dataesr/scientific-paragraphs-categorization huggingface dataset:
For detection of population structure without prior geographic assumptions, the Bayesian clustering software STRUCTURE  (Pritchard et al. 2000)   we used the genetic admixture model and correlated allele frequencies between populations, 10 000 reiterations for the burn-in and 100 000 Markov chain Monte Carlo (MCMC) repetitions. For the population genetic overview containing 17 sampling sites (Dataset B), 6 replicates were run for each value of K (number of clusters) from 1 to 10. According to the method proposed by Evanno et al. (  2005 ), the uppermost level of population structure can be detected as an increase in log likelihood as K is increased. For this data set, the strongest increase in log likelihood was observed for 2 clusters (data not shown) as K increased, additional sublevels of structuring were observed both within the southern clade (K = 3) and in the northern clade (K = 4).
For the northern time series (Dataset A), containing samples from 3 sampling sites, 6 replicate runs were made for clusters from 1 to 5. To investigate relatedness within the southern invasion event and to specifically identify the source of the Mediterranean populations, an allele frequency data set containing all southern sites was ge nerated in Genetix  (Belkhir et al. 1996 ) and exported into the PHYLIP package  (Felsenstein 1993). A neighbour-joining (NJ) tree based on Cavalli-Sforza's and Edward's chord distance was generated (Cavalli-Sforza & Edwards 1967) with 1000 boot strap replicates using the PHYLIP subprograms SEQBOOT, GENDIST, NEIGHBOUR; CONSENSE and DRAW TREE. The resulting NJ tree was visualized with TreeView (Page 1996). To evaluate the different invasion/expansion scenarios within the framework of coalescence theory, we ran several models implemented in MIGRATE-N v.
RESULTS Given that Mnemiopsis leidyi is a holoplanktonic species, we observed high levels of genetic structuring between regions as well as substructuring within regions, demonstrated by significant F ST values (after correction) even over short geographic distances (Table  2 , Table  S1  in the Supplement). For the 136 pairwise comparisons of the population genetic over view, 120 were significant (Dataset A, Table  S1 ). In the northern time series from the North and Baltic Seas, 19 out of 36 comparisons were significant (Dataset B, Table  2 ). The strong genetic structuring allows identification of different clusters within the native and invaded ranges, through Bayesian clustering without prior definition of populations (Fig. 1 ). A very clear separation between both invasion waves was observed (Fig.
Time series northern invasion During the period from 2008 to 2010, the difference in genetic diversity (Fig. 2b ) among the North Sea and Baltic Sea sites showed only small and nonsignificant changes (Dataset A). Divergence between the regions was reflected in significant (p < 0. 05) pairwise F ST values (0. 018 to 0. 056, Table  2 ). Genetic diversity was significantly different between the North and Baltic Seas in all years, with comparisons among Central/Western Baltic and the North Sea always highly significant (p < 0. 001). In contrast, within the Baltic there was no significant difference (p = 0. 084, Table  S2  in the Supplement). The mean number of alleles was consistently higher in the Western Baltic than in the North Sea (Fig. 2b ). The levels of allelic richness stayed virtually constant for Helgoland and Western Baltic Sea, whereas in the.
Southern invasion and spread into the Mediterranean Sea When applying Bayesian clustering to Dataset B, all Mediterranean Mnemiopsis leidyi were firmly placed into the previously identified southern cluster that originates from the Gulf of Mexico (Fig. 1a ). The Mediterranean samples do not form a new separate cluster (Fig. 1a-c ), suggesting that no novel genotypes from yet another source were present. If the number of clusters was increased to K = 3 (Fig. 1b ) additional genetic subdivision became visible: Caspian Sea (CAS) and Mediterranean Sea (MS) samples were grouped into different clusters while the Black Sea (BS) samples have some probability for both clusters. M. leidyi from Barcelona had the smallest pairwise divergence compared to Black Sea Turkey (MS-BS × BS-T, F ST = 0. 051, p < 0.
DISCUSSION Mnemiopsis leidyi is a prime example of a globally successful gelatinous plankton species with a wide native distribution and the ability to quickly invade new habitats. Here we provide novel data on introduction pathways and processes that take place after successful introduction into a given region. To this end, we monitored the temporal stability of genetic diversity and divergence. In the recently invaded North and Baltic Seas, we found no signs of immigration of new genotypes from known or unknown source regions. Instead, a distinct genetic composition was maintained in both seas (Fig. 3 ). Our microsatellite data revealed both significant and almost constant genetic divergence between Mnemiopsis leidyi populations in North and Western Baltic Sea, combined with little variability across years at the same sampling location (Fig.
