dataesr/scientific-paragraphs-categorization huggingface dataset:
The homoplasy index ϕw test was done on pub MLST web site (http://www. pubmlst. org) or split tree. Recombination events were detected from aligned concatenated sequences using seven different methods with default parameters of the RDP v3. 44  (Martin et al. , 2010)  software package: general, RDP, GENECONV, Bootscan, MAxChi, CHIMAERA, and Siscan. The r/m ratio, i. e. , the relative impact of recombination and mutation in the diversification of the lineages, was calculated by LDhat  (McVean et al. , 2004)  implemented in RDP v3. 44. Recombination events were also visualized by decomposition analyses with SplitsTree 4. 0 software using a distance matrix in nexus format generated from the concatenated sequence (http://www. splitstree. org/).
Only 14 STs (18%) were represented by multiple isolates. Three of them (ST255, 259, and 242) grouped strains isolated at different dates and sites, and in different salinity conditions. Seven other STs were each represented by isolates collected at the same date but in different sites  (ST200, 201, 223, 246, 265, 270, 273). The 4 STs formed by strains isolated in a same site at the same date could probably be considered as replicates of a unique strain  (ST 218, 219, 221, 226)  (Supplementary Table  S1 ). None of the STs described in this study except ST2 were documented in databases. A similarly high genetic diversity was observed for V. parahaemolyticus isolates with 68 STs, 53 STs being represented by a single isolate and 15 STs (22. 1%) by 2 to 5 isolates. All STs but two, represented by multiple isolates (n = 13), grouped strains originating from different sites, the most represented being ST481, ST2000 and ST2005 (Supplementary Table  S2 ).
Eleven of the 68 STs were previously described in databases. The STs clustering in clonal complexes (CCs) by goeBURST confirmed the high level of genetic diversity within the two species. The population of V. cholerae displayed seven small CCs containing 2 to 3 STs (Figure  2 ) (Supplementary Table  S1 ). Seven CCs, each formed by only 2 STs, were also detected in the population of V. parahaemolyticus (Figure  3 ) (Supplementary Table  S2 ). The genetic diversity (H) was 0. 9082 ± 0. 0369 and 0. 9706 ± 0. 0081 for V. cholerae and V. parahaemolyticus, respectively. The genetic diversity at individual loci (h) and the number of single nucleotide polymorphism (SNP) are given in Table  1. For the two species, the rarefaction curve for each locus did not reach a plateau suggesting that we only partially explored the genetic diversity present in the ecosystem, thus confirming the high genetic diversity of the populations studied (Supplementary Figure  S1 ).
Genetic Diversity of V. cholerae and V. parahaemolyticus from Mediterranean Lagoons Compared to Worldwide Population We compared the multi-locus genetic data of the Vibrio population studied herein with those available in pubMLST databases for clinical and environmental isolates originating from various countries and collected at different times. Reconstruction of minimum-spanning trees from MLST profiles obtained in pubMLST databases and in this study showed no specificity in the distribution of the strains from Mediterranean coastal lagoons. They were equally distributed in the different clusters and globally reflected the overall diversity of V. cholerae and V. parahaemolyticus strains available in pubMLST databases (data not shown). H and ST/strain scores were similar in a collection sampled during 6 months in Mediterranean lagoons and in Vibrio collections from databases.
The H score was 0. 8836 in database vs. 0. 9082 in this study for V. cholerae and H was 0. 9536 in database vs. 0. 9705 in this study for V. parahaemolyticus. Therefore, the very high genetic diversity observed locally in the coastal lagoon systems for the two Vibrio species was similar to that observed in strains collected from many countries (five continents) over the past 60 years (data not shown). Among the 78 STs detected in this study for V. cholerae population, ST2 was the only ST previously deposited in the database. It corresponded to ctx-strains of serotype O49 isolated in Bangladesh in 2000 in a context of sporadic digestive infections  (Octavia et al. , 2013). It belonged to the same CC as ST1 (serotype O49) previously isolated in the same epidemiological context. ST223 and ST238 belonged to CCs that grouped clinical strains of V.
cholerae. ST223 was related to ST65 corresponding to O37 strains isolated in the environment in Germany in 1993 and in sporadic digestive infections in Bangladesh in 2000. ST238 was related to ST30 isolated in human in Peru in 1994. For V. parahaemolyticus population, 11 STs among the 68 detected herein were previously deposited in pubMLST database, which is larger than the V. cholerae database. Most of them corresponded to strains isolated from water or shellfish, worldwide (USA, China, Thailand, Vietnam and Northern Europe) from 1997 to 2012. They presented the virulence genotype tdh-/trh-, except for one environmental strain isolated in USA (Pacific coast) in 2006 that was tdh+/trh+. The ST363 that contained 2 strains isolated in sites 5 and 10 in July 2011 was composed of clinical strains (O3, tdh+/trh+) isolated in a patient with gastro-enteritis in Thailand in 1991.
