dataesr/scientific-paragraphs-categorization huggingface dataset:
Comparative analyses of diversification indicated a very rapid adaptive radiation by the permanently inbreeding and fungus-cultivating lineage Xyleborini beginning around 20 Ma: the highest speciation rate for any lineage of Scolytinae. More detailed analyses using the software SLOUCH revealed significant effects of inbreeding and deep host shifts for the diversification of the subfamily  [120]. High diversification rates were further emphasized by the likely high levels of cryptic species in some inbreeding lineages, e. g. , Hypothenemus eruditus (Westwood) and allied species groups  [121]. Over larger evolutionary time spans, it is also clear that radical host shifts have facilitated high diversification rates given the radically new host opportunities in these lineages.
The Rhynchophorini was also monophyletic, albeit also with less than 95% PP support, with the possible inclusion of Cryptoderma Ritsema, which is currently classified in its own tribe as the Cryptodermatini within this clade. She provided an overview of known host plant preferences and possible evolutionary shifts of these preferences among major groups within dryophthorines. She is currently working to add additional molecular markers as well as morphological data of the adults and immatures. She concluded with an overview of ongoing efforts to generate two-dimensional (2D), and possibly three-dimensional (3D), images of all North American weevil types housed at the United States National Museum (USNM). These images and corresponding occurrence data are being made available through the Symbiota Collections of Arthropods Network (SCAN) as part of the Weevils of North America (WoNA) project http://scan-bugs.
The option of sampling thousands of genera is probably unrealistic and so reducing this number to a few hundred units, the monophyly of each of which is testable, seems a sensible move. Undoubtedly, other clades will become apparent whether there is a formal name available for them or not. From this, it is more feasible to develop trees at the higher level. It is also important to understand the sampling intensity necessary to deliver a robust tree; e. g. the tree in [79] is far more coherent for Old-World Cryptorhynchini than other cryptorhynchines and Molytinae with a lower sampling density. Establishing phylogenetically reliable bricks may help us build the larger construction that is the phylogeny of the CCCMS clade. 2. 3. 9. Regional Databases in Curculionidae: An Example for the Naupactini (Curculionidae: Entiminae) from Argentina and Uruguay (M.
Guadalupe del Río) Guadalupe del Río talked about cybertaxonomy (e-taxonomy = web-based taxonomy) and how systematics has evolved, integrating standardized electronic tools, cyber-infrastructure, computer science and computer engineering. Through user-friendly interfaces, these tools make it easier for taxonomists and the general public to identify species and access the world´s total knowledge of biodiversity  [133]. She gave a screenshot of the main biodiversity portals, e. g. , taxonomic data (Antweb, Avibase, FishBase, species file OSF); biodiversity data (GenBank, iBol, BOLD); morphological data (Morphbank); phylogenetic data (Tree of Life); biodiversity initiatives (Species 2000, GBIF, CoL, EOL); bibliographic information (Biodiversity Heritage Library); and tools for registration and recovery of taxonomic collections (life science identifiers [LSIDs], Darwin Core, digital object identifiers [DOIs]).
In the case of weevils, there is an International Weevil Community Website [134] that facilitates cooperation and information sharing worldwide and that also includes a very useful glossary of weevil structures  [135]. There are several other websites, for example Wtaxa: Electronic Catalogue of weevil names  [136] , New Zealand weevil Images  [137] , Potential invasive weevils of the world  [138] , Coleoptera Neotropical  [139] , Symbiota Collections of Arthropods Network (SCAN)  [140]  and Beetles and Coleopterists  [141]  among others. Analía Lanteri and M. Guadalupe del Río generated a regional database of "Naupactini (Curculionidae: Entiminae) from Argentina and Uruguay" that includes more than 120 species, some of which are also distributed in other South American countries and have been introduced in other continents.
