Defining what constitutes a reliable dataset to test for hybridization and introgression in marine zooplankton: Comment on Choquet et al. 2020 “No evidence for hybridization between Calanus finmarchicus and C. glacialis in a subarctic area of sympatry”

The article ‘No evidence for hybridization between Calanus finmarchicus and C. glacialis in a subarctic area of sympatry’ (Choquet et al. 2020) concludes that “no evidence supports a potential for hybridization between C. finmarchicus and C. glacialis”. We argue that the InDel markers used by Choquet et al. (2020) may have limited capacity to detect admixed genotypes between C. finmarchicus and C. glacialis due to an inappropriate choice of reference sample for each species during the marker development. We first review terms and concepts used in genetic classification using reference samples and describe problems associated with the selection of genetic markers in the context of possible hybridization. We reanalyze InDel genotypes provided with Choquet et al. (2017) and identified an admixed individual. We then contrast methods used by Choquet et al. (2017) and Parent et al. (2012) and explain how Parent et al. (2012) developed microsatellite markers capable of discriminating admixed genotypes from parental species. In this comment, we have identified a major issue that must be considered when selecting reference samples in the context of testing for possible hybridization.publishedVersio

Insect herbivory (Choristoneura fumiferana, Tortricidea) underlies tree population structure (Picea glauca, Pinaceae)

Variation in insect herbivory can lead to population structure in plant hosts as indicated by defence traits. In annual herbaceous, defence traits may vary between geographic areas but evidence of such patterns is lacking for long-lived species. This may result from the variety of selection pressures from herbivores, long distance gene flow, genome properties, and lack of research. We investigated the antagonistic interaction between white spruce (Picea glauca) and spruce budworm (SBW, Choristoneura fumiferana) the most devastating forest insect of eastern North America in common garden experiments. White spruces that are able to resist SBW attack were reported to accumulate the acetophenones piceol and pungenol constitutively in their foliage. We show that levels of these acetophenones and transcripts of the gene responsible for their release is highly heritable and that their accumulation is synchronized with the most devastating stage of SBW. Piceol and pungenol concentrations negatively correlate with rate of development in female SBW and follow a non-random geographic variation pattern that is partially explained by historical damage from SBW and temperature. Our results show that accumulation of acetophenones is an efficient resistance mechanism against SBW in white spruce and that insects can affect population structure of a long-lived plant

The lack of genetic variation underlying thermal transcriptomic plasticity suggests limited adaptability of the Northern shrimp, Pandalus borealis

Introduction: Genetic variation underlies the populations’ potential to adapt to and persist in a changing environment, while phenotypic plasticity can play a key role in buffering the negative impacts of such change at the individual level. Methods: We investigated the role of genetic variation in the thermal response of the northern shrimp Pandalus borealis, an ectotherm species distributed in the Arctic and North Atlantic Oceans. More specifically, we estimated the proportion transcriptomic responses explained by genetic variance of female shrimp from three origins after 30 days of exposure to three temperature treatments. Results: We characterized the P. borealis transcriptome (170,377 transcripts, of which 27.48% were functionally annotated) and then detected a total of 1,607 and 907 differentially expressed transcripts between temperatures and origins, respectively. Shrimp from different origins displayed high but similar level of transcriptomic plasticity in response to elevated temperatures. Differences in transcript expression among origins were not correlated to population genetic differentiation or diversity but to environmental conditions at origin during sampling. Discussion: The lack of genetic variation explaining thermal plasticity suggests limited adaptability in this species’ response to future environmental changes. These results together with higher mortality observed at the highest temperature indicate that the thermal niche of P. borealis will likely be restricted to higher latitudes in the future. This prediction concurs with current decreases in abundance observed at the southern edge of this species geographical distribution, as it is for other cold-adapted crustaceans. Keywords : phenotypic plasticity ; climate change ; ocean warming ; crustacean ; decapod ; fisheries ; RNA-seq

Mutations in TUBG1, DYNC1H1, KIF5C and KIF2A cause malformations of cortical development and microcephaly

The genetic causes of malformations of cortical development (MCD) remain largely unknown. Here we report the discovery of multiple pathogenic missense mutations in TUBG1, DYNC1H1 and KIF2A, as well as a single germline mosaic mutation in KIF5C, in subjects with MCD. We found a frequent recurrence of mutations in DYNC1H1, implying that this gene is a major locus for unexplained MCD. We further show that the mutations in KIF5C, KIF2A and DYNC1H1 affect ATP hydrolysis, productive protein folding and microtubule binding, respectively. In addition, we show that suppression of mouse Tubg1 expression in vivo interferes with proper neuronal migration, whereas expression of altered gamma-tubulin proteins in Saccharomyces cerevisiae disrupts normal microtubule behavior. Our data reinforce the importance of centrosomal and microtubule-related proteins in cortical development and strongly suggest that microtubule-dependent mitotic and postmitotic processes are major contributors to the pathogenesis of MCD

Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes

Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts’ maps could uncover functionally and clinically related genes.Molecular Psychiatry advance online publication, 31 May 2016; doi:10.1038/mp.2016.84

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Acclimatation thermique de la palourde américaine, Mercenaria mercenaria : expérimentation en jardin commun

Chez les poïkilothermes, l'adaptation homéovisqueuse est le paradigme le plus utilisé pour expliquer le remodelage des lipides membranaires en fonction de la température. La présente étude vise à déterminer la capacité adaptative de la palourde américaine (Mercenaria mercenaria) à l'aide des différents mécanismes de remodelage des lipides membranaires en comparant, en jardin commun, des animaux de différentes origines de la côte est canadienne. Les résultats obtenus montrent que lors d'une diminution de température les différentes modifications apportées au sein des membranes cellulaires sont semblables et ne varient pas en fonction de l' origine des animaux. Ces résultats concordent avec la faible différentiation génétique observée entre les sites. Toutefois, une séquence de mécanismes de remodelage des lipides membranaires, qui semble liée à la physiologie de l'espèce, est observée chez tous les animaux. De plus, il semble que les branchies de M mercenaria soient soumises à une régulation stricte de leur contenu lipidique puisqu'il diffère des sources environnementales de lipides. Finalement, cette étude montre un lien important entre l'environnement, la physiologie de l'espèce et l'adaptation homéovisqueuse chez les poïkilothermes

Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species

Abstract Background Reference genomes provide a foundational framework for evolutionary investigations, ecological analysis, and conservation science, yet uncertainties in the assembly of reference genomes are difficult to assess, and by extension rarely quantified. Reference genomes for monodontid cetaceans span a wide spectrum of data types and analytical approaches, providing the context to derive broader insights related to discrepancies and regions of uncertainty in reference genome assembly. We generated three beluga (Delphinapterus leucas) and one narwhal (Monodon monoceros) reference genomes and contrasted these with published chromosomal scale assemblies for each species to quantify discrepancies associated with genome assemblies. Results The new reference genomes achieved chromosomal scale assembly using a combination of PacBio long reads, Illumina short reads, and Hi-C scaffolding data. For beluga, we identified discrepancies in the order and orientation of contigs in 2.2–3.7% of the total genome depending on the pairwise comparison of references. In addition, unsupported higher order scaffolding was identified in published reference genomes. In contrast, we estimated 8.2% of the compared narwhal genomes featured discrepancies, with inversions being notably abundant (5.3%). Discrepancies were linked to repetitive elements in both species. Conclusions We provide several new reference genomes for beluga (Delphinapterus leucas), while highlighting potential avenues for improvements. In particular, additional layers of data providing information on ultra-long genomic distances are needed to resolve persistent errors in reference genome construction. The comparative analyses of monodontid reference genomes suggested that the three new reference genomes for beluga are more accurate compared to the currently published reference genome, but that the new narwhal genome is less accurate than one published. We also present a conceptual summary for improving the accuracy of reference genomes with relevance to end-user needs and how they relate to levels of assembly quality and uncertainty

L’évaluation structurée du risque de récidive des personnes placées sous main de justice : méthodes et enjeux

International audienceAlors que la prévention de la récidive est en train de subir nombre de transformations en France, l’évaluation du risque de récidive des personnes placées sous main de justice constitue un enjeu majeur. L’absence de structuration et de standardisation des évaluations soulevé des doutes a propos de leur validité et souligne la nécessite de recourir a des méthodes d’évaluation cliniquement et scientifiquement validées. Les professionnels et leurs administrations bénéficient désormais d’un éventail de stratégies pour effectuer une évaluation la plus juste, la plus transparente et la plus cohérente possible. Cet article retrace l’évolution de l’évaluation du risque de récidive, les principales stratégies et méthodes, les familles de facteurs de risque les plus couramment utilises, en plus d’illustrer deux stratégies d’évaluation typiques dans le champ de l’évaluation du risque récidive, l’évaluation intégrée a l’aide du LS/CMI et l’évaluation basée sur le jugement professionnel structure a l’aide de la HCR-20

Hydroxyacetophenone defenses in white spruce against spruce budworm

We review a recently discovered white spruce (Picea glauca) chemical defense against spruce budworm (Choristoneura fumiferana) involving hydroxyacetophenones. These defense metabolites detected in the foliage accumulate variably as the aglycons, piceol and pungenol, or the corresponding glucosides, picein and pungenin. We summarize current knowledge of the genetic, genomic, molecular, and biochemical underpinnings of this defense and its effects on C. fumiferana. We present an update with new results on the ontogenic variation and the phenological window of this defense, including analysis of transcript responses in P. glauca to C. fumiferana herbivory. We also discuss this chemical defense from an evolutionary and a breeding context.publishedVersio