BUSCADOR RECOLECTA

The dataset is an Excel file with five sheets that contain the following information: Sheet 1 ("1st experiment, 3 strains"): MLH1 foci count per spermatocyte per mice, strain and diet Sheet 2 ("2nd experiment, B6 males"): MLH1 foci count per spermatocyte per C57BL/6 mice treated with two diets (2nd experiment). Columns indicate the mouse ID and number of spermatocytes analyzed in parenthesis. Sheet 3 ("intercrossover distances"): Interfocus distances in control mice (maintenance diet) of 3 strains. Values are shown as percentage of synaptonemal complex length. Sheet 4 ("synaptonemal c. length, 1st"): Total autosomal length of synaptonemal complexes per strain, control groups (maintenance diets) Sheet 5 ("synaptonemal c. length, 2nd"): Total autosomal length of synaptonemal complexes per diet in C57BL/6 mice (2nd experiment), We performed two studies: in the initial one, adult males from the three strains were analyzed for the effect of two diets on recombination (undernourishment (reduction to 50% daily intake) and breeding diets (Teklad Global 18% Protein Rodent Diet)) provided during 24 days relative to a control group kept ad libitum with maintenance diet (Teklad Global 14% Protein Rodent Maintenance Diet). After the 24-day diet period, adult male mice were euthanized by cervical dislocation and weighed. After removing and weighing the testes, chromosome spreads for immunostaining as previously described (Anderson et al. 1999; de Boer et al. 2009; Milano et al. 2019). MLH1 immunostaining allows for identification of about 90% of mammalian crossover sites (Anderson et al. 1999; Cole et al. 2012). All slides were imaged on a Zeiss LSM 710 confocal microscope and analyzed using Zeiss Zen lite software. Only mid and mid-late pachytene stage spermatocytes were scored. For each spermatocyte, we counted the number of foci localizing to the SC of the 19 autosomes (Anderson et al. 1999); total SC length and interfocus distances were also measured in autosomes only., Meiotic recombination is a critical process for sexually reproducing organisms. This exchange of genetic information between homologous chromosomes during meiosis is important not only because it generates genetic diversity, but also because it is often required for proper chromosome segregation. Consequently, the frequency and distribution of crossovers are tightly controlled to ensure fertility and offspring viability. However, in many systems it has been shown that environmental factors can alter the frequency of crossover events. We have explored for the first time the effect of dietary changes on crossover frequency per nucleus. Our study was performed in spermatocytes of 3 mouse inbred strains by analyzing the number and position of crossovers along the synaptonemal complexes, as well as the length of such synaptonemal complexes, by immunostaining with antibodies against MLH1 (which allows the identification of the crossover sites) and SYCP3 (a component of the synaptonemal complex). Our results show that male recombination rate is sensitive to dietary changes, and this sensitivity depends on the genetic background in mice. This is first to report a nutrition effect on genome-wide levels of recombination., Peer reviewed

Repeat Explorer 2 comparative analysis. Repeat content data for phylogenetically analyzed clusters (repeat families) in each of the four evolutionary groups of Loliinae: (A) Loliinae; (B) broad-leaved (BL) Loliinae; (C) fine-leaved (FL) Loliinae; (D) Schedonorus., The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups [Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages]. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the Lolium clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses., Peer reviewed

ANNEX 1 - Questionnaire on sea turtle bycatch. ANNEX 2 - Content validation., Peer reviewed

Phylogenetic signal based on Blomberg’s K values of repeat cluster contents obtained from the comparative RE2 analysis of Loliinae samples assessed in each of the four Loliinae groups: (A) Loliinae (38 samples, 38 clusters), (B) Broad-leaved (BL) Loliinae (15 samples, 96 clusters), (C) fine-leaved (FL) Loliinae (17 samples, 122 clusters), (D) Schedonorus (16 samples, 167 clusters), using the phylosig option of the phytools R package. Cluster abundance values (number of PE reads) are indicated in Supplementary Table 4. K values close to one indicate phylogenetic signal, values close to zero phylogenetic independence, and values >1 more phylogenetic signal than expected. p-Values based on 1000 randomizations. Significant values are highlighted in bold., The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups [Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages]. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the Lolium clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses., Peer reviewed