Figures  2, 3  show the qualitative distribution of STs by goeBURST according to sampling dates and salinity. For the two species, clustering by reconstruction of minimum spanning tree gave the same results as goeBURST clustering (data not shown). A large majority of V. cholerae STs and strains was represented at only one date of sampling. Indeed, only one ST (ST259), containing five isolates, was found during the three campaigns in four different sites while two others (ST242 and ST255) were found in July and September 2011 (Figure  2 ). As expected, high salinities were recorded in July and low salinities in November whereas the high and low salinities observed in September were dependent on the sampling stations. Most STs (all but ST273) found only in September were detected either at high or low salinity whereas only a few STs found in July and September (ST242, ST255, and ST259) were detected in both salinity conditions.
Clade B was atypical due to an external position and long branches. In monogenic-based trees (data not shown), clade B isolates were either in the V. cholerae clade (adk, mdh, pntA, and pyrC-based trees) or in V. metoecus and Vibrio parilis clades (gyrB and purM-based trees) remote from V. cholerae or on an independent lineage (metE-based tree). Comparison of metE and purM gene sequences of strains N1-12 and N5-13 with sequences of databases showed a best match of only 93% with other published sequences of Vibrio spp. The gyrB gene of N1-12 and N5-13 gave the best match with strains Vibrio sp. W0706-81 (HM009674), L8M (HM009590), and HB0308-2A5 (HM009568) non-affiliated to the species level and detected in coastal marine water in California and Hawaii. The third member of clade B, N6-9, was generally related to N1-12 and N5-13, except for purM phylogeny that placed it on a long independent branch remote from all other Vibrio spp.
7% identity with V. mimicus ATCC 33655 dnaE sequence. Other best matches were V. cholerae strain 7449 (98. 5%), and Vibrio sp. HB0308 and L8M (96. 3%), which were previously found related to V. cholerae clade B strains (N5-13, N1-12) in gyrB phylogeny. This result indicated genetic exchanges between Vibrio sp. related to V. cholerae and V. parahaemolyticus. It is noteworthy that Vibrio sp. N5-13 and V. parahaemolyticus S5. 61 were isolated in the same station in November and September, respectively. V. parahaemolyticus J8. 24 and S11. 38 were also placed on long branches due to very polymorphic dtdS and gyrB alleles, respectively. Comparison   to databases showed that the best matches of isolate J8. 24 for dtdS was 94% with Vibrio campbelli and Vibrio harveyi type strains. The recA gene of strain S11.
These emerging branches were similar to the branches corresponding to the speciation of V. mimicus, V. metoecus, and V. parilis (Figure  7 ). These results suggested that recombination was a major force driving diversification and speciation of vibrios in Mediterranean coastal lagoon systems. Recombination was then evaluated in V. cholerae and V. parahaemolyticus by the determination of standardized index of association (sI A ), the homoplasy index ϕw test and by using RDP software. The sI A , expected to be null when a population is at linkage equilibrium, was significantly different from zero for both V. cholerae (sI A = 0. 1697; p = 0. 0002) and V. parahaemolyticus (sI A = 0. 3307; p < 10 3 ). No significant sI A difference was observed according to dates, stations, and salinities for both species (data not shown).
The sI A values indicated significant linkage disequilibrium suggesting that V. cholerae and V. parahaemolyticus population conserved a clonal backbone despite frequent events of recombination. In contrast, the homoplasy index ϕw test, which discriminates between recurrent mutation and recombination, found statistically significant evidence for recombination (p = 0. 0) in both V. cholerae and V. parahaemolyticus populations. Recombination events within these two Vibrio populations were further analyzed by RDP software. In V. cholerae population detected by at least 4 out of the 7 methods performed by RDP, 34 strains (31. 2% of isolates) underwent at least one recombination event (Supplementary Table  S6 ). Recombination events involved metE, pyrC, and pntA genes. For V. cholerae, the sampling month and the salinity influenced slightly the frequency of recombining isolates, a low salinity being associated with a lower frequency of recombining isolates.
