bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group
Authors: Shang Huiying , Hess Jaqueline , Pickup Melinda , Field David L. , Ingvarsson Pär K. , Liu Jianquan , Lexer Christian 
Published: July 2020

Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, usingPopulusas an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing onPopulus,our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
The evolution of strong reproductive isolation between sympatric intertidal snails
Authors: Stankowski Sean , Westram Anja M. , Zagrodzka Zuzanna B. , Eyres Isobel , Broquet Thomas , Johannesson Kerstin , Butlin Roger K. 
Published: July 2020

The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology,Littorina arcanaandLittorina saxatilisdiffer in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
The ecological stage changes benefits of mate choice and drives preference divergence
Authors: Tinghitella Robin M. , Lackey Alycia C. R. , Durso Catherine , Koop Jennifer A. H. , Boughman Janette W. 
Published: July 2020

Preference divergence is thought to contribute to reproductive isolation. Ecology can alter the way selection acts on female preferences, making them most likely to diverge when ecological conditions vary among populations. We present a novel mechanism for ecologically dependent sexual selection, termed ‘the ecological stage’ to highlight its ecological dependence. Our hypothesized mechanism emphasizes that males and females interact over mating in a specific ecological context, and different ecological conditions change the costs and benefits of mating interactions, selecting for different preferences in distinct environments and different male traits, especially when traits are condition dependent. We test key predictions of this mechanism in a sympatric three-spine stickleback species pair. We used a maternal half-sib split-clutch design for both species, mating females to attractive and unattractive males and raising progeny on alternate diets that mimic the specialized diets of the species in nature. We estimated the benefits of mate choice for an indicator trait (male nuptial colour) by measuring many fitness components across the lifetimes of both sons and daughters from these crosses. We analysed fitness data using a combination of aster and mixed models. We found that many benefits of mating with high-colour males depended on both species and diet. These results support the ecological stage hypothesis for sticklebacks. Finally, we discuss the potential role of this mechanism for other taxa and highlight its ability to enhance reproductive isolation as speciation proceeds, thus facilitating the evolution of strong reproductive isolation.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Anthropogenic hybridization at sea: three evolutionary questions relevant to invasive species management
Authors: Viard Frédérique , Riginos Cynthia , Bierne Nicolas 
Published: July 2020

Species introductions promote secondary contacts between taxa with long histories of allopatric divergence. Anthropogenic contact zones thus offer valuable contrasts to speciation studies in natural systems where past spatial isolations may have been brief or intermittent. Investigations of anthropogenic hybridization are rare for marine animals, which have high fecundity and high dispersal ability, characteristics that contrast to most terrestrial animals. Genomic studies indicate that gene flow can still occur after millions of years of divergence, as illustrated by invasive mussels and tunicates. In this context, we highlight three issues: (i) the effects of high propagule pressure and demographic asymmetries on introgression directionality, (ii) the role of hybridization in preventing introduced species spread, and (iii) the importance of postzygotic barriers in maintaining reproductive isolation. Anthropogenic contact zones offer evolutionary biologists unprecedented large scale hybridization experiments. In addition to breaking the highly effective reproductive isolating barrier of spatial segregation, they allow researchers to explore unusual demographic contexts with strong asymmetries. The outcomes are diverse, from introgression swamping to strong barriers to gene flow, and lead to local containment or widespread invasion. These outcomes should not be neglected in management policies of marine invasive species.
This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
Genome-wide patterns of divergence and introgression after secondary contact betweenPungitiussticklebacks
Authors: Yamasaki Yo Y. , Kakioka Ryo , Takahashi Hiroshi , Toyoda Atsushi , Nagano Atsushi J. , Machida Yoshiyasu , Møller Peter R. , Kitano Jun 
Published: July 2020

Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species,Pungitius pungitiusandP. sinensis, whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
Sympatric ecological divergence with coevolution of niche preference
Authors: Payne Pavel , Polechová Jitka 
Published: July 2020

Reinforcement, the increase of assortative mating driven by selection against unfit hybrids, is conditional on pre-existing divergence. Yet, for ecological divergence to precede the evolution of assortment, strict symmetries between fitnesses in niches must hold, and/or there must be low gene flow between the nascent species. It has thus been argued that conditions favouring sympatric speciation are rarely met in nature. Indeed, we show that under disruptive selection, violating symmetries in niche sizes and increasing strength of the trade-off in selection between the niches quickly leads to loss of genetic variation, instead of evolution of specialists. The region of the parameter space where polymorphism is maintained further narrows with increasing number of loci encoding the diverging trait and the rate of recombination between them. Yet, evolvable assortment and pre-existing assortment both substantially broaden the parameter space within which polymorphism is maintained. Notably, pre-existing niche preference speeds up further increase of assortment, thus facilitating reinforcement in the later phases of speciation. We conclude that in order for sympatric ecological divergence to occur, niche preference must coevolve throughout the divergence process. Even if populations come into secondary contact, having diverged in isolation, niche preference substantially broadens the conditions for coexistence in sympatry and completion of the speciation process.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
What cost decisiveness? A cost benefit analysis of the lockdown to contain COVID-19 in India
Authors: Dutta Mousumi , Husain Zakir 
Published: July 2020

