dataesr/scientific-paragraphs-categorization huggingface dataset:
To capture the processes underlying species dissimilarity among communities, we partitioned the overall β-diversity values into their species replacement (change in diversity due to species turnover) and species richness (change in diversity due to differences in species richness) components  [47]. We calculated β-diversity within sites in exotic and in native forests using the function "beta. div" in the R package "adespatial" version 0. 3-14  [48]. In order to assess the uniqueness of study sites in term of species composition, we computed the local contributions to beta diversity (LCBD indices) of each site  [49]  using the functions beta. div. comp and LCBD. comp in adespatial  [48]. LCBD indices were computed within each type of forest (native and exotic). High LCBD values indicate sites that have a unique species composition  [50].
Acknowledgments: We thank the many people who have assisted us with fieldwork, collecting specimens. A large number of students financed by the  EU Programs ERASMUS  and EURODYSSÉE sorted the samples prior to species assignment by one of us (PB), and we are grateful to all of them: Adal Humberto  Díaz Raya ,  David Rodilla Rivas ,  Daniel Ehrhart ,  Juan Ignacio Pitarch Peréz ,  Juan Manuel Taboada Alvarez ,  Helena Marugán Páramo ,  Laura Cáceres Sabater ,  Laura Gallardo ,  Marija Tomašic ,  Óscar García Contreras ,  Percy de Laminne de Bex ,  Ruben Murillo Garcia ,  Rui Carvalho ,  Rui Nunes ,  Sergio Fernandez ,  Sophie Wallon , and  William Razey. We are grateful to three anonymous reviewers for their comments on a previous version of this paper.
Genome analysis followed by searches in protein databases revealed that more than 36% of the proteins were novel, being Ectocarpus or phaeophyte specific, with no counterpart in other taxonomic groups. These significant differences suggested that a large number of evolutionary innovations took place in this group, leading to the occurrence of many novel genes in addition to considerable divergence from homologous sequences  [12]. Therefore, Ectocarpus genomic data represent a valuable resource with a great potential to discover novel genes and pathways involved in stress adaptation or specific bioactivities that are absent in other taxonomic groups. However, phaeophyte research is challenging, especially when the aim is to characterize and understand functions of novel genes, coding proteins of unknown function.
The presence of such domains makes protein expression in any system problematic. No transmembrane domains have been predicted for Esi0017_0056. Homology modelling using PSIPRED provided an overall prediction of the secondary structure of this protein with a MW of 43. 1 kDa and an isoelectric point (pI) of 8. 74 (Supplementary Figure  S1 ). To gain more information about Esi0017_0056 protein structure, homology-modelling was carried out using the SWISS-MODEL server. The best model (26. 71% sequence identity) was built using the hypothetical protein ybiA from E. coli as a template. Modelling of the region between residues 132 to 291 suggested that Esi0017_0056 is well-structured with several alpha-helices and short beta-strands (Supplementary Figure  S2a, b ). Modelling information and data coming from similarity searches of other proteins harboring domains from the DUF1768 superfamily as well as from the automatic prediction output from PSIPRED, HMMTOP v.
2. 0 and TMHMM v. 2. 0 indicated that Esi0017_0056 is a soluble, monomeric protein. A full-length tertiary structure, built by DMPfold, revealed a protein with a globular structure, and additional alpha helices (Supplementary Figure  S2c ). Blastp similarity searches of Esi0017_0056 in GenBank RefSeq non-redundant proteins database revealed that the closest relatives are two other proteins from Ectocarpus, which are also labeled as unknown conserved proteins (GenBank accession # CBJ32535 and CBJ27468). The next > 100 organisms harboring protein sequences with significant similarity (E-value: 8 × 10 -45 -1 × 10 -37 ) to these Ectocarpus proteins were of prokaryotic origin, including delta proteobacteria, gamma proteobacteria, firmicutes and cyanobacteria. The middle part of the 391 amino acids long Esi0017_0056 protein, that is, residues 132 to 291, was found to have strong similarity with DUF1768, a protein domain of unknown function (pfam08719).