For each species, the authors give the synonyms, a short diagnosis in English and Spanish, complete data of distribution, host plants and biological observations. This information is complemented with pictures of adult females and males and maps of their distribution in Argentina and Uruguay. The database will be available through the "Portal of Biodiversity of Insects from Argentina" hosted at CEPAVE (Centro de Estudios de Parásitos y Vectores, CONICET-UNLP) and will facilitate the rapid identification of naupactines harmful to agriculture. Guillermo (Willy) Kuschel dictated various topics to Richard Leschen who presented these after a brief introduction to Willy's career  [36]  that highlighted weevil specialists who had studied in or visited New Zealand. Ventral structures of beetles: The current sternal structures of beetles are based on the invagination of what are thought to be primitively external structures and referred to as meso-, meta-, or abdominal ventrites.
Curculionidae Classification: Viewpoints and Vision (Chris Lyal) Chris Lyal discussed his work on the classification of Curculionidae. An overarching vision is of a time when we know everything about weevil phylogeny, when fitting new taxa into the model is simple, when phylogeny illuminates hypotheses of biology and evolution and when we can address novel questions based on a clear phylogenetic framework supported by a digital databank of all known information about weevils and their associations. Until then. we are currently in a key position. We have a working community that is building on a long-term engagement around the goal of a functioning classification based on phylogeny and with a recent record of successful interactions in creating the Handbook  [142]. We are using multiple methodologies, but these are increasingly interlocking.
h. howdenae, G. conwayensis Lanteri, and G. ashlocki Lanteri (in Santa Cruz Island) and G. galapagoensis Lanteri, G. collaris Lanteri, and G. vandykei Lanteri (in San Cristóbal). Range expansion of G. h. howdenae into the highlands prompts us to ask if the introduced population could be hybridizing with the highland endemic G. ashlocki, which is also a single-island endemic. We predicted that if hybridization is occurring and is recent, larger estimates of genetic exchange should be found between the introduced G. h. howdenae and the Santa Cruz endemics G. conwayensis and G. ashlocki. Moreover, the effects of hybridization should be greater when analyzing patterns with mitochondrial DNA than with nuclear DNA due to the maternal inheritance of mtDNA. We estimated six parameters for six pairwise comparisons using IMa2  [149, 150]  using mitochondrial and nuclear DNA sequence datasets.
In its last project phase, MWI now investigates, among other aspects, the feasibility of using 'barcode gaps' in a quick approximation to pre-assign unknown specimens to species or to get a first heuristic hypothesis on species limits that will be subsequently tested by additional evidence (morphology, ecology). While a general barcode gap for such a diverse group of organisms would not hold, adapted gap values can still be conveniently applied for the various taxonomic and ecological groups. Currently, the MWI reference database contains roughly 1400 species, with usually several specimens per species, from 330 genera  [160, 161]. Using synergies with the ZFMK-coordinated project German Barcode of Life (www. bolgermany. de), a regional sampling focus of MWI lies on the weevil species occurring in Germany.
In summary, MWI compiles a validated reference database with DNA barcodes of western Palearctic weevils (to be released soon) and offers cross-linked morphological and molecular collections that we encourage entomologists to use. New Zealand has a diverse broad-nosed weevil (Coleoptera: Curculionidae: Entiminae) fauna, which is particularly speciose in alpine regions of the southern South Island  [83, 162]. A number of species show remarkable sexual dimorphism, where females possess exaggerated structures on the elytra and abdominal ventrites  [83]. These structures can be classified into five forms: (1) tubercles at the top of the elytral declivity; (2) prolongation of the apex of the elytra; (3) swelling of the disc of ventrite V; (4) emargination of the apex of ventrite V; and (5) the posterior margin of ventrite IV produced into a lamina.
The Bayesian approach enjoyed a considerable popularity in the decades that followed (see dos  Reis et al. 2016  for a recent review). Part of this success comes from the ease with which new models can be integrated without affecting the inference techniques (see for instance the "plug-in" architecture implemented in BEAST2,  Bouckaert et al. 2014). The first technique that combined fossil and genetic data in Bayesian molecular dating relied on the socalled "node-dating" approach. The age of a given fossil's stratigraphic range along with its morphological features are examined in a first step. This analysis is usually conducted by experts, following a wellestablished protocol  (Benton and Donoghue 2007; Parham et al. 2011 ). As a result, subsets of extant (and sampled) species are identified that share a MRCA with one or more fossils.