Reusch et al. (2010) Datasets A and B. For both analyses Mnemiopsis leidyi. Samples analysed in this study, sampling locations, coordinates, collectors and number of samples included in the final analysis. Dataset A: Samples from the time series of the northern invasion wave. Dataset B: Population genetic overview including samples from the native range (Gulf of Mexico, NW Atlantic), from the invaded seas in Northern Europe (North Sea, Kattegat, Baltic Sea) and from the southern invasion wave (Black Sea, Caspian Sea and Mediterranean Sea). Samples marked with an asterisk* are taken fromReusch et al. (2010).
Acknowledgements. For collection of specimen we thank the crews of the  RV 'Alkor' and RV 'Dana'  and the following colleagues:  P. Schubert ,  H. Hammer ,  L. Friis Möller ,  M. Acevedo ,  D. Edelist ,  N. Nakar ,  K. Stefanova ,  A. Gubanova  and  L. Bat. K. Beining  assisted with the laboratory analysis. We also thank  P. Beerli  for his patient comments on the MIGRATE-N analysis. The study was funded by the  DFG (Deutsche Forschungsgemeinschaft)  to T. B. H. R. and  EU   FP 7 project VECTORS  (Grant no. 266445 ). Jaspers C,  Haraldsson M, Lombard F, Bolte S, Kiorboe T (2013) Seasonal dynamics of early life stages of invasive and native ctenophores give clues to invasion and bloom potential in the Baltic Sea. J Plankton Res Javidpour J, Sommer U, Shiganova T (2006) First record of Mnemiopsis leidyi A.
The phylogenetic relationships between the different groups of Paleozoic gnathostomes are still debated, mainly because of incomplete datasets on Paleozoic jawed vertebrate fossils and ontogeny of some modern taxa. This issue is illustrated by the condition of the glossopharyngeal nerve relative to the parachordal plate, the otic capsules and the metotic fissure in gnathostomes. Two main conditions are observed in elasmobranchs (shark and rays) and osteichthyans (bony fishes and tetrapods). The condition in the other chondrichthyan taxon, the holocephalans, is still poorly known, and without any information on this taxon, it remains difficult to polarize the condition in gnathostomes. Based on the anatomical study of an embryo of the holocephalan Callorhinchus milii by means of propagation X-Ray Synchrotron phase contrast microtomography using both holotomography and single distance phase retrieval process, we show that, contrary to what was previously inferred for holocephalans (i.
Introduction Chondrichthyans are a clade of cartilaginous fishes comprising two, morphologically distinct modern sister groups: the elasmobranchs (sharks, skates, and rays) and the holocephalans (ratfishes). The relationships between these two monophyletic groups and the other gnathostomes (jawed vertebrates) are easy to establish when only extant forms are considered: both morphological and molecular data support the monophyly of osteichthyans and chondrichthyans, together forming the modern gnathostomes, sister group of the cyclostomes (hagfishes and lampreys)  [1] [2] [3]. The phylogenetic relationships between the different groups of gnathostomes are much more debated when Paleozoic forms are considered. Debate about the phylogenetic position of particular gnathostome taxa is a result of incomplete datasets on Paleozoic fossils and ontogeny of some modern gnathostomes.
The results are very close to what can be reached using the much more complex holotomographic approach, for a scanning time typically 10 times shorter, and a straightforward and rapid processing. The full sample was scanned in 6 sub-scans of 4 minutes each, using 2499 projections of 0. 1 s each over 360 degrees. The detector was based on a 750 mm thick LuAG scintillator, coupled to a FReLoN (Fast Readout Low Noise) CCD camera through a lens based optic system. Volumes were reconstructed using ESRF software PyHST, that includes the single distance phase retrieval algorithm  [15]. Sub-volumes were corrected for ring artefacts, and then concatenated to generate a single stack of 16bits tif slices. Segmentation and 3D rendering were performed with MI-MICSH 15. 01 64 bit software (Materialise Inc.
