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The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual drones, multiple drones, and pooled workers. Here, we compare introgression estimates via three genetic approaches: SNP array, individual RAD-seq, and pooled colony RAD-seq. We also compare two statistical approaches: a maximum likelihood cluster program (ADMIXTURE) and an incomplete lineage sorting model (ABBA BABA). Overall, individual approaches resulted in lower introgression estimates than pooled colonies when using ADMIXTURE. However, the pooled colony ABBA BABA approach resulted in generally lower introgression estimates than all three ADMIXTURE estimates. These results highlight that sometimes one individual is not enough to assess colony-level introgression, and future studies that do use colony pools should not be solely dependent on clustering programs for introgression estimates.

We used the methanol-to-hydrocarbon (MTH) reaction as a shape-selective model reaction to investigate coke formation in zeolite H-Ferrierite. Despite being a 2D topology in terms of channel propagation, the FER framework displays a lattice expansion in all three dimensions of space upon deactivation. Therefore, the volume of the unit cell is an excellent X-Ray diffraction (XRD) descriptor for the catalyst deactivation. A model with dummy atoms added, also proved to be an accurate approach to measure the amount of internal coke and/or water inside the pore network correlated with thermogravimetric analysis results. While the catalyst deactivation of the H-Ferrerite during the MTH was fast, a comparably long induction period was observed. We were able to track such fast deactivation with the aforementioned descriptors by means of an operando XRD study by a standard laboratory diffractometer.

This study presents the adsorption capability of a filter composed of sand coated with cobalt nanomaterials (CoNM) for the extraction of manganese ions from aqueous media. The study was performed in both batch and dynamic modes in order to evaluate the adsorption capabilities of free-standing CoNM and CoNM-coated sand. The Langmuir and Freundlich isotherm models were applied to the adsorption of manganese ions in batch-mode. The Langmuir model estimated a maximum adsorption capacity of 17.86 mg/g corresponding to a single layer adsorption. Nevertheless, the Freundlich model also characterized the adsorption with a high coefficient of determination, suggesting a multilayered adsorption mechanism of Mn on CoNM. Dynamic mode studies were conducted with different influent Mn concentrations, pH and in the presence of foreign or competing ions (Fe3+, As3+, As5+ and Cu2+). The experimental data was fitted with linearized Thomas and Yoon-Nelson models in order to determine adsorption capacities. The multilayered adsorption mechanism was confirmed owing to a high adsorption capacity of 3360 mg/g of active nanomaterials at pH = 6.

Honey bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environ-ment and mate naturally with queens from the local subspecies. The resulting ad-mixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to sub-species, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP- chip or by low- pass sequencing, or (iii) selecting SNPs compatible with the re-quirements of genotyping chips. This work was performed in collaboration with the GeT platform, Toulouse (France), a partner of the National Infrastructure France Génomique, thanks to support by the Commissariat aux Grands Invetissements (ANR-10- INBS-0009). Bioinformatics analyses were performed on the GenoToul Bioinfo computer cluster. This work was funded by a grant from the INRA Département de Génétique Animale (INRA Animal Genetics division) and by the SeqApiPop pro-gramme, funded by the FranceAgriMer grant 14-21- AT. We thank John Kefuss for helpful discussions. We thank Andrew Abrahams for providing honey bee samples from Colonsay (Scotland), the Association Conservatoire de l'Abeille Noire Bretonne (ACANB) for samples from Ouessant (France), CETA de Savoie for sample from Savoie, ADAPI for samples from Porquerolles and all beekeepers and bee breeders who kindly participated in this study by providing sam-ples from their colonies. info:eu-repo/semantics/publishedVersion

We have used operando 5D synchrotron total scattering computed tomography (TSCT) to understand the cycling and possible long term deactivation mechanisms of the lithium-ion battery anode bismuth vanadate. This anode material functions via a combined conversion/alloying mechanism in which nanocrystals of lithium-bismuth alloy are protected by an amorphous matrix of lithium vanadate. This composite is formed in situ during the first lithiation of the anode. The operando TSCT data were analyzed and mapped using both pair distribution function and Rietveld methods. We can follow the lithium-bismuth alloying reaction at all stages, gaining real structural insight including variations in nanoparticle sizes, lattice parameters and bond lengths, even when the material is completely amorphous. We also observe for the first time structural changes related to the cycling of lithium ions in the lithium vanadate matrix which displays no order beyond the first shell of V-O bonds. The first 3D operando mapping of the distribution of different materials in an amorphous anode reveals a decline in coverage caused by either agglomeration or partial dissolution of the active material, hinting at the mechanism of long-term deactivation. The numerous observations from the operando experiment are backed up by post mortem HRTEM studies and theoretical calculations to provide a complete picture of an exceptionally complex cycling mechanism.

