dataesr/scientific-paragraphs-categorization huggingface dataset:
Initial analysis of the pruned dataset recovered 2528 most parsimonious trees with a length of 1678 steps, with a strict consensus topology similar to that of our pruned dataset (see below), but with Edgarosaurus and Manemergus as the earliest-branching polycotylids. We suspected that the finding of the holotype of Manemergus in this basal position resulted from its highly juvenile ontogenetic status, and that this was influencing the optimization of character states in polycotylid phylogeny. Therefore, we conducted the analysis excluding Manemergus, in addition to the wildcard taxa listed above. This yielded 3584 most parsimonious trees each with a length of 1667 steps (figure  8 ; electronic supplementary material, figure  S3 ). The rescaled consistency index of these trees is 0. 1662. The trees have a very good fit to stratigraphy (electronic supplementary material, ESM1 and figure  S4 ).
The strict consensus of analysis of this reduced dataset yielded a well-resolved Leptocleidia. Edgarosaurus muddi is recovered as the earliest-branching polycotylid. No clade in our reduced consensus could bear the name Palmulasaurinae as both Pahasapasaurus and Palmulasaurus form an unresolved polytomy as sister taxa to the more derived polycotylids. This polytomy could be resolved by information from future studies or new discoveries as either a clade (to which 'Palmulasaurinae' could be correctly applied) or a paraphyletic grade. Plesiopleurodon and the 'Richmond pliosaur' (QM F18041) form a clade that we also find to include the Maastrichtian taxon Sulcusuchus erraini. We hereby chose to formally name and define this clade, Occultonectia clade nov. (see below). Thililua longicollis and Mauriciosaurus fernandezi form the successive sister lineages of Polycotylinae.
The generic content of Polycotylinae is similar to that specified by  Albright et al. [15] : Eopolycotylus, Polycotylus, Trinacromerum and Dolichorhynchops. In both datasets, we failed to recover a monophyletic Dolichorhynchops, notably because Dolichorhynchops tropicensis occupies a more basal position among polycotylines and because Georgiasaurus penzensis forms an unresolved clade with the species Dolichorhynchops herschelensis, Dolichorhynchops bonneri and Dolichorhynchops sp. (ROM 29010) (in the analysis of the full dataset). This questions the generic attribution of Dolichorhynchops tropicensis.
Tempo of polycotylid evolution Uncertainty has surrounded the timing and intensity of the early polycotylid radiation. Indeed, the presence of derived leptocleidids during the Valanginian (Leptocleidus capensis) results in a lengthy basal polycotylid ghost lineage that extends from the earliest Cretaceous up to the earliest fossil records of polycotylids, the 'Richmond pliosaur' (QM F18041) from the Upper Albian of Australia  [67]  and Edgarosaurus muddi from the Upper Albian of North America  [14]. The phylogenetic position of Plesiopleurodon implies that a series of cladogenetic events took place before the Early-Late Cretaceous boundary: at least seven polycotylid lineages (including the ancestor of polycotylines) were present by the end of the Middle Albian (figure  8 ) and our phylogenetic diversity estimates suggest that this number possibly reached 11 (see electronic supplementary material, table S4 for the phylogenetic diversity estimates, under different methods of reconstruction of branch lengths and datasets).
Phylogenetic definitions As discussed by O'Keefe  [16] , the definition of Palmulasaurinae is difficult to use, as it has been solely based on Palmulasaurus quadratus and UMUT MV 19965, a poorly known specimen from Japan. The content of the inclusive clade containing Palmulasaurus and excluding polycotylines and Edgarosaurus (as per  Albright et al. [15] ) has been widely varying in most phylogenetic analyses of polycotylids, including our full and reduced datasets. Therefore, we concur with O'Keefe  [16]  that the phylogenetic data presently available prevent the use and the formalization of the clade Palmulasaurinae. A stable clade of non-polycotyline polycotylids unites Plesiopleurodon wellesi and the 'Richmond pliosaur' (QM F18041)-this association has been recovered in several other studies  [9, 19, 27, 34, 68] , and we find for the first time that it also includes Sulcusuchus erraini.
