dataesr/scientific-paragraphs-categorization huggingface dataset:
Any bins for which less than 7 of the 16 marker proteins were present were discarded. Finally, a maximum-likelihood phylogenetic tree was inferred using IQTREE (-m TEST --b 1000)  [30]. Taxonomic assignments of newly recovered draft genomes from Lac Pavin were manually assigned using the tree topology and taxonomy of proximal reference sequences. For all other bacteria and archaea, phylum-level taxonomy was assigned using a combination of GTDB-Tk results, protein annotations from ggKbase, and manual BLAST searches of the S3 or L6 ribosomal proteins. Finally, reads from all samples were re-mapped to the refined bin set using bowtie2. Bin coverage was analyzed using CoverM (https:// github. com/ wwood/ CoverM) with a 95% identity threshold for read mapping and 50% breadth threshold (fraction of genome covered by reads).
Taxonomic affiliation was assigned at the phylum level using three separate pieces of evidence: the taxonomy of the bin containing the representative scaffold (where relevant), the taxonomy of the top UniRef100 BLAST hit to the representative protein sequence, and the consensus taxonomy of the representative scaffold. Consensus scaffold taxonomy was computed by comparing each predicted protein against UniRef100 using a custom DIAMOND database (diamond blastp)  [33]. Hits were filtered to those with 70% or greater coverage of the query sequence and an e value less than or equal to 1x10 -10 , as done previously  [34] , and the most common phylum-level designation was taken. If the same phylumlevel designation was predicted by any two pieces of evidence, it was assigned as the final taxonomy; otherwise, scaffold taxonomy was manually curated using BLAST searches and annotation information.
Finally, relative abundance of species groups was assessed by mapping all raw sequencing reads to the combined scaffold set using Bowtie2 (default parameters). Coverage was calculated using CoverM with a stringent mapping threshold (99% read identity) and a minimum coverage breadth of 50% of representative scaffolds. Relative coverage of each species group was calculated by dividing its mean coverage value by the total coverage of all species groups in a given sample. To examine overall similarity in community composition across samples, the relative coverage metrics computed above were subsequently used to generate a Bray-Curtis distance matrix (skbio's diversity package in Python) and subjected to a principal coordinates analysis (implemented in skbio's stats module).
Alternatively, if such a scaffold was considered a provirus by CheckV, it was assigned likely provirus status. If a given scaffold had fewer than 5 times the number of viral genes than host genes, or no viral genes but less than 4 host genes, it was flagged for manual curation regardless of provirus status. Manual curation was performed by examining taxonomic and functional affiliations of proteins using a combination of databases as well as BLAST. To further refine the set of putative viral genomes, we programmatically scanned for evidence of eukaryotic viruses. First, all viral proteins were predicted using Prodigal (-p meta)  [17]  and compared against UniRef100 as described above for rps3-bearing scaffolds. Taxonomic information for best, abovethreshold hits for each protein was collected, and those scaffolds with ≥25% of annotated proteins affiliated with eukaryotes or eukaryotic viruses were discarded.
Where host assignment methods were conflicting, assignment based on CRISPR-Cas targeting was prioritized, followed by taxonomic affiliation of regions surrounding prophages, where relevant. Finally, we re-predicted proteins for the refined set of phage genomes using Prodigal (-m single). To account for the possibility of alternatively-coded phages, predictions were made in genetic codes 11, 15, and 4, and coding density was compared. If an "alternate" code (15 or 4) displayed an increase in coding density ≥10% relative to standard  (11)  code for a given phage  [48] , protein predictions in that code were retained. Otherwise, protein predictions in standard code were retained. Phage metabolic potential with depth was then analyzed as described above for CPR bacteria. Recovered phage pmoC genes were combined with those recovered from bacterial draft genomes, aligned using MAFFT and trimAl  [49] , and incorporated into a maximum-likelihood tree using IQTree with reference phage/host pmoC  [50].