16 pages. -- Figure S1. Simplified interaction potential energy surface (iPES) between theobromine and adenine. -- Figure S2. Extended interaction potential energy surface (iPES) between theobromine and adenine. -- Figure S3. Simplified interaction potential energy surface (iPES) between theobromine and 4- aminopyrimidine. -- Figure S4. Extended interaction potential energy surface (iPES) between theobromine and 4-aminopyrimidine. -- Table S1. Relative stability of TB+A conformers. ZPE and BSSE corrected binding energy (BE) values are computed at 0 and 298 K. The colours match those in the iPES presented. -- Table S2. Relative stability of TB+AP conformers. ZPE and BSSE corrected binding energy (BE) values are computed at 0 and 298 K. The colours match those in the iPES presented. -- Figure S5. REMPI spectra of a) Adenine, b) Theobromine, c) Adenine + Theobromine dimer and d) 4-aminopyrimidine + Theobromine dimer. -- Figure S6. Comparison between the experimental IRIDS spectra and the computed simulated ones for TB+A dimer at B3LYP-ED=GD3BJ/def2TZVP level. -- Figure S7. Comparison between the experimental IRIDS spectra and the computed simulated ones for TB+A dimer at M06-2X/6-311++G(d,p) level. -- Figure S8. Comparison between the experimental IRIDS spectra and the computed simulated ones for TB+AP dimer at B3LYP-ED=GD3BJ/def2TZVP level. -- Figure S9. Comparison between the experimental IRIDS spectra and the computed simulated ones for TB+AP dimer at M06-2X/6-311++G(d,p) level. -- Figure S10. Structures of different dimers forming W-C mimic interactions, computed at B3LYPED=GD3BJ/def2TZVP. -- Table S3. Results from a second-order intramonomer/third-order intermonomer SymmetryAdapter Perturbation Theory (SAPT2+(3)/aug-cc-pVDZ) binding energy decomposition of dimers presented in Table 1 and Figure S10. values in kJ·mol-1, Peer reviewed

I. Collective chaos in Eq.(1) II. Boundary of Incoherence for Eq.(1) Thermodynamic limit: Perturbed Density Perturbation dynamics Self-consistency condition Final result III.Derivation of Eq. (2) IV.Boundary of Incoherence for Eq.(2), Peer reviewed

The supplemental files include: the description of the methods, figures of the dipole patterns as a function of temperature for periodicities of n=8 and n=14, derivation of the structural order-parameter, and a discussion on the normalization of the helicity., Peer reviewed

Supplementary Table 1. Hi-C experimental statistics. Statistics shown separated by replicates (top table) and merged datasets (middle table for valid pairs and bottom table for filtered reads). Supplementary Table 2. Mass-spectrometry analysis of histone H1 peptides after immunoprecipitation with H1 variant specific antibodies., Peer reviewed

[EN] It contains a netCDF file which needs specific data analysis software. [ES] Contiene un fichero netCDF que necesita software de análisis de datos específico., [ES] El dataset SEDIDatabase se actualiza periódicamente, se puede consultar y descargar en el siguiente enlace: https://sedi.csic.es/ [EN] The SEDIDatabase dataset is updated periodically, it can be consulted and downloaded at the following link: https://sedi.csic.es/, [EN] This dataset includes series of the Standardized Evapotranspiration Deficit at 0.25º spatial resolution and monthly time resolution at global scale from 1980., [ES] Esta base de datos proporciona el Standardized Evapotranspiration Deficit Index a escala global con una resolución espacial de 0.25 grados y una resolución temporal mensual desde 1980., This work was supported by the research projects PCIN-2015-220 and CGL2014-52135-C03-01 financed by the Spanish Commission of Science and Technology and FEDER. IMDROFLOOD financed by the Water Works 2014 co-funded all of the European Commission and INDECIS, which is part of ERA4CS, an ERA-NET initiated by JPI Climate, and funded by FORMAS(Sweden), DLR(Germany),BMWFW(Austria), IFD (Denmark), MINECO (Spain), and ANR (France), with co-funding by the European Union (Grant 690462)., Peer reviewed

The supplementary material provides (1) detailed derivations of formulae used in the main text: of the NS-subhalo encounter rate accounting for subhalo non-rigidity, and of the probabilities of observing neutron stars in certain temperature ranges, (2) brief discussion on tidal effects of neutron stars on subhalo accretion, (3) elaboration on the applicability of previous cosmic ray and paleo-detector limits to our scenario of clumped dark matter, (4) additional information on the sensitivities of and target regions for future telescopes., Peer reviewed