It was proposed in an attempt to analyze genetic sequences along with morphological characters in a unified statistical framework  (Pyron 2011; Ronquist et al. 2012). The inferred position of fossil taxa in the phylogeny is here determined by the similarities of morphological features displayed by extant and extinct (i. e. , fossil) taxa. While node-dating relies on expert knowledge to translate fossil data into calibration information, totalevidence instead tackles this issue using a statistical modeling approach. Uncertainty around the placement of calibration constraints is thus dealt with in a proper probabilistic framework, thereby giving this tip-dating technique a clear edge on node-dating approaches. The implementation of the total-evidence technique proposed by  Pyron (2011)  and  Ronquist et al.
If one uses g(e,i|α,θ) := Z θ instead of the definition given in Equation  2 , the above density simplifies to give the following: p(t,,e,i,θ|α) := p T (t,|θ)(t,,e,i)f (θ). ( 5 ) This expression is in fact similar to that used by  Gavryushkina et al. (2017)  in the context of a totalevidence approach combined to the FBD tree process. It also corresponds to using uniform priors on calibrated node ages in the "product-of-marginals" technique implemented in the BEAST software. This particular approach thus relies implicitly on substituting g(e,i|α,θ) with Z θ , which indeed corresponds to the probability of the calibration constraint given the fossil data under the tree process considered. This choice makes perfect sense from a mathematical and a modeling perspective. Yet, as shown above, using the tree process to define the distribution of e,i|α,θ is not a requirement.
They used a nucleotide sequence data set with 154 taxa and three genes (18S, atpB, and rbcL) totaling 4533 bp. The fossil data available provide calibration time intervals for 33 sets of taxa. The authors performed two analyses: one with a maximum age for the origin of eudicots set to 125 Ma and another without this particular constraint. Because geographical and morphological evidence suggest an earlier origin for that clade, this datum was discarded and the analysis conducted here focuses on the remaining 32 calibration intervals. Smith et al. (2010)  used the "product-of-marginals" approach implemented in BEAST 1. 4. 7. A lognormal probability density was used to model the marginal distribution corresponding to each fossil. FIGURE 4. Impact of ignoring Z θ on the inferred timing of speciation in lands plants.
Smith et al. (2010)  data set was analyzed with a subsample of 16 fossils (randomly sampled in the full set of 32 fossils). The timing of diversification of land plants, angiosperms and eudicots were estimated using the "traditional" tree-dependent approach that ignores Z θ (in blue) and the exchange algorithm that implements the tree-independent technique (in pink). and land plants. The 95% credibility intervals for these three events are  [159;225], [221;303] and [428;990]  Ma, respectively under the tree-independent model. Using the tree-dependent approach, the equivalent intervals are  [177;337], [240;448, and [475;1367]  Ma. Substantial differences in the posterior distribution of the birth parameter are also observed: the 95% credibility intervals with the tree-independent and the treedependent techniques are [0.
ACKNOWLEDGMENTS The work presented in this article greatly benefited from in depth discussions with  Alexandra Gavryushkina. I would also like to thank  Pierre Pudlo  for pointing me to Murray et al. (2012) article about sampling from doubly intractable distributions;  Jeremy Beaulieu  along with  Michael Donoghue  for sharing with me the plant data set;  Tanja Stadler ,  David Welch ,  Emmanuel Douzery  and  Sophie Mignon  for discussions;  David Bryant ,  Mario dos Reis  and an anonymous reviewer for excellent remarks and suggestions that improved this work.
Participants A tentative power analysis was performed through the G*Power software  (Faul, Erdfelder, Lang, & Buchner, 2007). We computed a priori power for our ANOVA design (F tests family, repeated measures e within factors). We used, as input parameters, an effect size f ¼. 17, alpha level ¼. 05, and correlation among repeated measures ¼. 5. We assumed no violations of sphericity, and thus did not apply any correction. Our design only considered 1 group of subjects with 18 repeated measures (GVS by Reward by Validity, 3 Â 3 Â 2). A power of 90% was found to be achievable at N ¼ 25. To properly counterbalance all conditions in our design (see below in the methods) we needed a sample size with a multiple of 6 subjects (3 levels of GVS Â 2), thus we back-computed achieved power for N ¼ 24 (89.
