Sex Differences in Recombination in Sticklebacks.

Recombination often differs markedly between males and females. Here we present the first analysis of sex-specific recombination in Gasterosteus sticklebacks. Using whole-genome sequencing of 15 crosses between G. aculeatus and G. nipponicus, we localized 698 crossovers with a median resolution of 2.3 kb. We also used a bioinformatic approach to infer historical sex-averaged recombination patterns for both species. Recombination is greater in females than males on all chromosomes, and overall map length is 1.64 times longer in females. The locations of crossovers differ strikingly between sexes. Crossovers cluster toward chromosome ends in males, but are distributed more evenly across chromosomes in females. Suppression of recombination near the centromeres in males causes crossovers to cluster at the ends of long arms in acrocentric chromosomes, and greatly reduces crossing over on short arms. The effect of centromeres on recombination is much weaker in females. Genomic differentiation between G. aculeatus and G. nipponicus is strongly correlated with recombination rate, and patterns of differentiation along chromosomes are strongly influenced by male-specific telomere and centromere effects. We found no evidence for fine-scale correlations between recombination and local gene content in either sex. We discuss hypotheses for the origin of sexual dimorphism in recombination and its consequences for sexually antagonistic selection and sex chromosome evolution

3D designed and printed chemical generators for on demand reagent synthesis

Modern science has developed well-defined and versatile sets of chemicals to perform many specific tasks, yet the diversity of these reagents is so large that it can be impractical for any one lab to stock everything they might need. At the same time, isssues of stability or limited supply mean these chemicals can be very expensive to purchase from specialist retailers. Here, we address this problem by developing a cartridge -oriented approach to reactionware-based chemical generators which can easily and reliably produce specific reagents from low-cost precursors, requiring minimal expertise and time to operate, potentially in low infrastructure environments. We developed these chemical generators for four specific targets; transition metal catalyst precursor tris(dibenzylideneacetone)dipalladium(0) [Pd2(dba)3], oxidising agent Dess-Martin periodinane (DMP), protein photolinking reagent succinimidyl 4,4’-azipentanoate (NHS-diazirine), and the polyoxometalate cluster {P8W48}. The cartridge synthesis of these materials provides high-quality target compounds in good yields which are suitable for subsequent utilization

Spin-other-orbit operator in the tensorial form of second quantization

The tensorial form of the spin-other-orbit interaction operator in the formalism of second quantization is presented. Such an expression is needed to calculate both diagonal and off-diagonal matrix elements according to an approach, based on a combination of second quantization in the coupled tensorial form, angular momentum theory in three spaces (orbital, spin and quasispin), and a generalized graphical technique. One of the basic features of this approach is the use of tables of standard quantities, without which the process of obtaining matrix elements of spin-other-orbit interaction operator between any electron configurations is much more complicated. Some special cases are shown for which the tensorial structure of the spin-other-orbit interaction operator reduces to an unusually simple form

The fitness of an introgressing haplotype changes over the course of divergence and depends on its size and genomic location

The genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature of evolution. Examples of both adaptive and deleterious introgression exist in a variety of systems. What is unclear is how the fitness of an introgressing haplotype changes as species diverge or as the size of the introgressing haplotype changes. In a simple model, we show that introgression may more easily occur into parts of the genome which have not diverged heavily from a common ancestor. The key insight is that alleles from a shared genetic background are likely to have positive epistatic interactions, increasing the fitness of a larger introgressing block. In regions of the genome where few existing substitutions are disrupted, this positive epistasis can be larger than incompatibilities with the recipient genome. Further, we show that early in the process of divergence, introgression of large haplotypes can be favored more than introgression of individual alleles. This model is consistent with observations of a positive relationship between recombination rate and introgression frequency across the genome; however, it generates several novel predictions. First, the model suggests that the relationship between recombination rate and introgression may not exist, or may be negative, in recently diverged species pairs. Furthermore, the model suggests that introgression that replaces existing derived variation will be more deleterious than introgression at sites carrying ancestral variants. These predictions are tested in an example of introgression in Drosophila melanogaster, with some support for both. Finally, the model provides a potential alternative explanation to asymmetry in the direction of introgression, with expectations of higher introgression from rapidly diverged populations into slowly evolving ones

An Edgeworth expansion for finite population L-statistics

In this paper, we consider the one-term Edgeworth expansion for finite population L-statistics. We provide an explicit formula for the Edgeworth correction term and give sufficient conditions for the validity of the expansion which are expressed in terms of the weight function that defines the statistics and moment conditions.Comment: 14 pages. Minor revisions. Some explanatory comments and a numerical example were added. Lith. Math. J. (to appear

Searching for signatures of sexually antagonistic selection on stickleback sex chromosomes.

Intralocus sexually antagonistic selection occurs when an allele is beneficial to one sex but detrimental to the other. This form of selection is thought to be key to the evolution of sex chromosomes but is hard to detect. Here we perform an analysis of phased young sex chromosomes to look for signals of sexually antagonistic selection in the Japan Sea stickleback (Gasterosteus nipponicus). Phasing allows us to date the suppression of recombination on the sex chromosome and provides unprecedented resolution to identify sexually antagonistic selection in the recombining region of the chromosome. We identify four windows with elevated divergence between the X and Y in the recombining region, all in or very near genes associated with phenotypes potentially under sexually antagonistic selection in humans. We are unable, however, to rule out the alternative hypothesis that the peaks of divergence result from demographic effects. Thus, although sexually antagonistic selection is a key hypothesis for the formation of supergenes on sex chromosomes, it remains challenging to detect. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'

Automatic generation of 3D-printed reactionware for chemical synthesis digitization using ChemSCAD

We describe a system, ChemSCAD, for the creation of digital reactors based on the chemical operations, physical parameters, and synthetic sequence to produce a given target compound, to show that the system can translate the gram-scale batch synthesis of the antiviral compound Ribavirin (yield 43% over three steps), the narcolepsy drug Modafinil (yield 60% over three steps), and both batch and flow instances of the synthesis of the anticancer agent Lomustine (batch yield 65% over two steps) in purities greater than or equal to 96%. The syntheses of compounds developed using the ChemSCAD system, including reactor designs and analytical data, can be stored in a database repository, with the information necessary to critically evaluate and improve upon reactionware syntheses being easily shared and versioned

Applying Machine Learning to Kinematic and Eye Movement Features of a Movement Imitation Task to Predict Autism Diagnosis

From Springer Nature via Jisc Publications RouterHistory: received 2019-12-04, accepted 2020-04-30, registration 2020-05-05, pub-electronic 2020-05-20, online 2020-05-20, collection 2020-12Publication status: PublishedAbstract: Autism is a developmental condition currently identified by experts using observation, interview, and questionnaire techniques and primarily assessing social and communication deficits. Motor function and movement imitation are also altered in autism and can be measured more objectively. In this study, motion and eye tracking data from a movement imitation task were combined with supervised machine learning methods to classify 22 autistic and 22 non-autistic adults. The focus was on a reliable machine learning application. We have used nested validation to develop models and further tested the models with an independent data sample. Feature selection was aimed at selection stability to assure result interpretability. Our models predicted diagnosis with 73% accuracy from kinematic features, 70% accuracy from eye movement features and 78% accuracy from combined features. We further explored features which were most important for predictions to better understand movement imitation differences in autism. Consistent with the behavioural results, most discriminative features were from the experimental condition in which non-autistic individuals tended to successfully imitate unusual movement kinematics while autistic individuals tended to fail. Machine learning results show promise that future work could aid in the diagnosis process by providing quantitative tests to supplement current qualitative ones