Honey bee subspecies originate from specific geographic areas in Africa, Europe and the Middle East. The interest of beekeepers in specific phenotypes has led them to import subspecies to regions outside of their original range. The resulting admixture complicates population genetics analyses and population stratification can be a major problem for association studies. As a typical example, the case of the French population is studied here. We sequenced 870 haploid drones for SNP detection and identified nine genetic backgrounds in 629 samples. Five correspond to subspecies, two to isolated populations and two to human-mediated population management. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long on chromosome 11, representing 1.6 % of the genome and has two major haplotypes, corresponding to the two dominant genetic backgrounds identified.

Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanningBMP15, suggesting this to be the primary candidate prolificacy gene in the breed. The analysis also identified several candidate regions spanning genes not reported before in prolific sheep but underlying fertility and reproduction in other species. The genes associated with female reproduction traits includedSPOCK1(age at first oestrus),GPR173(mediator of ovarian cyclicity),HB-EGF(signalling early pregnancy success) andSMARCAL1andHMGN3a(regulate gene expression during embryogenesis). The genes involved in male reproduction wereFOXJ1(sperm function and successful fertilization) andNME5(spermatogenesis). We also observed genes such asPKD2L2,MAGED1andKDM3B, which have been associated with diverse fertility traits in both sexes of other species. The results confirm the complexity of the genetic mechanisms underlying reproduction while suggesting that prolificacy in the Bonga sheep, and possibly African indigenous sheep is partly under the control ofBMP15while other genes that enhance male and female fertility are essential for reproductive fitness.

Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

East Coast fever, a tick-borne cattle disease caused by theTheileria parvaparasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Boran cattle demonstrating heritable tolerance to infection byT. parva(h2= 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region onBos tauruschromosome 15 that is significantly associated with survival outcome followingT. parvaexposure. Testing this locus in an independent cohort of animals replicates this association with survival followingT. parvainfection. A stop gained polymorphism in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa’s most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection byT. parva.Author SummaryMore than a million cattle die of East Coast fever in Africa each year, the impact of which disproportionately falls onto low-income, smallholder farmers. The lack of a widely accessible vaccine, heavy reliance on chemicals to control the tick vector and inadequate drug treatments means that new approaches for controlling the disease are urgently required. Through a genetic study of an extended pedigree of Boran cattle that are more than three times less likely to succumb to the disease than matched controls, we identify a region on chromosome 15 of the cattle genome associated with a high level of tolerance to the disease. We show that a variant in this region is also associated with survival in an independent cohort, and is linked to rates of cell expansion during infection. This genetic variant can therefore support marker-assisted selection, allowing farmers to breed tolerant cattle and offers a route to introduce this beneficial DNA to non-native breeds, enabling reduced disease incidence and increased productivity, which would be of benefit to millions of rural smallholder farmers across Africa.

International audience; Throughout western Europe, the endemic honeybee subspecies Apis mellifera mellifera, the black bee, has gradually been replaced in many beekeeper operations by other subspecies and hybrids of A. m. ligustica, A. m. carnica, A.m. caucasica, (C-type bees) and A. m. mellifera (M-type bees), which were found to be more efficient producers of honey or royal jelly, and also to be less aggressive. In order to understand the impact of these practices on the genomes of bee populations we followed two complementary approaches. The first was to produce a high-continuity reference genome for M-type bees by PacBio sequencing, for comparison with the current Amel_HAv3.1 reference-a C-type bee. A single haploid drone from a closed population was selected for sequencing and the overall genome assembly obtained is 227 Mb for the 16 chromosomes. The longest contig obtained is 11.6 Mb, the N50 contig size is 5.1 Mb and chromosome 16 was obtained as a single 7.2 Mb contig. Contigs were ordered along chromosomes by minimizing genetic recombination. Comparison with Amel_HAv3.1 allowed the high confidence detection of inversions between the two reference genomes. Long-read sequencing also allowed the discovery of new highly repeated elements. The second approach is the sequencing of several hundred haploid drones from separate colonies, which includes black bee conservatories, French queen breeders (honey and royal jelly production) as well as out-groups from various European regions from where genetic stock is imported for breeding purposes. Varying degrees of admixture between the M-and C-type bees are observed, often reflecting different breeding practices. Regions of high differentiation between the two genetic types are also detected.

