dataesr/scientific-paragraphs-categorization huggingface dataset:
COI genotyping A fragment of the mitochondrial Cytochrome c Oxidase Subunit I (COI) gene of 336 individuals (Table  S4 ) was amplified using primers 1/2COI_Fol-F and 1/2COI_Fol-R following the protocol of  Muñoz et al. (2010). Because these primers turned out to lack specificity and resulted in the amplification of a large number of numts (see below), we amplified the COI sequence of 23 additional individuals using the more specific primers Co1APAR-F(5'-TTTGGAGCTTGAGCAGGAAT-3') and Co1APAR-R(5'-TGCGGGATCAAAGAAAGAAG-3') (see sup. mat. 2). PCR products were purified and directly sequenced (i. e. with no cloning), using an ABI Prism Big Dye Terminator Kit (Applied Biosystems, Warrington, UK) on an ABI PRISM 3130xl sequencer. After removing sequences with indels and sequences from the same individual that were identical, we recovered 359 sequences that were split into two datasets: dataset1, which only included high quality sequences (198 sequences including at least 538 sites in the final alignment and without any ambiguous position), and dataset2, which included all other sequences (161 sequences that were either too short or included one or more ambiguous positions).
COI phylogenetic inferences are often biased by the inclusion of numts (Buhay 2009) or chimeric sequences that result from the coamplification by PCR of mitochondrial sequences with contaminating sequences (either numts or mitochondrial sequences from other individuals; e. g. Dubey et al. 2009 ). We developed a new method to identify potential chimeric sequences based on a dataset composed of known numts sequences (see "chimera detection" section below). To build this dataset, we performed additional cloning and sequencing of PCR fragments amplified either from total DNA or from DNA enriched from mitochondrial DNA (sup. mat. 2, Table  S4 ). Cloning allowed the recovery of 32 numt sequences without indels (which we identified as minority sequences among those obtained from the same individual through cloning, sup.
mat. 2) and seven mitochondrial sequences (hereafter dataset3). We built a dataset that combined these 39 sequences (dataset3), our 198 sequences (dataset1) and 748 Artemia spp. high quality sequences from GenBank without any indel (sup. mat. 2). All analyses of the final dataset of 985 COI sequences were performed in R 3. 6. 3 (www. rproject. org).
Analyses of mitochondrial data (3): chimera detection We designed a quantitative test to detect and exclude potential chimeric sequences. The principle of the method is to determine, for each focal sequence, how many mutations could be "explained" by assuming that this sequence represents a chimera. We compared each haplotype sequence to the remaining 229 sequences in the dataset to identify the most similar one. For each mutation differing between the focal sequence and the most similar one, we provide a score of one if this mutation (i. e. the same SNP) was found in another unrelated sequence of the dataset or zero otherwise. For each of the 230 haplotype sequences, we computed the sum of this score over the different SNPs of each haplotype. We considered that each sequence could have acquired a mutation which happened to be present in an unrelated sequence of the dataset (score =1), but that it could not have acquired two or more of these mutations (score >1).
Analyses of mitochondrial data (4): haplotype assignation To study the phylogenetic relationship among major asexual and sexual taxa (Ap2n-kaz, Ap2n-urm, Ap3n, Ap4n, Ap5n, Aurm, Akaz, Atib, Asin), we built a haplotype network based on the 123 reference haplotypes and using the parsimnet function (95% probability of parsimony,  Templeton et al. 1992 ) of the package haplotypes (v1. 1. 2; Aktas 2020). We found the same tree topology when building a maximum likelihood phylogeny with the phangorn package (v2. 5. 5 Schliep 2011). In addition, we assigned the 61 Ap2n sequences in dataset2 to either Ap2n-kaz, Ap2nurm or other sequences (i. e. numts or chimeras). To do so, we aligned them with the 123 reference haplotype sequences and with the 107 numt and chimeric sequences and estimated pairwise genetic distances as described above.
Microsatellite genotyping We genotyped 432 individuals with a panel of 12 microsatellite markers (see  Muñoz et al. 2008; Nougué et al. 2015a  for details regarding markers and amplification protocol). Data from  Nougué et al. (2015b)  were added to the dataset, resulting in 489 typed individuals (Table  S4 , sup. mat. 5). Standardization was achieved by adding DNA from the same individual onto the different plates. Genotype data at three microsatellite markers (Apdq01TAIL, Apdq02TAIL, Apdq03TAIL) were only used when investigating the relationship among Ap2n, but excluded when analyzing the full dataset due to the presence of null alleles in polyploids and sexuals  (Maniatsi et al. 2011).