Phylogenetic definition. The branch-based clade comprising all taxa more closely related to Plesiopleurodon wellesi than to Polycotylus latipinnis, Pahasapasaurus haasi or Palmulasaurus quadratus. Occultonectia should not be used in cases where the specifiers of Palmulasaurinae (Palmulasaurus quadratus) or Polycotylinae (Polycotylus latipinnis) are found to be more closely related to Sulcusuchus erraini than to Plesiopleurodon wellesi or the 'Richmond plesiosaur'. Diagnosis. Occultonectia is supported by the following non-unique unambiguous synapomorphies in the analysis of the full dataset: (i) reduced preorbital skull length (in between 0.
Pattern of morphospace occupation We visualized the morphospace of polycotylids by applying principal coordinate analyses to the Bauplan dataset that summarizes the body shape of polycotylids (figure  9 ; electronic supplementary material, ESM1, ESM7 and tables S1-S3). We also computed a phylomorphospace, visible in electronic supplementary material, ESM1 and figure S5. The earliest polycotylid Edgarosaurus muddi and the occultonectian Plesiopleurodon occupy a distinct region of the morphospace, especially in the first principal coordinate. This morphotype is convergent with that of pliosaurids  [9]. Despite its phylogenetic position, which is intermediate between Edgarosaurus and Occultonectia (figure  8 ), Pahasapasaurus haasi falls close to a region of the morphospace that is otherwise typical of the derived, polycotyline polycotylids such as Dolichorhynchops, predominantly due to the presence of a long, gracile snout and dentition.
Polycotylids (figure  8 ) are unusual among other fast-swimming marine reptiles of the Early Cretaceous in increasing their diversity and their disparity during the Late Albian-Turonian interval; ichthyosaurs met their demise in a two-step extinction event during and at the end of the Cenomanian  [70, 79] , while the last pliosaurids had low disparity, belonging to the same global morphotype [9], and disappeared by the Middle Turonian  [76]. The phylogenetic diversity estimate of polycotylids seems to follow the global temperature trend, decreasing after the Turonian climatic optimum. To test this, we used the median phylogenetic diversity estimate, using equal reconstruction of branch lengths of the most parsimonious trees from the analysis of the pruned dataset (figure  8c ; electronic supplementary material, table  S4 ) and compared it to the isotopic record reported in Prokoph et al.
45 and 0. 55 compared with the total skull length) (4. 2 → 4. 1); (ii) undulating, 'scalloped' alveolar margin of the upper jaw in lateral view (13. 0 → 13. 1); (iii) elongate dorsomedian ridge of the premaxilla, extending from the interorbital region to the tip of the rostrum (19. 1 → 19. 2); (iv) raised ventral keel on the symphysis (114. 0 → 114. 1); (v) coarse longitudinal enamel ridges (137. 1 → 137. 0); (vi) large number of maxillary teeth (greater than 28) (138. 1 → 138. 2); (vii) absence of a second postaxial accessory ossicle articulating with propodial (233. 1 → 233. 0) and (viii) narrow forefin (aspect ratio in between 3. 1 and 3. 5 (235. 0 → 235. 1)). The analysis of the pruned dataset recovered 12 non-unique unambiguous synapomorphies supporting Occultonectia: those found in the full dataset (except iv, v and viii) plus the following ones: rounded dorsal crest of the squamosal in the squamosal arch (54.
Acknowledgements. We warmly thank the staff from the  Museum d'histoire naturelle de Grenoble , especially  C. Durand , for assistance, logistic help and valuable discussions. We also thank  B. Schumacher  for sharing images of Pahasapasaurus and for discussion (with R. B. J. B. ), and two anonymous reviewers who provided sensible and thoughtful comments and suggestions that improved all aspects of this manuscript.
onFigure 8. 8 Figure 8. Phylogenetic relationships and diversification of leptocleidian plesiosaurians. (a) Focus on Leptocleidia from the strict consensus of the 50 000 most parsimonious trees arising from the maximum-parsimony analyses of the full dataset. Each tree has a length of 1706 steps. Thililua longicollis is indicated by the blue outline. (b) Focus on the Leptocleidia clade from the strict consensus of the 3584 most parsimonious trees arising from the maximum-parsimony analyses of the pruned dataset. Each tree has a length of 1667 steps. Thililua longicollis is indicated by the blue outline. None of the analyses yielded resampling values (bootstrap and jackknife) above 50% for leptocleidian clades and were thus not indicated. (c) Median phylogenetic diversity estimates using all the most parsimonious trees from the analysis of the pruned dataset in 'equal' time scaling, with 95% confidence interval.
