cerrado habitats. The study was conducted on ten in situ populations of Z. boliviana at sexual maturity (tertiary sex ratio). We estimated the populations’ sex ratio and performed a redundancy analysis to assess the relationship between biotic traits, such as sex ratio, and associated environmental features. Soil texture classes were used to classify the cycad habitats and were expressed in a ternary phase diagram. The results show a significant male-biased sex ratio in seven of the ten populations surveyed. Environmental factors did not explain the redundancy in the reproductive characteristics. However, the cycad occurs in different habitats in their endemic zone. Our study provides new biological data for Z. boliviana, suggesting that the differential reproductive expenditure of sexes in reproduction is governing the mechanisms of sex ratio variation, compared to local environmental factors in this cycad. The pattern of effective sex ratio found here improves our understanding of mechanisms causing biased sex ratios in cycads and other dioecious species from tropical ecosystems.

Connection of COX-2 variants to ankylosing spondylitis susceptibility.

This study aimed to explore the associations of COX-2 polymorphisms rs5275, rs20417, and rs2745557 with the susceptibility to ankylosing spondylitis among Chinese Han people. Polymerase chain reaction-restriction fragment length polymorphism (PCR/RFLP) was adopted for genotyping COX-2 polymorphisms rs5275, rs20417, and rs2745557 among 109 AS patients and 122 healthy controls. Genotype distribution in the control group was examined for these three polymorphisms to test whether it conformed to Hardy-Weinberg equilibrium (HWE) expectation. A χ2 -test was employed to compare genotype and allele frequencies between the two groups. Besides this, logistic regression analyses were also performed to adjust age and gender. Apless than .05 represented a significant level. Genotype distribution of our studied polymorphisms showed fine conformity to HWE in the controls. An increasing effect on AS risk was detected for the polymorphism rs5275 under GG versus AA contrast (crude: OR,3.040; 95% CI,1.015-9.104), and the adjustment for age and gender did not change such a relationship (adjusted OR,3.307; 95% CI,1.065-10.268). After adjusting age and gender, both polymorphisms of rs20417 and rs2745557 demonstrated a negative relationship with the disease susceptibility. The GC genotype and C allele of rs20417 reduced the disease risk to 0.248 (adjusted: 95% CI,0.089-0.692) and 0.269 (95% CI,0.098-0.733), respectively, while the AA genotype and A allele of the latter to 0.413 (adjusted: 95% CI,0.191-0.893) and 0.676 (adjusted: 95% CI,0.466-0.981), respectively. Among Chinese Han people, COX-2 polymorphism rs5275 may contribute to increased risk of developing AS, while the polymorphisms rs20417 and rs2745557 may offer protection against disease incidence.