The title compound, an (N^C)-cyclo­metalated gold(III) diazide, namely, di­azido­[5-eth­oxy­carbonyl-2-(5-eth­oxy­carbonyl­pyridin-2-yl)phenyl-κ2 C 1,N]gold(III), [Au(C17H16NO4)(N3)2] or Au(ppyEt)(N3)2, was synthesized by reacting Au(ppyEt)Cl2 with NaN3 in water for 24 h. The complex features a gold center with a square-planar environment., The title compound, an (N^C)-cyclo­metalated gold(III) diazide, namely, di­azido­[5-eth­oxy­carbonyl-2-(5-eth­oxy­carbonyl­pyridin-2-yl)phenyl-κ2 C 1,N]gold(III), [Au(C17H16NO4)(N3)2] or Au(ppyEt)(N3)2, was synthesized by reacting Au(ppyEt)Cl2 with NaN3 in water for 24 h. The complex has been structurally characterized and features a gold center with a square-planar environment. The Au—N(azide) bond lengths are significantly different depending on the influence of the atom trans to the azide group [Au—N(trans to C) of 2.067 (2) Å versus Au—N(trans to N) of 2.042 (2) Å]. The azide groups are twisted in-and-out of plane by 56.2 (2)°.

BackgroundHybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chickenGallus gallus domesticusis the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes.ResultsIn this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wildGallusspecies. We first assess the genome-wide phylogeny and divergence time across the genusGallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowlG. sonneratiiand Ceylon junglefowlG. lafayettii. Both species form a clade that is sister to the Red junglefowlG. gallus, with the Green junglefowlG. variusthe most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system.ConclusionsOur study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.

The extent to which the impact of regulatory genetic variants may depend on other factors, such as the expression levels of upstream transcription factors, remains poorly understood. Here we report a framework in which regulatory variants are first aggregated into sets, and using these as estimates of the total cis-genetic effects on a gene we model their non-additive interactions with the expression of other genes in the genome. Using 1220 lymphoblastoid cell lines across platforms and independent datasets we identify 74 genes where the impact of their regulatory variant-set is linked to the expression levels of networks of distal genes. We show that these networks are predominantly associated with tumourigenesis pathways, through which immortalised cells are able to rapidly proliferate. We consequently present an approach to define gene interaction networks underlying important cellular pathways such as cell immortalisation., For most human genes nearby regulatory variants explain only a small proportion of their expression variation between individuals. Here the authors show how the impact of a gene’s set of nearby regulatory variant is often linked to the expression levels of distal genes, providing insights into gene networks.

Dromedary camels (Camelus dromedarius) are single-humped animals found throughout the deserts of Africa, the Arabian Peninsula and the southwest of Asia. This well-adapted species is mainly used for milk and meat production, although some specific types exhibit superior running performance and are used in racing competitions. However, neither performance nor production camels are bred under intensive genomic selection programmes with specific aims to improve these traits. In this study, the full genome sequence data of six camels from the Arabian Peninsula and the genotyping-by-sequencing data of 44 camels (29 packing and 15 racing) from Sudan were analysed to assess their genome diversities, relationships and candidate signatures of positive selection. Genome admixture and principle component analyses indicate clear geographic separation between the Sudanese and the Arabian Peninsula camels, but with no population-specific genetic distinction within populations. Camel samples from the Arabian Peninsula show higher mean heterozygosity (0.560 ± 0.003)than those from Sudan (0.347 ± 0.003). Analyses of signatures of selection, using pooled heterozygosity (Hp) approach, in the Sudanese camels revealed 176, 189 and 308 candidate regions under positive selection in the combined, packing and racing camel populations, respectively. These regions host genes that might be associated with adaptation to arid environment, dairy traits, energy homeostasis and chondrogenesis. Eight regions show high genetic differentiation, based on Fst analysis, between the Sudanese packing and racingcamel types. Genes associated with chondrogenesis, energy balance and urinary system development were found within these regions. Our results advocate for further detailed investigation of the genome of the dromedary camel to identify and characterize genes and variants associated with their valuable phenotypic traits. The results of which may support the development of breeding programmes to improve the production and performance traits ofthis unique domesticated species.