This work has been supported by the Ministerio de Economía y Competividad of Spain, through Grant Nos. AYA2008-00446 (Plan Nacional I + D + I (2004-2007)) and FIS2011-28738-C02-02, and computing resources of CESGA. Also this work is partly supported by a joint project within the framework of a CNRS (France) and CSIC (Spain) agreement (Code No. : 2011 FR0018). I. K. acknowledge the financial support provided by ANR-08-BLAN-0054 and the support provided by the French PCMI (Programme National de Physique Chimie du Milieu Interstellaire).
-Collection of critical ancillary data wherever NH 3 flux are measured in the field. In addition to classical (micro-) meteorological data, measured ancillary data must include variables that are likely to be useful later for model parameterization or validation. Efforts should be made to measure the following according to the issues being addressed: LAI and leaf density profile; leaf wetness profile; soil texture, porosity, wilting point, organic matter content, pH, [NH + 4 ] and [NO - 3 ]; slurry pH, TAN, dry matter content and application rate; bulk leaf N and NH + 4 content; leaf litter pH and [NH + 4 ]; leaf surface water (dew, rain) pH and [NH +  4 ]. More difficult to measure, but equally important, would be apoplastic pH and [NH + 4 ], such as by the vaccuum infiltration technique  (Husted and Schjoerring, 1995) ; in-canopy vertical NH 3 profiles; ambient concentrations of SO 2 , HNO 3 , HNO 2 and HCl, and particulate NH + 4 and NO - 3.
Overall 3D-recording of the cave's structural elements The overall recording of the cave by terrestrial laser scanning was our first goal since it ensures the georeferencing of any type of object, image or measurement and an accurate indexing compatibility of the data between the researchers involved in the project. The study began with the consolidation of the topography network and the creation of polygonal traverses inside the cave thanks to a total station. This network is connected outside by several points measured by differential GPS. All the data was recorded in the French Geodetic Reference System (Lambert 2). First campaigns of recording were done with the scanner Photon 120 FARO, which well adapted in the middle underground passage. Since 2012, data acquisition has been performed using a FARO Focus 3D.
Acknowledgements: The study of Les Fraux takes place in a planned multi-year archaeological excavation funded by the regional office of Aquitaine of the French Ministry of Culture and Communication. The French National Research Council is also supporting this project labeled as a research site in Global Ecology (called SEEG). We would like to thank the FARO Company for its scientific partnership in this project. Thanks also to E. Moisan, V. Léglise and B. Cazalet for their contribution as a part of their training at INSA. With our warmest thanks to Edmond ( †) and Marcelle Goineaud, owners of the cave « Les Fraux » who allowed us to publish the images produced in the cave.
Contribution of remote sensing To complete glaciological data time series in terms of changes in surface area and volume before the beginning of field measurements, and to calculate these changes at a regional scale, remote-sensing techniques have proved to be very efficient. Brecher and Thompson (1993)  used terrestrial photogrammetry to quantify the retreat of Qori Kalis Glacier (Quelccaya ice cap, Peru). Aerial photographs (available since the 1950s) and satellite images (available since the late 1970s) have been widely used for glacier inventories  (Jordan, 1991; Georges, 2004; Silverio and Jaquet, 2005; Jordan et al. , 2005; Morris et al. , 2006; Raup et al. , 2007; Racoviteanu et al. , 2007; Poveda and Pineda, 2009; UGRH, 2010)  and to quantify variations in glacier surface area at a decadal to interannual timescale since the mid-20th century   (  Rabatel et al.
Direct annual measurements began between 1968 and 1980, but additional information for 1949 was added based on aerial photographs. For glaciers for which data are available for the late 1970s, a change in the trend appeared in 1976-1977. Before this date, changes in glacier length were limited (between 100 and 300 m in about 30 yr); Broggi Glacier even advanced in the 1970s. Since the end of the 1970s, glacial withdrawal has increased and the glaciers have retreated between 500 and 700 m in length (i. e. more than twice the rate of the former period). El Niño years  (e. g. 1982-1983, 1997-1998, 2004-2005)  resulted in a more pronounced retreat, whereas persistent La Niña conditions at the turn of the 21st century resulted in a slight slowdown in the retreating trend.
