dataesr/scientific-paragraphs-categorization huggingface dataset:
Studies quantifying base cation and other ion exchange with leaf surfaces are also needed. -Fundamental analytical research is needed to provide guidance on the most appropriate soil NH + 4 extraction method for the development of representative soil values. Many studies have demonstrated the variability of extracted/extractable NH + 4 depending on the electrolyte used (eg KCl, CaCl 2 ) and its concentration in the extraction solution (see for example Fig. 1  in the Supplement on http://www. biogeosciences-discuss. net/10/C2954/ 2013/bgd-10-C2954-2013-supplement. pdf). Provided a better understanding of the relationships between extractable NH + 4 and soil , historical soil chemistry datasets from long-term ecological sites, agricultural experiment stations, soil surveys, etc, could be put to use within the context of soil/vegetation/atmosphere NH 3 modelling.
Acknowledgements. We gratefully acknowledge financial support from the project " Effects of Climate Change on Air Pollution Impacts  and  Response Strategies for European Ecosystems" ( ÉCLAIRE) , funded under the  EC 7th Framework Programme  (Grant Agreement No. 282910 ), from the  COST Action ES0804  " Advancing the integrated monitoring of trace gas exchange between biosphere and atmosphere" (ABBA ), and from the project " Pan-European Gas-AeroSOl-climate interaction Study " (PEGASOS) funded under the  EC 7th Framework Programme  ( FP7-ENV-2010-265148 ). We are thankful to the  UK National Environment Research Council and Centre for Ecology and Hydrology  for underpinning input through National Capacity funding and contributing to open access page charges. This review paper was originally written as a background document in preparation for the international workshop "From process scale to global scale: integrating our knowledge on biosphere atmosphere exchange modelling of trace gases and volatile aerosols", co-organised by  INRA ,  AgroParisTech ,  ÉCLAIRE  and  COST  action  ES0804 , and held in Paris, 25-27 September 2012.
Acknowledgements We thank anonymous reviewers for helpful comments. GM was supported by a grant from  Academic Research Cluster 1 of Rhône-Alpes Region. This work was partially funded by the grant  EC2CO   CNRS , and was carried out with the support of  CMIRA Coopéra Rhône-Alpes and within the frameworks of GDRIs "Biodiversité et Développement Durable à Madagascar" and "Biodiversity and Infectious Diseases " as well as  COST action F0701 'Arthropod Symbioses : from fundamental to pest disease management'. Received: 19 March 2013 Accepted: 8 May 2013 Published: 20 May 2013.
Raptor Abundance The breeding bird community at study sites was censused by means of standard point counts with unlimited recording distance  [42]. Censuses were made during the springs 2009-2010 in both urban and rural habitats in all study locations at the same sites where FID information was recorded  [35]. From these data we derived an index of abundance of raptors (mostly hawks Accipiter spp. , kestrels Falco spp. and buzzards Buteo buteo) by summing the numbers of individuals detected at each site divided by the number of sampling points (data in  [35] ). Briefly, we placed 25-50 points in each urban and rural site at distances of at least 100 m between two consecutive points. The exact location of each point was determined with a GPS, allowing us to make the second census in exactly the same sites as the first census.
This phylogeny considers Corvus corone and C. cornix as conspecifics, so that we have also assigned a genetic distance between them of 1?10 210. The R script and the edited phylogeny file are supplied as Files S1 and S2, respectively. Sequential (type I) models were fitted, including first the effect of body size to test for effects of latitude and habitat, and the sequential effects of body size and raptor abundance to ascertain whether latitudinal and habitat effects changed when raptor abundance effects were included first. We evaluated the magnitude of associations between FID and predictor variables based on effect sizes and its 95% CI, as computed from P values of t-tests according to Cohen  [47]. Cohen's criteria were small (Pearson r ,0. 10, explaining ,1% of the variance), intermediate (r = 0.
