BUSCADOR RECOLECTA

6 pages. -- Table S1. Coordinates of sampling sites and related Meteorological stations. -- Table S2. Summary of the available metabolic data per species, region and season. -- Table S3. Summary of statistical analyses, performance of mixed models with random factor “publication”, summary of fixed effects through additional ANOVA analysis. -- Figure S1. Metabolic rates (CR, NCP and GPP in mmol O2 m-2 day-1) in relationship with the in situ temperature in the Posidonia oceanica benthic chambers data (top plot) and for all sensor data (bottom plot) in the Western basin. -- Figure S2 A. Seasonal metabolic rates (GPP, NCP and CR in mmol O2 m-2 day-1) in the Western Mediterranean basin calculated with sensor data. -- Figure S2 B. Seasonal metabolic rates (GPP, NCP and CR in mmol O2 m-2 day-1) calculated with benthic chamber data for Posidonia oceanica. -- Figure S3. Changes over time (Year) in metabolic rates (GPP, NCP and CR in mmol O2 m-2 day-1) for A) rates calculated with sensor data (both basins) and B) incubations of Posidonia oceanica., Peer reviewed

Supplementary Table S5: Important features identified by One-way ANOVA and post-hoc analysis (Fisher’s LSD) comparing the expression of immune genes in the IMMETCOLS Clusters., Existing immune signatures and tumor mutational burden have only modest predictive capacity for the efficacy of immune check point inhibitors. In this study, we developed an immune-metabolic signature suitable for personalized ICI therapies. A classifier using an immune-metabolic signature (IMMETCOLS) was developed on a training set of 77 metastatic colorectal cancer (mCRC) samples and validated on 4,200 tumors from the TCGA database belonging to 11 types. Here, we reveal that the IMMETCOLS signature classifies tumors into three distinct immune-metabolic clusters. Cluster 1 displays markers of enhanced glycolisis, hexosamine byosinthesis and epithelial-to-mesenchymal transition. On multivariate analysis, cluster 1 tumors were enriched in pro-immune signature but not in immunophenoscore and were associated with the poorest median survival. Its predicted tumor metabolic features suggest an acidic-lactate-rich tumor microenvironment (TME) geared to an immunosuppressive setting, enriched in fibroblasts. Cluster 2 displays features of gluconeogenesis ability, which is needed for glucose-independent survival and preferential use of alternative carbon sources, including glutamine and lipid uptake/β-oxidation. Its metabolic features suggest a hypoxic and hypoglycemic TME, associated with poor tumor-associated antigen presentation. Finally, cluster 3 is highly glycolytic but also has a solid mitochondrial function, with concomitant upregulation of glutamine and essential amino acid transporters and the pentose phosphate pathway leading to glucose exhaustion in the TME and immunosuppression. Together, these findings suggest that the IMMETCOLS signature provides a classifier of tumors from diverse origins, yielding three clusters with distinct immune-metabolic profiles, representing a new predictive tool for patient selection for specific immune-metabolic therapeutic approaches., Peer reviewed

Fig. S1. Conceptual model of avoidance. A primary repellent evokes reflexive withdrawal immediately after exposure. A secondary repellent is avoided because an animal associates a conditional stimulus (sound, sight, taste) to an aversive experience (e.g., illness, pain) with a sensory stimulus. A generalized conditional aversion may occur against the food that previously contained the chemical and it is avoided by only the type of food as the cue to refusing it. Fig. S2. Diagram of test of avoidance to treated sorghum seeds. Fig. S3. Diagram of experiment of avoidance to soybean seeds treated with imidacloprid. Fig. S4. Diagram of experiment of avoidance to soybean cotyledons treated with neonicotinoids. Fig. S5. Frequency of signs of intoxication observed over the days in each treatment during the Exposure 1 (A) and Exposure 2 (B) periods of the sorghum experiment. Signs of intoxication were measured as present or absent at each moment of observation, consisting of from lethargy to motionless. Letters indicate significant differences among treatments. IMI: red bars, CLO: green bars, THI: blue bars. Fig. S6. Body weights of survivors and dead in the sorghum experiment. The deaths only occurred in the sorghum experiment, during the Exposure 1 period, in birds treated with imidacloprid (3 dead) and clothianidin (1 dead). In the dead, the BWs were measured at the time of death. In survivors, BWs were measured at the end of the Exposure 1 period. Table S1. Records of maximum and minimum temperature and humidity in each period, and average daily thermal amplitude. Table S2. Doves that consumed soybeans (12 of the 40). Consumption was measured from the fourth day of the "Pre-Exposure 1" period. The number of seeds consumed was calculated based on the average daily weight of soybeans used to measure the humidity factor. Table S3. Average mass in grams of seeds and cotyledons. "Ad Sur" sorghum is the AD75STA commercial hybrid sorghum of "adSur, Agrosemillas del Sur SA", used in COM, IMI and THI treatments of the sorghum test. “DK” sorghum is the “Dekalb” commercial hybrid sorghum seeds of Syngenta®, used in CLO treatment of the sorghum test. Table S4. Average consumption in grams (mean ± SE) of test food and the total consumption (grams of test food + grams of maintenance food) during periods of exposure to neonicotinoids. In the sorghum seeds, CON is the untreated sorghum control and COM is the commercial sorghum control. Table S5. Video records of the behavior of some doves during the first 15 minutes of exposure to food in the different treatments and periods. “1rt peck” indicates the time in seconds when the bird first pecked at the food inside the feeder after it was offered; “n peck food” is the number of times the bird pecked at the feeder food during the first 15 minutes of its exposure to the food; “n grit peck” is the number of times the bird pecked at the grit; “n drink” is the number of times the bird drank water from the drinking fountain; “n grooming” is the number of times the bird groomed itself; “n shaking” is the number of times the bird shook; “on perch” is the number of times the bird climbed on the perch. In the sorghum experiment, CON is the untreated sorghum control and COM is the commercial sorghum control. Table S6. Body condition index (SMI) and the p-value of the paired Wilcoxon test used to compare the initial and final body conditions of each treatment in the three experiments. In the sorghum experiment, CON is the untreated sorghum control and COM is the commercial sorghum control., Peer reviewed

