Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing.

The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes

How recent learning shapes the brain: Memory-dependent functional reconfiguration of brain circuits

The process of storing recently encoded episodic mnestic traces so that they are available for subsequent retrieval is accompanied by specific brain functional connectivity (FC) changes. In this fMRI study, we examined the early processing of memories in twenty-eight healthy participants performing an episodic memory task interposed between two resting state sessions. Memory performance was assessed through a forced-choice recognition test after the scanning sessions. We investigated resting state system configuration changes via Independent Component Analysis by cross-modeling baseline resting state spatial maps onto the post-encoding resting state, and post-encoding resting state spatial maps onto baseline. We identified both persistent and plastic components of the overall brain functional configuration between baseline and post-encoding. While FC patterns within executive, default mode, and cerebellar circuits persisted from baseline to post-encoding, FC within the visual circuit changed. A significant session × performance interaction characterized medial temporal lobe and prefrontal cortex FC with the visual circuit, as well as thalamic FC within the executive control system. Findings reveal early-stage FC changes at the system-level subsequent to a learning experience and associated with inter-individual variation in memory performance

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens.

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales

Compact Labelings For Efficient First-Order Model-Checking

We consider graph properties that can be checked from labels, i.e., bit sequences, of logarithmic length attached to vertices. We prove that there exists such a labeling for checking a first-order formula with free set variables in the graphs of every class that is \emph{nicely locally cwd-decomposable}. This notion generalizes that of a \emph{nicely locally tree-decomposable} class. The graphs of such classes can be covered by graphs of bounded \emph{clique-width} with limited overlaps. We also consider such labelings for \emph{bounded} first-order formulas on graph classes of \emph{bounded expansion}. Some of these results are extended to counting queries

Pursuing a fast robber on a graph

AbstractThe Cops and Robbers game as originally defined independently by Quilliot and by Nowakowski and Winkler in the 1980s has been much studied, but very few results pertain to the algorithmic and complexity aspects of it. In this paper we prove that computing the minimum number of cops that are guaranteed to catch a robber on a given graph is NP-hard and that the parameterized version of the problem is W[2]-hard; the proof extends to the case where the robber moves s time faster than the cops. We show that on split graphs, the problem is polynomially solvable if s=1 but is NP-hard if s=2. We further prove that on graphs of bounded cliquewidth the problem is polynomially solvable for s≤2. Finally, we show that for planar graphs the minimum number of cops is unbounded if the robber is faster than the cops

Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation.

The genetic architecture of speciation, i.e., how intrinsic genomic incompatibilities promote reproductive isolation (RI) between diverging lineages, is one of the best-kept secrets of evolution. To directly assess whether incompatibilities arise in a limited set of large-effect speciation genes, or in a multitude of loci, we examined the geographic and genomic landscapes of introgression across the hybrid zones of 41 pairs of frog and toad lineages in the Western Palearctic region. As the divergence between lineages increases, phylogeographic transitions progressively become narrower, and larger parts of the genome resist introgression. This suggests that anuran speciation proceeds through a gradual accumulation of multiple barrier loci scattered across the genome, which ultimately deplete hybrid fitness by intrinsic postzygotic isolation, with behavioral isolation being achieved only at later stages. Moreover, these loci were disproportionately sex linked in one group (Hyla) but not in others (Rana and Bufotes), implying that large X-effects are not necessarily a rule of speciation with undifferentiated sex chromosomes. The highly polygenic nature of RI and the lack of hemizygous X/Z chromosomes could explain why the speciation clock ticks slower in amphibians compared to other vertebrates. The clock-like dynamics of speciation combined with the analytical focus on hybrid zones offer perspectives for more standardized practices of species delimitation

Hierarchical Micro/Nano-Porous Acupuncture Needles Offering Enhanced Therapeutic Properties

Acupuncture as a therapeutic intervention has been widely used for treatment of many pathophysiological disorders. For achieving improved therapeutic effects, relatively thick acupuncture needles have been frequently used in clinical practice with, in turn, enhanced stimulation intensity. However due to the discomforting nature of the larger-diameter acupuncture needles there is considerable interest in developing advanced acupuncture therapeutical techniques that provide more comfort with improved efficacy. So motivated, we have developed a new class of acupuncture needles, porous acupuncture needles (PANs) with hierarchical micro/nano-scale conical pores upon the surface, fabricated via a simple and well known electrochemical process, with surface area approximately 20 times greater than conventional acupuncture needles. The performance of these high-surface-area PANs is evaluated by monitoring the electrophysiological and behavioral responses from the in vivo stimulation of Shenmen (HT7) points in Wistar rats, showing PANs to be more effective in controlling electrophysiological and behavioral responses than conventional acupuncture needles. Comparative analysis of cocaine induced locomotor activity using PANs and thick acupuncture needles shows enhanced performance of PANs with significantly less pain sensation. Our work offers a unique pathway for achieving a comfortable and improved acupuncture therapeutic effect. © The Author(s) 2016.1