Evolutionary origin of Ap3n, Ap4n and Ap5n We assumed the maternal origin of the ancestor of Ap3n, Ap4n and Ap5n lineages to be known based on mitochondrial data (see results below). For each ploidy level, we compared different scenarios involving different paternal origins (see sup. mat. 7 for details). For each ploidy level and each scenario, we simulated 10,000 synthetic hybrids using a custom script in R. For each hybrid, we first randomly sampled a mother with the observed mitochondrial haplotype in our dataset (i. e. Ap2n-kaz for Ap3n, Asin for Ap4n and Ap4n for Ap5n). Second, to draw a haploid genotype (representing the sperm genotype), we randomly sampled an individual for each paternal origin (i. e. Akaz, Ap2n-kaz, Ap2n-urm, Aurm, Atib or Asin) and randomly sampled one allele of this individual at each locus.
We assumed that the 12 microsatellite loci were unlinked, so that probabilities of sampling alleles were independent across loci. We assumed that alternative scenarios involving fertilization by an unreduced sperm were less likely (e. g. origin of Ap3n through the fertilization of a reduced Ap2n-kaz egg by an unreduced sperm or origin of Ap4n through the fertilization of an unreduced Asin egg by an unreduced sperm). We then computed average Lynch genetic distance based on the 100 synthetic hybrids closest to Ap3n, Ap4n or Ap5n individuals in our dataset.
COI genotyping Ap2n, Ap3n, Ap4n and Ap5n were found in 24, 3, 7 and 5 populations respectively (Table  S4 , Fig. 2 ). Among the 37 populations sampled, only five (ATA, IZM, NAR, COQ and DON) were composed of individuals with different ploidies. Similarly, among the 24 Ap2n populations, 13 comprised only individuals with Ap2n-kaz haplotypes, five comprised only individuals with Ap2n-urm haplotypes and six (AIM, ATA, VIL, SAG, IZM, NAR) comprised individuals with both Ap2n-kaz and Ap2n-urm haplotypes (Fig. 2 ). Consistent with previous studies, Ap2n-kaz is the clade with the largest geographic distribution (Fig. 2 ). When including all sequences found in GenBank, the distribution of Ap2n-urm is restricted to the Mediterranean area (Spain, France, Italy and Turkey), around the Black sea (Atanasovko Lake, Bulgaria; Oybuskoye Lake, Ukraine) and in Western China (Aibi Lake, Lagkor Co).
Polyploids also have a large geographic distribution (Fig. 2 ). Among the 950 sequences from dataset1 and from GenBank, we found 47 sequences that had a large change in the polarity of the amino-acid sequence and 88 sequences that included two or more mutations found in another unrelated sequence of the dataset. These sequences were likely to be numts and chimeras respectively. The remaining 850 COI sequences were collapsed into 123 unique haplotypes of diploid mt-2nk, diploid mt-2nu, triploid, tetraploid and pentaploid asexual lineages and related sexual species (Fig. 5 ). In line with Maccari et al. (2013a), we found three networks separated by more than 30 mutation steps. The fourth network described in their study corresponded to pseudogenes (GenBank accession: EF615587-8) that differ from other sequences by several non-synonymous mutations that changed polarity.
5 , Table  2 ). A second network consisted of one Atib sequence from Lagkor Co (AtibLAG2) and sequences from other sexual populations (Haiyan Lake, Jingyu Lake, Nima, Yangnapengco, Qi Xiang Cuo, etc. ) from the Qinghai-Tibet plateau, that we refer to as mt-tib2 (Fig. 5 ). This haplogroup differed by more than 35 mutation steps from mt-tib1 and segregates at a frequency of ~3% in Lagkor Co (1 over 34 Atib sequences). No sequence from the mt-tib1 haplogroup was found in populations from Haiyan and Jingyu Lakes. Only a few sequences per population were available from GenBank, so making general conclusions is not possible. The third network included sequences from Ap4n, Ap5n and Asin. We found that some Ap4n and Ap5n samples shared the same mitochondrial haplotype (Fig. 5 ). We found low haplotype diversity among Ap4n and Ap5n haplotypes (in contrast to Asem et al.
Monophyly of Ap2n mitochondrial clades The NJ tree based on our genetic distance for automicts, which accounts for recombination and null alleles, is represented in Fig. 7. Individuals that cluster together in this tree often had the same mitochondrial haplotype group (Ap2n-kaz or Ap2n-urm). In other words, nuclear genetic distance between pairs of individuals with mt-2nk and mt-2nu mitochondrial haplotypes was larger, on average, than that between pairs of individuals with the same mitochondrial haplotype group (Fig. 7 ; distance d(Ap2n-kaz-Ap2n-urm)=9. 23; d(Ap2n-urm-Ap2n-urm)=8. 51; d(Ap2n-kaz-Ap2n-kaz)=8. 22). This association between mitochondrial haplotype and nuclear background was highly significant: among 10000 randomizations of the dataset, the estimated genetic distance between pairs of individuals with the same mitochondrial haplotype was never lower than observed genetic distances of 8.