6 pages. -- Supplementary Table S1.Results of the 3-way PERMANOVA for isotopes (δ13C and δ15N), C and N content and C/N ratio in the mussel Mytilus galloprovincialis for the monitoring experiment. -- Supplementary Table S2. Average and standard deviation in δ13C, δ15N, carbon and nitrogen content and C/N ratio of pooled mussels’ tissues of Mytilus galloprovincialis infected and uninfected with the African pea crab Afropinnotheres monodi. -- Supplementary Table S3. Results of the 3-way (Model 2) and 1-way (Model 3) PERMANOVA for isotopes (δ13C and δ15N), C and N content and C/N ratio in the mussel Mytilus galloprovincialis for the monitoring experiment. -- Supplementary Table S4. Average and standard deviation in δ13C, δ15N, carbon and nitrogen content and C/N ratio of pooled mussels’ tissues of Mytilus galloprovincialis and the African pea crab Afropinnotheres monodi after 30 days reared under ad libitum food (Day 30) and subsequently exposed to no access to food during 21 days (Day 51). -- Supplementary text: Isotopic variability of the symbiont and the host species. -- Supplementary Figure S1. Relationships between the carbon and nitrogen isotopic signal (‰) of Afropinnotheres monodi and the muscle of the host bivalve species Mytilus galloprovincialis (locations 2 and 3) and Scrobicularia plana (location 1) in the three locations studied., Peer reviewed

13 pages. -- This PDF file includes: Figures S1 to S7 and Tables S1 to S2. -- Fig. S1. Characterization of scFab-apoferritin fusions. -- Fig. S2. Multabody affinity-purification scheme. Protein A and Protein L sequential affinity purification. -- Fig. S3. Generation of a Multabody that cross-targets the HIV-1 Env and the CD4 receptor. -- Fig. S4. Biophysical characterization of HIV-1 Multabodies. Comparison of the Tm and Tagg temperatures of T-01/T-02 MB, 12-mer ferritin fusions, parental IgGs and the N6/PGDM1400x10E8v4 trispecific antibody. -- Fig. S5. Binding characteristics of IgGs binding to four different antigens. -- Fig. S6. Multabody v2 features. -- Fig. S7. PsV neutralization and inhibition of primary PBMC infection by Multabodies. -- Table S1. IC50 of individual and IgG mixtures, PGDM1400/N6x10E8v4 trispecific and HIV-1 Multabodies against a 14-PsV panel and 25-PsV panel (additional 11 HIV-1 strains highly resistant to PGDM1400). -- Table S2. Potency of parental and IgG mixtures and T-01 Multabody versions against a 118-PsV panel., Peer reviewed

36 pages. -- Supplementary Figure 1 | (A) Combined (plastome + 35S rDNA) Loliinae coalescent species tree computed through Singular Value Decomposition quartets (SVDq) analysis showing bootstrap support values on branches. (B–D) Maximum Likelihood phylogenomic trees of 47 Loliinae samples based on (B) Combined (plastome + 35S rDNA) data, (C) plastome data, (D) nuclear 35S rDNA data, (E) Histograms of repeat contents per holoploid genome (1C) retrieved from the individual Repeat Explorer 2 analyses of the studied Loliinae samples mapped onto the Maximum Likelihood combined phylogenomic tree (plastome + nuclear 35S rDNA cistron) of Loliinae. -- Supplementary Figure 2 | Correlation plots of repeat content and genome size variation (1Cx) for the 23 Loliinae taxa with known genome sizes. -- Supplementary Figure 3 | Evolutionary networks based on standardized repeat data sets obtained from the comparative RE2 analysis of the four Loliinae evolutionary groups: (A) Loliinae, (B) broad-leaved (BL) Loliinae, (C) fine-leaved (FL) Loliinae, (D) Schedonorus. -- Supplementary Figure 4 | Maximum Likelihood Loliinae tree cladograms (combined plastome + nuclear 35S rDNA cistron) showing the relationships among the studied samples in each of the four evolutionary groups of Loliinae and phyloheatmaps of normalized values for different sets of repeat clusters retrieved by RE2 from the comparative analysis of each group: (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). -- Supplementary Figure 5 | Maximum Likelihood nuclear 5S rDNA cistron tree showing the relationships among the 47 studied Loliinae samples., 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

Taxa included in the repeatome analysis of Loliinae. Taxonomic rank, taxon authorship, detailed localities and vouchers, and source of cytogenetic and genomic data. Group: BL, broad-leaved Loliinae; FL, fine-leaved Loliinae; Sch, Schedonorus. Chromosome number (2n), ploidy, genome size (2C, pg), monoploid genome size (1Cx, pg; 1Cx, Mbp) and GenBank accession codes for plastome and nuclear ribosomal 35S and 5S genes are given for each sample. Values in bold correspond to new data generated in this study. Outgroups used in the phylogenomic analyses: Oryza sativa, Brachypodium distachyon., 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

Loliinae samples used in the repetitive DNA analysis. Genome skimming paired-end (PE) reads per sample and PE reads selected by Repeat Explorer 2 per sample in each of the comparative analyses of the four Loliinae groups: Loliinae, BL (broad-leaved Loliinae), FL (fine-leaved Loliinae), 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

Repeat Explorer 2 comparative analysis. Repeat content data for top 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

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