DUF1768 contains members such as E. coli N-glycosidase YbiA (COG3236), involved in riboflavin biosynthesis, which was initially characterized as a swarming motility protein. More recently, this family was included in the NADAR (NAD and ADP-ribose) superfamily which comprises proteins predicted to be involved in NAD-utilizing pathways, likely to act on ADP-ribose derivatives. Blastp similarity searches of Esi0017_0056 protein in GenBank RefSeq non-redundant proteins database, with restricted searches for eukaryotes, revealed that the closest eukaryotic organisms harboring a similar protein is the apusomonad Thecamonas trahens ATCC 50062 (E-value: 1 × 10 -38 ). The organisms within this range of similarity were found to be extremely diverse, including the metazoans Strongylocentrotus purpuratus and Dendronephthya gigantea, the haptophyte Emiliania huxleyi, the amoebozoa Entamoeba invadens and the fungus Cercospora berteroae.
Means and SE followed by the same letter are not significantly different. The plants were photographed at 9 days after transfer in standard and under salinity stress conditions. In order to verify if the enhanced stress tolerance observed in seedlings can be observed in plants grown in soil, 15-days-old transgenic plants were irrigated with 200 mM NaCl, and concentrations of around 100 mM were maintained in the peat pellet. After one week of exposure to salinity stress, wild type plants exhibited symptoms of growth retardation and leaf chlorosis whereas transgenic plants grew better (Figure  4 ). Analysis of biomass data suggested that transgenic plants had significantly higher fresh weight and dry weight as compared to the wild type plants (Figure  4 ). When the effect of promoters (constitutive and stress-inducible) was contrasted, transgenic lines generated using stress inducible promoter showed slightly reduced fresh weight under standard conditions as compared to the wild type plants, while the lines generated using constitutive promoter showed slightly reduced dry weight.
1; structure solved by NMR). As the model generated by SWISS-MODEL covered only the DUF1768-domain, another tertiary structure homology-modelling was carried out using DMPfold  [51]. The PDB files generated by ProMod3 v. 3. 0. 0 and DMPfold were visualized using iCn3D  [52]. To assess the evolutionary relationship of Esi0017_0056, the amino acid sequence was compared with that of similar protein sequences retrieved from GenBank by running a blastp search. Alignments of selected protein sequences were performed using MUS-CLE [53] implemented in MEGA X  [54]. Sequences were trimmed to a total of 163 amino acid positions in the final dataset. The evolutionary history was inferred by using the Maximum Likelihood method and JTT matrix-based model  [55]. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.
Recombinant Esi0017_0056 Protein Analysis by LC-MS/MS The excised gel slices were processed for LC-MS/MS as described by  [57] , with minor modifications. The samples were transferred to a 300 µL HPLC vial and were subjected to analysis by LC-MS/MS on a VelosPRO orbitrap mass spectrometer (ThermoFisher Scientific, Mississauga, ON, Canada) equipped with an UltiMate 3000 Nano-LC system (ThermoFisher Scientific, Mississauga, ON, Canada). Chromatographic separation of the digests was performed on PicoFRIT C18 self-packed 75 µm × 60 cm capillary column (New Objective, Woburn, MA, USA) at a flow rate of 300 nl/min. MS and MS/MS data were acquired using a data-dependent acquisition method in which a full scan was obtained at a resolution of 30,000, followed by ten consecutive MS/MS spectra in both higher-energy collisional dissociation (HCD) and collision-induced dissociation (CID) mode (normalized collision energy 36%).
Internal calibration was performed using the ion signal of polysiloxane at m/z 445. 120025 as a lock mass. Raw MS data were analyzed using Proteome Discoverer 2. 2 (ThermoFisher Scientific, Mississauga, ON, Canada). Peak lists were searched against all the available protein databases as well as the cRAP database of common contaminants (Global Proteome Machine Organization). Cysteine carbamidomethylation was set as a fixed modification, while methionine (Met) oxidation, N-terminal Met loss and phosphorylation on serine, threonine and tyrosine were included as variable modifications. A mass accuracy tolerance of 5 ppm was used for precursor ions, while 0. 02 Da for HCD sucrose and solidified with 0. 4% Phytagel (w/v) and containing ammonium glufosinate 40 µg/mL. Plates were maintained at 22 • C in a 16-h light/8-h dark cycle.
