dataesr/scientific-paragraphs-categorization huggingface dataset:
Recall indeed that our candidate model only used ASM-V data, whereas all other candidate models used nominal L1b VFM data [whenever using Swarm data, see  Alken et al. (2021b)  and references therein]. An additional illustration of the increased value of the new ASM-V data for global geomagnetic field modeling purposes is provided in Fig. 4b. This map of the difference between our DGRF 2015. 0 candidate model and its twin illustrates the impact of using the new ASM-V data in place of the L1b VFM data, all else being equal. This leads to differences well within the 1 nT range, except in a few localized regions, such as above South America, where differences can reach 2 nT. The reason for this is unknown. It could of course be related to a remaining unidentified ASM calibration issue, but other causes may come into play, such as small distortions of the boom, or, more likely, artifacts linked to the so-called dBSun perturbations currently corrected for in the L1b VFM data by assuming that only the VFM instrument is affected (see  Tøffner-Clausen et al.
Availability of data and materials Swarm nominal L1b data are available from https:// earth. esa. int/ web/ guest/ swarm/data-access. The experimental ASM-V data used in this study are ASMV data version 050X (0505, 0506, 0507 or 0508) produced by IPGP/CEA-Léti using the ASM CEA-Léti designed/ CNES Customer Furnished Instrument. These ASM-V data as well as the ASM-V derived models (parent model and DGRF 2015 candidate model with associated error estimates) are accessible at https:// swarm. ipgp. fr/. ASM-V data are also intended to later be made available through the "Form@Ter-Data and Service for the Solid Earth" Center (https:// en. polet erres olide. fr/).
2021). Lastly, inspection of allele sharing patterns derived from analyses conducted between modern individuals and populations on the highly fragmented and contiguous reference genomes revealed widespread introgressive signals between P. dactylifera, P. atlantica, P. sylvestris, and P. theophrasti, all of which were statistically significant (supplementary tables S4-S7, Supplementary Material online). In particular, our finding of introgression between modern individuals P. dactylifera and P. sylvestris is in line with the study of  Flowers et al. (2019) , where an excess of derived allele sharing between Asian individuals of P. dactylifera and P. sylvestris was reported. To obtain a time tree for Phoenix and further tease apart the signal of incomplete lineage sorting (ILS) from the introgressive relationships revealed by the D-statistics, we used three approaches: 1) the molecular-clock dating of plastid and nuclear genomic data sets; 2) the comparison of tree and quartet frequencies genome-wide and in scaffolds, and 3) an explicit statistical test of introgression based on ultrametric trees and DNA distance matrices.
datcylifera to P. sylvestris. Lastly, to statistically test for the presence of introgressed sequences among date palm populations, we compared the minimum pairwise distance between simulated and empirical data sets as implemented in the software JML v. 1. 3. 1  (Joly 2012) , using as a framework the posterior distribution species trees obtained by StarBEAST2 for each nuclear scaffold. The test revealed significant (Bonferroni adjusted P < 0. 05; supplementary table S10, Supplementary Material online) widespread gene flow between North African-Asian populations of P. dactylifera, P. sylvestris and P. theophrasti, thus providing support to the findings produced by our D-statistic analyses conducted to population level (supplementary tables S6 and S7, Supplementary Material online). Our multiple lines of evidence (i.
C. E. ) to second intermediate period, but they become only common from the New Kingdom (1,570-1,070 B. C. E. ) onward (see reviews in  Zohary et al. [2015] , and database in  Flowers et al. [2019] ). The importance of date culture during the New Kingdom is also reflected artistically, for instance in garden scenes within tomb wall paintings  (Parkinson 2008). More limited evidence from the Old Kingdom (2,700-2,100 B. C. E. ) includes findings of two date stones, and occasional fragments of other plant parts, from Giza  (Malleson and Miracle 2018). Textual evidence from the Old Kingdom additionally refers to imported dates  (Tallet 2017 ). Some early finds may therefore represent either imports or cultivated trees (Gros-Balthazard and Flowers 2021). Examples of date stones recovered from earlier pre-Dynastic sites, notably from El Omari and Hierakonpolis, however, might be intrusive and lack reliable context (Friedman R, personal communication to.