International audience; Honeybee is native from Africa, Europe and western Asia and its presence elsewhere in the world is due to human imports. In New Caledonia, importation of Western-Europe M lineage honeybees from France started in the 19th century and these black honeybees were dominant until the late 1980’s when an American foulbrood infestation decimated the colonies and Eastern-Europe C Lineage importation began from Australia, New Zealand and Italy. Nowadays, the hybrid honeybee is the most frequently bred but A. m. mellifera persists. The New Caledonia Islands offers the opportunity to study the genetic admixture of two human-mediated driven and temperate European subspecies into a favorable tropical landscape. Within the framework of the INRA-ITSAP SeqApiPop project, we sequenced the whole-genome of 40 honeybees sampled from Grande Terre, the largest island of the archipelago, and from 3 medium size islands (Lifou, Maré and Ouvéa). When compared with population samples from Europe including A. m. mellifera, A. m. ligustica, A. m. carnica and A. m. caucasica, the New Caledonia honeybee population indeed reveals a mixed composition of A. m. mellifera and A. m. ligustica. The honeybees from Grande Terre have a higher proportion of A. m. ligustica background whereas the honeybees from Lifou have a higher proportion of A. m. mellifera. Maré shows an intermediate profile with a higher proportion of A. m. mellifera background than Grande Terre. The Ouvéa honeybee’s background is similar to Grande Terre, and yet the Ouvéa colonies originate from a recent importation of A. m. ligustica queens. Despite a substantial importation of A. m. ligustica and the decline of the first introduced black honeybee, the genetic composition of New Caledonia honeybees is still characterized by a strong presence of an A. m. mellifera background. Our whole-genome results comfort previous studies on Lifou, suggesting this island could be considered as a black honeybee conservatory in the South Pacific Ocean.

The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of a pathogenic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota.

The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large- scale introductions of commercial strains (C- lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M- lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C- lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST = 1) is introduced when the sample size is small (N ≤ 10) and when sampling only captures a small fraction of a population’s genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise FST between the Iberian and C- lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time- and cost- effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations. We thank numerous researchers, beekeepers and beekeeping associations who provided samples and assisted with sampling in the several countries. João Costa, Instituto Gulbenkian Ciência, designed the multiplexes with the Assay Design tool. José Rufino provided computational resources at IPB. A. m. ligustica drone samples were kindly provided by Cecilia Costa, from the Council for Agricultura Research and Economics Honey Bee and Silkworm Unit, Bologna, Italy. John C. Patton, Phillip San Miguel, Paul Parker, Rick Westerman, from the University of Purdue, USA, sequenced most honeybees and many reference samples. Reference samples were also sequenced at the GeT PlaGe platform in Toulouse, France. An earlier version of the manuscript was improved by the constructive comments made by two anonymous reviewers. Dora Henriques was supported by a PhD scholarship from the Fundação para a Ciência e Tecnologia (FCT) (SFRH/BD/84195/2012) and Melanie Parejo by the Swiss Federal Office for Agriculture FOAG and the Sur-la- Croix foundation, Basel. MAP is a member of and receives support from the COST Action FA1307 (SUPER-B). Analyses were performed at UPPMAX, Uppsala University, and UBELIX, University of Bern. The Roslin Institute was supported by the Biotechnology and Biological Services Research Council (BBS/E/D/20211551). This research was funded through the projects PTDC/BIA-BEC/ 099640/2008 (FCT and COMPETE/ QREN/EU) and the 2013-2014 BiodivERsA/FACCE-JPI joint call for research proposals, with the national funders FCT (Portugal), “Agence Nationale de la Recherche” (France) and “Ministério de Economia y Competividade” (Spain) to MAP. info:eu-repo/semantics/publishedVersion

