dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2012)  to select the best model of nucleotide substitution for each gene under the Bayesian information criterion (BIC) resulting in the GTR + G model for both mitochondrial markers and the HKY + G for the two nuclear markers. We performed phylogenetic analyses of the partitioned concatenated datasets (complete, mitochondrial and nuclear) and of the individual markers under maximum likelihood (ML) and Bayesian inference (BI) frameworks. We conducted ML analyses using RAxML v. 8. 1. 2 (Stamatakis, 2006)  as implemented in rax-mlGUI v. 1. 5 (Silvestro & Michalak, 2012). The ML analyses were performed with the thorough bootstrap analysis setting, GTRGAMMA model of sequence evolution and 100 random addition replicates. Nodal support was assessed with 1000 bootstrap replicates. We conducted BI analyses using MrBayes v.
, 2018). We explored patterns of intraspecific diversity and nuclear allele sharing within the Tropiocolotes nattereri species complex by inferring statistical parsimony networks for the two individual nuclear phase genes with the program TCS v. 1. 21 (Clement et al. , 2000 ; connection limit of 95%), consisting of all sampled specimens for each marker (Table  1 ). We used tcsBU (Múrias dos  Santos et al. , 2016)  for visualization of the nuclear networks. Letters in parentheses at the end of the species' names denote lineages presented in Figure  1. Accession numbers of sequences generated in this study are in bold. The meristic characters are: dorsal scales, counted from the forelimbs to the hindlimb level; ventrals, from the forelimbs to the hindlimb level; scale rows around the midbody; interorbitals, scales across the interorbital region at level of the mid orbits; supralabials; infralabials; gular scales, from the postmentals to the mandibular level; lamellae under the fourth finger; and lamellae under the fourth toe.
We statistically tested whether similarities/differences were supported. Meristic characters and measurements were analyzed separately, but together when using the false discovery rate method to adjust alpha levels. Additionally, we performed two principal component analyses (PCA) with the groups of Tropiocolotes nattereri delimited by molecular analyses and T. steudneri (the species of which T. nattereri was previously considered as senior synonym): one PCA including all examined specimens and all meristic characters; and another including all specimens and all measurements (except tail length). Statistical analyses were implemented in PAST v. 3. 26 software  (Hammer et al. , 2001). Colouration in preservative was described on the basis of the neotype/holotype, and variations thereof on the basis of specimens deposited in the herpetological collections mentioned above.
| Molecular analyses The datasets of the Tropiocolotes nattereri species complex and the remaining species of Tropiocolotes, respectively, included 30 and 40 sequences of 12S, 23 and 36 sequences of ND2, 18 and 35 sequences of c-mos, and 18 and 33 sequences of MC1R (ND2, c-mos and MC1R could not be reliably obtained from specimens from Sinai) (see Figures  S1  and S2  for the individual gene trees). Both the ML and BI phylogenetic trees of the complete concatenated dataset recovered identical topologies with all nodes wellsupported (Figure  1 ). Our phylogenetic analyses recovered F I G U R E 1 Bayesian inference phylogenetic tree of Tropiocolotes based on the complete concatenated dataset (12S, ND2, c-mos, MC1R). Support values are indicated near the nodes (Bayesian posterior probabilities/ML bootstrap).
Sample codes correlate with specimens in Table  1  two major clades, one of T. algericus and T. tripolitanus (with two subclades A and B for the latter species), and another one in which the T. nattereri species complex is monophyletic and sister to the remaining species. In both phylogenetic analyses, T. nattereri samples were divided into two clades with a total of four geographical lineages. The concatenated nuclear phylogenetic tree (Figure  2 ) recovered most species as monophyletic, with low support values for interspecific relationships. The four geographical lineages within the Tropiocolotes nattereri species complex were also recovered as constituting a monophyletic group. The nuclear haplotype networks showed a structure similar to the two major clades recovered from the phylogenetic trees of the concatenated datasets, and a clear segregation of clade A and subclade B within the T.
nattereri sensu lato. Tropiocolotes sp. n. from Israel, Jordan, Sinai and Saudi Arabia is not conspecific with T. nattereri or with any previously recognized congener. Therefore, based on the overall congruence with lineages identified and species delimited in the molecular analyses, here we redefine and redescribe T. nattereri, F I G U R E 2 Phylogenetic relationships of Tropiocolotes based on the nuclear dataset. Colours correspond to those in Figures  1  and 3. Left: Bayesian inference phylogenetic tree of the concatenated nuclear dataset (c-mos and MC1R). Support values are indicated near the nodes (Bayesian posterior probabilities/ML bootstrap). Sample codes correlate with specimens in Table  1. Right: Phylogenetic networks based on nuclear haplotypes for the CMOS (top) and MC1R (bottom) gene fragments.