Predicted proteins were also used to compare newly reported phages from Lac Pavin (viral_region_length ≥ 50 kbp, Table  S9 ) to those from reference databases/previous publications  [46, 50, 51]  using vContact2  [52]. The network was created using default parameters with the "ProkaryoticViralRefSeq201-Merged" reference database (--pcs-mode MCL --vcs-mode Cluster-ONE). Clusters reported by vContact2 were further classified as those containing only reference sequences, both Lac Pavin and reference sequences, and only Lac Pavin sequences. The network was visualized using Cytoscape v3. 9. 1  [53]  in a prefuse force directed layout with a modified spring coefficient of 1x10 -6. One large subnetwork containing multiple clusters was manually extracted from the broader network for the purposes of visualization.
Acknowledgements We thank  Yue Clare Lou ,  Spencer Diamond ,  Shufei Lei ,  Adair Borges ,  Marie Schoelmerich ,  Lin-Xing Chen ,  Alex Thomas , and  Rohan Sachdeva  for helpful discussions and informatic support. We also thank  Guillaume Borrel  and  François Enault  for their comments on the manuscript, and  Lily Law ,  Christopher Lefevre , and  Didier Jézéquel  for their assistance with sampling logistics. We also thank the  Innovative Genomics Institute at UC Berkeley ,  Y. Justin Choi ,  Shana McDevitt , and  QB3 Genomics at UC Berkeley.
Availability of data and materials Read data and draft genomes from this study are available through NCBI at PRJNA852163. Genome accession information for bacterial/archaeal genomes is also listed in Table  S3. Custom code for the described analyses are available on GitHub (https:// github. com/ alexa nderj affe/ lac-pavin-metag enomi cs). All supplementary figures, tables, data files, and genomes (including phage/viral genomes) are also available through Zenodo (https:// doi. org/ 10. 5281/ zenodo. 68575 90).
Creating a participatory platform The KFA has an online, freely available data platform for viewing and uploading information about kelp forest conservation projects (see kelpforestalliance. com). This platform will be used to track and monitor the success and outcomes of the Kelp Forest Challenge. On the platform, users can create individual profiles, organizational profiles, restoration and conservation project locations and outcomes, and pledges to the Kelp Forest Challenge will be displayed on the same platform. The platform tracks the amount of area pledged for protection and restoration as well as the self-reported area restored or protected. There will also be an emphasis for reporting relevant indicators such as the ecosystem services or benefits resulting from that conservation, the number of people involved in the kelp forest community, and non-area-based pledges such as the dollar value of those pledges, the number of person-hours contributed, or the audience reached by an activity.
Yearly progress updates are requested and they will be openly accessible on The Alliance website. We are also continuing the development of monitoring and reporting standards for kelp ecosystems and associated ecosystem services. This work will be done in collaboration with the Kelp Forest Alliance community and will help ensure a gold standard of data collection and allow for better data aggregation and comparison. This standardized and aggregated data can then help guide future decision making, enable large scale synthesis, benefit researchers, and communicate the importance of kelp forests to the public  (Adams and Sandbrook 2013). National pledges will also be included in the IUCN Restoration Barometer.
The construction of the Iron Age Mediterranean chronology began in the Levant based on historical evidence and has been additionally supported in recent decades by means of radiocarbon analysis, although with variable precision and ratification. It is only in recent years that new evidence in the Aegean and the western Mediterranean has opened discussion towards its further acceptance as an authoritative i. e. highly reliable, and widely applicable historiographic network. Altogether, the Mediterranean Iron Age chronology has only undergone minor changes during the last hundred years. The Phoenician metropolis of Sidon in southern Lebanon now provides a new, large and robust dataset obtained through a combination of archaeological and 14 C-radiometric analysis of materials from stratified contexts that allow their statistical assessment.
The appearance of substantial amounts of pottery of Greek, Cypriot and Egyptian origin together with Phoenician local wares in a long stratigraphy is a benefit for the synchronisation of regional pottery styles and allows wider geographic correlation of relative chronological systems. The close association of the archaeological data with a long series of AMS-14 C-dates on short-lived samples provides new evidence for the absolute dating of many of the regional pottery styles that are represented in the stratigraphy of Sidon, and contributes towards a considerable improvement of the Mediterranean chronology.