It is now over 10 years since the first avian genome [International Chicken Genome Sequencing Consortium, 2004] and the first complete avian karyotype [Masabanda et al., 2004] were both published; however, until 2014, avian cytogenetics has focused heavily on descriptive studies [e.g. Griffin et al., 2007, 2008; Skinner et al., 2009; Volker et al., 2010] with less attention to its functional relevance. Last year, however, saw 2 landmark efforts in the chromosomal studies of birds: a special issue of Chromosome Research in April and the announcement of recently completed sequences of multiple new avian genomes in Science and the BMC journals (taking the total number sequenced to over 50) in December. Studying the chromosomes of birds is, perhaps for the first time, telling us more about avian biology, function and evolution than it ever has... Conclusions. The most recent advances in avian cytogenetics have culminated in great promise not only for the study of bird karyotypes, but also for providing insight into the mechanisms of chromosome evolution in general. New avenues for investigation include gene regulation; for instance, it will become necessary to map accurately the physical location of polyadenylation and transcription start sites, important reference points that define promoters and post-transcriptional regulation. It will also become possible to sequence full-length transcripts, to allow accurate identification of alternate splicing events and their controlling elements. The ENCODE (Encyclopedia of DNA Elements) project has helped to define functional elements of the human genome, including those aforementioned as well as other chromatin signals, e.g. active chromatin, enhancers, insulators, methylation domains, etc. An effort of agENCODE is underway to include agriculturally important birds such as chicken, turkey, duck, quail, and perhaps ostrich. The study of cytogenetics will be essential here in helping to define higher-order structures in nuclear organization that show regulatory interactions within and between chromosomes. Finally, reconstruction of evolutionary events allows us to study genome organization and function not only in extant but, by extrapolation, in extinct species also. Reconstruction of avian-reptilian ancestral karyotypes will allow us to define chromosomal rearrangements in long-dead species that have captured the public imagination. Here be dragons!

National audience

Na-ion batteries (NIBs) are considered the most attractive and cost-effective alternative to Li-ion batteries (LIBs), due to the widespread abundance of sodium and its chemical similarity with Li, facilitating the conversion of battery technologies. Meanwhile, replacing the liquid electrolyte in traditional batteries with a super-ionic conductor material in the solid-state presents additional advantages in terms of safety and stability. The research for solid-state electrolytes (SSE) is consequently a very active field. Layered tellurates with formula Na2 M 2TeO6 (M = Co, Mg, Zn, Ni) have been reported to exhibit high Na-ion conductivity, around 10-4 S/cm, and crystallize into two distinct P2-layered modifications, structurally related to Na-deficient Na xMO2 (x < 0.7; M = Co, Fe, Mn) materials. Na2Ni2TeO6 (NNTO) adapts an AA stacking of hexagonal Ni-Te layers (P63/mcm), while Na2 M’ 2TeO6 (M’ = Zn, Co) adapts an alternative AB stacking (P6322) [1]. However, the structure of the Na2 M’ 2TeO6 compounds is not yet fully resolved, because the refinements reported in literature do not account for the broadening of a low-angle peak in the X-ray diffraction pattern which could be ascribed to the presence of stacking faults [1,2]. In this study, Na2Zn2TeO6 (NZTO) was synthesized via conventional solid-state methods. Synchrotron X-ray diffraction (SXRD) experiments were performed to verify the presence and quantify the amount of stacking faults in the structure. The standard Rietveld refinement against SXRD data shows that NZTO crystallizes into the P6322 structure (a = 5.289 Å, c = 11.244 Å), consistent with previous reports. The refinement exhibits a poor fit of Bragg intensity and could not describe the significant broadening of the (0 1 1) reflection, as shown in Figure 1. We performed density functional theory (DFT) calculations to verify the nature of these faults. We modeled two different NZTO modifications, the standard one (space group P6322) and the one obtained by substituting Zn for Ni in the NNTO structure. The energy difference is smaller than 10 meV, indicating the possible coexistence of these phases at room temperature or, indeed, the presence of the associated stacking faults in the P6322 structure. The latter hypothesis was directly tested by simulating the effect of NNTO-type stacking faults in NZTO and subsequent refinement against SXRD data employing the FAULTS software [3]. The simulated XRD patterns reveal that only the (0 1 1) reflection is drastically broadened and its intensity decreases as the fraction of NNTO-type stacking faults increases. Notably, the other peaks remain largely unchanged. The FAULTS-refined profiles exhibit a better fitting of the Bragg intensity and peak broadening of the (0 1 1) reflection, revealing 3% NNTO-type stacking faults in NZTO. In conclusion, a more accurate structural model of the NZTO compound is proposed and validated. Figure 1: Rietveld refinement (without stacking faults) and FAULTS refinement (with stacking faults) against SXRD data (λ = 0.3149 Å) for NZTO. References [1] M A. Evstigneeva, V B. Nalbandyan, A A. Petrenko, B S. Medvedev, A A. Kataev. A new family of fast sodium ion conductors: Na2 M 2TeO6 (M = Ni, Co, Zn, Mg), Chem. Mater., 2011, 23, 1174-1181. [2] Y Li, Z Deng, J Peng, E Chen, Y Yu, X Li, J Luo, Y Huang, J Zhu, C Fang, Q Li, J Han, Y Huang. A P2-type layered superionic conductor Ga-doped Na2Zn2TeO6 for all-solid-state sodium-ion batteries, Chem. Eur. J., 2018, 24, 1057-1061. [3] M C. Cabanas, M Reynaud, J Rikarte, Pavel Horbach, J R. Carvajal. FAULTS: a program for refinement of structures with extended defects. J. Appl. Cryst., 2016, 49, 2259-2269. Figure 1