One clade (clade A) includes specimens occurring in the Sinai Peninsula and southern Israel (from Eilat Mountains north to Yotvata) (n = 6). The second clade (clades B-D) includes: (1) subclade B (Eilat and S. Jordan) occurring in southern Israel within and around the city of Eilat and southern Jordan (n = 5); (2) subclade C (Dead Sea and Arava Valley) ranging along the western shores of the Dead Sea and northern Arava Valley, Israel (n = 6); and (3) subclade D (Negev) distributed in the Negev Desert, Israel (n = 13). According to the topologies of the concatenated datasets (Figures 1-2 and S3), clade A diverged first, followed by subclade B diverging from clades C and D.
ACKNOWLEDGMENTS We are grateful to the following curators and staff from museums who granted access to specimens:  L. Scheinberg  and  E. Ely  ( California Academy of Science, San Francisco ),  J. Streicher  ( Natural History Museum, London ),  A. Resetar  and  J. Mata  ( Field Museum, Chicago ),  L. Vonnahme  ( American Museum of Natural History, New York ) and  J. Moravec  ( Národní Muzeum, Prague ). We thank  Aviad Bar  and  Jonathan Ben-Simon  for sending pictures of specimens in life. This work was supported by the  Gans Collections and Charitable Fund Inc. [M. A. R-J. grant],  SYNTHESYS + , Synthesis of Systematic Resources  funded by the  European Commission  [M. A. R-J. grants:  ES-TAF-1276 ;  GB-TAF-2393 ;  CZ-TAF-1260 ;  DE-TAF-2418 ], the Rector scholarship,  Tel Aviv University  [M.
In particular, they called for clarification of the origin of the water at the TSF outlet and better knowledge of saturation conditions in the TSF, as a first step for geochemical modeling. The purpose of this paper is to answer these hydrological questions in order to clarify the current and future hydrogeological functioning of the site, through data analysis and modeling. This article first presents the analysis of data acquired in the site to better understand the dynamics of the hydrosystem after rainfall events and to clarify the interactions between the waste rocks, the TSF and the water table. Cross-correlations of groundwater level and observed discharges with daily rainfall recorded at the nearby weather station of Rodez were performed. A water balance was calculated using Thornthwaite's approach and based on site observations (rainfall, discharges).
A 3D numerical model of the aquifer system of the Balaures catchment was developed based on the recharge calculated from the water balance and the first conclusions of the data analysis. It runs in steady sate and saturated conditions representing the average state of the hydrogeological system. The popular and common MODFLOW modeling software  (Harbaugh, 2005)  has been used in its basic configuration, coupled with GMS visual interface. MODFLOW appears as an international standard to simulate or manage groundwater flows, validated by the authorities, which justifies the choice of this software for the present study. The model helps identify the sub-catchments and test reclamation scenario with a cover over the TSF. The model also allows using particle tracking to identify the preferential flow paths from the potential contamination sources within the catchment.
Since the AMD should occur at least during 50 years, the site must also be managed with a long-term view. It is located at the limit between the North and the South of France where the climate change predictions are uncertain regarding the rainfall variation and the modification of extreme events. The impact of climate change on the future hydrological functioning of the catchment was then investigated using daily rainfall and temperature data sourced from the Coupled Model Intercomparison Project (CMIP5) for three climatic scenarios (RCP2. 6, RCP4. 5 and RCP8. 5). The evolution of the water balance as well as the frequency and intensity of extreme events over the next 100 years are evaluated with the CMIP5 simulated data. The study of extreme events observed at the study site complete the analysis to understand the site response to rain events.