Behavioural tasks Participants were tested in a dimly lit, quiet room. Their head was restrained by a chinrest, facing a 15 inches large screen at a distance of approximately 57 cm. The open-source software OpenSesame  (Mathôt, Schreij, & Theeuwes, 2011 , http:// osdoc. cogsci. nl/) was used to display experimental stimuli on the screen and record the subjects' response. Participants provided responses by means of keyboard presses (on a standard QWERTY keyboard) using the index and middle fingers of their dominant hand. Two tasks were administered during GVS. The main task evaluates attentional assets and their modulation according to the rewards at stake (attention and reward task e ART). This part was designed to last a maximum of 25 min. A control task (subjective visual vertical e SVV) was also administered before the main task.
SVV requires rotating visual segments until they appear to be in a vertical position. It was meant to provide independent evidence of GVS effectiveness, given that displacements occur towards the site of labyrinthine dysfunction  (B€ ohmer & Rickenmann, 1995; Vibert, H€ ausler, & Safran, 1999)  or anodal GVS stimulation  (Mars et al. , 2001; Saj, Honor e, & Rousseaux, 2006). It was therefore meant to provide evidence of a successful stimulation, and means to correlate the perceptual effects of GVS (effectiveness of the stimulation) with results obtained from the ART task. The scripts to run these tasks can be found in the supplementary materials. Finally, a brief evaluation of subjective feelings and sensations experienced during each session was administered. It was meant to monitor participants' distress and task compliance across the different days of the experiment and GVS protocols.
2. 4. 2. Statistical analyses 2. 4. 2. 1. ART. Results were analysed through mixed-effects multiple regression models  (Baayen, Davidson, & Bates, 2008)  using the lme4 package for R  (Bates, Maechler, Bolker, & Walker, 2014). Models had a logistic link-function, appropriate for binary variables, when assessing accuracy. As a first step, we defined a model containing the most appropriate random effects. Theoretically, models including all the possible random effects (justified by experimental design) would lead to the most informative solution. However, complicated matrices often result in convergence problems in the face of a negligible increase in the amount of information provided or even overfitting  (Bates, Kliegl, Vasishth, & Baayen, 2015). Random effects were thus introduced sequentially, their effect on model fit assessed through likelihood ratio tests (LRT): residuals of each model were compared, and the one with significantly lower deviance as assessed by a chi-squared test was chosen.
We used p-values adjustments for multiple testing (see below) and an alpha level of. 043 (see section 2. 1). For a Bayesian counterpart, Bayes Factors (BF) were obtained through objective Cauchy-distributed priors (i. e. , assuming that 50% of observed normalized effect sizes might fall in the À. 7 to þ. 7 interval; Rouder, Morey, Speckman, & Province, 2012) using the BayesFactor package for R  (Morey, Rouder, & Jamil, 2015) , in the context of an ANOVA design. A Bayes Factor larger than 1 supports the alternative hypothesis, while a BF smaller than 1 supports H0; it is best used to grade the strength of evidence for one model over another. Procedure for dealing with non-convergence. Despite the selection procedure mentioned above, convergence problems could still arise during the testing of both random and fixed effects.
Results Raw data, the full analysis pipeline and scripts, and additional graphical depictions are available in the supplementary materials and at the following link: https://data. mendeley. com/datasets/b5grw3pz3r/draft?a¼a7556d48-1f30-4b2c-a9e4-2031012e3541. As previously stated, we eventually enrolled 30 participants because the first interim analysis (N ¼ 24) only provided evidence for the GVS by Reward interaction (but not for the other key tests of this work, e. g. , the three way GVS by Reward by Validity). The following packages for R greatly eased our work: afex  (Singmann, Bolker, Westfall, & Aust, 2015) ; BayesFactor  (Morey, Rouder, & Jamil, 2015) ; lme4  (Bates et al. , 2014) ; tidyverse  (Wickham, 2017) , and notably ggplot2  (Wickham, 2016).
