dataesr/scientific-paragraphs-categorization huggingface dataset:
Measured traits Courtship display, ejaculate size, number of eggs laid and body mass per year were analysed to assess change in breeding values over time. Measurements of these traits were available for thousands of birds with a known pedigree that reached 74 528 individuals in 2011. Full statistics on pruned pedigrees used in analyses are given in Appendix S1. We used phenotypic data collected from 1999 to 2011 on 3230 males and females born in 1986 and onwards. Body mass (AE1 g) was measured in both males and females several times per year. Because body mass shows some within-year variation  (Saint Jalme et al. 1996) , we yearly corrected each measure by the day of measurement (R software, lmer function: body mass ~day + day 2 + 1| bird identity + 1|year, with day 1 = 1 January). Houbara sexual display is characterized by a complex behaviour including a circular running with the white feathers on the neck and the head fully erected.
Calculation of selection coefficients We estimated selection coefficients using a linear regression between traits and relative fitness (i. e. individual fitness divided by population average) as described by  Lande and Arnold (1983). Because a dumping strategy is in use in this breeding programme, fitness was estimated by the number of chicks recruited to the captive breeder flock and not the total number of offspring produced. To compare patterns of selection between traits, phenotypic values were standardized (mean = 0, SD = 1) within years. We first estimated selection differentials for each year using linear regressions with a normal distribution of errors (R software, lm function) because estimates are not affected by the non-normality of data  (Lande and Arnold 1983). However, to test the statistical significance of models, a second regression model was performed on nonstandardized values of number of chicks with a Poisson distribution of errors (R software, glm function).
The Houbara supportive breeding managed by ECWP was a unique opportunity to investigate potential genetic changes because the captive population was established ~70 founders, regularly reinforced by wild-laid eggs (~500), leading to a very large captive population of about 10 000 adult breeders (~7000 still alive in 2012), reared and bred individually for 15 years (~5 generations) so that impressive pedigree records and precise phenotypic dataset were available. The aim of the Houbara breeding management was fourfold: (i) avoiding inbreeding, (ii) equalizing the representation of each founder line by forming pairs based on their mean kinship, (iii) maintaining high genetic diversity by regularly integrating new founders, from wild-laid eggs, to the captive broodstock and (iv) limiting best breeders to be over-represented in the captive population by preferentially releasing in the wild offspring sired by the most represented breeders (i.
Acknowledgements The  Emirates Centre for Wildlife Propagation  (ECWP, www. ecwp. org)provided the data and funding for this project under the leadership of the  International Fund for Houbara Conservation (IFHC). We are grateful to  H. H. Sheikh Mohammed  bin  Zayed Al Nahyan ,  Crown Prince of Abu Dhabi and Chairman of the International Fund for Houbara Conservation (IFHC)  and  H. E. Mohammed Al Bowardi ,  Deputy Chairman  of  IFHC  for their support. We also thank  Gw ena€ elle Levêque  who coordinated data collection, and to all ECWP staff involved in behavioural observations, eggs and chicks care and assessments of ejaculate quality and a final thank to two anonymous reviewers for their valuable comments.
DAPI Staining of Mitosis Seven days after germination, root tips were fixed for 45 min in 4% paraformaldehyde in PME (50 mM PIPES, pH 6. 9, 5 mM MgSO4, and 1 mM EGTA) and then washed 3 times for 5 minutes each in PME. Root tips were then digested for 30 min in 1% (w/v) cellulase, 0. 5% (w/v) cytohelicase, and 1% (w/v) pectolyase (from Sigma-Aldrich; Refs. C1794, C8274, and P5936) solution prepared in PME and then washed 3 times 5 minutes in PME. Digested root tips were gently squashed onto slides  (Liu et al. , 1993) , air dried, and mounted using Vectashield mounting medium with 1. 5 mg/mL DAPI (Vector Laboratories) and observed by fluorescence microscopy. Images were further processed and enhanced using Adobe Photoshop software.
Flow Cytometry Analysis Nuclei were prepared with the Cystain UV Precise P kit (#05-5002; Partec GmbH, Germany. http://www. partec. com), following the manufacturer's instructions. Briefly, nuclei of approximately 20 seven-day-old seedlings were chopped with a razor blade in 200 ml of Cystain UV Precise P extraction buffer, 800 ml of Cystain UV Precise P staining buffer was added and the sample filtered through 30 mm nylon mesh. Flow cytometry was performed using an Attune Acoustic Focusing Cytometer (Life Technologies), following the manufacturer's protocols. Results were analysed using the Attune Cytometric Software version 1. 2. 5.