2010, Maccari et al. 2013a, Eimanifar et al. 2014, Eimanifar et al. 2015)had the same APD05 haplotype as Ap3n individuals in our dataset. The TU13 Asin sequences from Siberia was found to be chimeric between the Ap4nARS1 mitochondrial haplotype and an Ap5n numt, it was.
Acknowledgements We thank  Christ Mahieu  ( Laboratory of Aquaculture & Artemia Reference  Center),  Paco Amat  ( Instituto de Acuicultura de Torre de la Sal ) and  Marta Sanchez  ( University of Sevilla ) for providing samples and  Emmanuel Douzery  ( ISEM, University of Montpellier ) and  Arnaud Estoup  ( CBGP, INRAE ) for advice on phylogenetic and population genetic methods. We thank  Marie-Pierre Dubois  and the  GEMEX molecular platform of CEFE laboratory , and the  GENSEQ platform of the Centre Méditerranéen Environnement Biodiversité (LABEX CEMEB, Montpellier, France)  for assistance with molecular laboratory work. We also thank  Maria Orive  and two anonymous reviewers for their useful comments.
2010, Maccari et al. 2013a, Eimanifar et al. 2014, Eimanifar et al. 2015)had the same APD05 haplotype as Ap3n individuals in our dataset. The TU13 Asin sequences from Siberia was found to be chimeric between the Ap4nARS1 mitochondrial haplotype and an Ap5n numt, it was included to illustrate that Ap4n and Ap5n likely originated from Siberian Asin. c e.
Necroses Analyses The desiccation cone zones, spur diameter and necrosis lengths were analysed 4 or 8 months after pruning. The desiccation cone samples were cut longitudinally in order to observe the internal necroses. Each sample was first soaked in 5% bleach solution, to distinguish between living wood (yellow-green) and necrotic wood (beige-brown), and then examined using scanner Hitachi X-300 (Hitachi, Ltd. , Tokyo, Japan). The fact that the extended necrosis did not show any additional infection, confirmed us in our decision to focus specifically on internal necrosis. Software ImageJ (Java software, NIH, Rockville, MD, USA) was employed to analyse the images, with the protocol for calculating the necrosis being adopted from the procedure pioneered by Abramoff et al. [19]. This software allowed us to calculate necrosis lengths, the proportion of necrosis between the top of the cut and the diaphragm, and the entire length of the cuttings.
During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E.
Phylogenetic analyses Potentilla-type ITS and partial ETS sequences retrieved from bacterial artificial chromosome (BAC) clones and Illumina datasets of Erythronium were added into a recent backbone phylogeny of Potentilla  (Feng et al. , 2017). This phylogeny was supplemented with additional Potentilla taxa having publicly available ITS sequences that were potentially closely related to the alien ITS of Erythronium. A maximum likelihood (ML) phylogeny was computed using the IQ-TREE  (Nguyen et al. , 2014)  web server (http://iqtree. cibiv. univie. ac. at/). The strategy for public Potentilla ITS sequence gathering and details of their aligning and parameters of the ML phylogeny applied are provided in Methods S1. GenBank accession numbers for newly generated and previously published Potentilla and Erythronium sequences included into the study are listed in Tables  S1, S3 , S4.
Chromosomes were counterstained with 4 0 ,6diamidino-2-phenylindole (2 µg ml -1 ) in Vectashield antifade. Fluorescence signals were analyzed and photographed using a Zeiss Axioimager epifluorescence microscope and a CoolCube camera (MetaSystems, Altlussheim, Germany). Individual images were merged and processed using the PHOTOSHOP CS software (Adobe Systems, San Jose, CA, USA).
Additionally, a semi-quantitative PCR (SQ-PCR) approach was employed using Maxima SYBR Green qPCR Master Mix (Thermo Scientific, Waltham, MA, USA) and primers for eudicot and monocot ITS2 in order to establish the relative fold difference (RFD) between native and alien rDNA in E. dens-canis and E. caucasicum. The latter species also tested positive for Potentilla-type ITS2 in PCR screenings. Along with the single accession of E. caucasicum, this experiment included gDNAs of five E. dens-canis samples (Table  S1 ) from distant localities of the longitudinally wide and latitudinally narrow species' range in order to get a first insight into monocot/eudicot rDNA RFD variation between populations. Each sample-primer pair combination was run in triplicate. Raw fluorescence data provided by a Rotor-Gene 6000 instrument (Corbett Research, Mortlake, VIC, Australia) were analyzed in the LINREGPCR v.