Lexical olfaction recruits olfactory orbitofrontal cortex in metaphorical and literal contexts

The investigation of specific lexical categories has substantially contributed to advancing our knowledge on how meaning is neurally represented. One sensory domain that has received particularly little attention is olfaction. This study aims to investigate the neural representation of lexical olfaction. In an fMRI experiment, participants read olfactory metaphors, their literal paraphrases, and literal olfactory sentences. Regions of interest were defined by a functional localizer run of odor processing. We observed activation in secondary olfactory areas during metaphorical and literal olfactory processing, thus extending previous findings to the novel source domain of olfaction. Previously reported enhanced activation in emotion-related areas due to metaphoricity could not be replicated. Finally, no primary olfactory cortex was found active during lexical olfaction processing. We suggest that this absence is due to olfactory hedonicity being crucial to understand the meaning of the current olfactory expressions. Consequently, the processing of olfactory hedonicity recruits secondary olfactory areas

Performance and automation of ancient DNA capture with RNA hyRAD probes

DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analys- ing ancient DNA (aDNA) extracts, which are often dominated by exogenous environ- mental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic re- striction of fresh DNA extracts to produce RNA probes that cover only a fraction ofthe genome and can serve as baits for capturing homologous fragments from aDNA li- braries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing ex- tremely low endogenous content (20%¿30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensi- tive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypo- methylated regions, which improved data quality by reducing post-mortem DNA dam- age and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture process- ing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.This project received funding from: the University Paul Sabatier IDEX Chaire d’Excellence (OURASI); the CNRS Programme de Recherche Conjoint (PRC); the CNRS International Research Project (IRP AMADEUS); the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 797449; the Russian Foundation for Basic Research, project No. 19-59-15001 “Horses and their importance in the life of the ancient population of Altai and adjacent territories: interdisciplinary research and reconstruction”; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement 681605)

The Afrotropical breeding grounds of the Palearctic-African migratory painted lady butterflies (Vanessa cardui)

Migratory insects are key players in ecosystem functioning and services, but their spatiotemporal distributions are typically poorly known. Ecological niche modeling (ENM) may be used to predict species seasonal distributions, but the resulting hypotheses should eventually be validated by field data. The painted lady butterfly (Vanessa cardui) performs multigenerational migrations between Europe and Africa and has become a model species for insect movement ecology. While the annual migration cycle of this species is well understood for Europe and northernmost Africa, it is still unknown where most individuals spend the winter. Through ENM, we previously predicted suitable breeding grounds in the subhumid regions near the tropics between November and February. In this work, we assess the suitability of these predictions through i) extensive field surveys and ii) two-year monitoring in six countries: a large-scale monitoring scheme to study butterfly migration in Africa. We document new breeding locations, year-round phenological information, and hostplant use. Field observations were nearly always predicted with high probability by the previous ENM, and monitoring demonstrated the influence of the precipitation seasonality regime on migratory phenology. Using the updated dataset, we built a refined ENM for the Palearctic-African range of V. cardui. We confirm the relevance of the Afrotropical region and document the missing natural history pieces of the longest migratory cycle described in butterflies.This work was funded by the National Geographic Society (grant WW1-300R-18); by the British Ecological Society (grant LRB16/1015); by the Research and Conservation Projects of the Fundació Barcelona Zoo; by the grant PID2020-117739GA-I00/MCIN/AEI/10.13039/501100011033 of the Spanish Ministry of Science and Innovation and the Spanish State Research Agency to G.T.; by the grant LINKA20399 from the Spanish National Research Council iLink program to G.T., C.P.B., N.E.P., and R.V.; by fellowship FPU19/01593 of the program Formación de Profesorado Universitario (FPU) to A.G.-B.; by the Turkana Basin Institute, National Geographic Society, and Whitley Fund for Nature to D.J.M.; and by grant 2018-00738 of the New Frontiers in Research Fund (Government of Canada) to G.T. and C.P.B.Significance Abstract Results Field Surveys, Larval Hostplants, and Field-Based Model Validation Monitoring Results and Population Dynamics across Regions A Refined Model for the Afrotropical Region Discussion The Afrotropical Breeding Grounds of V. cardui: Multiple Generations Shift South Toward the Tropics Diversity and Phenology of Larval Hostplants in the Afrotropics The Ecological Relevance of Delimiting Spatiotemporal Distributions in Migratory Insects Conclusion Methods December-January Field Surveys and Year-Round Monitoring Spatiotemporal Ecological Niche Modeling Data, Materials, and Software Availability Acknowledgments Supporting Information Reference