Data Analysis Raw sequence files from the Illumina pipeline were used for alignment against the TAIR10 Arabidopsis genome sequence release using BWA software. First, the original 100-mers were aligned with a tolerance of up to five mismatches. On average, we found a unique hit for 85% of the reads, giving approximately 16 million reads per library mapped uniquely to the Arabidopsis genome. Seqmonk software was used for visualization and analysis of mapped sequence. The genes for which less than 20 hits were recorded in all samples were discarded from the data set. Comparisons of relative levels of transcripts in wild type, tertG2 and tertG7 plants in two independent experiments were carried out as described in the main text. Gene ontology classification of the transcripts was done according to classical gene ontology categories using the web-based tool Classification Super-viewer (http://bar.
The sequences were aligned to the TAIR10 reference Arabidopsis genome sequence using the BWA tool and the SEQMONK program used to identify and quantitate transcript levels of individual genes. In two independent repetitions, the RNAseq analyses yielded approximately 20 million sequences per sample, with quantifiable transcripts (at least 20 reads per transcript) from 18893 genes present in samples from both repetitions (Table  S1 ). We note that, notwithstanding the presence of elevated levels of mitotic chromosome bridges and the continuous induction of the DDR (presence of TIFs) in tertG7 plants, no evidence for higher levels of single nucleotide polymorphisms (SNPs) and DNA insertions/deletions (InDels) is seen in the RNAseq data from these plants (Figure  4 ). The results of screening for genes with altered expression in the WT versus tertG2, WT versus tertG7, and/or tertG2 versus tertG7 plants are presented as a Venn diagram in Figure  5.
This work was partly financed by a  European Union  research grant ( LSHG-CT-2005-018785 ), a  French Government ANR grant  ( ANR-07-BLAN-0068 ), the  Centre National de la Recherche Scientifique , the  UniversiteBlaise Pascal , the  Universited'Auvergne , and the  Institut National de la Santeet la Recherche Medicale. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Colonies Collection and Data Collection Insecticide fogging and the use of baited traps are common sampling methods in studies of ant diversity  [21]. However, they are not suited for evaluating myrmecophile diversity within ant nests  [2]. Here we chose to directly evaluate the macrofauna within ant nests through exhaustive colony sampling and careful examination of every individual within the nest under a stereomicroscope. The laborious nature of our approach and the need to sacrifice all individuals dictated the assessment of reduced colony sample sizes. Three complete C. sp. aff. textor nests were collected at the INIFAP Experimental Field Station at Rosario Izapa, Tuxtla Chico municipality, Chiapas, Mexico (14u5892599N, 92u0991999W, 430 m above sea level), and in an adjacent family-run orchard, at a distance of 300 m, during the dry season (February 2010).
However, the sub-castes were not counted individually, and their relative proportions were not estimated. Four adult males were found within a nest, but no alate females were present in any of the colonies (Table  1 ). Male and female pupae were present in considerable numbers in the two largest nests. A sex ratio of 0. 61 (proportion male) was calculated from the data on sexual pupae from these two nests. Eggs and larvae in different developmental stages were present in all three nests. The average colony size (mean 6 SE, n = 3) consisted of 16,73464,039 workers, 2,6566556 cocoons and 7,38062,242 larvae (Table  1 ).
Acknowledgments We are indebted to  Jacques Delabie ,  William Mackay ,  John Heraty ,  Jeyaraney Kathirithamby ,  Michael Gates  and  Jens Prena  for their help with insect identification, to  Mrs. Lucia Lopez Escobar  and her son  Mr. Francisco Lopez Lo  ´pez for permission to collect nests in their orchard and to JoseAntonio Lopez Mendez and  Wendy Xool  for technical assistance. An anonymous referee provided very helpful comments on an earlier version of this manuscript.