Instrumentation and field measurements The rainfall data from January 2006 to November 2021 was provided by an in-situ station. These data were originally measured daily and then weekly or monthly since January 2016. To complete the analysis of daily events and catchment reactivity, meteorological data provided by the Météo France station at Rodez have been used to perform daily cross-correlations and extreme-events analysis. It provides daily rainfall and minimum and maximum temperatures for the period 2006-2021. This station is located 25 km away from the Bertholène site at an altitude of 579 m. a. s. l while the mining site is at 700 m. a. s. l. For the period November 2006 to October 2021, the rainfall recorded by Météo France in Rodez (837 mm/year) was 23 % lower than that recorded in Bertholène (1083 mm/year).
Eq. (  6 ) describes the PET formula from  Oudin et al. (2005)  used in this study: if T + 5 > 0 • C → PET = Re γρ × ( T + 5 100 ) if not → PET = 0 (6) where Re is the extraterrestrial radiation (MJ/m 2. d) given by the Julian day and the latitude, γ is the latent heat of water vaporization (kJ/kg), ρ is the density of water (kg/m 3 ) and T is the mean daily temperature ( • C). In the Bertholène case, two different hydrological units were considered: the storage facility sub-catchment upstream of the BC (34 ha) and the sub-catchment with Q Venturi as the outlet (230 ha). The discharges for each sub-catchment were respectively measured at Q BC and Q Venturi. The water balances were estimated from monthly data recorded on-site and cumulated by hydrological year for each sub-catchment (November 2006 to October 2021).
Numerical modeling A three-dimensional (3D) steady-state groundwater flow model of the catchment aquifer system has been developed using the finite difference code MODFLOW-2005 via the GMS software interface (version 10. 4, Aquaveo, 2017). MODFLOW was used with the native packages (recharge (RCH1), well (WEL1)), the solver Preconditioned Conjugate Gradient Solver (PCGS) and the flow package Layer-Property Flow (LPF). Those packages can work with few information about materials properties (horizontal hydraulic conductivity and anisotropy). The saturated flow equation is solved in steady-state conditions with the Preconditioned Conjugate Gradient (PCG) solver with the convergence criteria on head change (HCLOSE) and residual change (RCLOSE) of 0. 0001 m and 0. 0001 m 3 /s. The model is a simplified version of the catchment with only two layers: a 60 m thick unconfined layer corresponding to the weathered bedrock and alluvial deposits, over a 150 m thick confined layer which represents the less permeable deeper bedrock (Fig.
5 (9) where h o is the observed water level, h s is the simulated water level and n is the number of observation piezometers. The estimator values must be as low as possible and close to zero. Once the model had been calibrated, particle tracking (the MODPATH package available for MODFLOW) was used to visualize the pathlines according to different starting zones and to delineate the hydrogeological sub-catchments. Only forward tracking was used in this study. The use of this package allows us to validate groundwater sources and to visualize groundwater flow pathlines in each subcatchment as well as within the alluvial area.
Extreme events and their influence on the observed hydraulic head The impact of extreme events on groundwater level was studied from acquired data on piezometers BE10 and V1 which are the only two piezometers located in the center of the valley. BE10 is located upstream of the storage and V1 is located in the middle of the facility downstream the storage and it is screened at the base of 40 m of precipitates and tailings. The studied events correspond to the maximum water level recorded during the period June 2018 -November 2021. They result from a succession of rainy days between the 19th of January and the 9th of February 2021 for the two piezometers during the wet period. Fig. 13a  shows the water level change in BE10. The peak is reached with a lag of 4 days after 7 rainy days, with a total of 50 mm during the last 3 days.
In any case, however, it facilitates the recovery of any water that has seeped into the TSF and is then stored in the control basin. Finally, we cannot exclude the possibility that the quality of the flow measurement at the control basin is part of the explanation for the water balance discrepancy. In addition, the potential evapotranspiration calculated for the catchment is 662 mm/year, which represents 61 % of the rainfall. The PET/P ratio for the Bertholène site is the same as for other small catchments in the area when using the same Oudin evapotranspiration formula (French Hydro database,  Brigode et al. , 2020). In the equivalent catchments (1. 2-24 km 2 ) located around the Bertholène site (O5010535, O5000510, O5445510 and O5055310), this ratio is less than 65 %. We can therefore assume that the Thornthwaite water balance calculation does work at Q Venturi between November 2006 and October 2021 and can be used to estimate the water balance in the context of climate change, considering all other parameters equal, including vegetation.