Salinity Stress Tolerance Four days old uniform seedlings produced as described earlier were transferred on plates containing half strength MS medium and 100 mM NaCl. Root length was marked on the day of transfer, and on the 7th day, plates were scanned with a high-resolution scanner (Epson Expression 10000 XL, Epson, Markham, ON, Canada). Root length and the number of lateral roots per cm of primary root were measured using Image J software (Research Services Branch, NIH, Bethesda, MD, USA). Percent leaf chlorosis was visually estimated on 7th day after transfer. Nine-days-old plants were used to determine the fresh and dry weight. The experiment was repeated 3 times with 30 plants in each treatment in all experiments. To assess the effect of salinity stress, plants were grown on Jiffy peat pellets (Jiffy, Shippagan NB, Canada).
This cleavage site is thought to be critical to its replication and pathogenesis, with a notable link to virus transmission. Here, we examine the spike protein across coronaviruses identified in both bat and rodent species and address the role of furin as an activating protease. Utilizing two publicly available furin prediction algorithms (ProP and PiTou) and based on spike sequences reported in GenBank, we show that the S1/ S2 furin cleavage site is typically not present in bat virus spike proteins but is common in rodent-associated sequences, and suggest this may have implications for zoonotic transfer. We provide a phylogenetic history of the Embecoviruses (betacoronavirus lineage 2a), including context for the use of furin as an activating protease for the viral spike protein. From a One Health perspective, continued rodent surveillance should be an important consideration in uncovering novel circulating coronaviruses.
A second Alphacoronavirus, canine coronavirus 23/03, also possesses a furin cleavage site, but the role in disease is less well defined  [76]. In bat spike sequences from Alphacoronaviruses, no obvious S1/S2 furin cleavage site was identified based on ProP and PiTou predictions. Two proposed alphacoronavirus from rodents, AcCoV-JC34 and Lucheng Rn rat coronavirus Lijiang-170, had a shared, weakly predicted furin cleavage site (S-R-R-A-R), based on the PiTou program. A caveat to using bioinformatics programs lies in the correlation between a software prediction and biological plausibility. A predicted site, for example, may not be accessible to furin and thus, nonfunctional and the action of other proteases, needs also to be considered. It is also presently unclear how the presence or absence of a cleavage site and its relative cleavability score translates into a given biological process, such a transmissibility, cross-species tropism or pathogenicity.
, 1994; Le Roy et al. , 2020) , which may lead to uncorrelated patterns of diversification. To investigate whether species and phenotypic diversification dynamics are coupled and to identify potential drivers of variations, we inferred a time-calibrated molecular phylogeny of the genus that we combined to a dataset of geographical distributions and morphometric measurements of wing size and shape. We applied an integrative approach and addressed the following questions: (1) Have rates of phenotypic diversification varied across the tree? We investigated potential variations in rate of phenotypic diversification among clades using phenograms and models of trait evolution to compare evolutionary rates for wing size and shape. (2) Is species diversification better explained by global processes or clade-specific (ecological) factors? First, we fitted different models of species diversification testing for global drivers of diversification, specifically past temperatures and Andean orogeny.
Time-calibrated phylogeny Phylogenetic relationships and divergence time were inferred with Bayesian inference. We concatenated DNA data for one mitochondrial (COI) and four nuclear genes (CAD, EF-1α, GAPDH and MDH) using published sequences  (Cassildé et al. , 2012; Penz et al. , 2012; Chazot et al. , 2016)  retrieved from GenBank, generating a molecular dataset of a total length of 5001 nucleotides. Our dataset includes all Morpho species (i. e. 30 species sensu  Blandin, 2007). Morpho helenor, which harbours many subspecies, is distributed throughout the entire Neotropical region, resulting in unresolved biogeographic reconstructions in preliminary analyses. To help resolving the biogeographic inferences, M. helenor was represented in the biogeographic analyses by six subspecies that each occupies a distinct Neotropical area.
Morphological data Our morphological dataset (published by  Chazot et al. 2016 ) consists in the size and shape of the fore and hind wings, as assessed by morphometric measurements. A total of 911 collection specimens of both sexes and representing all Morpho species were photographed. Wing shape was described using landmarks and semi-landmarks placed at vein intersections and wing margins, respectively (see  Chazot et al. , 2016  for details), which were superimposed with tpsRelw  (Rohlf, 1993). Wing size was measured using the logtransformed mean centroid size per species. Importantly, for analyses involving wing shape we used the residuals of a multivariate regression of species mean Procrustes coordinates on species mean centroid size (log-transformed), which allows focusing on the non-allometric shape variation.