Nanopore long-read sequencing and data analysis Oxford Nanopore Technologies' (ONT) long-read sequencing service was ordered from Deep Seq (University of Nottingham, Nottingham, UK). Bulb-extracted gDNA of c. 25 kbp in size was used as input for the preparation of the standard SQK-LSK109 library as per ONT's protocol (ONT, Oxford, UK). The library was run over one PromethION flow cell. Base calling was completed in PromethION's sequencing software MINKNOW by using the default quality threshold of 7. The resulting 12. 6 million reads (c. 68. 2 Gb of data) had an N50 read length of 9. 9 kbp. A total of 64 998 contigs with minimum, maximum, and average lengths of 1 kbp, 1. 38 Mbp, and 5. 69 kbp, respectively, were assembled using CANU v. 1. 8 (Koren et al. , 2017)  from the raw Nanopore data.
Polishing of the CANU assembly was attempted using PILON  (Walker et al. , 2014)  (https://github. com/broadinstitute/pilon) with default parameters, using a preprocessed paired-end Illumina dataset (see later). Both the raw reads and the contigs were screened for eudicot/monocot ITS1/ ITS2 fragments (Table  S5 ) in GENEIOUS PRIME. In terms of the number and the length of Nanopore reads containing Potentillaspecific rDNA sequences, the assembly did not turn out to be superior to the original read dataset (Table  S6 ). Raw Nanopore sequences that were analyzed and presented in the current study were included in the supplementary dataset (Datasets S1, S2).
Illumina whole genome shotgun sequencing and read analysis A TruSeq shotgun library (of 350 bp insert-size) was prepared from gDNA of E. dens-canis and paired-end (150 bp) sequenced via a HiSeqX platform at Macrogen B. V. Then, 50 Gb of raw reads were preprocessed to remove low-quality reads and controls and to trim adapter sequences by using a combination of tools provided in the BBMap project  (Bushnell, 2016; Bushnell et al. , 2017). A de novo assembly of Illumina reads into contigs was performed in SPADES  (Bankevich et al. , 2012). Potentilla-specific ITS and partial ETS sequences were extracted from contigs following a screen in GENEIOUS PRIME with eudicot ITS1/ITS2 sequences (Table  S5 ). In the case of E. caucasicum, 5 Gb of whole genome shotgun (WGS) data were obtained. A shotgun gDNA library of 350 bp insert size was prepared and paired-end (150 bp) sequenced at Novogene (Cambridge, UK) using the Novaseq6000 platform.
, 2017; Dunning et al. , 2019; Graham & Davies, 2021)  suggests that they could play a role in the DNA transfer. Moreover, DNA fragments similar to the Potentillasister Fragaria DNA transposon CACTA-class elements found within BAC clone 1J24 (Table  S7 ) suggest TEs might have also been participating in the actual transfer. Simultaneous presence of native and alien rDNA was not detected in the sequenced BAC clones, although a chimeric sequence read containing parts of both native and alien rDNA (Fig. S5 ; Dataset S1) was found within the Nanopore WGS dataset (Table  S6 ). The fragmentation of native rDNA observed in this sequence is possibly the result of pseudogenization. Nevertheless, given the rarity of this sequence type, one cannot rule out its origin as a sequencing artefact. Presumed pseudogenization of alien rDNA at a larger scale was caught in action in the longest Nanopore read containing Potentilla-specific rDNA (Fig.
S6 ; Dataset S2). Here, disruption of rDNA subunits has a more or less symmetrical pattern within a palindromic structure that renders little likelihood for the artefact origin. Numbers of polymorphic nucleotide sites were also assessed in alignments of native and alien 18S and 26S sequences from the two BAC clones analyzed. Pseudogenization of alien rDNA is further supported by the fact that the number of polymorphic nucleotide sites is several fold higher in alien 18S and 26S sequences when compared with their native homologues (Table  S8 ). Still, conclusions in this respect must be taken cautiously since nucleotide variation in two BAC clones cannot truly reflect variation of target regions across the whole-genome level. Although the presence of horizontally transferred rDNA was demonstrated previously in eukaryotes  (Yabuki et al.