Whole-genome sequence data from these taxa were obtained from the NCBI Sequence Read Archive repository. Twenty million reads were downloaded for each accession using the tool fastq-dump of the SRA toolkit. Nearly all accessions sampled are linked to vouchers and have known origins  (Gros-Balthazard et al. 2017; Flowers et al. 2019) ; detailed information on their provenance, average read length and number of bases downloaded are provided in supplementary tables S1 and S2, Supplementary Material online.
Genome Skimming of L. montana We extracted genomic DNA from silica-dried leaf tissue of L. montana using the Qiagen DNeasy Plant kit, following the manufacturer's protocol. A genomic Illumina paired-end library was prepared using the NEBNext Ultra II library preparation kit, following the manufacture's protocol and with an average insert size of 464 bp. Library sequencing was performed by the company Genewiz (NJ) on a HiSeq platform. A total of four million paired-end reads were produced. The newly generated sequence read data of L. montana have been made available in the Sequence Read Archive project PRJNA739191.
High-Throughput Read Data Processing The Illumina raw reads were quality filtered using Trim Galore v. 0. 4  (Krueger 2015) , discarding sequences with an average phred33 score below 20 and a length <25. Preand posttrimming read quality was assessed using FASTQC v. 0. 1  (Andrews et al. 2015). The proportion of endogenous DNA sequences present in the ancient Saqqara date palm leaf extract was assessed by mapping the trimmed read data against two nuclear genomes (Khalas variety: assembly GCA000413155. 1, Al-Mssallem et al. 2013 ; Bahree cultivar: assembly GCA0009389715. 1,  Hazzouri et al. 2019 ) and one plastid genome of P. dactylifera (assembly NC013991;  Yang et al. 2010 ) using Magic-BLAST v. 1. 5. 0  (Boratyn et al. 2019 ), a word size value of 18 (-word_size), and a penalty for nucleotide mismatch (-penalty) and score (-score) threshold of 4 and 20, respectively.
The full reports of our Magic-BLAST analyses are freely available in supplementary file S1, Supplementary Material online. We then determined the proportion of nuclear/plastid ancient date palm read data sequenced by filtering the number of hits mapped by Magic-BLAST onto nuclear and organellar scaffolds. Given the low proportion of nuclear genomic data recovered from the ancient Saqqara date palm leaf (see Results), we mapped trimmed reads of both modern and ancient accessions on nuclear and plastid targeted scaffolds (i. e. , scaffolds with Saqqara date palm leaf reads mapped). These represented 198 contigs, or 26. 8% (149. 01 Mb) of the P. dactylifera' nuclear genome assembly. We investigated the proportion and position of mis-incorporated nucleotides in the Saqqara date palm leaf DNA following the protocol of  Latorre et al.
(2020) , that is, using aligned aDNA reads and the tool mapDamage2 v. 2. 0. 9  (J onsson et al. 2013). We compared nucleotide mis-incorporation patterns between the aligned aDNA reads of the Saqqara date palm leaf and DNA reads of modern date palm accessions (SRR5120110). Finally, to reduce the fraction of mis-incorporated nucleotides mapped onto the reference genome, which were found to occur with higher frequency on the first 1-3 positions of DNA fragments (fig. 1  and supplementary fig. S1 , Supplementary Material online), we trimmed two bases at the 3 0 and 5 0 end of the aDNA reads, using Trim Galore v. 0. 4. Read mapping, alignment, and DNA damage analyses were implemented through the pipeline PALEOMIX v. 1. 2. 13  (Schubert et al. 2014). The trimmed read data were mapped using the software bowtie v.
If mis-incorporations are pervasive in the aDNA fragments, a deviation of Ti/Tv and error rates is expected when compared with values derived from modern accessions. Ti/Tv ratios were computed by first obtaining a matrix of 7,599 called genotypes from genotype likelihoods (GLs) using the software PLINK v. 1. 9 (Purcell et al. 2007 ). The GLs were obtained from read mappings against the P. dactylifera Bahree cultivar reference genome and retaining only sites that were common across all sets of modern individuals and the Saqqara date leaf (see Population Structure, Nuclear Phylogenomics, and Gene Flow of the Saqqara Date Palm). The resulting 7,599 genotyped sites were then used as input in vcftools v. 0. 1. 16 (Danecek et al. 2011)  to produce the Ti/Tv ratios. Error rates were computed for the same set of samples in ANGSD v.