Acknowledgements The authors wish to thank  Pr. Leonardo Chelazzi  for insightful discussions around both the early and final stages of this project. EB received funding from the  People Programme  ( Marie Curie Actions ) of the European Union's  Seventh Framework Programme  ( FP7/2007-2013)  under  REA  grant agreement  PCOFUND-GA-2013-609102 , through the  PRESTIGE program  coordinated by  Campus France , and then from the  European Union 's  Horizon 2020 research and innovation programme (Marie Curie Actions)  under grant agreement  MSCA-IF-2016-746154. AF was supported by the  James S. McDonnell Scholar award. FHB received funding from the  French National Research Agency (ANR)  ( ANR-14-CE13-0005-1 ). The study was performed within the framework of the  LABEX CORTEX  ( ANR-11-LABX-0042 ) of the  University of Lyon  within the program " Investissements d'Avenir"  ( ANR-11-IDEX-0007 ) operated by the  ANR.
In addition, species that are visually similar in pictures must be avoided, and the chosen species must be well illustrated in the predictive model training database. In addition to these criteria that allow automatic species identification, we must take into account the requirements using SDM on presence-only data to acquire meaningful results. More precisely, the species must have contrasted environmental preferences regarding the study domain, its realized habitat must not be overly constrained by its dispersal capacity or important historical perturbations, and there must be enough observation points regarding the environmental variables considered. Considering these constraints on species selection, the available data, and the potential use-cases, we applied our protocol to the modeling of the distribution of five species classified in major and moderate categories of invasion by the National Mediterranean Botanical Conservatory of Porquerolles for the southeastern region of France (Conservatoire botanique national méditerranéen de Porquerolles, 2018).
Invasive species represent a major economic cost to our society (estimated at nearly €12 billion a year in Europe) and are one of the main threats to biodiversity conservation  (Weber and Gut, 2004). The early detection of the appearance of these species is a key element in managing them and reducing the cost of such management. The analysis of Pl@ntNet data can provide a highly valuable response to this problem because the presence of these species is often correlated with that of human activity (and thus to the density of Pl@nt-Net data occurrences), and the constant flow of observations enables annual monitoring of species distributions.
g. , faces, animals, manufactured objects). These species cover a large part of the European and North African floras, according to the network of people initially involved in the production and validation of these data (this network was initiated with the Tela Botanica nongovernmental organization [http://www. tela-botanica. org] and the network of French-speaking botanists, composed of professionals and amateurs). This data set also includes a few hundred species of common tropical plants from two tropical regions: the Indian Ocean region and tropical Amazonia. Data from these two regions were collected by scientists and engineers from research institutes and universities working on these flora, representatives of the Tela Botanica network in these regions, and Pl@ntNet users. The data validation process was conducted using the IdentiPlante web tool (http://www.
tela-botanica. org/appli:identiplante), essentially dedicated to the Tela Botanica community, and was also accessible on the Pl@ntNet Android app. These applications display all botanical records shared by the project members. Logged-in users are able to provide new identifications, post comments, and vote on previous identifications. The revised data are regularly crawled by the visual search engine, which picks up observations considered correctly identified according to a predefined set of rules on the votes and on possible conflicts. These validation tools allow coverage of a growing number of species, from 800 in 2013 up to 11,000 in 2016.
Species distribution modeling using automatically identified Pl@ntNet observations We performed SDM based on the unvalidated Pl@ntNet observations made in France in 2016. In total, the data represent approximately 2 million observations (most observations have only one image and some have up to five images). Each image x was passed to the CNN to receive an automated species prediction in the form of a categorical distribution p(k|x) estimating the probability that the image x is from the k-th species (according to the softmax classification layer of the CNN). For the observations composed of several images, the predictions were simply averaged (i. e. , p(k|x) = 1/n x • ∑p(k|x i ) for an observation x composed of n x images x i ). We then kept only the observations for which the most probable species (denoted as k max ) belonged to the set of the five potential invasive species considered in our study: Acer negundo L.