Acknowledgements We would like to thank  Adela Jurković  ( University of Zagreb ) for providing guidance to LB in regard to the Southern blotting technique. Chemiluminescence detection was achieved with the assistance of  László-Csaba Bencze  and  Alina Filip  ( Babes ¸-Bolyai University ), whose help is also acknowledged. We thank  Kunigunda Macalik ,  Jānis Rukšāns  and the  Rare Bulb Nursery (Latvia) ,  Andrey Dedov ,  Sergey Banketov ,  Julianna Lingvay ,  Paul-Marian Szatmari ,  Gábor Sramkó ,  Boštjan Surina ,  Polina A. Volkova ,  Nikolay V. Stepanov , and  Alexander L. Ivanov  for their help in the acquisition of plant material. This work was supported by a grant of the  Romanian Ministry of Research and Innovation ,  CNCS-UEFISCDI , project no. PN-III-P1-1. 1-PD-2016-0919 ,within PNCDI III.
PAB was supported by research grant no. 20-12496X  ( Grant Agency of the Czech Republic ). The cytogenetic work was supported by the  Czech Science Foundation  grant to TM and AK ( 22-16826S ). The work of VM was supported by the long-term research development project RVO 67985939 of the  Czech Academy of Sciences. We would like to acknowledge the support of the  GENTYANE platform of Clermont-Ferrand INRAE Centre  (http://gentyane. clermont. inra. fr/)for providing assistance in next-generation sequencing and of the  Genotoul bioinformatics platform Toulouse Midi-Pyrenees  ( Bioinfo Genotoul ,  10. 15454/1. 5572369328961167E12 ,http://bioinfo. genotoul. fr)for providing computing resources.
2D scattering profiles were radially averaged and normalized to the sample transmission and sample thickness. Corrections for the detector sensitivity, background noise and empty cell signal were applied  (Brûlet, Lairez, Lapp, & Cotton, 2007). The absolute scattering cross sections I(q) per unit sample volume in cm -1 was obtained using normalization of 1 mm thick water cell. The experimental scattering profiles of all the gel samples were fitted with a Two Lorentzian model available in SasView software (http://www. sasview), described by Eq. (1): I(q) = A 1 + (qξ) n + C 1 + (qΞ) m + Bkg (1) where the 1st term, dominating at high q range, characterizes scattering from elementary components of the gel (i. e. , individual proteins), while the 2nd term, dominating at low q, characterizes the structural order and interactions between the elementary components in the gel (i.
Acknowledgments We thank  Laboratoire Léon Brillouin  for beam time allocation on PAXY spectrometer and financial support of the internship of  Urielle Randrianarisoa. We thank  Daniel Dudzinski  for help and discussions on the rheometer. We thank the  INRAE team  for purification of the proteins and  Williams. N. Ainis  for sharing the protein isolate. We thank  CNRS  for the financial support of M. Napieraj thesis.
Hydrology Three major regions can be recognized from the paleohydrological records: The Sahel and Savannah zones, with drying trend; the center of the Congo Basin, which exhibit an opposite trend of increasing humidity; and the boundary between the dry and humid domains defined by the equatorial sectors closest to the coast or in mountain, where an alternation of wet and dry phases is recorded. Two paleo-records differ from this general picture: that of Lake Chad, where a period of flooding is recorded ca 1600CE, and that of the Diorom Boumak, where the LIA is entirely characterized by a wet period (Fig. 4 ). As evoked above, the multiple origins of the data and the complex hydrological system of Lake Chad may have introduced a bias into the hydrological record and may explain (at least partly) the difference with the other Sahelian archives.
Acknowledgements This work contributes to the  ACCEDE ANR Belmont Forum  project ( 18 BELM 0001 05 ). This work was undertaken in the framework of the  French L-IPSL LABEX  and the  IPSL Climate Graduate School EUR  and benefited from the  FNS  " SYNERGIA EffeCts of lArge voLcanic eruptions on climate and societies: UnDerstanding impacts of past Events and related subsidence cRises to evaluate potential risks in the future" (CALDERA)  project under  French CNRS  grant agreement number  CRSII5_183571 -CALDERA. MK acknowledges support from the  HPC  resources of TGCC under the allocations  2020-A0080107732  and  2021-A0100107732  (project gencmip6) provided by  GENCI  ( Grand Equipement National de Calcul Intensif)  and  2020225424  provided by  PRACE (Partnership for Advanced Computing in Europe).
This study benefited from the ESPRI computing and data centre (https://mesocentre. ipsl. fr) which is supported by  CNRS ,  Sorbonne Université ,  Ecole Polytechnique  and  CNES  as well as through national and international grants. Thanks are due to the African Pollen Database for data access. AML, MC and JV were funded by  CNRS , and MK by  IRD. We acknowledge the  World Climate Research Programme' s Working Group on Coupled Modelling.