Use and limitations of the hydrogeological model In its native version, MODFLOW cannot simulate unsaturated flow. The UZF package has been developed to meet this need but it is mainly designed to compute the evapotranspiration and the recharge in unsaturated areas. Despite that, MODFLOW has been chosen in this study. First, the knowledge of the particle size and the parameters to describe the unsaturated medium within the TSF was very imperfect and not sufficient to run adequately the UZF package. Second, the goal was to simulate the average groundwater flow at the catchment scale. The TSF that overlies gneiss formations over only 3 % of the total model surface, was therefore removed from the aquifer system model domain due its unsaturated functioning inferred from the available data (see Section 4.
To document early-branching crocodylomorph palatal anatomy, we developed an anatomical comparative dataset using computed tomography scan data and literature, comprising 12 early-branching crocodylomorph taxa. To understand discrete phenotypic changes in palatal structure, we compiled a phylogenetically broadly sampled character-taxon matrix from the existing literature, and revised its palatal characters, adding 10 new palatal characters. Our comparative anatomical investigations allow us to propose an adapted hypothesis for the closure of the palate and the posterior migration of the choana. Our phylogenetic findings corroborate previous research showing that non-crocodyliform crocodylomorphs ("sphenosuchians") are paraphyletic, with the exclusion of the clade Hallopodidae. Non-mesoeucrocodylian crocodyliforms ("protosuchians") are paraphyletic, but form three monophyletic clades: Notochampsoidea, Shartegosuchoidea, and Gobiosuchidae.
| Premaxilla The premaxilla of most early-diverging crocodyliforms contributes a smaller portion to the secondary palate than in the later-branching members of Mesoeucrocodylia. The condition is not well known in Nominosuchus, Sichuanosuchus, and Shartegosuchus because the palatal surface of the premaxilla is either not preserved, or is concealed by the dentary symphyseal region (and CT scan data are not available). The palatal surfaces of the premaxillae in Orthosuchus, Protosuchus, Shantungosuchus, and Fruitachampsa are separated along the midline of the palate posterior to the tooth-bearing region. Only the paired premaxillae of UCMP 97638 and Gobiosuchus possess palatal shelves that meet along the midline of the palate and form a portion of a secondary palate. Gobiosuchus is unique among the early branching crocodyliforms in that the premaxilla has two smaller foramina followed by a much larger foramen that receives an enlarged dentary caniniform (Figure  4d ).
| Vomer Only the vomer of Orthosuchus, Shartegosuchus, and Gobiosuchus (Osm olska et al. , 1997) are observable. The vomers of Orthosuchus are paired. They are anteroposteriorly long and mediolaterally narrow and exposed on the palatal surface. The vomer is u-shaped in transverse cross-section, as in "sphenosuchians," forming a hemicylinder that extends between maxilla, palatine, and pterygoid. The CT scan data of Orthosuchus shows that the contact between the vomer, palatine, and pterygoid resembles the "sphenosuchian" condition, with the pterygoid overlapped by the vomer, which is in turn overlapped by the palatine. The vomer of Orthosuchus extends much farther posteriorly along the pterygoid than in other "protosuchians," terminating at a level between the midpoint of the suborbital fenestra.
The presence of a choanal groove is homoplastically distributed throughout the tree. The presence of a choanal groove is traced as originating at the node that includes Junggarsuchus and all later-branching crocodylomorphs, but this optimization is uncertain given the lack of data of the choanal region throughout this part of the tree. Character 505 (new): Choanal groove present and positioned: (0) anterior to the choana; (1) posterior to the choana. This character is developed to test the relationship between the position of the choanal groove and the choana (Figure  4 ). Character 506 (new): choanal septum: (0) present; (1) absent. The choanal septum is a slender sheet of bone that partitions the paired nasal passages as they pass through the nasal cavity into the throat via the choana. The choanal septum is reconstructed as synapomorphic for Crocodylomorpha but is independently lost within UCMP 97638, shartegosuchoids, and Gavialis.
| The implications of a shift to herbivory on secondary palate evolution One of the prevailing hypotheses for the evolution of a secondary palate in mammals is that it is a functional adaptation for increased chewing ability, particularly of tough plant parts  (King, 1996). The palatal data collected here, paired with information from recent research hypothesizing that crocodylomorph teeth repeatedly adapted for herbivory  (Melstrom & Irmis, 2019)  warrants evaluation of herbivory as a causative model for palate ossification in Crocodylomorpha. Within Crocodylomorpha, Melstrom and Irmis (2019) hypothesize that herbivory evolves within notochampsoids, specifically Edentosuchus and UCMP 97638. They propose either a single origin for herbivory as ancestral for Notosuchia, or alternatively at least three independent occurrences of herbivory within that group (Simosuchus, Pakasuchus, and Chimaerasuchus).