0  (Stamatakis 2014) , using the GTR substitution model, 25 gamma rate categories, and 1,000 bootstrap replicates. The number of informative sites and proportion of missing data of the whole-plastid genome alignment are available in supplementary table  S3 , Supplementary Material online. Population Structure, Nuclear Phylogenomics, and Gene Flow of the Saqqara Date Palm Given the low-depth of the high-throughput sequencing data produced for the ancient Saqqara date palm leaf, we relied on GL to place the aDNA nuclear genomic data of the Saqqara date in range with genomic sequences of modern Phoenix samples. We computed nuclear GL using the software ANGSD v. 0. 929  (Korneliussen et al. 2014) , by implementing the GATK GL model, inferring the minor and major alleles, and retaining polymorphic sites with a minimum P value of 1e 6.
Such approach has been widely used in studies involving the analysis of modern and ancient DNA samples in phylogenomic frameworks (see  Sheng et al. 2019; Westbury et al. 2020). The resulting alignments were then concatenated into a supermatrix and subsequently trimmed in Geneious v. R. 8. 0 to consider only sites that were homologous to those retrieved from the Saqqara nuclear genome. We computed a NeighborNet network derived from uncorrected P-distances using the software SplitsTree4  (Huson 1998)  and the supermatrix as input. The support at edges was estimated by conducting 1,000 bootstrap replicates (supplementary file S3, Supplementary Material online). The number of informative positions and proportions of missing data for this alignment are provided in supplementary table  S3 , Supplementary Material online.
We next conducted principal component (PCA) and population structure analyses using nuclear GLs and the tools PCangsd  (Meisner and Albrechtsen 2018) , and NGSadmix  (Skotte et al. 2013)  of the software ANGSD, respectively. Because PCA can be particularly affected by the proportion of overlapping sites between modern and ancient populations  (Ausmees 2019) , we computed covariance matrices by using only GLs derived from sites that were shared across all the modern individuals and the ancient Saqqara date palm leave (i. e. , option -minInd set to 35), and a maximum of 1,000 iterations. Admixture analyses were conducted with number of population (K) set from two to eight and a maximum of 20,000 iterations. The best K was selected by comparing the resulting likelihood values derived from each K iteration.
As such, discussions regarding gene flow between the Saqqara leaf and modern populations of Phoenix are based only on the test considering all sites. The significance of the analyses was assessed by executing a block-Jacknife test which derived SEs and Z scores, using a block size of 5 Mb. For population level analyses, P values were derived. The admixture of the Saqqara date palm was discussed based solely on significant P-and D-statistic values (i. e. , jZj > 3). D-statistic values, SDs, Z scores, and the number of evaluated sites for each topological permutation are provided in supplementary tables S4-S7, Supplementary Material online. NGSadmix and D-statistic analyses were conducted on filtered GLs derived from read data mapped on: 1) 198 contigs representing 26. 8% of the P. dactylifera genome (assembly GCA000413155.
A total of 18 alignments were produced (supplementary file S4, Supplementary Material online). To reduce the influence of missing data on phylogenetic analyses, we trimmed positions including more than 10% of gaps in each alignment, which subsequently were split into nonoverlapping blocks of 10,000 bp. This approach was chosen to account for potential differences in the evolutionary histories of loci along each scaffold which ultimately can lead to producing contrasting tree topologies, while allowing for a number of loci sufficiently low to render computational analyses tractable. The total number of blocks and their corresponding features, including number of informative positions and proportions of missing data, are provided in supplementary table  S3 , Supplementary Material online. ML phylogenies were inferred from each block, using the same settings mentioned above to infer the plastid genome phylogeny (see Plastid Phylogenomic Analyses of Phoenix).
We employed the resulting 1,143 ML phylogenies to infer a species tree under an MSC framework as implemented in the software ASTRAL-III v. 5. 6  (Mirarab and Warnow 2015) , after collapsing Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf. doi:10. 1093/molbev/msab188 MBE branches with less than 10% of LBS, as recommended in  Zhang et al. (2018). To determine the frequency of gene tree quartets supporting (LBS ¼ 0 and >90) the species tree or any other alternative relationship, we compared each ML tree produced from 10,000 bases blocks against the species tree using the software DiscoVista v. 1. 0 (Sayyari et al. 2018). Each internal branch of a resolved, bifurcating tree has four taxa (or groups of taxa) around itself, and there are only three possible topologies for the arrangement of these four taxa around the branch; these three topologies are often referred to as three alternative quartets.