Methods The SITVIT2 global repository and PUBMED were searched for spoligotype and published genotype data respectively, of M. tuberculosis from Africa. M. tuberculosis lineages in Africa were described and compared across regions and with those from 7 European and 6 South-Asian countries. Further analysis of the major lineages and sub-lineages using Principal Component analysis (PCA) and hierarchical cluster analysis were done to describe clustering by geographical regions. Evolutionary relationships were assessed using phylogenetic tree analysis.
Introduction The development and application of genotyping tools for Mycobacterium tuberculosis has greatly enhanced our understanding of the epidemiology of tuberculosis (TB) on a local  [1]  and global scale  [2] [3] [4] [5]. Three internationally standardized genotyping methods, IS6110 DNA fingerprinting  [6] , Mycobacterial Interspersed Repetitive Unit-Variable Number of Tandem Repeat (MIRU-VNTR) typing  [7]  and spoligotyping  [8]  have been used extensively to quantify transmission  [9] , describe genetic diversity  [3] , determine the epidemiology of drug resistance  [10] [11] [12]  and identify mixed infections  [13, 14]. Spoligotyping data represents the largest body of genotyping data which has been formally organized into a global repository termed SpolDB  [2] [3] [4] 15]. This database has been through a number of reiterations and has recently been expanded to include MIRU-VNTR data, and is now called SITVIT  [16].
Within this database clinical isolates have been grouped into distinct lineages such as Beijing, Central Asian (CAS), East-African Indian (EAI), Cameroon, Haarlem (H), Latin American Mediterranean (LAM), T, S, and X according to defined spoligotype signatures  [17, 18]. In 2002, Filliol et al used spoligotype data from SpolDB to present the first view of the global phylogeny of M. tuberculosis  [2]. Subsequent studies described the population structure of M. tuberculosis complex (MTBC) on the different continents  [4, 19]. Findings from these studies are largely concordant with those from studies using the Long Sequence Polymorphism (LSP) to describe the global phylogeny of the 6 LSP lineages  [5, 20]. In Africa, the Euro-American lineage was found to be dominant. The CAS and EAI lineages were confined to East Africa  [21] , the East Asian lineage (i.
Geographical distribution To gain a broad overview of the African M. tuberculosis population structure, isolates were assigned to major lineages. The distribution of genotypes was described by country of origin. A map of Africa was prepared showing the proportion of isolates belonging to the respective spoligotype lineages for the respective countries (3 letter country codes according to http://en. wikipedia. org/wiki/ISO_3166-1_alpha-3). Country specific spoligotyping data was included in the analysis if spoligotype data for ! 100 isolates was available. Isolates belonging to the Turkey and Ural (U) lineages were excluded owing to their limited frequency in Africa. In addition, maps were prepared to show the proportion of M. tuberculosis isolates belonging to the different sub-lineages of the respective major spoligotype lineages if the major lineage constituted ! 15% of the M.
Principal component analysis Given the complex nature of the data, a principal component analysis (PCA) is an appropriate mathematical tool to reveal underlying patterns within the data. This analysis was completed using R (version 3. 2. 0) [40]  and visualized using the ggbiplot R package  [41]. PCA analysis of the geographical distribution of the major lineages in countries belonging to Africa, Europe and Western, South and South East Asia was done using the proportions of the different lineages and not the spoligotype itself. This analysis included spoligotyping data for the Beijing, Cameroon, CAS, EAI, H, LAM, Manu, and S lineages. Spoligotype data for the T lineage was excluded from the PCA analysis, since these isolates were present in most countries included in the analysis. In addition, data for the X lineage (based on the small proportion of strains in this group) and isolates with unassigned spoligotypes were excluded.
Phylogenetic tree analysis BioNumerics software version 6. 6 (Applied Maths, Sint-Martens-Latem, Belgium; available at the following link: http://www. applied-maths. com/bionumerics) was used to highlight evolutionary relationships between main spoligotypes present in Africa. Minimum spanning trees were drawn based on spoligotyping patterns having a SIT number, and belonging to the following lineages: LAM, T, H, Beijing, CAS, X, Cameroon, EAI, S, and Manu. Minimum Spanning Trees are undirected graphs in which all samples are connected together with the fewest possible connections between nearest neighbors.