, 2013). For each paleoenvironmental variable, we designed three models to be tested: (i) the speciation rate varies exponentially with the environment and the extinction rate is constant, (ii) the speciation rate is constant and the extinction rate varies exponentially with the environment, and (iii) both speciation and extinction rates vary exponentially with the environment. We repeated these three models with a linear dependence to the environmental variable, instead of exponential dependence. For temperature we relied on the well-known Cenozoic temperature dataset published by  Zachos et al. (2008). The orogeny of the Andes is a highly complex process, with important differences in uplift tempo and mode from the south of Central Andes to Northern Andes  (Blandin & Purser, 2013, and references therein).
Several general phases have been identified from the late Eocene to present, but they are difficult to synthetize in a unique model. As  Blandin & Purser (2013)  suggested that the early diversification of the Morpho occurred along the proto-Central Andes, we used the model of surface uplift inferred by  Leier et al. (2013)  for the eastern cordillera of the southern Central Andes to test the possible influence of Andean orogeny on the diversification of the Morpho. We used the R-package PSPLINE 1. 0-17 to reconstruct smooth lines of the paleo-data for each environmental variable. The smooth line is introduced in the birth-death model to represent the variation of the environment through time. Given the dated phylogeny, the model then estimates speciation and extinction rates, as well as their respective variations according to the environment  (Condamine et al.
Historical biogeography To assess where and when diversification occurred, we estimated ancestral areas using the dispersal-extinction-cladogenesis (DEC,  Ree and Smith, 2008)  model as implemented in the R-package BioGeoBEARS 0. 2. 1  (Matzke, 2014). The analyses were performed using the MCC tree (outgroups removed) and included six subspecies of M. helenor (each subspecies was assigned to its current distribution). The distribution of Morpho is restricted to South America and Central America (all Neotropics except the Caribbean Islands). A geographic model was incorporated to include operational areas, defined as geographic ranges shared by at least two or more species and delimited by geological, oceanic or landscape features, which may have acted as barriers to dispersal. The model comprised 7 component areas: (A) Central America, (B) trans-Andean South-America, (C) slopes of northern Andes, (D) eastern slopes of central Andes, Orinoco-Amazonian basin north of the Amazon, including the Guyanas, (E) Amazonian basin, south of the Amazon River, and (F) Atlantic forest.
Hence, our results do not exclude the possibility that the Andes played a role in diversification, but rather suggest that their effect on the shape of the phylogenetic tree was less significant than other factors. Nevertheless, the extent to which the effects of these ecological drivers can be generalised is unknown given the scale of our dataset. In particular future work at a larger phylogenetic scale should shed light on the importance of major hostplant transitions on the evolution of body size and the dynamics of diversification. Our study also highlights that both phenotypic and ecological information are of key relevance for understanding macroevolutionary patterns of diversification. Table  1. Summary results obtained from fitting three models of trait evolution on 100 trees, using the rjmcmc.
bm function as implemented in the R package GEIGER on a) males and b) females. bm=single Brownian rate, rbm=relaxed Brownian rates, jbm=jumps of Brownian rates. AICbm, AICrbm, AICjbm = mean AIC score across the 100 trees for all three models. ΔAIC bm-rbm, ΔAIC bm-jbm, ΔAIC rbm-jbm = pairwise AIC differences between models for each tree. Diversification rates (speciation minus extinction) for the best models identified for the different subclades (canopy and monocotyledon) and the remaining lineages (background). The early background diversification is elevated and decreases through time until it becomes negative in the early Miocene. The canopy clade has constant rates of diversification, while the monocotyledon clade conforms to an early-burst pattern with high rates that decrease toward the present.
The authors have no conflict of interest to declare. F. L. C. has benefited from an " Investissements d'Avenir " grant managed by  Agence Nationale de la Recherche  (CEBA, ref. ANR-10-LABX-25-01 ). P. B benefited from the  Programme Pluriformation "Etat et structure phylogénétique de la biodiversité actuelle et fossile ". CC-BY-NC-ND 4. review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is.
