Genome scan to assess the respective role of host-plant and environmental constraints on the adaptation of a widespread insect

<p>Abstract</p> <p>Background</p> <p>The evolutionary success of phytophagous insects could result from their adaptation to different host-plants. Alternatively, the diversification of widespread species might be driven by adaptation along environmental gradients. To disentangle the respective roles of host-plant versus abiotic environmental variables acting on the genome of an oligophagous insect, we performed a genome scan using 83 unlinked AFLP markers on larvae of the large pine weevil collected on two host-plants (pine and spruce) in four forestry regions across Europe.</p> <p>Results</p> <p>At this large geographic scale, the global genetic differentiation was low and there was no isolation by distance pattern, suggesting that migration is overwhelming genetic drift in this species. In this context, the widely used frequentist methods to detect outliers (e.g. Dfdist), which assume migration - drift equilibrium are not the most appropriate approach. The implementation of a recently developed Bayesian approach, conceived to detect outliers even in non-equilibrium situations, consistently detected 9 out of 83 loci as outliers. Eight of these were validated as outliers by multiple logistic regressions: six correlated with environmental variables, one with host-plant and one with the interaction between environmental variables and host-plant.</p> <p>Conclusion</p> <p>These results suggest a relatively greater importance of abiotic environmental variables, as opposed to factors linked with the host-plant, in shaping genetic differentiation across the genome in this species. Logistic regression allows the nature of factors involved in locus-specific selection to be precisely identified and represents another step forward in the process of identifying adaptive loci.</p

Plant chemical defence: a partner control mechanism stabilising plant - seed-eating pollinator mutualisms

<p>Abstract</p> <p>Background</p> <p>Mutualisms are inherently conflictual as one partner always benefits from reducing the costs imposed by the other. Despite the widespread recognition that mutualisms are essentially reciprocal exploitation, there are few documented examples of traits that limit the costs of mutualism. In plant/seed-eating pollinator interactions the only mechanisms reported so far are those specific to one particular system, such as the selective abortion of over-exploited fruits.</p> <p>Results</p> <p>This study shows that plant chemical defence against developing larvae constitutes another partner sanction mechanism in nursery mutualisms. It documents the chemical defence used by globeflower <it>Trollius europaeus </it>L. (Ranunculaceae) against the seed-eating larvae of six pollinating species of the genus <it>Chiastocheta </it>Pokorny (Anthomyiidae). The correlative field study carried out shows that the severity of damage caused by <it>Chiastocheta </it>larvae to globeflower fruits is linked to the accumulation in the carpel walls of a C-glycosyl-flavone (adonivernith), which reduces the larval seed predation ability per damaged carpel. The different <it>Chiastocheta </it>species do not exploit the fruit in the same way and their interaction with the plant chemical defence is variable, both in terms of induction intensity and larval sensitivity to adonivernith.</p> <p>Conclusion</p> <p>Adonivernith accumulation and larval predation intensity appear to be both the reciprocal cause and effect. Adonivernith not only constitutes an effective chemical means of partner control, but may also play a key role in the sympatric diversification of the <it>Chiastocheta </it>genus.</p

Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations

<p>Abstract</p> <p>Background</p> <p>Genome scans are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation, but on their own, they are often helpless at identifying the specific gene(s) or mutation(s) targeted by selection. This shortcoming is hopefully bound to disappear in the near future, thanks to the wealth of new genomic resources that are currently being developed for many species. In this article, we provide a foretaste of this exciting new era by conducting a genome scan in the mosquito <it>Aedes aegypti </it>with the aim to look for candidate genes involved in resistance to <it>Bacillus thuringiensis </it>subsp. <it>israelensis </it>(<it>Bti</it>) insecticidal toxins.</p> <p>Results</p> <p>The genome of a <it>Bti</it>-resistant and a <it>Bti</it>-susceptible strains was surveyed using about 500 MITE-based molecular markers, and the loci showing the highest inter-strain genetic differentiation were sequenced and mapped on the <it>Aedes aegypti </it>genome sequence. Several good candidate genes for <it>Bti</it>-resistance were identified in the vicinity of these highly differentiated markers. Two of them, coding for a cadherin and a leucine aminopeptidase, were further examined at the sequence and gene expression levels. In the resistant strain, the cadherin gene displayed patterns of nucleotide polymorphisms consistent with the action of positive selection (e.g. an excess of high compared to intermediate frequency mutations), as well as a significant under-expression compared to the susceptible strain.</p> <p>Conclusion</p> <p>Both sequence and gene expression analyses agree to suggest a role for positive selection in the evolution of this cadherin gene in the resistant strain. However, it is unlikely that resistance to <it>Bti </it>is conferred by this gene alone, and further investigation will be needed to characterize other genes significantly associated with <it>Bti </it>resistance in <it>Ae. aegypti</it>. Beyond these results, this article illustrates how genome scans can build on the body of new genomic information (here, full genome sequence and MITE characterization) to finally hold their promises and help pinpoint candidate genes for adaptation and speciation.</p

