Dynamic evolution of size and colour in the highly specialized Zodarion ant-eating spiders.

Ecological specialists constitute relevant case studies for understanding the mechanisms, potential and limitations of evolution. The species-rich and strictly myrmecophagous spiders of the genus Zodarion show diversified defence mechanisms, including myrmecomorphy of different ant species and nocturnality. Through Hybridization Capture Using RAD Probes (hyRAD), a phylogenomic technique designed for sequencing poorly preserved specimens, we reconstructed a phylogeny of Zodarion using 52 (approx. a third of the nominal) species that cover its phylogenetic and distributional diversity. We then estimated the evolution of body size and colour, traits that have diversified noticeably and are linked to defence mechanisms, across the group. Our genomic matrix of 300 loci led to a well-supported phylogenetic hypothesis that uncovered two main clades inside Zodarion. Ancestral state estimation revealed the highly dynamic evolution of body size and colour across the group, with multiple transitions and convergences in both traits, which we propose is likely indicative of multiple transitions in ant specialization across the genus. Our study will allow the informed targeted selection of Zodarion taxa of special interest for research into the group's remarkable adaptations to ant specialization. It also exemplifies the utility of hyRAD for phylogenetic studies using museum material.

Querying the In Vitro Proteome Cysteine Reactivity of 8:2 Fluorotelomer Acrylate.

Despite the phase out of legacy per- and polyfluoroalkyl substances (PFAS), fluorotelomer-based polymers (FTP) have been used for many applications, notably textile surface coatings. FTPs are of a health concern due to their breakdown into legacy PFAS and the co-occurrence of fluorotelomer acrylate (FTAC) monomers, of which the latter may potentially react with cellular thiols. To evaluate this hypothesis, we employed fluorous-solid-phase extraction (FSPE), to enrich peptides covalently modified by 8:2 fluorotelomer acrylate (8:2 FTAC) and coupled it to a modified nano-liquid chromatography method for the identification of in vitro protein adducts using bottom-up data-dependent proteomics analysis. Using this method, over 100 unique peptides were detected with 8:2 FTAC modifications, although none of the modified cysteine residues were annotated active site nucleophiles. In parallel, a synthetic C6F13-iodoacetamide (F13-IAM) chemical probe was used to gauge the upper bound of PFAS-thiol reactivity. Over seven hundred peptides were detected with modifications but only 9 of 28 annotated active site cysteines in this dataset were modified by F13-IAM. Further exploration of the impacts of 8:2 FTAC adducts on protein function revealed that 8:2 FTAC modification promotes protein aggregation in vitro. These results suggest that 8:2 FTAC may exhibit significant proteome thiol reactivity and imply a more general mechanism of toxicity of PFAS-induced protein aggregation.

Identifying Unknown Fluorine-Containing Compounds in Environmental Samples Using 19F NMR and Spectral Database Matching.

The ubiquity of per- and polyfluorinated alkyl substances (PFAS) in the environment is a continuing concern. While typical analytical methods for the analysis of PFAS include both targeted and non-targeted mass spectrometry, there remains a significant portion of fluorinated compounds that are not accounted for by these routine methods. It has been previously demonstrated that 19F NMR can be used to identify these compounds, helping to close the mass balance on total fluorine in the environment. 19F NMR offers an unbiased method of analysis that requires no anticipation of fluorine-carbon bonds or functional groups. However, there is resistance to further uptake of NMR spectroscopy as an analytical tool, owing to perceived difficulties in sensitivity and spectral overlap. In this study, we measure the 19F NMR spectrum of hundreds of fluorinated compounds and use this constructed database to determine the concentration of PFAS in an extracted sample of a known aqueous firefighting foam-contaminated site. The 19F NMR database has been included for use by other researchers, and we discuss the intricacies of 19F NMR as applied to environmental samples.

The identity of Argyrialacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens.