Acknowledgments  J. J. Cuervo  and  J. J. Soler  helped us with the phylogenetic analyses. Comments by  D. Blumstein  and an anonymous referee were very helpful. This paper is a contribution by  MD  to the project  MONTES  ( CSD2008-00040 ) and RiskDisp ( CGL2009-08430 ) of the  Spanish Ministerio de Ciencia e Innovacion  and to the thematic network GlobiMed (www. globimed. net).
TG was supported by the  Human Frontier Science Program  ( RGY69/07 ) and MSM6198959212. JJ was supported by the  EU Regional Development Foundation  for the project ( A31026 ). MD was funded by the project  RISKDISP  ( CGL2009-08430 ) of the  Spanish Ministerio de Ciencia e Innovacion. GM was supported by  TA   ´MOP-4. 2. 1. /B-09/1-KMR-2010-0005and TA ´MOP-4. 2. 2. /B-10/1-2010-0023  grants. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Background: The detection and exploitation of genetic variation underpins crop improvement. However, the polyploid nature of the genomes of many of our most important crops represents a barrier, particularly for the analysis of variation within genes. To overcome this, we aimed to develop methodologies based on amplicon sequencing that involve the incorporation of barcoded amplification tags (BATs) into PCR products. Results: A protocol was developed to tag PCR products with 5' 6-base oligonucleotide barcode extensions before pooling for sequencing library production using standard Illumina adapters. A computational method was developed for the de-convolution of products and the robust detection and scoring of sequence variants. Using this methodology, amplicons targeted to gene sequences were screened across a B.
napus mapping population and the resulting allele scoring strings for 24 markers linkage mapped to the expected regions of the genome. Furthermore, using one-dimensional 8-fold pooling, 4608 lines of a B. napus mutation population were screened for induced mutations in a locus-specific amplicon (an orthologue of GL2. b) and mixed product of three co-amplified loci (orthologues of FAD2), identifying 10 and 41 mutants respectively. Conclusions: The utilisation of barcode tags to de-convolute pooled PCR products in multiplexed, variation screening via Illumina sequencing provides a cost effective method for SNP genotyping and mutation detection and, potentially, markers for causative changes, even in polyploid species. Combining this approach with existing Illumina multiplexing workflows allows the analysis of thousands of lines cheaply and efficiently in a single sequencing run with minimal library production costs.
Illumina's GoldenGate  [11] , one of the most popular technologies for analysis of SNP markers, is based on BeadArray/Chips and offers genotyping with low costs per data point when large numbers of markers are assayed in parallel, but unlike DArT requires previous sequence knowledge. Genomic DNA is bound to paramagnetic particles and an oligonucleotide pool is added that contains allele-specific primers with universal priming sites and SNP-linked locus-specific primers carrying bead address sequences. Following extension and ligation, an allelespecific fluoro-labelled PCR is performed and the resulting products hybridised against beads carrying locus address sequences arrayed on a glass slide. Genotyping is then performed by reading the fluorescence at each address. Fairly large collection of samples (maximum 384) can be genotyped for a customized pool of markers, up to 1536 SNPs, simultaneously  [9].
PCR amplification of all 35 amplicons was successfully conducted across a subset of 46 lines of the B. napus TNDH mapping population (plus parent cultivars, Tapidor and Ningyou 7) with PCR products amplified in many separate tubes (with different barcodes) and combined for the production of an Illumina sequencing library. The risk of the incorporation of the same base in a large proportion of clusters during one cycle of the Illumina run triggering an error and terminating the run was prevented by the addition of a "spike" sequencing library designed to complement the base composition over the barcode and M13(-21) region of the read. The spike (of ~280 base lengths) was added to the sample libraries at an approximately 1:10 ratio of final library molar concentration prior to cluster generation.
One lane (76 base single-end reads) of Illumina sequencing on a GAII platform produced 8,002,602 single-end reads for genotyping. These were analysed for composition, with the results shown in Table  1. Of the sequence reads, 1. 1% (89,517) corresponded to the 'spike' library and 22%  (1, 725, 988)  included the M13(-21) sequence. Of the latter, only 2. 3% carried an intact 6 base barcode, 18. 4% carried a 5 base barcode, 42. 2% carried a 4 base barcode and 37% had barcodes of less than 4 bases. This truncation of the barcodes is likely to have been due to exonucleases degrading the ends of molecules prior to ligation to Illumina adapters. However, as only the final four bases of the barcode were needed for the address space used in the experiment, 63% of the reads carrying M13(-21) tags were usable for genotyping.