For each internal branch in the species tree, DiscoVista computes the relative frequencies at which the three alternative quartets are found in the gene trees, thereby providing a measure of the relative support for each alternative. The analysis was performed by first looking at conflict among all 1,143 blocks, and then separately for each of the 18 scaffolds to test for conflict among the blocks derived from each scaffold. Inferring absolute ages of divergence in the presence of gene tree discordance is challenging because distinct evolutionary histories can lead to differences in estimated ages of divergence  (Widhelm et al. 2019). We relied on the program StarBEAST2 v. 2. 5  (Ogilvie et al. 2017)  to estimate absolute ages of lineage divergence from nuclear and plastid genomic data, using the same taxon sampling employed to calculate ML trees across the 18 scaffolds.
The software implements MSC methods in conjunction with various molecular clock models, allowing species tree calibration in the presence of reticulation. One downside of the analysis is that it becomes time intractable whenever large numbers of partitions are being analyzed  (Ogilvie et al. 2017; Widhelm et al. 2019; Mello et al. 2021 ). To render the Bayesian time estimations tractable, we independently analyzed one plastid and 18 scaffolds, the latter divided each in nonoverlapping blocks of 100,000 bases, with an average of 913 parsimony informative sites. The number of variable and parsimony informative sites, proportion of missing data and A/T, G/C content for nuclear and plastid alignments were obtained using the program AMAS v. 1. 0 (Borowiec 2016). The total number of plastid and nuclear blocks and their corresponding features are provided in supplementary table  S3 , Supplementary Material online.
Given that nuclear-wide genome data are not available for L. montana, we relied on the ages of divergence of Phoenix derived from our plastid chronogram to calibrate the root of our nuclear tree (including P. reclinata, P. sylvestris, P. theophrasti, and individuals representing Asian and African populations of P. dactylifera; see Results). The prior probability distribution of the root age was set to follow a Normal distribution of arithmetic mean 12. 5 Ma and SD of 1, reflecting the posterior age distribution yielded by our plastid analysis for this node. We used the same priors and models employed to obtain absolute ages from the plastid data set, with the exception that: 1) the mean rate of the relaxed molecular clock was set to a uniform distribution with lower and upper values of 0. 0001 and 0.
01, respectively, following  Gaut et al. (1992)  and  Gros-Balthazard et al. (2017)  while allowing substantial deviation from them; and 2) the ploidy level was set to 2 (option "autosomal nuclear") as recommended for nuclear diploid data sets  (Jatt et al. 2019). Nineteen ultrametric Maximum Clade Credibility (MCC) consensus trees were produced in TreeAnnotator v. 2. 5 (available at https://www. beast2. org/treeannotator/) for plastid and nuclear scaffolds based on the posterior tree distribution from each analysis using the median node heights option and a burn-in fraction of 10%. Median node ages and 95% highest posterior density intervals are provided in supplementary table  S8 , Supplementary Material online.
Validation Tests of Gene-Flow Processes To determine whether the conflicting, strongly supported relationships observed in our nuclear genome-wide ML and Bayesian phylogenies are the product of gene flow and not ILS, we conducted statistical tests involving the comparison of minimum pairwise distance between simulated and empirical data sets in the software JMLv. 1. 3. 1  (Joly 2009 ). The program relies on posterior predictive checking to assess whether the minimum distance between any two given DNA sequences is smaller than expected assuming the absence of gene flow  (Joly 2012). To this end, we employed 396,000 post-burnin randomly subsampled posterior trees from the dating analyses conducted on the 18 nuclear scaffold data sets (i. e. , 22,000 trees per analysis) and their corresponding DNA alignments.
A total of 396,000 simulations were run using an average mutation rate of 0. 005 (option locusrate), a heredity scalar P erez-Escobar et al. doi:10. 1093/molbev/msab188 value of 1 as recommended for nuclear data sets (option heredityscalar), the GTR substitution model (option seqgecommand), and a P value of 0. 05 (option significancelevel). The resulting P values were adjusted by implementing a Bonferroni correction. The minimum distances between the ingroup taxa and their statistical significance are provided in supplementary table S10, Supplementary Material online.