Acknowledgements. This study was conducted within the framework of the  International Joint Laboratory GREAT-ICE , an initiative of the  French Institute of Research for Development (IRD)  and universities and institutions in Bolivia, Peru, Ecuador and Colombia. IRD researchers:  B. Pouyaud ,  R. Gallaire ,  E. Cadier ,  P. Garreta  and  A. Coudrain  are acknowledged for their participation in the development of the glacier monitoring program in the tropical Andes. We are grateful to all those who took part in field campaigns for mass balance measurements. We also appreciate collaboration with  Nadine Salzmann ,  Mario Rohrer ,  Walter Silverio ,  Cesar Portocarrero  and  Bryan Mark. This study was funded by the  French IRD (Institut de Recherche pour le Développement)  through the Andean part of the French glaciers observatory service: GLACIOCLIM (http: //www-lgge.
Digital land-cover information was extracted from the CORINE land-cover database for Martinique (French Ministry of Ecology, http://www. statistiques. developpement-durable. gouv. fr/donnees-ligne/t/telechargement-donnees-sig-corine-land-cover-dom. html; see also  Cruiskshank and Tomlison (1996) ). This database was generated from orthorectified satellites images and provides thematic GIS map layers including up to 24 land-cover classes with a mapping scale of 1:100 000.
We estimated the pure effects of geomorphology and anthropogenic disturbance as the sum of eigenvalues of canonical axes in analyses (1) and (2), respectively. The effect shared by both groups of variables (shared variance fraction) was obtained by subtracting the sum of variability of (1) and (  2 ) from the amount of variability explained by (3)  (Lepš and Šmilauer, 2003). Variation partitioning was first applied to the entire dataset (51 sampling stations), and then to each cluster individually. Finally, in order to provide further indication of invertebrate community responses, the distributions of species richness, community evenness (Simpson index) and entropy (Shannon index) were compared among Ward clusters using Kruskall-Wallis tests. These statistical tests were performed using the Past software (version 2.
, 1995; Céréghino and Park, 2009). Overall, our results highlight the importance of geomorphology (particle size, river competence and erosive forces in relation to elevation, conductivity from headwaters to seashore) and land cover (e. g. , agricultural lands and related alterations of water chemistry) in delineating ecological sub-regions for the freshwater biota. It should be noted however that the unexplained variation for the entire dataset (all stations) was quite important (39. 7%); therefore, important variables that were not included in our analysis would deserve further investigation. Most stations that formed clusters were geographically adjacent and there was no major spatial discontinuity in invertebrate distribution. Sampling stations were included in our multivariate analysis regardless of a priori consideration of disturbance.
The caddisfly Smicridea sp. (Trichoptera Hydropsychidae), a common taxa in our dataset, showed high to moderate densities in clusters 1 and 2, but was absent in plain rivers from cluster 3. Although some taxa were specific of a given cluster, such invertebrates usually occurred in very low densities (<1 individual per m 2 ). In fact, most taxa were common; 24 and 42 taxa out of 84 occurred in two and three clusters, respectively. Despite this general trend for ubiquity, individual stations only contained 9 to 38 taxa. This situation raise concerns as to how to define water quality classes in the later phase of applied research, and how to identify sensitive indicator species when (i) local communities are rather poor (insular context,  Smith et al. , 2003 ; Hughes, 2005 ; Gonçalves et al. , 2008) , (ii) mean or median values for structural indices (e.
ACKNOWLEDGEMENTS This study was funded by the  French Direction de l'Environnement, de l'Aménagement et du Logement de Martinique (Ministère de l'Ecologie, du Développement Durable, des Transports et du Logement/ DEAL Martinique) , the  Office de l'Eau Martinique  and the  Office National de l'Eau et des Milieux Aquatiques (ONEMA). CB is supported by an  ANRT-CIFRE  grant No. 460/2010 ; HTP is supported by an  ANRT-CIFRE  grant No. 912/2010. Two anonymous reviewers provided helpful comments on an earlier version of this paper.
We use IASI measurements over boreal Eurasia (see Fig. 1 ) that have been processed with the Fast Optimal Retrievals on Layers for IASI (FORLI) algorithm  (Hurtmans et al. , 2012). FORLI-CO data v20100815 were downloaded from the Ether database (http://ether. ipsl. jussieu. fr) and only the measurements with "super quality flag = 0" have been selected with a solar zenith angle smaller than 90 AK. The AK is stored in the FORLI product, and is needed for a proper comparison of TIR satellite measurements and models  (George et al. , 2009). Apart from the IASI observations, measurements from the NOAA network are also assimilated. These more sparse measurements are used to anchor CO surface mixing ratios outside our study area. Very few NOAA observations are present in boreal Eurasia (16 of the 246 assimilated NOAA measurements in July and August 2010), and emission changes here will therefore be almost entirely driven by IASI observations.