Overview of M. tuberculosis genotypes in Africa A total of 112,683 mycobacterial isolates in the SITVIT2 database were screened for eligibility. All isolates from non-African countries (n = 99,196), non-human hosts (n = 965), members of the MTBC other than M. tuberculosis (n = 598), and atypical mycobacteria (n = 41) were excluded, leaving 11,883 M. tuberculosis isolates. These isolates represented spoligotype data from individual patients in 25 countries in the Africa region (S1 Table ). Review of the literature added isolates from an additional 11 countries resulting in a total of 15522 M. tuberculosis isolates with spoligotype data in Africa (S1 Table ). African countries not represented included Botswana, Burundi, Cabo Verde, Chad, Congo, Republic of the Congo, Equatorial Guinea, Eritrea, Gabon, Lesotho, Liberia, Mauritania, Niger, Sao Tome and Principe, Seychelles, Somalia, South Sudan, Swaziland, and Togo.
Phylogeographical clustering of major M. tuberculosis lineages in African countries We assessed the intra-country lineage proportions in 25 African countries for which data for >100 isolates was available. percentage of isolates classified as belonging to the H lineage (Central African Republic, Guinea, Gambia, and Tunisia) showed a loose grouping together, however these countries generally showed a mixed distribution of lineages, with an influence of LAM lineages preventing a close clustering. Egypt showed a uniquely dominant Manu lineage and therefore did not cluster closely with other Northern African countries. Similarly, Madagascar showed a higher proportion of EAI than other African countries and therefore did not belong to a cluster. Countries Tunisia, South Africa, Egypt, and Madagascar have the highest lineage diversity and were therefore positioned towards the center of the PCA plot.
Phylogeographical clustering of major M. tuberculosis sub-lineages in African countries In order to describe the M. tuberculosis population structure in finer detail, the proportion of isolates representing the sub-lineages of each major lineage (CAS, EAI, LAM, H and T) were plotted onto their country of origin if they contributed ! 15% of the isolates causing disease in the respective country, as assessed by the present dataset (Figs 3, 4, 5 and 6 and S1-S6 Figs, and S2 Table ). LAM sub-lineages. Isolates belonging to this lineage were seen to a lesser extent in other countries: Mozambique (6. 9%), Madagascar (5. 5%) and Tanzania (6. 4%) from the Southern African region; Guinea (5. 3%) and Gambia (5. 2%) from the West African region; and Tunisia (7. 7%) in North Africa. X lineages. Isolates belonging to the X family were over represented in South Africa (15.
First, our data was not substantiated with more robust analysis like MIRU-VNTR or whole genome sequencing. This could have increased the discriminatory power, thereby optimizing the classification of the M. tuberculosis strains. Second, the PCA was carried out using either lineages or sub-lineages, and not the SITs. Considering that some of the sub-lineages might be polyphyletic, corresponding strains between countries may not fully represent a true monophyletic branch, and in such cases a shared evolutionary history for the strains in question might have not occurred. Nevertheless, it would have been too cumbersome to perform PCA analysis of M. tuberculosis isolates based on thousands of SITs, with inherently complicated results and interpretations. We therefore chose to perform PCA using either lineages or sub-lineages for the time being.
When the next database is released with a significantly greater number of strains and SITs worldwide in near future, and SITs from Africa are better characterized, it might be worthwhile to run PCA analysis of selected SITs. Third, the strain population structure in many of the countries was defined by a single study. This could introduce bias depending on how representative the study was. However, our observation of geographical clustering suggests that the data included largely reflects the strain diversity of that country. Fourth, data from a number of countries was not available. This together with the exclusion of countries with less than 100 isolates may have prevented the detection of new regional clustering. Fifth, it is not possible to determine whether the observed clustering of M.