Introduction Many details of the Iron Age chronology of the Mediterranean have been questioned during the last two decades by new dendro-and radiocarbon data from several sites in the Aegean, central and eastern Mediterranean as well as through archaeological critique  [1] [2] [3] [4] [5] [6] [7]. Some of these studies, that were conducted in the central Mediterranean, put into question for the first time the conventional Mediterranean chronology  [1] [2] [3] , an otherwise vague term that has not yet been adequately defined. More recent data from the Aegean  [4, 6]  stressed the need for a revision of conventional Iron Age chronology based on robust stratigraphic data. In the meantime it became evident that a new definition of the Mediterranean chronology is required, one based on the systematic correlation among many different regional relative chronological systems that have been developed over the years and which range from the Iberian Peninsula to Cyprus and the Levant, and from Italy and Greece to the northern African coast.
Interestingly, many of these early synchronisms that were based on evidence from culture-historical methods were later confirmed, at first sight, by scientific dating in Israel. It is this evidence that has been recently questioned  [1] [2] [3] [4] [5] [6] [7]  and which is further scrutinized in this paper through juxtaposition to our new 14 C-AMS-data from the site of Sidon (Fig  1 ). This large radiocarbon dataset is not only valuable for the dating of regional ceramic sequences but also provides an opportunity to reevaluate the Iron Age Mediterranean chronology based on new scientific and archaeological evidence. The Early Iron Age levels at Sidon's College Site that provided our AMSdata yielded, next to local Phoenician pottery, one of the largest assemblages of well-dated Protogeometric and mainly Geometric Greek pottery in the Levant as well as Cypriot and Egyptian wares.
In this way the new scientific and archaeological data from Sidon provides us with a starting point for reexamination of the Iron Age chronology in a wider Mediterranean context. We approach this topic, in the present paper, through a study of all predominant regional pottery categories, as well as on the basis of comprehensive 14 C-analysis of the AMS-data from Sidon and other sites. The first and most significant impact of our dating project is on the Iron Age chronology of what is known as Phoenicia, most of which is today in modern Lebanon. A substantial amount of literature on the chronology of the southern Levant in the Late Bronze and Early Iron Age transpired already from the screening, selection, and explorative stratigraphic modelling of over 350 radiocarbon dates carried out on samples from prominent sites such as Megiddo (N = 147), Tel Rehov (N = 113), Tel Dor (N = 21), Tel Lachish (N = 61), and Ata Haroa (N = 16).
Put together, for Israel, the CalPal-database contains a total of around 100 14 C-dates for the Late Bronze Age and more than 350 14 C-dates for the Iron Age. But the data availability is not only highly disperse, in terms of sampling quality and dating precision, but also in geographic terms. In contrast to Israel, on the northern littoral of Levantine Phoenicia, the tells in long settled sites such as Tyre and Sarepta with their long stratigraphic sequences dating up to the Iron Age, have up until now, only been correlated to sites in the southern Levant by means of ceramic typological criteria  [8]. Phoenicia has long been considered one of the few areas where a smooth transition between the Late Bronze and Iron Age took place thus accounting for the interchangeable use of the terms 'Canaanite' and 'Phoenician'  [9] [10] [11].
These IDs are used, below, to abbreviate the identification of dated samples (e. g. ID1 = OxA-32124: 2908 ± 28 BP). Then follows the laboratory identifier (LabCode) and measured 14C-age. The following columns show the dated MATERIAL (olive stone, bone), the PHASE (A, B, C, C1, D, D1, E, I) to which the sample is attributed, the sample DEPTH [m], the ROOM number from which the sample was taken, and the excavation CONTEXT number. The last column contains the calibrated age with units [calBC ± 68%], calculated by CalPal-software based on IntCal20. This notation is used in preference of multiple calendric age intervals, for which unitary probabilities are often wrongly assumed (see below). Analytical methods. CalPal calibration software is programmed in Win10 1 and uses Intel 1 Visual Fortran Intel 1 VS64 Compiler XE in combination with Winteracter 1 (Version 14.