In this way 64. 4% (699,449) of reads processed by Maq were mapped to a reference sequence and associated with individual lines via the munged BAT. A Perl script was used to identify variants in amplified sequences relative to the ancestral reference  sequence and call genotypes based on counts of the bases read at the SNP position (subject to a minimum of 20 reads). Conventional marker scoring strings were produced (based on the convention of A allele for that of the maternal parent of the population, Tapidor, B allele for the paternal parent, Ningyou7, and U where the allele could not be called, for example because of insufficient read depth). The resulting scoring strings for 24 markers (derived from 17 amplicons) were successfully linkage mapped, as shown in Figure  3  and listed in Additional file 3, to the expected regions of the genome, i.
Conclusion We describe a robust and cost-effective methodology for oligonucleotide barcoding via one-step incorporation into PCR products suitable for Illumina sequencing by standard workflows. Computational methods then allow the deconvolution of the sequences and both the scoring of known polymorphisms and the detection of mutations. We have demonstrated the use of 4 base oligonucleotide barcode address space, but using this methodology much larger numbers of PCR products could be pooled and analysed if more of the address space of the tails (which could be longer than 6 bases) were used, although the inclusion of some unused bases helps mitigate the effects of any exonuclease contamination. The panel of 192 BAT oligonucleotides synthesised and validated can be re-used with many different M13tailed specific primers, making the approach much more cost effective than synthesising locus-specific PCR primers or locus-specific library adapters incorporating barcodes.
Reference sequences for the mapping of Illumina sequence reads were designed to represent the amplified sequences with the ancestral base at the hemi-SNP position (i. e. the resolved base allele) (see Additional file 2, for reference sequences). Each of the 46 TNDH lines to be genotyped (plus Tapidor and Ningyou7) was assigned a specific barcode (see Additional file 5 for barcode allocations). PCR products were pooled for each of the 35 assays, PAGE was used to clean and concentrate the sample prior to Illumina mRNA-seq single-end library production from the adapter ligation reaction stage of the protocol following the manufacturer's instructions. Library preparation methods were as described in  Bancroft et al. 2011 [17].
Spike sample preparation Ordinarily the Illumina real time analysis software would fault a situation in which all clusters report incorporation of the same nucleotide on a given cycle, yet this would occur for the universal primer portion of reads derived from the PCR amplicons. To overcome this, experimental samples were spiked with a 1:10 ratio, based on library molar concentration (libraries being nomalised to approximately 10 nM), with DNA comprising sequences that should complement those of the M13 and barcode regions. Two sets of spike samples were prepared, one of ~130 bases in length, the other of ~280 bases on length, each comprising two different amplicons. For the ~130 base spike, PCR was conducted using DNA from B. napus cultivar Tapidor and primer pairs R00005 and D00002 (BBNNNNVHVBBBBDHBDHHDDBHVCA GAGCACGTGGAGCAG and TGCATTTTTCTGTTGG Libraries for these spikes were produced following the same protocol as for the pooled barcoded experimental samples, resulting in one library for spiking the sequencing of smaller size range amplicons (~130 base spike) and one library for spiking the sequencing of larger size range amplicons (~280 base spike).
Data processing To address reads back to barcodes, and hence individual PCR wells or pools, we developed a novel method based on techniques reported previously  [16, 17]. We used Maq v0. 7. 1  [27]  to align reads against reference sequences comprising the target amplicons and to identify mismatches (SNPs or mutations). However, mismatches between read and reference sequence within the barcode region (that encodes sample origin) must be partitioned from those in the target region (that would signal SNPs or mutations). With very high levels of multiplexing (as in this experiment), in which a large part of the 4 K address space offered by 6 base barcodes is occupied, individual barcodes may differ by only one base. Ordinarily this could result in cross-alignment, i. e. wild type reads derived from a given barcode could potentially be mapped to an incorrect barcode closely neighbouring in address space.