Amplified fragment length homoplasy: in silico analysis for model and non-model species

<p>Abstract</p> <p>Background</p> <p>AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species.</p> <p>Results</p> <p>In this study we performed <it>in silico </it>AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (<it>Bacillus thuringiensis </it>ser. <it>konkukian</it>), a plant (<it>Arabidopsis thaliana</it>) and an animal (<it>Aedes aegypti</it>). In addition, we compared <it>in silico </it>AFLPs to empirical data obtained from three related non-model species (<it>Bacillus thuringiensis </it>ser. <it>israelensis, Arabis alpina </it>and <it>Aedes rusticus</it>). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in <it>Ae. aegypti</it>. Finally, we show that <it>in silico </it>AFLPs can help to accurately predict AFLP profiles in related non-model species.</p> <p>Conclusions</p> <p>These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at <url>http://www-leca.ujf-grenoble.fr/logiciels.htm</url>.</p

A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection

<p>Abstract</p> <p>Background</p> <p>For most organisms, developing hundreds of genetic markers spanning the whole genome still requires excessive if not unrealistic efforts. In this context, there is an obvious need for methodologies allowing the low-cost, fast and high-throughput genotyping of virtually any species, such as the Diversity Arrays Technology (DArT). One of the crucial steps of the DArT technique is the genome complexity reduction, which allows obtaining a genomic representation characteristic of the studied DNA sample and necessary for subsequent genotyping. In this article, using the mosquito <it>Aedes aegypti </it>as a study model, we describe a new genome complexity reduction method taking advantage of the abundance of miniature inverted repeat transposable elements (MITEs) in the genome of this species.</p> <p>Results</p> <p><it>Ae. aegypti </it>genomic representations were produced following a two-step procedure: (1) restriction digestion of the genomic DNA and simultaneous ligation of a specific adaptor to compatible ends, and (2) amplification of restriction fragments containing a particular MITE element called <it>Pony </it>using two primers, one annealing to the adaptor sequence and one annealing to a conserved sequence motif of the <it>Pony </it>element. Using this protocol, we constructed a library comprising more than 6,000 DArT clones, of which at least 5.70% were highly reliable polymorphic markers for two closely related mosquito strains separated by only a few generations of artificial selection. Within this dataset, linkage disequilibrium was low, and marker redundancy was evaluated at 2.86% only. Most of the detected genetic variability was observed between the two studied mosquito strains, but individuals of the same strain could still be clearly distinguished.</p> <p>Conclusion</p> <p>The new complexity reduction method was particularly efficient to reveal genetic polymorphisms in <it>Ae. egypti</it>. Overall, our results testify of the flexibility of the DArT genotyping technique and open new prospects as regards its application to a wider range of species, including animals which have been refractory to it so far. DArT has also a role to play in the current burst of whole-genome scans carried out in various organisms, which track signatures of selection in order to unravel the basis of genetic adaptation.</p

Écosystème numérique DESIIR : Données Environnementales et de Santé Intégrées pour une Infrastructure de Recherche