, 2002; Deter et al. , 2010). Studies in cholera-free temperate or cold regions are scarce but all have underlined the absence of ctx+ isolates in environmental strains  (Zo et al. , 2009; Schuster et al. , 2011; Haley et al. , 2012)  whereas toxigenic strains were mainly detected in outbreak contexts (Tobin-D  'Angelo et al. , 2008; Haley et al. , 2014). Databases comparison showed that most STs described in this study were detected for the first time, demonstrating that the V. cholerae and V. parahaemolyticus populations are extremely diverse and their genetic diversity under-reported. In this study, the distribution of STs, as well as the H and ST/strain scores, are in agreement with the overall diversity of V. cholerae and V. parahaemolyticus. Indeed, we observed locally a genetic diversity similar to or higher than that observed worldwide in the last fifty years.
Acknowledgments This work was supported by funding provided by the  GIS  " Climat Environnement Société ", by the  Observatoire Homme Milieux (OHM)  " Littoral méditerrannéen ", by the  Programme National EC2CO "Ecosphère Continentale et Côtière , " and by the association ADEREMPHA (Sauzet, France), and a doctoral fellowship (KE. ) from  CNRS  and  Université Montpellier  2. The authors are thankful to  Mylène Toubiana  and  Anne Lotthé  for their involvement in the critical reading of the manuscript.
(f ) Female wing coloration measurements The wings of female Hetaerina vary from nearly clear to nearly black (figure  1a-e ). To quantify this variation, we measured wing reflectance spectra using an Ocean Optics spectrometer (USB 2000) equipped with a reflectance probe (Ocean Optics R200 -7-UV-VIS) and a pulsed xenon light source (Ocean Optics PX-2), with reference to a Labsphere certified reflectance standard using Ocean Optics' OOIBase32 software. We placed the reflectance standard behind the wings when taking readings, and the light path was oriented 458 relative to the wing surface to eliminate glare. The resulting measurements include both light reflected off the wings and light transmitted through the wings. We took three repeat measurements at three positions (base, middle and tip) on the forewings and hindwings and averaged the repeats.
, Tokyo). In ImageJ (http:// imagej. nih. gov/), we used the 'Color Balance' plugin in the MBF package to standardize the white balance in each photo relative to the white background of the scale paper included in each photograph. We then used the polygon tool and the 'Measure RGB' plugin to analyse the RGB profile of each wing. The average, weighted greyscale calculated in 'Measure RGB' provided a photographic measure of wing lightness that correlated well with the spectroradiometric measure of wing lightness (Pearson's product-moment correlation r ¼ 0. 78, n ¼ 49, p , 0. 001).
(h) Statistical analysis To obtain a relative measure of interspecific aggression, we divided the mean attack rate towards heterospecific tethered males by the mean attack rate towards conspecific tethered males. Likewise, to obtain a relative measure of reproductive interference, we divided the proportion of tethered females that elicited sexual responses in trials with heterospecific males by the proportion of tethered females that elicited sexual responses in trials with conspecific males. We obtained two measures of interspecific aggression and reproductive interference at each study site, one for each species, but only one measure of the species difference in female wing coloration. To test for correlations between these variables, while circumventing potential non-independence caused by the data structure, we used the following randomization approach: one of the two species at each site was dropped at random and a Spearman correlation coefficient (r) was calculated using the remaining data points in STATA 12.
Acknowledgements. We thank  A. Gonzalez-Karlsson ,  F. Gould ,  K. Peiman ,  T. B. Smith  and two anonymous reviewers for comments and discussion. For assistance in the field, we thank  T. Alvey ,  M. Benitez ,  E. Berlin ,  A. Chao ,  S. Giovanetti ,  P. Green ,  K. Henderson ,  S. Hu ,  L. Karlen ,  E. Khazan ,  R. Musker  and  S. Sanford. For assistance with transcription and image analyses, we thank  C. Antaky ,  S. Ellis ,  N. Gentry ,  O. Mckenzie ,  L. Perng  and  N. Synstelien. We thank  S. Bybee  for providing extracted DNA or tissue for several specimens,  E. Toffelmier ,  R. Ellingson ,  S. Lao  and  S. Chin  for assistance with laboratory work and sample processing,  T. B. Smith  for use of laboratory facilities,  R. Garrison  for access to the Hetaerina morphological character data,  M.