This is in sharp contrast with  Konovalov et al. (2011) , who report a large impact of the diurnal emission cycle. However, we use large-scale satellite data to constrain our emissions. These measurements have only a small sensitivity to surface CO. Redistribution of the emissions in the PBL apparently lowers the sensitivity to the emission diurnal cycle. As noted before, convective mixing during daytime appears an efficient mechanism to loft the emitted CO to altitudes at which the IASI instrument can detect it. We also argued that the vertical mixing in the model may have been systematically overestimated, since the radiative effects of smoke are not considered in the driving ECMWF model. Since the IASI instrument lacks sensitivity to the surface CO, a too strong vertical mixing would imply an underestimate in the emissions.
This leads to improved performance in the presence of discontinuities, i. e. changes of disparity, where traditional window based matchers tend to perform poorly. This is particularly important in the determination of SPIH; as traditional window based matchers tend to smooth over disparities leading to the loss of smaller disparity features such as smoke plumes. M6s modification involves using a subset of the pixels from the local neighbourhood determined by similarity to the pixel of interest, in both the normalisation and the matching stages. A processing chain for the generation of the AATSR SPIH dataset has been developed using the Java based BEAM visualisation toolkit (http://www. brockmann-consult. de/cms/web/beam/). The processing chain outputs pixel level accuracy SPIHs using the algorithm described above and from this product, Smoke Plume Masks (SPMs).
The idea behind the MERGED scenario is therefore to give the system freedom to place emissions in grid cells where some kind of fire activity has been detected by either MERIS or MODIS. The Global Fire Assimilation System (GFAS) system has been described in  Kaiser et al. (2012)  and is applied in  Huijnen et al. (2012). These daily emission maps account for the assumed heavy peat burning east of Moscow by including a peat map for Russia in combination with observations of fire radiative power (FRP). The Global Fire Emission Database (GFED3) emissions used in this study are monthly averages that have been obtained as described in van der  Werf et al. (2010).
Acknowledgements. This study has been supported by  NSFC (National Natural Science Foundation of China)  under grant agreement no. 41204057  and 12th  Five-Year Plan of National Science and Technology Support  ( 2012BAK19B02-03 ). This work was also supported by  China Earthquake Administration. Edited by: M. E. Contadakis Reviewed by:  T. Chelidze  and two anonymous referees The publication of this article is financed by  CNRS-INSU.
2012 ) and corresponding to two distinct morphospecies were added to the data set. These two specimens were collected off the Sepik River in Broken Bay together with many empty shells attributed to the two same morphospecies but also with other organisms typically found at cold seep sites (e. g. , tubes of Lamelibrachia sp. and Escarpia sp. , vesycomyid clams, and thyasirids). Both these two morphospecies were attributed to the genus Gigantidas (R. von Cosel, pers. comm. ) and here referred to as G. sp. 1 Broken Bay and G. sp. 2 Broken Bay. We also have obtained four specimens assigned to the species Idas simpsoni from the collection of the Museum of London. These were trawled at 162 m in the northern Atlantic Ocean off Rockall between Iceland and Ireland, associated with whale bones. Last, an additional unstudied morphospecies was found within the collection of the MNHN.
These mussels were registered in the MNHN database as collected on vertebrate bones in South Atlantic at 3900 m depth. The shells are similar to those of Benthomodiolus mussels (R. von Cosel, pers. comm. ). Following  Samadi et al. (2007) , Modiolus modiolus was used as an outgroup. All specimens corresponding to the 51 terminal taxa used in this study are listed in the Table  1.
Phylogenetic analyses Chromatograms were edited with Sequencher 4. 1. 4, DNA sequences were aligned with the Clustal W module in Mega 4. 0  (Tamura et al. 2007) , and ambiguous sites were excluded. For each of the seven genes, one specimen of each species or ESUs  (Samadi et al. 2007; Lorion et al. 2009 Lorion et al. , 2010) )  was used to evaluate the phylogenetic relationships among them. Best-fitting substitution models were estimated for each gene separately and for a data set that combined the seven single-gene data sets using MrModel-Test 3. 7 with the Akaike information criterion (AIC)  (Posada and Crandall 1998). Each of the seven single-gene data sets and the combined data set were fitted to a general time-reversible model with a proportion of invariant sites and gamma-distributed rates (GTR+I+Γ).