Research Foundation of South Africa, award number UID 86539. The study was also supported by the South African Medical Research Council (SAMRC). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NRF or SAMRC. David Couvin was awarded a Ph. D. fellowship by the European Social Funds through the Regional Council of Guadeloupe, while the work done at Institut Pasteur de la Guadeloupe was supported by a FEDER grant, financed by the European Union and Guadeloupe Region (Programme Operationnel FEDER-Guadeloupe-Conseil Regional 2014-2020, Grant number 2015-FED-192). XW participated in this project through the South African Tuberculosis Bioinformatics Initiative, funded by a Strategic Health Innovation Partnership (SHIP) grant from the South African Department of Science and Technology (DST) and South African Medical Research Council (SAMRC) to Gerhard Walzl.
Acknowledgments VN Chihota was supported by the  Wellcome Trust  (Research Leave Grant  01680/Z//00/Z ). EM Streicher was supported by the  National Research Foundation (NRF)   Research Career Advancement Award. SL Sampson is funded by the  South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation of South Africa , award number  UID 86539. The study was also supported by the  South African Medical Research Council (SAMRC). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NRF or SAMRC. David Couvin  was awarded a Ph. D. fellowship by the  European Social Funds through the Regional Council of Guadeloupe , while the work done at  Institut Pasteur de la Guadeloupe  was supported by a  FEDER grant , financed by the  European Union and Guadeloupe Region  ( Programme Operationnel FEDER-Guadeloupe-Conseil Regional 2014-2020 , Grant number  2015-FED-192 ).
National Research Foundation of South Africa, award number UID 86539. The study was also supported by the South African Medical Research Council (SAMRC). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NRF or SAMRC. David Couvin was awarded a Ph. D. fellowship by the European Social Funds through the Regional Council of Guadeloupe, while the work done at Institut Pasteur de la Guadeloupe was supported by a FEDER grant, financed by the European Union and Guadeloupe Region (Programme Operationnel FEDER-Guadeloupe-Conseil Regional 2014-2020, Grant number 2015-FED-192). XW participated in this project through the South African Tuberculosis Bioinformatics Initiative, funded by a Strategic Health Innovation Partnership (SHIP) grant from the South African Department of Science and Technology (DST) and South African Medical Research Council (SAMRC) to Gerhard Walzl.
Significance The cuticle, mainly composed of chitin and cuticular proteins (CPs), is a multifunctional structure of arthropods. CPs usually account for >1% of the total insect proteins encoded in the genome. Why does an insect need so many different CPs? In this study, we use comprehensive large-scale technologies to study the full complement of CPs and their functions in the brown planthopper (BPH). A total of 32 of the 140 BPH CP genes are found to be essential for nymph/adult development, egg production, or embryo development; in addition, redundant and complementary functions of CPs are revealed. sequences, first, 135 of the above 140 N. lugens CP gene sequences were successfully verified and revised through PCR, RACE, and gene clone sequencing (Dataset S1). To further validate and authenticate the CPs of N.
lugens at the protein level, proteins from four tissue samples were collected and digested with trypsin. The resulting peptides were analyzed by shotgun ultra-performance liquid chromatography (UPLC)-tandem MS (MS/ MS). The four protein samples were cast first-instar nymph cuticles (CC1), cast third-to fifth-instar nymph cuticles (CC3-5), adult long wings (LW), and fifth-instar nymph abdominal cuticles (AC). Only proteins with at least two peptide-spectrum matches and a score of >4. 0 were considered reliable. Under these conditions, we identified a total of 519; 686; 1,341; and 710 proteins from CC1, CC3-5, LW, and AC protein samples, respectively (Dataset S2 A-D). It is possible that not all peptides could be detected because they were too long for detection or because cuticle components were cross-linked to each other  (7).
See SI Appendix, section 2 for functional classification of four MS/MS results according to Gene Ontology. To determine the functions of BPH CPs, we conducted RNAi experiments. Double-stranded RNA (dsRNA) for 135 of the 140 CP genes had been successfully synthesized (Dataset S1). Three groups of BPHs were treated with dsRNAs targeting BPH CP genes: 0-to 12-h second-instar nymphs (representing early instar nymphs), 0-to 12-h fifth-instar nymphs (representing late-instar nymphs), and 0-to 1-h female adults (for reproduction and embryos). To avoid off-target effects, RNAi experiments were replicated by choosing two nonoverlapping regions as targets to the fifth-instar nymphs (SI Appendix, section 3). The results showed that no off-target effects had happened in the dsRNA injection experiments.