La pandémie de COVID-19 a souligné l’interdépendance des espèces vivantes et de leur environnement, menant au concept de « One Health ». Celui-ci implique une démarche intersectorielle afin de répondre aux enjeux complexes de santé incluant l’impact des changements climatiques sur la santé respiratoire et allergique. Ainsi, ce projet vise à regrouper les données de recherche générées au Saguenay–Lac-Saint-Jean (SLSJ) depuis les années 1970 en environnement, en santé physique et psychosociale et sur la structure populationnelle au sein d’un écosystème numérique nommé DESIIR (Données Environnementales et de Santé Intégrées pour une Infrastructure de Recherche). Le premier volet de ce projet vise à regrouper ces données dans un environnement sécurisé répondant aux principes FAIR et respectant les lois québécoises sur la protection des données. Le deuxième volet utilisera l’asthme comme modèle afin de démontrer l’ampleur des possibilités qu’offrira DESIIR. Le troisième volet aura comme objectif d’évaluer la complétude des différents ensembles de données, de planifier des programmes de recherche pour combler les lacunes identifiées et de développer un plan de valorisation de DESIIR pour maximiser sa visibilité et son utilisation. DESIIR est un vaste projet d’infrastructure qui implique une équipe de 30 chercheuses et chercheurs provenant de 9 établissements universitaires qui sera réalisé en partenariat avec le Centre intégré de santé et de service sociaux du SLSJ, le Cégep de Jonquière, ville Saguenay ainsi que « Secure Data 4 Health » pour la construction de l’infrastructure. Ces chercheurs, chercheuses et partenaires assurent actuellement la gestion des données qui seront regroupées dans DESIIR et la gouvernance du projet. À terme, DESIIR fournira des données conformes aux principes FAIR, de multiples opportunités pour le développement de nouveaux projets de recherche novateurs, des modèles d’analyse qui pourront être élargis à d'autres traits complexes ainsi qu’une preuve de concept de la valeur ajoutée d'un tel écosystème. Il favorisera le développement d’une approche holistique de la recherche en santé durable conduisant au développement et à l’application de nouveaux modèles de prévention et de gestion de la santé. DESIIR contribuera à bâtir un modèle socioéconomique innovant en santé durable pour la population du SLSJ

Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation (PERSPECTIVE I&I).

Early detection of breast cancer through screening reduces breast cancer mortality. The benefits of screening must also be considered within the context of potential harms (e.g., false positives, overdiagnosis). Furthermore, while breast cancer risk is highly variable within the population, most screening programs use age to determine eligibility. A risk-based approach is expected to improve the benefit-harm ratio of breast cancer screening programs. The PERSPECTIVE I&I (Personalized Risk Assessment for Prevention and Early Detection of Breast Cancer: Integration and Implementation) project seeks to improve personalized risk assessment to allow for a cost-effective, population-based approach to risk-based screening and determine best practices for implementation in Canada. This commentary describes the four inter-related activities that comprise the PERSPECTIVE I&I project. 1: Identification and validation of novel moderate to high-risk susceptibility genes. 2: Improvement, validation, and adaptation of a risk prediction web-tool for the Canadian context. 3: Development and piloting of a socio-ethical framework to support implementation of risk-based breast cancer screening. 4: Economic analysis to optimize the implementation of risk-based screening. Risk-based screening and prevention is expected to benefit all women, empowering them to work with their healthcare provider to make informed decisions about screening and prevention

The CardioMetabolic Health Alliance Working Toward a New Care Model for the Metabolic Syndrome

AbstractThe Cardiometabolic Think Tank was convened on June 20, 2014, in Washington, DC, as a “call to action” activity focused on defining new patient care models and approaches to address contemporary issues of cardiometabolic risk and disease. Individual experts representing >20 professional organizations participated in this roundtable discussion. The Think Tank consensus was that the metabolic syndrome (MetS) is a complex pathophysiological state comprised of a cluster of clinically measured and typically unmeasured risk factors, is progressive in its course, and is associated with serious and extensive comorbidity, but tends to be clinically under-recognized. The ideal patient care model for MetS must accurately identify those at risk before MetS develops and must recognize subtypes and stages of MetS to more effectively direct prevention and therapies. This new MetS care model introduces both affirmed and emerging concepts that will require consensus development, validation, and optimization in the future