1) for archaeological 14 C-age modelling. Once the chronological results have been established by Gaussian Monte Carlo Wiggle Matching (GMCWM), for which we use Fortran IMSL6. 0™; GAMMQ, CSNDF non-central χ 2 routines  [6] ; for the final graphic processing we routinely make use of the CalPal-dialog shown in (  Fig 7). This dialog provides further analytical and graphical functions, which can be used to enhance the already completed chronology, as well as for additional chronological studies. These functions include (1) the construction of a new calibration curve that allows insertion of the recently modelled dataset (for which we use cubic splines with variable stiffness, with polynomial representation of curve variability; in Fortran IMSL6. 0™; CSSMH, CSVAL; SPLEZ routines), (  2 ) the age-shifting on both scales ( 14 C-and calendric) of the different curve construction component files, (3) the graphic addition of these files as well as previously modelled archaeological site 14 C-chronologies to the study graph, (4) the recently established 14 C-offset functionality (described below), and (5), the new Miyake functionality.
g. use of point vs interval dates; numeric abbreviation of continuous distributions; interpolation for missing data). In support of ongoing 14 C-calibration research, we have added new functions to CalPal, including a dialog called 'Delta 14 C-Composer' that is needed to transfer the Miyake events (which are typically published on the Δ 14 C-domain) onto the 14 C-BP-scale, as well as viceversa. The CalPal Δ 14 C-dialog utilizes data import/export in Excel™-format through the Windows 1 ODBC 1 -interface, and which supports (user-convenient) spreadsheet-processing. This database functionality makes extensive use of Winteracter 1 libraries.
Similarly unrealistic is the dating of a lower wall and base fragment of a bowl to the Late (!) Middle Geometric period (no 14). Equally ambiguous was also the attribution of two rim sherds from bowls to Middle Geometric (nos 12 and 13). Greek pottery and the new radiocarbon dates from Tell Tayinat in the Amuq plain, northern Levant. A large dataset of 49 radiocarbon determinations has recently become available from Tell Tayinat, a major site in the Orontes valley, where large amounts of Greek Geometric pottery were consumed  [28]. In Fig  9  (see above) we provide a detailed comparison of the chronological results achieved by age-modelling using OxCal and CalPal. Looking beyond the details, what we judge important is that we have independently confirmed the results of Manning et al. 2020  [28].
If the ascription of the use of pendent semicircle skyphoi to this Period is not due to a stratigraphic deficit, it certainly represents a chronological misperception of BP 3. According to recent secure stratigraphic data from several sites in the Aegean and Mediterranean  [51] , pendent semicircle skyphoi cannot be dated after Late Geometric Ia. Additionally, this Greek period can by no means be dated to the last third of the 8 th century BC or later. The modelled radiocarbon dataset from Tell Tayinat was recently interpreted in support of the conventional chronology  [28]. In the first place, the earliest use of 'LH IIIC-style ceramics' was attested in layers of Field Phase (FP) 6c that was 14 C-dated to the 12 th century calBC. This occurrence of 'LH IIIC-style pottery' was taken to contradict the data presented at Assiros in the northern Aegean that suggested that the transition from the Late Bronze Age to the Early Iron Age dates to the 12 th century  [28].
The consistency of the AMS-dates and their stratigraphic sequence at Sidon speaks for the general reliability of the combined 14 C-scientific and archaeological evidence. We note, in particular, the high consistency of our model-based 14 C-redating of Megiddo, Tel Rehov, and Tel Tayinat with the previously published chronologies. This comparison is all the more satisfactory, since the results (purposely utilising the same data and models) were achieved using two quite different analytical approaches (Bayesian Sequencing, Gaussian Monte Carlo Wiggle Matching) and corresponding software (OxCal, CalPal). The precision of the 14 C-analysis was contrasted, whenever possible, with the independently undertaken Phoenician, Greek, Cypriot and Egyptian pottery dating, but significant differences were not found.
Conclusions The new data from Sidon provide support for the high Aegean chronology, in the present case specifically by raising the Early and Middle Geometric period to the 11 th and 10 th centuries BC. The results of this study are thus consistent with the chronological data recently obtained in the northern Aegean  [4, 6] , at Phoenician sites in southern Spain  [7, 107] , in northern Africa  [1, 5]  as well as with recent suggestions about a higher Mediterranean chronology deriving evidence from holistic examination of available data in the central and western Mediterranean  [108]. This suggests not only a much longer time span for the Geometric period in the Aegean but also a different periodisation pattern. The implications of the revised Aegean chronology on what has been called Mediterranean chronology and especially the Iron Age chronology of the Levant must now be reassessed not only for the wider regional ceramic synchronisms between the Aegean and the eastern Mediterranean, but also among several microregions along the Levantine coast.