In this study the aim was to resolve the taxonomy of several species of Argyria Hübner (Pyraloidea, Crambinae) with previously unrecognised morphological variation. By analysing the DNA barcode (COI-5P) in numerous specimens, the aim was to reconstruct phylogenetic relationships between species, to provide better evidence for synonymies, and to circumscribe their geographical distribution. Using an innovative DNA hybridisation capture protocol, the DNA barcode of the lectotype of Argyrialacteella (Fabricius, 1794) was partially recovered for comparison with the 229 DNA barcode sequences of Argyria specimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. The same protocol was used for the following type specimens: the Argyriaabronalis (Walker, 1859) holotype, thus confirming the synonymy of this name with A.lacteella, the holotype of A.lusella (Zeller, 1863), syn. rev., the holotype of A.multifacta Dyar, 1914, syn. nov. newly synonymised with A.lacteella, and a specimen of Argyriadiplomochalis Dyar, 1913, collected in 1992. In addition, nine specimens of A.lacteella, A.diplomochalis, A.centrifugens Dyar, 1914 and A.gonogramma Dyar, 1915, from North to South America were sampled using classical COI amplification and Sanger sequencing. Argyriagonogramma Dyar, described from Bermuda, is the name to be applied to the more widespread North American species formerly identified as A.lacteella. Following morphological study of its holotype, Argyriavestalis Butler, 1878, syn. nov. is also synonymised with A.lacteella. The name A.pusillalis Hübner, 1818, is considered a nomen dubium associated with A.gonogramma. The adult morphology is diagnosed and illustrated, and distributions are plotted for A.lacteella, A.diplomochalis, A.centrifugens, and A.gonogramma based on slightly more than 800 specimens. For the first time, DNA barcode sequences are provided for the Antillean A.diplomochalis. This work provides a modified, improved protocol for the efficient hybrid capture enrichment of DNA barcodes from 18th and 19th century type specimens in order to solve taxonomic issues in Lepidoptera.

A field-validated equilibrium passive sampler for the monitoring of per- and polyfluoroalkyl substances (PFAS) in sediment pore water and surface water.

A simple equilibrium passive sampler, consisting of water in an inert container capped with a rate-limiting barrier, for the monitoring of per- and polyfluoroalkyl substances (PFAS) in sediment pore water and surface water was developed and tested through a series of laboratory and field experiments. The objectives of the laboratory experiments were to determine (1) the membrane type that could serve as the sampler's rate-limiting barrier, (2) the mass transfer coefficient of environmentally relevant PFAS through the selected membrane, and (3) the performance reference compounds (PRCs) that could be used to infer the kinetics of PFAS diffusing into the sampler. Of the membranes tested, the polycarbonate (PC) membrane was deemed the most suitable rate-limiting barrier, given that it did not appreciably adsorb the studied PFAS (which have ≤8 carbons), and that the migration of these compounds through this membrane could be described by Fick's law of diffusion. When employed as the PRC, the isotopically labelled PFAS M2PFOA and M4PFOS were able to predict the mass transfer coefficients of the studied PFAS analytes. In contrast, the mass transfer coefficients were underpredicted by Br- and M3PFPeA. For validation, the PC-based passive samplers consisting of these four PRCs, as well as two other PRCs (i.e., M8PFOA and C8H17SO3-), were deployed in the sediment and water at a PFAS-impacted field site. The concentration-time profiles of the PRCs indicated that the samplers deployed in the sediment required at least 6 to 7 weeks to reach 90% equilibrium. If the deployment times are shorter (e.g., 2 to 4 weeks), PFAS concentrations at equilibrium could be estimated based on the concentrations of the PRCs remaining in the sampler at retrieval. All PFAS concentrations determined via this approach were within a factor of two compared to those measured in the mechanically extracted sediment pore water and surface water samples obtained adjacent to the sampler deployment locations. Neither biofouling of the rate-limiting barrier nor any physical change to it was observed on the sampler after retrieval. The passive sampler developed in this study could be a promising tool for the monitoring of PFAS in pore water and surface water.

First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies.

The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.

Transcriptomic analysis of deceptively pollinated Arum maculatum (Araceae) reveals association between terpene synthase expression in floral trap chamber and species-specific pollinator attraction.