ACKNOWLEDGMENTS Kimi Chapelle  and  Serjoscha Evers  are thanked for their discussions on this topic. The  Evolutionary Studies Institute (University of Witwatersrand, South Africa), American Museum of Natural History (New York ), the  Institute of Vertebrate Paleontology and Paleoanthropology (Beijing, China) , and the  Iziko South African Museum (Cape Town, South Africa ) are thanked for allowing access to research specimens. This research was funded by grants from the  NRF African Origins Platform  ( 98800  and  118974  to J. N. C. ) and  Competitive Programme for Rated Researchers  ( 98906  to J. N. C. ), and the  NSF  grant  EAR 1636753. The support of the  DST-NRF Centre of Excellence in Palaeosciences (CoE-Pal) University of the Witwatersrand, Johannesburg  (Grant  86073 ) toward this research is hereby acknowledged.
Acknowledgments C. R. , S. K. , and  M. I. V-R. , acknowledge the  ERC Starting Grant  project  O 2 RIGIN (636808 ) to S. K. for funding this research. M. I. V-R. additionally acknowledges funding from the  DFG  project  VA 1568/1-1. C. R. further acknowledges funding from the  Federal Ministry of Education and Research (BMBF)  and the  Baden-Württemberg Ministry of Science as part of the Excellence Strategy of the German Federal and State Governments , contract:  PRO-ROSCA-2021-11. S. K additionally acknowledges the contracts: Ramon y Cajal  RYC2020-030014-I  and  EMERGIA20_38349. A. Finizola ,  T. Staudacher  and  J-P. Toutain  are thanked for their participation in the fumarole sampling. Eva Stüeken  and one anonymous reviewer are thanked for their constructive comments and suggestions, and  Catherine Chauvel  for the effective editorial handling of the manuscript.
, 2007; Olsson & Folke, 2001). One reason behind the increased reliance on LEK is its complementarity with existing databases and academic knowledge, allowing researchers to screen through large pools of native tree species to identify locally suitable ones  (Smith Dumont et al. , 2019; Uprety et al. , 2012). In addition, the use of participatory methods results in higher levels of engagements from local stakeholders, better fits between agroforestry system designs and farmers' needs, and therefore increased adoption rates  (Smith Dumont et al. , 2019). Therefore, the use of participatory methods and reliance on LEK to develop locally adapted tree species recommendations is gaining popularity in conservation studies  (Charnley et al. , 2007; de Albuquerque et al. , 2009) , forest restoration studies  (Chechina & Hamann, 2015; Fremout et al.
| Linking LEK to socio-economic groups and environmental factors In order to ensure the reliability of LEK and of subsequent recommendations from the online tool, priority should be given to gathering knowledge from local experts rather than from a pool of respondents representative of the study area  (Davis & Wagner, 2003; Ruddle & Davis, 2013). These local experts should be agroforesters with first-hand experience of ES provision by shade trees. The richer the respondents' experience, the more comprehensive the results  (Cerdán et al. , 2012). Most ShadeTreeAdvice studies relied on existing databases of cooperatives, NGO programs, and certification schemes to identify smallholder farmers with agroforestry systems, considered local experts (Table  3 ). Extension workers provided an alternative source of contact information to identify local experts.
One consequence is that interviewed farmers are often better linked to market and international projects than average farmers in the study area. This could have an influence on the LEK as well since these farmers could be influenced by tree species promotion or the knowledge of the extension service. Most studies then used random sampling techniques to extract a sample of farmers from within these databases of local experts, or used semi-random techniques to include representatives of major socio-economic and demographic groups in their sample, often with a specific focus on gender (Table  3 ). Characterizing cultural, socio-economic, and demographic groups is important since LEK is known to be associated with criteria such as gender  (Ayantunde et al. , 2008)  impacts from organic farmers than conventional farmers.