We countered this problem by replacing one-to-one, in silico, the real six base barcodes with an artificial construct derived from a bigger address space and thus able to carry more discriminating information. Our simple implementation was to replicate the barcode four-fold ("munging") such that a one base difference became amplified to four, thus defeating cross-alignment by Maq with default parameters. This was done with simple Perl scripts mung_barcoded_reads. pl (Additional file 6) and mung_refseqs. pl (Additional file 7) operating on the reads and the references respectively. During our analysis it was found that a proportion of reads had incomplete barcodes which could nevertheless be rescued and so only those with a perfect match to the M13 primer and at least four bases of the barcode (and which could be reconstructed back to a unique, full barcode) were used.
Reads corresponding to the PCR spike amplicons were identified and removed and individual lines were associated with their sequence from the BAT. The munged reads were aligned by Maq, with default parameters, to the reference sequence for each marker and the genotype called, based on counts of the bases read at the SNP position, but only if the SNP position was covered by at least 20 high quality reads (otherwise the allele is defined as unclassified, U) using Perl script BAT_SNPs. pl (Additional file 8).
Mutation data processing Mutations were detected using an adaption of the program used for SNP assay. The munged reads were competitively aligned by Maq, with default parameters, to the munged references. The maq pileup -v command was then used to generate text files encapsulating these alignments and associated base quality information. A Perl script TILLING_parse. pl (Additional file 10) was developed to extract the called base frequency compositions at each EMS-mutable base within the target amplicon, using base qualities, by accessing pre-indexed versions of the pileup files. Pools were identified as potentially containing mutant line(s) based on a number of heuristics. First, the absolute number of reads carrying an EMS mutation candidate was required to exceed 10, then the signal, the ratio of calls of this candidate to the reference (wild-type) base, was required to be greater than 0.
Four close species were also sampled for use as outgroups in data analysis: L. aschenbornii S. Schauer, L. hintonii C. P. Sm. , L. splendens Rose and L. campestris Schltdl. & Cham, all collected in the TMVB  (MEXU voucher numbers 1297311, 1344434, 1344438, 1297272 , respectively) (Table  1 ). Dried plant material was ground using a Tissue Lyser QIAGEN® at 1800 rpm. DNA isolation was performed with DNeasy Plant Minikits (Qiagen, Paris, France) according to the manufacturer's instructions. DNA concentration was determined with a spectrophotometer at 260 nm.
Data analysis ISSR: Only clear, unambiguous, reproducible and strongly stained ISSR loci were taken into account in data analysis. Amplified fragments were scored as 1 (presence) or 0 (absence) for individuals, and matrices generated by each primer were assembled. A heuristic search for a dendrogram was done by tree-bisection-reconnection. The distance method is based on the mean character difference; shared bands are not informative in this technique. Distance analysis was performed using PAUP software version 4. 0b10  (Swofford, 2001). Dendrograms were visualised with TreeView version 1. 5  (Page, 1996). The binary data from ISSR fingerprinting was also subjected to principal coordinates analysis implemented in Genalex version 6  (Peakall and Smouse, 2006). ETS and COS: The two complementary strands were corrected and assembled with Sequencher version 4.
6 (Gene Codes Corporation, Ann Arbor, MI, USA). The total DNA matrix was aligned for each marker with the ClustalW algorithm in MEGA 5  (Tamura et al. , 2007). The sequences generated were deposited in GenBank (accession numbers KC914401-KC914424). Both maximum likelihood (ML) and partition-homogeneity testing of the molecular data were performed with PAUP. The congruence of the ETS and COS gene datasets was evaluated with the partitionhomogeneity test implemented using 1000 random distributions, with MAXTREES set to 5000  (Farris et al. , 1994). No starting trees were used, as it was possible to make taxon addition without them. ModelTest was used to determine the most reliable substitution model  (Felsenstein, 1985) ; the TVM + I + G model was chosen. For the final combined tree (ETS + COS genes), the following parameters were used in the ML analyses: unequal base frequencies (A: 0.