Wilms' tumours, paediatric kidney cancers, are the archetypal example of tumours caused through the disruption of normal development. The genetically best defined subgroup of Wilms' tumours is the group caused by biallelic loss of the WT1 tumour suppressor gene. Here we describe a developmental series of mouse models with conditional loss of Wt1 in different stages of nephron development before and after the mesenchymal to epithelial transition (MET). We demonstrate that Wt1 is essential for normal development at all kidney developmental stages under study. Comparison of genome-wide expression data from the mutant mouse models to human tumour material of WT1-mutant and WT1 wild-type datasets identifies the stage of origin of human WT1-mutant tumours, and emphasizes fundamental differences between the two human tumour groups due to different developmental stages of origin.
Since Wt1 is not expressed in the ureteric bud, the activity of Pax8 +/Cre there does not affect the analysis presented here. Finally we used a CreGFP fusion construct knocked into the endogenous Wnt4 locus  (Shan et al. , 2010). As described, this driver becomes active in the pre-tubular aggregates and subsequently traces the complete nephron (Fig. 1C  and Supp. Movie 1C). The GFP signal from the Wnt4 CreGFP allele is barely detectable on the time-lapse system  (Shan et al. , 2010 and data not shown) , therefore all signal comes from the eYFP reporter. Before crossing our Wt1 conditional allele  (Martinez-Estrada et al. , 2010)  to the three Cre drivers, we confirmed that it is a conditional version of the conventional Wt1 knockout  (Kreidberg et al. , 1993)  by crossing it to a germline Cre deleter strain expressing a CAGGsdriven Cre transgene to generate heterozygous Wt1 +/-mice.
Homozygosity for this recombined allele was found to be an exact phenocopy of the conventional knockout, including the kidney, gonad, epicardium and diaphragm phenotypes (Supp. Fig. 1  and data not shown). Next, the Wt1 conditional allele was crossed to each of the three Cre drivers we had characterized above. Cre-positive (all three drivers) / Wt1 conditional heterozygous mice were viable and healthy (data not shown). With one exception (see below), the Cre-positive Wt1 conditional homozygous genotypes were not compatible with postnatal life. Embryos developed up to birth and were macroscopically normal (though slightly smaller than control littermates in the case of Nes-Cre Wt1 co/co embryos), but died immediately after birth. As there is overlap between the activities of the Cre drivers and Wt1 outside the kidney, we used Optical Projection Tomography  (Sharpe et al.
In contrast, in Wnt4 +/CreGFP Wt1 co/co kidneys MET is possible as there is condensation, epithelialisation and early tubulogenesis (comma and S-shaped body stages), albeit at reduced levels. Expanded mesenchyme can be found in these kidneys as well, although glomerulogenesis and tubular maturation are absent. Pax8 +/Cre Wt1 co/co kidneys showed normal levels of condensation, epithelialisation and early tubulogenesis, but tubule maturation and glomerulogenesis are still absent. As was the case for the Nes-Cre Wt1 co/co kidneys  (Essafi et al. , 2011) , no differences in proliferation or apoptosis were found in the other two models (data not shown); the 'escaping nephrons' that develop completely normally but are still Wt1positive in the Nes-Cre driven mutant were not found in the other mutants either (data not shown).
We serendipitously identified one surviving Nes-Cre Wt1 co/co mouse. This mouse developed a lump on its back at 25 weeks of age. Macroscopic analysis identified a large tissue mass in place of the right kidney (Figure  2E, F ). Microscopic analysis identified this as a Wilms' tumour (Figure  2G ). The left kidney was relatively normal and contained many more escaping nephrons than usual (data not shown). We assume this left kidney provided sufficient renal function for this animal to survive, thereby giving the right kidney time to develop this tumour.