Deceptive pollination often involves volatile organic compound emissions that mislead insects into performing nonrewarding pollination. Among deceptively pollinated plants, Arum maculatum is particularly well-known for its potent dung-like volatile organic compound emissions and specialized floral chamber, which traps pollinators-mainly Psychoda phalaenoides and Psychoda grisescens-overnight. However, little is known about the genes underlying the production of many Arum maculatum volatile organic compounds, and their influence on variation in pollinator attraction rates. Therefore, we performed de novo transcriptome sequencing of Arum maculatum appendix and male floret tissue collected during anthesis and postanthesis, from 10 natural populations across Europe. These RNA-seq data were paired with gas chromatography-mass spectrometry analyses of floral scent composition and pollinator data collected from the same inflorescences. Differential expression analyses revealed candidate transcripts in appendix tissue linked to malodourous volatile organic compounds including indole, p-cresol, and 2-heptanone. In addition, we found that terpene synthase expression in male floret tissue during anthesis significantly covaried with sex- and species-specific attraction of Psychoda phalaenoides and Psychoda grisescens. Taken together, our results provide the first insights into molecular mechanisms underlying pollinator attraction patterns in Arum maculatum and highlight floral chamber sesquiterpene (e.g. bicyclogermacrene) synthases as interesting candidate genes for further study.

Noise-Reduced Quantitative Fluorine NMR Spectroscopy Reveals the Presence of Additional Per- and Polyfluorinated Alkyl Substances in Environmental and Biological Samples When Compared with Routine Mass Spectrometry Methods.

Per- and polyfluorinated alkyl substances (PFAS) are ubiquitous throughout the environment. Analysis of PFAS is commonly performed using both targeted and nontargeted mass spectrometry methods. However, it has been demonstrated that measurements of fluorinated compounds in the environment by mass spectrometry often fall short of the total fluorine concentration. In the present study, we employ a 19F NMR technique, which is capable of detailing fluorinated compounds in a sample while providing both quantitative and structural information. Inclusion of a noise-reduction strategy involving the acquisition of arrays of spectra with an increasing number of transients addresses the sensitivity challenges of environmental nuclear magnetic resonance (NMR), improving signal to noise. When this technique is applied to environmental and biological samples including rainwater, lake water, wastewater effluent, serum, and urine, the presence of PFAS, which may have been missed by routine mass spectrometric methods, is revealed. Important resonances in the 19F NMR spectrum such as that of trifluoroacetic acid are brought above the limit of quantification in all samples, allowing detection limits as low as 389 pg/L in rainwater. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, which was used to analyze 47 PFAS compounds, accounts for only 3.7-27% of the total fluorine concentration as determined by the NMR strategy in the present study.

Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly-The Ithomiini Melinaea marsaeus.

Ecological speciation entails divergent selection on specific traits and ultimately on the developmental pathways responsible for these traits. Selection can act on gene sequences but also on regulatory regions responsible for gene expression. Mimetic butterflies are a relevant system for speciation studies because wing colour pattern (WCP) often diverges between closely related taxa and is thought to drive speciation through assortative mating and increased predation on hybrids. Here, we generate the first transcriptomic resources for a mimetic butterfly of the tribe Ithomiini, Melinaea marsaeus, to examine patterns of differential expression between two subspecies and between tissues that express traits that likely drive reproductive isolation; WCP and chemosensory genes. We sequenced whole transcriptomes of three life stages to cover a large catalogue of transcripts, and we investigated differential expression between subspecies in pupal wing discs and antennae. Eighteen known WCP genes were expressed in wing discs and 115 chemosensory genes were expressed in antennae, with a remarkable diversity of chemosensory protein genes. Many transcripts were differentially expressed between subspecies, including two WCP genes and one odorant receptor. Our results suggest that in M. marsaeus the same genes as in other mimetic butterflies are involved in traits causing reproductive isolation, and point at possible candidates for the differences in those traits between subspecies. Differential expression analyses of other developmental stages and body organs and functional studies are needed to confirm and expand these results. Our work provides key resources for comparative genomics in mimetic butterflies, and more generally in Lepidoptera.

HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution.

Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosomaburchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.

The Sulfoximine Insecticide Sulfoxaflor and Its Photodegradate Demonstrate Acute Toxicity to the Nontarget Invertebrate Species Daphnia magna.

The environmental fate and persistence of sulfoxaflor is of significant interest given the potential for the insecticide to impact nontarget organisms, particularly pollinating and aquatic species. In the present study we examine the potential for sulfoxaflor, a new sulfoximine insecticide, to undergo degradation and transformation in sediments and the aquatic environment. Following application of the active substance as a foliar spray or seed coating, sulfoxaflor can be found in the soil at a mass percentage of up to 61% of the total applied concentration. The low soil sorption coefficient (KD ) of sulfoxaflor of 0.103 signifies the potential for sulfoxaflor to undergo transport into nearby surface waters via groundwater run-off. In soils and sediments sulfoxaflor produces a sulfoxaflor-urea analog with a varying half-life of 5.0 to 8.5 d depending on the sediment type. Once in surface waters, sulfoxaflor can undergo photolysis to a sulfoxaflor alcohol derivative with a half-life of 35 h. The photodegradate demonstrates reduced aquatic toxicity to Daphnia magna, but the photolytic half-life may be too long to mitigate the acute toxicity of the parent substance sulfoxaflor to D. magna, which was found to have a 48-h median effect concentration of 361 µg/L. Environ Toxicol Chem 2021;40:2156-2164. © 2021 SETAC.

Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization.

Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.

The Environmental Degradation and Distribution of Saflufenacil, a Fluorinated Protoporphyrinogen IX Oxidase-Inhibiting Herbicide, on a Canadian Winter Wheat Field.

Saflufenacil when applied to a field is susceptible to transport, degradation, and transformation. We used a laboratory-based approach to model the fate of saflufenacil in the environment, the results of which are compared directly with those observed in a field study where saflufenacil was applied to a crop of winter wheat at a standard rate of 63 g of active ingredient/hectare. The water solubility of 2.1 g/L for saflufenacil allows for vertical transport through soil at a rate of 4.3 cm/mL of rainwater, and a soil adsorption coefficient KOC of 28.8 suggests that some of the herbicide will absorb to the soil. Of the saflufenacil in the soil, 78 ± 2.1% (n = 18) partitioned into plants, including nontargeted crop species, where it was found primarily in leaves (78 ± 2.1%, n = 18) and roots (22 ± 1.7%, n = 18). The saflufenacil that does not partition into plants or undergo vertical transport followed a degradation pathway into 3 metabolites: a uracil-ring N-demethylated metabolite (Saf-µCH3 ), a doubly N-demethylated metabolite (Saf-2CH3 ), and a ring-cleavage metabolite (Saf-RC), identified using nontargeted mass spectrometry. In the field, saflufenacil was observed to degrade over 212 d to the persistent metabolite Saf-RC. This metabolite was found at a concentration that was 1/10th of that applied to the field, suggesting that the majority of saflufenacil had undergone transport through the soil, or uptake into the winter wheat crop. Field samples were further examined using F-19 nuclear magnetic resonance and nontargeted mass spectrometry to rule out the potential of other degradation products. Environ Toxicol Chem 2020;39:1918-1928. © 2020 SETAC.

What do tropical cryptogams reveal? Strong genetic structure in Amazonian bryophytes.

Lowland tropical bryophytes have been perceived as excellent dispersers. In such groups, the inverse isolation hypothesis proposes that spatial genetic structure is erased beyond the limits of short-distance dispersal. Here, we determine the influence of environmental variation and geographic barriers on the spatial genetic structure of a widely dispersed and phylogenetically independent sample of Amazonian bryophytes. Single nucleotide polymorphism data were produced from a restriction site-associated DNA sequencing protocol for 10 species and analyzed through F-statistics and Mantel tests. Neither isolation-by-environment nor the impact of geographic barriers were recovered from the analyses. However, significant isolation-by-distance patterns were observed for 8 out of the 10 investigated species beyond the scale of short-distance dispersal (> 1 km), offering evidence contrary to the inverse isolation hypothesis. Despite a cadre of life-history traits and distributional patterns suggesting that tropical bryophytes are highly vagile, our analyses reveal spatial genetic structures comparable to those documented for angiosperms, whose diaspores are orders of magnitude larger. Dispersal limitation for tropical bryophytes flies in the face of traditional assumptions regarding their dispersal potential, and suggests that the plight of this component of cryptic biodiversity is more dire than previously considered in light of accelerated forest fragmentation in the Amazon.

DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics.

Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism-SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.

Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland.

Erosion of biodiversity generated by anthropogenic activities has been studied for decades and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analysing museum collection specimens. While providing direct access to genetic variation over time, historical DNA is usually not optimally preserved, and it is necessary to apply genotyping methods based on hybridization-capture to unravel past genetic variation. In this study, we apply such a method (i.e., HyRAD), to large time series of two butterfly species in Finland, and present a new bioinformatic pipeline, namely PopHyRAD, that standardizes and optimizes the analysis of HyRAD data at the within-species level. In the localities for which the data retrieved have sufficient power to accurately examine genetic dynamics through time, we show that genetic erosion has increased across the last 100 years, as revealed by signatures of allele extinctions and heterozygosity decreases, despite local variations. In one of the two butterflies (Erebia embla), isolation by distance also increased through time, revealing the effect of greater habitat fragmentation over time.

Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone.

Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.

Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea.

Comparison of the molecular diversity in all plankton populations present in geographically distant water columns may allow for a holistic view of the connectivity, isolation and adaptation of organisms in the marine environment. In this context, a large-scale detection and analysis of genomic variants directly in metagenomic data appeared as a powerful strategy for the identification of genetic structures and genes under natural selection in plankton. Here, we used discosnp++, a reference-free variant caller, to produce genetic variants from large-scale metagenomic data and assessed its accuracy on the copepod Oithona nana in terms of variant calling, allele frequency estimation and population genomic statistics by comparing it to the state-of-the-art method. discosnp ++ produces variants leading to similar conclusions regarding the genetic structure and identification of loci under natural selection. discosnp++ was then applied to 120 metagenomic samples from four size fractions, including prokaryotes, protists and zooplankton sampled from 39 tara Oceans sampling stations located in the Atlantic Ocean and the Mediterranean Sea to produce a new set of marine genomic markers containing more than 19 million of variants. This new genomic resource can be used by the community to relocate these markers on their plankton genomes or transcriptomes of interest. This resource will be updated with new marine expeditions and the increase of metagenomic data (availability: http://bioinformatique.rennes.inria.fr/taravariants/).

Genetic footprints of adaptive divergence in the bracovirus of Cotesia sesamiae identified by targeted resequencing.

The African parasitoid wasp Cotesia sesamiae is a generalist species structured in locally adapted populations showing differences in host range. The recent discovery of Cotesia typhae, a specialist, sister species to C. sesamiae, provides a good framework to study the genetic determinants of parasitoid host range. To investigate the genomic bases of divergence between these populations and species, we used a targeted sequencing approach on 24 samples. We targeted the bracovirus genomic region encoding virulence genes involved in the interaction with the lepidopteran hosts of the wasps. High sequencing coverage was obtained for all samples, allowing the study of genetic variation between wasp populations and species. By combining population genetic estimations, such as nucleotide diversity (π), relative differentiation (FST ) and absolute divergence (dxy ), with branch-site dN/dS measures, we identified six of 98 bracovirus genes showing significant divergence and evidence of positive selection. These genes, belonging to different gene families, are potentially involved in host adaptation and in the specialization process. Fine-scale analyses of genetic variation also revealed mutations and large deletions in certain genes inducing pseudogenization and loss of function. The image emerging from these results is that adaptation mediated by bracovirus genes happens through selection of particularly adaptive alleles and loss of nonadaptive genes. These results highlight the central role of the bracovirus in the molecular interactions between the wasps and their hosts and in the evolutionary processes of specialization.