Acknowledgments We would like to thank  Valentina Gasperini  ( The British Museum ) for her advice on the Saqqara excavation contexts, and  Ren ee Friedman  (Director of excavations at the  Predynastic site of Hierakonpolis ) for her advice on the reliability of date stone archeological findings and the need for re-evaluation of date leaf finds. O. A. P. E. acknowledges support from the  Sainsbury Orchid Fellowship  at the  Royal Botanic Gardens ,  Kew , and the  Swiss Orchid Foundation ; a  Garfield Weston Foundation postdoctoral fellowship  to S. B. , the  Swedish Research Council , the  Swedish Foundation for Strategic Research , the  Knut and Alice Wallenberg Foundation  and the  Royal Botanic Gardens, Kew  to A. A. G. C. is funded by a  Natural Environment Research Council   Independent Research Fellowship  ( NE/S014470/1 ).
Acknowledgements We thank our advisory board for guidance,  Des Browne ,  Polly Courtice ,  Martin Rees , and  Mark Welland. For funding, we are grateful to The David and  Claudia Harding Foundation ,  Arcadia , and  MAVA. Mark Burgman ,  Lynn Dicks ,  Riikka Savolainen ,  Jonathan Spencer , and  Hannah Tankard  provided useful comments on earlier versions of the manuscript. For suggesting ideas on Twitter that we included, we thank  Steph Bradbeer @stephjbradbeer ,  Steven Byrnes @steve47285 ,  Lorna Cole @LornaC ,  Deano @Deano80783668 ,  Mike Hudson @DrMike_Hudson ,  Steve Jones @SteveCJjones , Liam Langan @langan_liam, Littlerobbergirl @lilrobbergirl, Grainne McCabe @grainne_mccabe,  Julie McMurray @figgyjam ,  Simon Miller  @simoncmiller,  Manu Saunders @ManuSaunders , Grania.
Optical microscopy Resuspended cells were mounted onto glass slides with Vectashield Vibrance mounting media (Vector Labs, Burlingame, CA) and analyzed using a Leica DM500 fluorescence microscope (Leica, Buffalo Grove, IL) or a Zeiss LSM 880 (Carl Zeiss, Jena, Germany) inverted confocal microscope, all the images were analyzed using Fiji Image J software  (45). Additionally, the supernatant from each microbial isolation from cecal contents was imaged for confirmation of the absence of bacteria with Hoechst 33342 (1 µg/mL) and imaged using a fluorescence microscope. Samples were imaged by using two color filter cubes-UV (359 nm/461 nm) for Hoechst to localize cells, and Cy5 (650 nm/670 nm) for AF647 to detect the presence of alkyne-containing metabolites.
5 min; and hold at 72°C for 10 min, and the duplicate final amplified products were pooled. 16S rRNA gene amplicons were cleaned with Mag-Bind® RxnPure Plus (Omega Bio-tek, Inc. , GA). Samples were mixed together in equimolar amounts prior to sequencing on Illumina's MiSeq platform. Sequence data was processed in QIIME 2 (Quantitative Insights Into Microbial Ecology 2)  (48). Libraries were demultiplexed, raw sequence pairs were joined, and the quality was trimmed based on an average quality score of 30. Sequences were clustered into de novo OTUs with 97% similarity using the Greengenes database (version 13. 8)  (49). The negative controls run with each MiSeq set for determining potential contaminants in PCR reagents and procedure were analyzed and removed  (50).
Untargeted Metabolomic Analysis RAW files generated from HPLC-HRMS acquisitions were converted to mzXML files utilizing MSconvertGUI software (proteowizard. sourceforge. net). Differential molecular features were determined by subjecting mzXML files to Metaboseek Software version 0. 9. 6 (metaboseek. com) utilizing the xcms package  (51). Differential features were filtered using the minFoldOverCtrl, minInt, and Fast_Peak_Quality filters, and then subjected to manual curation to remove adducts and isotopes. The curated features were assigned molecular formulas and then subjected to tandem mass spectrometry (MS2). MS2 fragments were also assigned molecular formulas and sphingolipid structures were inferred. was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
Acknowledgements: The authors would like to thank  Rebecca Williams  for her guidance with confocal imaging. We thank the  Genomics Facility of the Biotechnology Resource Center at the Cornell University's Institute of Biotechnology  for their help with sequencing experiments and financial support through their seed grant program. Additional grant support for data collected on the Zeiss LSM880 inverted confocal/multiphoton microscope (i880) came from grants  NYSTEM C029155  and  NIH S10OD018516. was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which this version posted June 8, 2020. ; https://doi. org/10. 1101/2020. 06. 08. 140665  doi: bioRxiv preprint.