Results The four selected ISSR primers gave a total of 103 loci for the 129 individuals sampled of which 100 (97. 1%) are polymorphic. The results of the partition-homogeneity test (P = 0. 39) indicated that the three sequences ETS, AroB and Eif3E (Partial: first 571 nucleotides) represent the same phylogeny, allowing the three gene datasets to be combined. The total length of the aligned combined nuclear DNA matrix was 1456 bp with 1400 (96. 2%) constant characters, 34 (2. 3%) parsimony uninformative characters and 22 (1. 5%) parsimony informative characters. Within L. montanus, 1433 (98. 4%) constant characters, 18 (1. 2%) parsimony uninformative characters and 5 (0. 4%) parsimony informative characters were determined. Whatever the technique considered, the topology obtained was very similar (Fig.
They establish a list of 48 different plesiobiotic species pairs that have been recorded from various habitat types of the Holarctic region and provide a good discussion of the possible reasons for the associations that have been recorded and of their possible role in the formation of other types of interspecific associations like cleptobiosis or lestobiosis. Pointing out the lack of reliable data, this review raises numerous questions that, hopefully, will promote collecting more and better defined data and extend our knowledge to arboreal species and to Tropical and Neotropical regions. More intricately specialized ant-ant relationships, involving permanently parasitizing species depending upon their hosts throughout their lives, have attracted more attention from numerous scientists. For slave-making ants and their hosts, most of the work has been made on Harpagoxenus and Polyergus  [21] [22] [23] , but some groups of species are less well known.
The home range of the community has been estimated to be 6. 78 km 2  [24]. Data were collected during two field seasons (January 17 th to March 25 th , 2009; September 3 rd , 2009 to September 3 rd , 2010) from 33 individuals (N=15 males, aged 8 to 49; N=18 females, aged 12 to 47). Data collection was based on focal animal sampling  [25]  by following subjects on their daily travels from 07:00 to 16: 00.
In particular, we were interested in behaviours that suggested that the focal animal was monitoring its audience and/or waiting for specific responses. Three behaviours appeared to fulfil these criteria: 'hooing', 'waiting' and 'checking' (table  2 ). Social factors. To investigate the impact of social factors on behavioural decisions during a travel event, we determined the social bonds and relative ranks of the focal animals and, for adult females, their relative stage of fertility. We used social bond data determined by another study conducted during the same time period  [8]  (see Data S1). We calculated dominance ranks from pant-grunting behaviour, a reliable indicator of rank relations in chimpanzees  [7]. For the females, pant-grunting between individuals was not so common, but it was still possible to group individuals into three rank classes: 'high', 'middle' and 'low'.
Statistical methods To analyse the sequential organisation of behaviours seen during the 'initiation phase', we used a Friedman test with the order of appearance of each of the five behaviours, the behaviour type, and the identity of the individuals as variables. To control for the identity of the focal animals and their different contributions to the dataset (individuals contributed 1 to 11 initiation phases with an average of 3. 54 sequences), we entered the average order of appearance of each behaviour per individual. We used post hoc Tukey-tests for pairwise comparisons. To analyse the effect of the presence of other group members on vocal production, we ran a Generalized Linear Mixed Model (GLMM) comparing vocal and non-vocal travel events during solitary and social travel. Call production was entered as the dependent variable coded as a binomial response, the presence of an audience as a fixed factor and the identity of the focal animals as a random covariate (as individuals contributed several data points).
1% of N=393 total). We found a significant difference between the number of cases excluded in non-vocal Table  3. Average order of appearance of the five key behaviours during the initiation phase. and vocal travel events (GLMM, Estimate=2. 092, Standard Error (S. E. )=0. 344, t=6. 086, p<0. 001), showing that travel events included a 'travel hoo' most often in the presence of an audience. 171 of the 263 vocal events (65. 2%) were single entries to the dataset (i. e. no more than one event per day per individual). 92 of 263 (34. 8%) vocal travel events were multiple entries from individuals that had been recorded more than once on the same day. 60 of these 92 vocal events were given during different travel events with different audiences. The average interval between two recorded travel events was 84.