Statistical analysis Data treatment and statistical analyses were performed with R (R Core Team, 2013) and MatLab Ò softwares (The MathWorks Inc. , Natick, Massachusetts, U. S. A). Exploratory statistics consisted in Principal Component Analysis of the chemical data and MALDI-TOF MS ion intensities. PCA was achieved using the functions of the library FactoMineR  (Husson, Joss, Le, & Mazet, 2009 ). Significant differences between individuals were evaluated by a Student test performed on PCA individual coordinates on principal components. Significant differences were set at a probability value of equality below 5%. Pearson correlation coefficients were computed within MALDI-TOF MS ion datasets.
2013) and with both rabbit RNA-seq data and the annotation of human orthologs (4) (Table  S3 ). Our analysis of rabbit domestication used Ensembl annotations as well as a custom pipeline for annotation of UTRs (168,286 unique features), non-coding RNA (n=9,666) and non-coding conserved elements (2,518,476 unique features). To identify genomic regions under selection during domestication we performed whole genome resequencing (10X coverage) of pooled samples (Table  S4 ) of six different breeds of domestic rabbits (Fig. 1A ), three pools of wild rabbits from Southern France, and 11 pools of wild rabbits from the Iberian Peninsula, representing both subspecies (Fig. 1B ). We also sequenced a close relative, snowshoe hare (Lepus americanus), to deduce the ancestral state at polymorphic sites.
We identified 78 outliers with F ST >0. 35 and H<0. 05 (Figs. 2A, S2, Database S1). We also used SweepFinder  (7) , which calculates maximum composite likelihoods for the presence of a selective sweep, taking into account the background pattern of genetic variation in the data, and with a significance threshold set by coalescent simulations incorporating the recent demographic history of domestic and wild rabbits (Figs. S3, S4, Databases S1, S2) (4). This analysis resulted in the identification of 78 significant sweeps (Fig. 2A , Database S1). Thirty-one (40%) of these were also detected with the F ST -H approach (Fig. 2A ). This incomplete overlap is likely explained by the fact that SweepFinder primarily assesses the distribution of genetic diversity within the selected population, while the F ST -H analysis identifies the most differentiated regions of the genome between wild and domestic rabbits.
We carried out an additional screen using targeted sequence capture on an independent sample of individual French wild and domestic rabbits. We targeted over 6 Mb of DNA sequence split into 5,000 1. 2 kb intronic fragments that were distributed across the genome and selected independently of the genome resequencing results above. Coalescent simulations, using the targeted resequencing dataset and incorporating the recent demographic history of domestic rabbit as a null model (Figs. S3, S4, Databases S1, S2) (  4 ), confirmed the majority of sweeps detected in our whole genome resequencing approach (76. 0% with SweepFinder and 73. 7% with F ST -H outlier regions, excluding regions without targeted fragments), a highly significant overlap (Fisher's exact test, P<1x10 -5 for both tests). Furthermore, 26 of the 31 sweep regions detected with both SweepFinder and the F ST -H approach were targeted in the capture experiment, 23 of these (88.
05). Of note, we detected a significant excess of SNPs at conserved non-coding sites for each bin ΔAF>0. 45 (χ 2 test, P=1. 8x10 -3 -7. 3x10 -17 ), whereas in coding sequence, a significant excess was only found at ΔAF>0. 80 (χ 2 test, P=3. 0x10 -2 -1. 0x10 -3 ). Compared to the relative proportions in the entire dataset, there was an excess of 3,000 SNPs at conserved non-coding sites with ΔAF>0. 45, whereas for exonic SNPs with ΔAF>0. 80 the excess was only 83 SNPs (Table  S6 ). Thus, changes at regulatory sites have played a much more prominent role in rabbit domestication, at least numerically, than changes in coding sequences. We selected the 1,635 SNPs at conserved non-coding sites with ΔAF>0. 80, which represent 681 non-overlapping 1 Mb blocks of the rabbit genome. In order not to inflate significances due to inclusion of SNPs in strong linkage disequilibrium we selected only one SNP per 50 kb, leaving 1,071 SNPs.