AbstractOn 24th March, 2020 the Government of India announced a national level lockdown to contain the spread of COVID. The lockdown policy has generated considerable controversy, with critics arguing that it was done without adequate notice or planning, exposed vulnerable section of the population to a humanitarian crisis, and failed to contain the spread of COVID. In response, the Government has claimed that lockdown slowed the transmission process of COVID, thereby reducing the number of cases and deaths substantially. The consequent pressure on the health infrastructure was also much less. To judge between competing claims, this study has undertaken the first cost-benefit analysis of the world’s biggest lockdown. Although the data for a proper cost-benefit analysis is currently not available, we have made a ball point estimate of the net benefit of the lockdown under alternative scenarios. Our estimates reveal the net benefits of lockdown to be negative; moreover, the results are robust under all scenarios.
SARS-CoV-2 RNA extraction using magnetic beads for rapid large-scale testing by RT-qPCR and RT-LAMP
Authors: Klein Steffen , Müller Thorsten G. , Khalid Dina , Sonntag-Buck Vera , Heuser Anke-Mareil , Glass Bärbel , Meurer Matthias , Morales Ivonne , Schillak Angelika , Freistaedter Andrew , Ambiel Ina , Winter Sophie L. , Zimmermann Liv , Naumoska Tamara , Bubeck Felix , Kirrmaier Daniel , Ullrich Stephanie , Miranda Isabel Barreto , Anders Simon , Grimm Dirk , Schnitzler Paul , Knop Michael , Kräusslich Hans-Georg , Dao Thi Viet Loan , Börner Kathleen , Chlanda Petr 
Published: July 2020

AbstractRapid large-scale testing is essential for controlling the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits followed by reverse transcription and quantitative PCR detection. As a result of the large demand for testing, commercial RNA extraction kits may be limited and alternative, non-commercial protocols are needed. Here, we provide a magnetic bead RNA extraction protocol that is predominantly based on in-house made reagents and is performed in 96-well plates supporting large-scale testing. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric RT-LAMP using N primers, as well as RT-qPCR using E gene primers showing that the here presented RNA extraction protocol can be combined with a variety of detection methods at high throughput. Importantly, the presented diagnostic workflow can be quickly set up in a laboratory without access to an automated pipetting robot.
Default(y) Mode Network: Important regions of DMN do not survive alterations in flip angles
Authors: Singhal Ishan , Soni Abhishek K. , Srinivasan Narayanan 
Published: July 2020

AbstractThe default mode network (DMN) is thought to capture intrinsic activity of the brain and has been instrumental in understanding the dynamics of the brain. However, the DMN has not been without critics; both conceptual and empirical. The empirical criticisms caution against physiological noise as a source for the reported connectivity in the DMN. Smaller flip angles (FAs) have been modelled and shown to reduce physiological noise in BOLD signal recordings. A previous functional MRI (fMRI) study with flickering checkerboard stimuli, manipulated FAs to show that activity in the posterior-cingulate cortex (PCC) and precuneus is prone to physiological noise. This raises questions about studies that show activations in these areas (PCC and precuneus) with a fixed FA and the role of these areas in brain networks like DMN. Given the prominent role of PCC and precuneus in DMN, we studied the effect of FAs on the resting-state functional connectivity involving these areas in DMN. We used four FAs and recorded resting-state activity in a 3-T scanner. The results show PCC and precuneus BOLD functional connectivity is inconsistent. We lend support to previous empirical criticisms of DMN, linking its activity to physiological noise. Our results add to concerns about PCC and precuneus related BOLD activity and their putative role in DMN. Alongside previous studies we advocate using smaller flip angles as an empirical tool to investigate physiological noise in fMRI studies.
The impact of the variation of imaging factors on the robustness of Computed Tomography Radiomic Features: A review
Authors: Reiazi Reza , Abbas Engy , Famiyeh Petra , Rezaie Aria , Kwan Jennifer Y. Y. , Patel Tirth , Bratman Scott V , Tadic Tony , Liu Fei-Fei , Haibe-Kains Benjamin 
Published: July 2020

ABSTRACTThe field of radiomics is at the forefront of personalized medicine. However, there are concerns regarding the robustness of its features against multiple medical imaging parameters and the performance of the predictive models built upon them. Therefore, our review aims to identify image perturbation factors (IPF) that most influence the robustness of radiomic features in biomedical research. We also provide insights into the validity and discrepancy of different methodologies applied to investigate the robustness of radiomic features. We selected 527 papers based on the primary criterion that the papers had imaging parameters that affected the reproducibility of radiomic features extracted from computed tomography (CT) images. We compared the reported performance of these parameters along with IPF in the eligible studies. We then proceeded to divide our studies into three groups based on the type of their IPF: (i) scanner parameters, (ii) acquisition parameters and (iii) reconstruction parameters. Our review highlighted that the reconstruction algorithm was the most reproducible factor and shape along with intensity histogram (IH) were the most robust radiomic features against variation in imaging parameters. This review identified substantial inconsistencies related to the methodology and the reporting style of the reviewed studies such as type of study performed, the metrics used for robustness, the feature extraction techniques, the image perturbation factors, the reporting style and their outcome inclusion. Finally, we hope the IPFs and the methodology inconsistencies identified will aid the scientific community in conducting research in a way that is more reproducible and avoids the pitfalls of previous analyses.
Huge Excess Mortality due to the delta strain of COVID-19 in Japan in August and September, 2021
Authors: Kurita Junko , Sugawara Tamie , Ohkusa Yasushi 
Published: July 2020