Materials Today, the mummy remains are kept at the Musee des Confluences, the former Musee d'Histoire naturelle de Lyon. In our descriptions below, we use the registration numbers assigned to the specimens since 2005, when the material was registered in the museum's database. Where possible, we mention the corresponding original numbers used by Lortet and Gaillard in their monograph. In the museum collections, eight clusters of bones are stored as skeletons, three of which clearly correspond to the descriptions given by Lortet and Gaillard. The five others are not mentioned in the original monograph and in three cases are composed of bones from more than one individual. In the early 1900s, attempts were made to reconstruct as many complete skeletons as possible, even using bones that did not belong to the same individual.
40. 6 in  [29] ; 104 # 1089-1116 in  [30] ; # T 323 in  [31] ); and by the presence of two amphora from the Byzantine period (  [28] ; Fig 109 in  [18] ; Pl. 29. 2 in  [30] ; # K 737 in  [31] ; MHNL 90000557). A much earlier date was obtained by radiocarbon dating of textiles used to wrap a baboon (MHNL 90001206), which is recorded in the museum's database as being of unknown provenance but must have come from the same locality: SacA40592: 2545 ± 35 BP (calibrated age 2σ: 803-544 cal. BC)  [2]. To better understand and clarify the exact dating of the baboon mummies, we performed additional radiocarbon datings, this time on bone collagen. A previous attempt to date cranial bone of one the baboon mummies (MHNL 90000176) was unsuccessful  (Richardin [Unpublished] ) because of the poor preservation and quality of the collagen.
Diagnosis of the pathologies observed on the skeletons A detailed description of the pathologies seen in the baboon remains from the Lyon collections is presented in the supporting information (S1 Text). First, observations we made on the skulls and mandibles are provided, then the more or less complete skeletons are described, and finally the isolated skeletal elements that showed pathological conditions but could not be linked to a particular individual. Only descriptions are given in the supporting information; the likely diagnoses of the observed pathologies are discussed below. Based on the data of Table  2. The 4 male Papio sp. individuals, whose dental stage could not be determined (indicated as "?" in Table  2 ) because only the skull roof was preserved, are taken into account as well.
Ongoing work includes dental microwear analysis which, combined with the available carbon and nitrogen stable isotope data, could further refine our knowledge concerning the diet of the baboons. These data will allow comparison with existing information from predynastic Hierakonpolis  [76]. A series of molars, sequentially sampled for strontium isotope analysis, is under study to try to distinguish between allochthonous individuals and those animals born locally. As shown by previous work  [44] , the isotopic signature could also provide information on the animals' provenance where-in the case of the hamadryas baboons-it is hoped to find out whether the Horn of Africa or rather the southern part of the Arabian Peninsula played a role. Previous ancient DNA research has shown that genetic material is very poorly preserved, but mitochondrial DNA could also help determine provenance  [57, 77].
Acknowledgments The authors acknowledge the  Musee des Confluences (Lyon, France) ; the  Agence National de la Recherche ; the  Ministère de la Culture et de la Communication , the  Service des Musees de France  and the  Labex ARCHIMEDE (Montpellier, France ), especially  Dominique Dupuis-Labbe  ´and  Fre  ´deric  Servajean  for their ongoing support. We wish to thank  Dr. Yannick Roussanne  for his help in the interpretation of the osteosarcoma pathology and  Anton Ervynck  for his help with the interpretation of the radiocarbon dates. We also thank  Jean-Philippe Degeai ,  Didier Berthet ,  Francois Vigouroux  and  Roger Lichtenberg  for their contribution to the project. This paper benefited from discussions with colleagues participating in the "2019 Colloque  du Groupe des Paleopathologistes de Langue  Francaise" held at the RBINS, co-organised by the  SocieteRoyale Belge d'Anthropologie  et Prehistoire, and in the 2023 workshop " Animating ancient trade routes through primate lifeways " held at the  Zukunftskolleg, University of Konstanz , co-funded by the  Wenner-Gren Foundation.