More than 60% of the SNPs were located 50 kb or more from the closest transcriptional start site (TSS; Fig. 2E ), suggesting that many differentiated SNPs are located in long-range regulatory elements. A gene ontology (GO) overrepresentation analysis (  11 ) examining all genes located within 1 Mb from high ΔAF SNPs showed that the most enriched categories of biological processes involved 'cell fate commitment' (Bonferroni P=3. 1x10 -3 -5. 4x10 -5 ; Table  1 , Database S3), while the statistically most significant categories involved brain and nervous system cell development (Bonferroni P=2. 9x10 -3 -3. 7x10 -10 ). Many of the mouse orthologs of genes associated with non-coding high ΔAF SNPs were expressed in brain or sensory organs, and this enrichment was highly significant (Table  1 ). We also examined phenotypes observed in mouse mutants (http:// www.
This is an important finding as it has been suggested that gene inactivation could be an important mechanism for rapid evolutionary change, for instance during domestication  (14). Of 69,985 autosomal missense mutations, there were no fixed differences and only 14 showed a ΔAF above 90%. On the basis of poor sequence conservation, similar chemical properties of the substituted amino acids, and/or the derived state of the domestic allele we assume that most of these result from hitchhiking, rather than being functionally important (Database S4). However, two missense mutations stand out; these may be direct targets of selection because at these two positions the domestic rabbit differs from all other sequenced mammals (>40 species). The first is a Q813R substitution in TTC21B (tetratricopeptide repeat domain 21B protein), which is part of the ciliome and modulates sonic hedgehog signaling during embryonic development  (15).
The other is a R1627W substitution in KDM6B (lysine-specific demethylase 6B) that encodes a histone H3K27 demethylase involved in HOX gene regulation during development  (16). Deletions unique to domestic rabbits were difficult to identify, because the genome assembly is based on a domestic rabbit, but some convincing duplications were detected with striking frequency differences between wild and domestic rabbits (Database S5). We observed a one bp insertion/deletion polymorphism located within an intron of IMMP2L (inner mitochondrial membrane peptidase-2 like protein), where domestic and wild rabbits were fixed for different alleles. The polymorphism occurs in a sweep region and it is the sequence polymorphism with highest ΔAF in the region (Fig. S6 ). Mutations in IMMP2L have been associated with Tourette syndrome and autism in humans  (17).
Cell fate determination was a strongly enriched GO category (Database S3) for genes near variants with high ΔAF. We examined the functional significance of twelve SOX2, four KLF4 and one PAX2 high ΔAF SNPs associated with this GO category and where all 17 SNPs were unique to domestic rabbits compared with other sequenced mammals. Electrophoretic mobility shift assay (EMSA) with nuclear extracts from mouse ES-cell derived neural stem cells revealed specific DNA-protein interactions (Figs. 3, S7, Table  S7 ). Four probes, all from the SOX2 region, showed a gel shift difference between wild and domestic alleles. Nuclear extracts from a mouse P19 embryonic carcinoma cell line before and after neuronal differentiation recapitulated these four gel shifts and revealed three additional probes, one in PAX2 and two more in SOX2 that showed gel shift differences between wild-type and mutant probes only after neuronal differentiation.
Acknowledgements The work was supported by grants from  NHGRI  ( U54 HG003067  to ESL),  ERC  project  BATESON  to LA,  Wellcome Trust  (grant numbers  WT095908  and  WT098051 ), the intramural research program of the  NIH ,  NIAID (RGM) , the  European Molecular Biology Laboratory, POPH-QREN  funds from the  European Social Fund and Portuguese MCTES  [postdoc grants to M. C ( SFRH/BPD/72343/2010 ) and  R. C. ( SFRH/BPD/64365/2009 ), and PhD grant to  J. Alves  ( SFRH/BD/72381/2010 )], a  NSF international postdoctoral fellowship  to  J. M. G. ( OISE-0754461 ), by  FEDER  funds through the  COMPETE program  and Portuguese national funds through the  FCT -Fundação para a Ciência e a Tecnologia - ( PTDC/CVT/122943/2010; PTDC/BIA-EVF/115069/2009; PTDC/BIA-BDE/72304/2006; PTDC/BIA-BDE/72277/2006 ), by the projects " Genomics and Evolutionary Biology " and " Genomics Applied to Genetic Resources " co-financed by North Portugal Regional Operational Programme 2007/2013 (ON.
