Analysis of historical selection in winter wheat

Winter wheat is a major crop with a rich selection history in the modern era of crop breeding. Genetic gains across economically important traits like yield have been well characterized and are the major force driving its production. Winter wheat is also an excellent model for analyzing historical genetic selection. As a proof of concept, we analyze two major collections of winter wheat varieties that were bred in western Europe from 1916 to 2010, namely the Triticeae Genome (TG) and WAGTAIL panels, which include 333 and 403 varieties respectively. We develop and apply a selection mapping approach, Regression of Alleles on Years (RALLY), in these panels, as well as in simulated populations. RALLY maps loci under sustained historical selection by using a simple logistic model to regress allele counts on years of variety release. To control for drift-induced allele frequency change, we develop a hybrid approach of genomic control and delta control. Within the TG panel, we identify 22 significant RALLY quantitative selection loci (QSLs) and estimate the local heritabilities for 12 traits across these QSLs. By correlating predicted marker effects with RALLY regression estimates, we show that alleles whose frequencies have increased over time are heavily biased towards conferring positive yield effect, but negative effects in flowering time, lodging, plant height and grain protein content. Altogether, our results (1) demonstrate the use of RALLY to identify selected genomic regions while controlling for drift, and (2) reveal key patterns in the historical selection in winter wheat and guide its future breeding.

Irritable bowel syndrome – a common problem, individual approach

Irritable bowel syndrome is a recurrent abdominal pain that occurs at least once a week for 3 months, with symptoms at least 6 months associated with at least two features: bowel movements, change in bowel frequency, change in the appearance of stools. According to the Rome IV Diagnostic Criteria, the disease is diagnosed on the basis of clinical symptoms. This does not apply to people over 50 years of age (and in the case of first-degree relatives of patients with colorectal cancer after 45 years of age) and patients with alarm symptoms. Due to the lack of a single etiological factor, the treatment of irritable bowel syndrome consists in reducing symptoms and improving the patient’s quality of life. Non-pharmacological treatment includes a high-fiber diet and modification of the microbiota. The most effective drugs are antispasmodics directly affecting the smooth muscle, inhibiting the influx of calcium, i.e. drotaverine, mebeverine and alverine. There has been proven effectiveness of antidepressants. This confirms that functional disorders of the gastrointestinal tract are a manifestation of the dysfunction of the brain–gut–microbiota axis.

The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America

Understanding the genetic basis of environmental adaptation in natural populations is a central goal in evolutionary biology. The conditions at high elevation, particularly the low oxygen available in the ambient air, impose a significant and chronic environmental challenge to metabolically active animals with lowland ancestry. To understand the process of adaptation to these novel conditions and to assess the repeatability of evolution over short timescales, we examined the signature of selection from complete exome sequences of house mice (Mus musculus domesticus) sampled across two elevational transects in the Andes of South America. Using phylogenetic analysis, we show that house mice colonized high elevations independently in Ecuador and Bolivia. Overall, we found distinct responses to selection in each transect and largely non-overlapping sets of candidate genes, consistent with the complex nature of traits that underlie adaptation to low oxygen availability (hypoxia) in other species. Nonetheless, we also identified a small subset of the genome that appears to be under parallel selection at the gene and SNP levels. In particular, three genes (Col22a1, Fgf14, and srGAP1) bore strong signatures of selection in both transects. Finally, we observed several patterns that were common to both transects, including an excess of derived alleles at high elevation, and a number of hypoxia-associated genes exhibiting a threshold effect, with a large allele frequency change only at the highest elevations. This threshold effect suggests that selection pressures may increase disproportionately at high elevations in mammals, consistent with observations of some high-elevation diseases in humans.

Measuring drift by mean deviation: unequal breeding sex ratio revisited

When it comes to estimating the magnitude of genetic drift, there is hardly any indexes other than the effective population size. Starting from the binomial sampling distribution, this research proposed using mean deviation of allele frequency change as a direct measurement of drift, then tested it in a classical example concerning unequal breeding sex ratio. This study found that: (1) mean deviation offers a new dimension in measuring the magnitude of drift; (2) the measurement displays a half-half pattern; (3) allele frequency determines the efficacy of hitchhiking effect of rare alleles, and in what way that half-half pattern should be divided.