Consensus phylogram (50 % majority rule) of 56 102 trees resulting from a Bayesian analysis of the LSU sequence alignment (179 sequences including outgroup; 832 aligned positions; 378 unique site patterns; 3 740 000 generations with trees sampled every 100 generations) using MrBayes v. 3. 2. 7a (Ronquist et  al. 2012). Bayesian posterior probabilities (PP) > 0. 84 are shown at the nodes and thickened lines represent nodes with PP = 1. 00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. Culture collection/voucher, GenBank accession (in superscript) and/or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Diaporthe perjuncta (GenBank NG_059064. 1) and the taxonomic novelties described in this study for which LSU sequence data were available are indicated in bold face.
The most basal branched was halved in length to facilitate layout. The alignment and tree were deposited in TreeBASE (Submission ID 28129). Consensus phylogram (50 % majority rule) of 91 128 trees resulting from a Bayesian analysis of the LSU sequence alignment (170 sequences including outgroup; 799 aligned positions; 295 unique site patterns; 6 075 000 generations with trees sampled every 100 generations) using MrBayes v. 3. 2. 7a (Ronquist et  al. 2012). Bayesian posterior probabilities (PP) > 0. 84 are shown at the nodes and thickened lines represent nodes with PP = 1. 00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. Culture collection/voucher, GenBank accession (in superscript) and/or Fungal Planet numbers are indicated behind the species names.
Overview Leotiomycetes phylogeny Consensus phylogram (50 % majority rule) of 408 002 trees resulting from a Bayesian analysis of the LSU sequence alignment (90 sequences including outgroup; 826 aligned positions; 283 unique site patterns; 2 720 000 generations with trees sampled every 10 generations) using MrBayes v. 3. 2. 7a (Ronquist et  al. 2012). Bayesian posterior probabilities (PP) > 0. 84 are shown at the nodes and thickened lines represent nodes with PP = 1. 00. The scale bar represents the expected changes per site. Families and orders are indicated with coloured blocks to the right of the tree. Culture collection /voucher, GenBank accession (in superscript) or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Xylaria hypoxylon (GenBank AY544648.
Vandijckellaceae Leotiales Consensus phylogram (50 % majority rule) of 87 002 trees resulting from a Bayesian analysis of the LSU sequence alignment (33 sequences including outgroup; 792 aligned positions; 203 unique site patterns; 290 000 generations with trees sampled every five generations) using MrBayes v. 3. 2. 7a (Ronquist et  al. 2012). Bayesian posterior probabilities (PP) > 0. 84 are shown at the nodes and thickened lines represent nodes with PP = 1. 00. The scale bar represents the expected changes per site. The family and order are indicated with coloured blocks to the right of the tree. Culture collection/voucher, GenBank accession (in superscript) or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Candida broadrunensis (GenBank KY106372. 1) and the taxonomic novelty described in this study for which LSU sequence data were available is indicated in bold face.
Overview Phytophthora phylogeny Consensus phylogram (50 % majority rule) of 64 502 trees resulting from a Bayesian analysis of the LSU sequence alignment (25 sequences including outgroup; 1 110 aligned positions; 68 unique site patterns; 215 000 generations with trees sampled every five generations) using MrBayes v. 3. 2. 7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0. 84 are shown at the nodes and thickened lines represent nodes with PP = 1. 00. The scale bar represents the expected changes per site. The higher taxonomic classification is indicated with coloured blocks to the right of the tree. Culture collection/voucher, GenBank accession (in superscript) or Fungal Planet numbers are indicated behind the species names. The tree was rooted to Absidia panacisoli (GenBank NG_063948.
Straminipila Stramenopiles Oomycetes Overview Saccharomycetes and Tremellomycetes phylogeny Consensus phylogram (50 % majority rule) of 136 502 trees resulting from a Bayesian analysis of the LSU sequence alignment (36 sequences including outgroup; 667 aligned positions; 432 unique site patterns; 910 000 generations with trees sampled every 10 generations) using MrBayes v. 3. 2. 7a (Ronquist et al. 2012). Bayesian posterior probabilities (PP) > 0. 84 are shown at the nodes and thickened lines represent nodes with PP = 1. 00. The scale bar represents the expected changes per site. The families, orders and classes are indicated with coloured blocks to the right of the tree. Culture collection/voucher, GenBank accession (in superscript) and/or Fungal Planet numbers are indicated behind the species names.