Histological phenotyping of Wt1 mutants through genome-wide expression analysis. It has previously been shown that many genes are expressed in more than one developmental stage in the kidney  (Brunskill et al. , 2008). The identification of true anchor genes, which are uniquely expressed in just one specific cell type or developmental stage, can be challenging, especially for the stages immediately before and after the MET, on which we focused our analysis  (Thiagarajan et al. , 2011). This limits the usefulness of analysing individual genes to describe developmental phenotypes like the ones found here. Instead, we hypothesized that global expression patterns could provide means to describe complex phenotypes. To test this we generated microarray data from E18. 5 total kidney RNA of the three mutant genotypes.
We first compared each Cre + Wt1 co/co dataset to the corresponding Cre + -only data to identify differentially expressed genes for each mutant and correct for changes due to expression of the Cre or, in the case of Wnt4 and Pax8-driven Cre alleles, haploinsufficiency of the driver gene (Supp. Fig. 2  and Supp. Table  1 ). Comparison of increased and decreased genes for each of the mutants showed 84 increased and 159 decreased genes were shared between two or three mutants, with larger numbers of genes being uniquely differentially expressed in individual mutants (Fig. 3A ). To identify candidate direct targets for Wt1 in the differentially expressed genes we compared the gene lists to Wt1 ChIP-seq data from a recently published study on E18. 5 mouse kidneys  (Motamedi et al. , 2014)  and identified multiple genes in each differential geneset that showed in vivo binding of Wt1 to their genomic loci (Supp.
We compared our differential gene sets to the kidney compartment-specific genome-wide expression patterns as they are being generated (via microarray and RNA-seq analysis of micro-dissected and FACS-sorted cell populations) and made available by the GUDMAP project  (Harding et al. , 2011). These data provide expression signatures of each compartment in the developing kidney, even if the genes that make up this signature are not unique for this compartment. Note that in this approach, we use differentially expressed genes solely as a signature for the stage where development is blocked, and that this is independent from whether or not the differential genes are direct targets for control by Wt1. Geneset enrichment analysis using the ToppCluster tool  (Kaimal et al. , 2010) , which analyses enrichment for each of these compartment-specific signatures (as well as to other biological datasets such as GO terms and phenotypic data sources), was used to further analyse the stage of developmental block in the different mutants.
We hypothesized that enrichment for certain compartment-specific signatures would be indicative of a developmental block at that stage or close to that stage. The increased genes in the three mutants significantly overlapped with many genes from early developmental stages from the GUDMAP data (Fig. 3B ). These include different cap mesenchyme datasets (including E15. 5 and early postnatal), E11. 5 metanephric mesenchyme and E15. 5 pelvic mesenchyme. This demonstrates that the three mutants expressed sets of genes that are normally (in wild-type kidneys) found in these cell types / developmental stages. More informative were the enrichment patterns that were found for one or two of the mutants, as they illustrated the order in which the phenotypes arise. For instance, enrichment for genes normally expressed in the S-shaped body was exclusively found in the Pax8 +/Cre Wt1 co/co mutant kidneys.
Accepted manuscript Confirmation of the differential srenal phenotypes. The combined data showed that Nes-Cre driven loss of Wt1 results in disturbance of the MET while Pax8-Cre Wt1 co/co reaches a developmental block after the MET but before tubule maturation and glomerulogenesis. The Wnt4 +/CreGFP Wt1 co/co appears to be a combination of both; the reduced epithelialisation suggests that in some cases the MET is still disturbed, whereas in cases where the MET was successful the resulting nephrons were blocked at the same stage as observed in the Pax8 +/Cre Wt1 co/co mutants. We therefore limited a more detailed phenotypic analysis to the Nes-Cre Wt1 co/co and Pax8 +/Cre phenotypes. We first analysed the nephrogenic progress in control and mutant kidneys on time-lapse using a Wt1 GFP knock-in allele  (Hosen et al.
movie 2) thereby closely mimicking the known Wt1 expression pattern. Mutant Nes-Cre Wt1 co/GFP kidneys showed the increase in GFP signal in the cap-mesenchyme but no further development (except in some escaping nephrons as discussed before), whereas the brightfield data showed a corresponding lack of epithelialized structures (Fig. 4B  and Supp. movie 2). The brightfield signal for Pax8 +/Cre Wt1 co/co kidneys showed the formation of condensed mesenchymes and some epithelialisation and nephron formation, accompanied by.