Fast magnetization reversal of a magnetic nanoparticle induced by cosine chirp microwave field pulse

We investigate the magnetization reversal of single-domain magnetic nanoparticle driven by the circularly polarized cosine chirp microwave pulse (CCMP). The numerical findings, based on the Landau-Lifshitz-Gilbert equation, reveal that the CCMP is by itself capable of driving fast and energy-efficient magnetization reversal. The microwave field amplitude and initial frequency required by a CCMP are much smaller than that of the linear down-chirp microwave pulse. This is achieved as the frequency change of the CCMP closely matches the frequency change of the magnetization precession which leads to an efficient stimulated microwave energy absorption (emission) by (from) the magnetic particle before (after) it crosses over the energy barrier. We further find that the enhancement of easy-plane shape anisotropy significantly reduces the required microwave amplitude and the initial frequency of CCMP. We also find that there is an optimal Gilbert damping for fast magnetization reversal. These findings may provide a pathway to realize the fast and low-cost memory device.

Time-dependent quantum harmonic oscillator: a continuous route from adiabatic to sudden changes

In this work, we give a quantitative answer to the question: how sudden or how adiabatic is a frequency change in a quantum harmonic oscillator (HO)? We do that by studying the time evolution of a HO which is initially in its fundamental state and whose time-dependent frequency is controlled by a parameter (denoted by ε) that can continuously tune from a totally slow process to a completely abrupt one. We extend a solution based on algebraic methods introduced recently in the literature that is very suited for numerical implementations, from the basis that diagonalizes the initial hamiltonian to the one that diagonalizes the instantaneous hamiltonian. Our results are in agreement with the adiabatic theorem and the comparison of the descriptions using the different bases together with the proper interpretation of this theorem allows us to clarify a common inaccuracy present in the literature. More importantly, we obtain a simple expression that relates squeezing to the transition rate and the initial and final frequencies, from which we calculate the adiabatic limit of the transition. Analysis of these results reveals a significant difference in squeezing production between enhancing or diminishing the frequency of a HO in a non-sudden way.

Simulation of an Adaptive Method of Improving the Accuracy and Extending the Range of Frequency Signal Processing in a Frequency-to-Code Converter

The article discusses the modification of one of the basic methods of converting successive periods of a variable frequency signal into numerical values representing them. The method performs the adaptive frequency selection of the clock signal in the system processing the consecutive periods of input signal. The signal processing error is analyzed on an ongoing basis, and the frequency change factor is selected. Algorithms describing the operation of the method are included. The program of the simulator of the measurement channel operation with a frequency carrier of information is described, which allows for the verification of the proposed method. Examples of the simulation results are included.

Experimental evolution reveals the synergistic genomic mechanisms of adaptation to ocean warming and acidification in a marine copepod

Metazoan adaptation to global change will rely on selection of standing genetic variation. Determining the extent to which this variation exists in natural populations, particularly for responses to simultaneous stressors, is therefore essential to make accurate predictions for persistence in future conditions. Here, we identify the genetic variation enabling the copepod Acartia tonsa to adapt to experimental ocean warming, acidification, and combined ocean warming and acidification (OWA) conditions over 25 generations. Replicate populations showed a strong and consistent polygenic response to each condition, targeting an array of adaptive mechanisms including cellular homeostasis, development, and stress response. We used a genome-wide covariance approach to partition the genomic changes into selection, drift, and lab adaptation and found that the majority of allele frequency change in warming (56%) and OWA (63%) was driven by selection but acidification was dominated by drift (66%). OWA and warming shared 37% of their response to selection but OWA and acidification shared just 1%. Accounting for lab adaptation was essential for not inflating a shared response to selection between all treatments. Finally, the mechanisms of adaptation in the multiple-stressor OWA conditions were not an additive product of warming and acidification, but rather a synergistic response where 47% of the allelic responses to selection were unique. These results are among the first to disentangle how the genomic targets of selection differ between single and multiple stressors and to demonstrate the complexity that non-additive multiple stressors will contribute to attempts to predict adaptive responses to complex environments.

Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed population

Sex-biased demography, including sex-biased survival or migration, can impact allele frequency changes across the genome. In particular, we can expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well as differences in effective population size, transmission modes, and the strength and mode of selection. Here, we demonstrate the role that sex differences in life history played in shaping short-term evolutionary dynamics across the genome. We used a 25-year pedigree and genomic dataset from a long-studied population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of sex-biased demography and inheritance in shaping genome-wide allele frequency trajectories. We used gene dropping simulations to estimate individual genetic contributions to future generations and to model drift and immigration on the known pedigree. We quantified differential expected genetic contributions of males and females over time, showing the impact of sex-biased dispersal in a monogamous system. Due to female-biased dispersal, more autosomal variation is introduced by female immigrants. However, due to male-biased transmission, more Z variation is introduced by male immigrants. Finally, we partitioned the proportion of variance in allele frequency change through time due to male and female contributions. Overall, most allele frequency change is due to variance in survival and births. Males and females have similar contributions to autosomal allele frequency change, but males have higher contributions to allele frequency change on the Z chromosome. Our work shows the importance of understanding sex-specific demographic processes in accounting for genome-wide allele frequency change in wild populations.