2 -O Novo Norte) under the National Strategic Reference Framework (NSRF) and  European Regional Development Fund (ERDF) , by travel grants to M. C. ( COST Action   TD1101 ) and S. S. was supported by  Higher Education Commission in Pakistan. We are grateful to  L. Gaffney  for assistance with figure preparation,  Paulo C. Alves  and  Scott Mills  for providing the snowshoe hare sample and  S. Pääbo  for hosting M. C. , S. A. and  R. C. Sequencing  was performed by the  Broad Institute Genomics Platform. Computer resources were supplied by  BITS  and  UPPNEX at Science for Life Laboratory. The O. cuniculus genome assembly has been deposited in Genbank under the accession number  AAGW02000000. The RNA-seq data have been deposited there under the bioproject  PRJNA78323 , the rabbit genome resequencing data under the bioproject  PRJNA242290 , and the sequence capture data under the bioproject  PRJNA221358.
The ERA Guidance Document (EFSA, 2010a) sets out a number of particular areas of potential environmental concerns for applications relating to GM crops: i) impacts on non target organisms (NTOs e. g. natural enemies and pollinators; Arpaia, 2010); ii) impacts of GM crops on soil biodiversity and biology; iii) long-term effects on the environment, biodiversity and biogeochemical cycles; iv) impact of farming practices, with the need to take into account the diversity of management systems that may be associated to GM crops. Statistical procedures are required in order to support the ERA with robust data analyses. Finally, the European Commission has requested that PMEM guidelines should be updated to strengthen the overall decision-making process, by incorporating long term effects of GM crops and related agronomic changes relative to the current baseline of agricultural practices over the last 30 years as a mechanism for estimating rates of change.
AMIGA objectives The AMIGA project aims to: i) reduce uncertainty in decision-making for the cultivation of GMPs in Europe by developing and verifying robust Environmental Risk Assessment methods based on testable hypotheses that seek to aid the decision making process; ii) increase confidence in the practicability of EFSA Guidance Documents for Environmental Risk Assessment; and iii) contribute to the development of more effective PMEM designs and risk mitigation procedures. The specific objectives are: i) to provide baseline data on biodiversity in selected agro-ecosystems and adjacent habitats through field surveys in non-GM cultivations in five different geographical European regions and build a database of species assemblages and ecological functional groups in the chosen crops (maize and potato); ii) to aid the translation of regional protection goals into measurable assessment endpoints by establishing a link between functional groups of arthropod species active in two selected agro-ecosystems (maize and potato), whilst taking into account the differences in the ecology of the different agroecosystems; iii) to outline potential bioindicators (species assemblages and/or ecosystem functions) fine-tuned for specific European regions and translate them into a decision matrix, which can provide guidance on the selection of relevant test species, experiments and monitoring targets/areas; iv) to improve knowledge on the potential long-term environmental effects of GMPs by assembling background information on changes in land use, cropping practices and the economic returns of arable farming for representative crops and areas in different regions (over the last 30 years) in order to help assess future effects of GMbased agro-ecosystems in the context of impacts due to other factors; v) to provide examples for testing the efficacy of the EFSA Guidelines for the ERA of GM plants and produce standardized protocols for ERA in laboratory as well as field conditions; vi) to explore possible strategies for data-driven post market monitoring of GMPs and develop a coherent framework, validated methods and tools, including exposure models, to help implement cost-efficient monitoring schemes; vii) to estimate the compatibility and sustainability of GM crops within the principles of Integrated Pest Management which represent the sole pest management options in the EU after 2014; viii) to evaluate the potential risks of GM crops for non-target pollinators and crop pollination services; ix) to Provide a systematic analysis of economic aspects of cultivation of GMPs; x) to provide a training and communication plan that addresses current public concerns about GMPs in Europe.
Past GM risk assessments in Europe have not explicitly considered such differences, exposing the risk assessment practice and its outcomes to criticism. The EFSA ERA Guidance Document (EFSA, 2010b), considers four classifications of geographical zones in Europe, but gives no clear instruction or standard on how to adopt them. AMIGA therefore aims to vali- date with real case studies, a logical road map for the selection of biogeographical zones. Further, through literature and ecological surveys conducted in 5 geographical zones in potato and maize growing areas, AMIGA research will identify region-specific characteristics of these agroecosystems and provide a decision-support tool for further supporting a correct selection of receiving environments. These will be reflected in databases of species assemblages to be used in the definition of geographical regions to be adopted for ERA of GM maize and potato in Europe and in a decision matrix to support guidance for any GM crop.