The Green-legged Partridgelike (GP) fowl, an old native Polish breed, is characterised by reseda green-coloured shanks rather than yellow, white, slate or black commonly observed across most domestic breeds of chicken. Here, we investigate the origin, genetic relationships and structure of the GP fowl using mtDNA D-loop sequencing and genome-wide SNP analysis. Genome-wide association analysis between breeds enables us to verify the genetic control of the reseda green shank phenotype, a defining trait for the breed. Two mtDNA D-loop haplogroups and three autosomal genetic backgrounds are revealed. Significant associations of SNPs on chromosomes GGA24 and GGAZ indicate that the reseda green leg phenotype is associated with recessive alleles linked to the W and Id loci. Our results provide new insights into the genetic history of European chicken, indicating an admixed origin of East European traditional breeds of chicken on the continent, as supported by the presence of the reseda green phenotype and the knowledge that the GP fowl as a breed was developed before the advent of commercial stocks.

Pas de Clé UT; International audience; Pollination is a key ecosystem service for agricultural systems and Western honey bees, Apis mellifera, are the most important managed pollinators. Major losses of managed honey bee colonies reinforced the need to take advantage of locally adapted subspecies and ecotypes to buffer populations against various stressors. However, introductions of non-native honey bees from distant lineages are likely to undermine respective conservation efforts unless reliable and cost effective tools can be used to identify hybridization. The purpose of this study is to characterize current population structure and genetic diversity, and to assess the degree of admixture between native and introduced honey bees. Moreover, we aim to select a reduced number of genetic markers to improve conservation management strategies. We take advantage of recent developments in next-generation sequencing and network-based clustering to investigate conservation efforts for the native European Dark honey bee, A. m. mellifera, which is threatened by introgression in most of its range. We collected whole-genome sequence information from haploid drones of A. m. mellifera, A. m. carnica, and Buckfast sampled throughout Switzerland (N = 81), as well as from four Swiss A. m. mellifera conservation areas (N = 39) and from one conservatory in the French Alps (N = 31). Population structure analyses based upon 3.375 M genome-wide SNPs discerned samples by subspecies and geographic origin (Switzerland or France). Ancestry inference indicated admixed individuals in all of the protected areas, calling for improved management efforts. After testing different subsets of ancestry informative SNPs using three different selection strategies (FST, PCA-based or at random), as few as 50 SNPs are found to be sufficient to differentiate native from introduced honey bees. Therefore, our data suggests that a low-density SNP panel can be a precise and cost-effective tool to support conservation management efforts for managed pollinators.

Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail.

We have used in situ energy dispersive synchrotron X-ray diffraction to study the crystallization of aluminum phosphate frameworks under ionothermal conditions with conventional and microwave heating. The reaction is shown to follow slightly different routes depending on the type of heating used and a kinetic analysis shows that the rate constant is 10 times higher under microwave heating (1.4 compared to 0.14 min−1). The conventionally heated reaction is shown to proceed by a transformation of SIZ-3 to SIZ-4 via an intermediate, while the microwave-heated reaction forms SIZ-4 directly. The kinetic analysis is used to rationalize the differences in reaction rate and the findings are supported by SEM images of the crystal morphologies which result from the two heating methods.