AbstractBackgroundNo remarkable mortality attributable to COVID-19 confirmed by PCR test has been observed in Japan.ObjectWe sought to quantify excess mortality using the National Institute of Infectious Diseases (NIID) model.MethodWe applied the NIID model to deaths of all causes from 1987 up through October, 2021 for the whole of Japan and up through August, 2021 for Tokyo.ResultsResults in Japan show huge number of excess mortality, up to 10 thousands in the two months, in August and September, 2021. On the other hand, in Tokyo, 1323 excess mortality was detectedDiscussion and ConclusionWe detected substantial excess mortality in Japan in August and September, 2021 and in Tokyo in August, 2021. It might be important to continue to monitor excess mortality of COVID-19 carefully hereafter.
Improving pandemic mitigation policies across communities through coupled dynamics of risk perception and infection
Authors: Silk Matthew J , Carrignon Simon , Bentley R. Alexander , Fefferman Nina H 
Published: July 2020

ABSTRACTDecisions to adhere to health-protective behaviors (e.g. mask-wearing, social distancing, etc.) that impact the spread of COVID-19 are not made in isolation by each individual. They are instead the result of the social construction of perceived risks and resulting community norms. In populations in which disease is unlikely to spread throughout all communities simultaneously, community-driven perception of risk can drastically alter collective outcomes. A community could respond to a few infections by becoming fearful and adopting anticipatory behaviors that protect them from disease spread. Similarly, there could be false reassurance, in which low disease incidence over time leads to community consensus that protective actions are unnecessary (even if they are the reason cases remains rare). We therefore model COVID-19 spread with three synergistic dynamics governing individual behavioral choices: (1) Social construction of concern, (2) Awareness of disease incidence, and (3) Reassurance by lack of disease. We use a multiplex network approach that captures social communication and epidemiological spread. We find that effective protective policies enacted too early may backfire by allowing a community to become reassured and therefore unwilling to adopt or maintain further protective behaviors. Based on these insights, we propose that public health policies for which success relies on collective action should be designed to exploit thebehaviourally receptive phase; the period between the generation of sufficient concern as to foster adoption of novel protective behaviors and the relaxation of adherence driven by reassurance fostered by avoidance of negative outcomes over time.
Assessing the impact of preventive mass vaccination campaigns on yellow fever outbreaks in Africa : a population-level self-controlled case-series study
Authors: Jean Kévin , Raad Hanaya , Gaythorpe Katy A. M. , Hamlet Arran , Mueller Judith E. , Hogan Dan , Mengistu Tewodaj , Whitaker Heather J. , Garske Tini , Hocine Mounia N. 
Published: July 2020

ABSTRACTIntroductionThe Eliminate Yellow fever Epidemics (EYE) strategy was launched in 2017 in response to the resurgence of yellow fever in Africa and the Americas. The strategy relies on several vaccination activities, including preventive mass vaccination campaigns (PMVCs). However, by how much PMVCs decrease the risk of outbreak to occur has not yet been quantified.MethodsWe used the self-controlled case series (SCCS) method to assess the association between the occurrence of yellow fever outbreaks and the implementation of PMVCs at the province level in the African endemic region. As all time-invariant confounders are implicitly controlled for, the SCCS method is an alternative to classical cohort or case-control study designs when the risk of residual confounding is high.The location and dates of outbreaks were identified from international epidemiological records, and information on PMVCs was provided by coordinators of vaccination activities and international funders. The study sample consisted of provinces that were both affected by an outbreak and targeted for a PMVC between 2005 and 2018. We compared the relative incidence of outbreaks before and after the implementation of a PMVC. The sensitivity of our estimates to a range of assumptions was explored, and the results of the SCCS method were compared to those obtained through a retrospective cohort study design. We further derived the number of yellow fever outbreaks that have been prevented by PMVCs.ResultsThe study sample consisted of 33 African provinces. Among these, outbreaks occurred during the pre-PMVC period in 26 (78.8%) provinces versus 7 (21.2%) occurring in the post-PMVC period. This corresponded to a significantly reduced incidence rate ratio of 0.14 (95% Confidence interval 0.06 to 0.34) for the post-PMVC versus pre-PMVC period. This estimate was robust across a range of sensitivity analyses, while the results of the cohort-style analyses were highly sensitive to the choice of covariates included in the model. Based on the SCCS results, we estimated that PMVCs have reduced the number of outbreaks by 34% (22% to 45%) in Africa over the study period.ConclusionOur estimates provide new empirical evidence of the high preventive impact of PMVCs on yellow fever outbreaks. This study illustrates that the SCCS method can be advantageously applied at the population level in order to evaluate a public health intervention.