dataesr/scientific-paragraphs-categorization huggingface dataset:
melanogaster: w[1118]; P{y[+t7. 7] Bloomington RRID:BDSC_39171 w[+mC]=GMR57C10-GAL4}attP2 Drosophila Stock Center D. melanogaster: pJFRC29-10XUAS-IVS-myr::GFP-p10 Jack Etheredge; N/A in attP40; pJFRC105-10XUAS-IVS-nlstdTomato in Etheredge, 2017 VK00040 D. melanogaster: w[1118]; P{y[+t7. 7] Bloomington RRID:BDSC_39786 w[+mC]=GMR72F11-GAL4}attP2 Drosophila Stock Center D. melanogaster: P{GawB}Tab2[201Y] Bloomington RRID:BDSC_4440 Drosophila Stock Center D. melanogaster: w[1118] P{y[+t7. 7] w[+mC]=20XUAS- Bloomington RRID: BDSC_55134 IVS-CsChrimson. mVenus}attP18 Drosophila Stock Center Software and Algorithms polyseq This paper https://github. com/j wittenbach/polyseq bcl2fastq Ilumina https://support. illumi na. com/sequencing/ sequencing_softwar e/bcl2fastq- conversion- software. html; RRID: SCR_015058 development.
The 5 unsampled genera are either monotypic  (Arlequinus, Callixalus, Chrysobatrachus, Kassinula)  or species poor (Alexteroon, 3 spp. ). Our sampling of the remaining genera is proportional to their recognized diversity and includes several known species complexes with lineages not reflected in the current taxonomy. We also sampled outgroup species from the following families: Arthroleptidae (7 spp), Brevicipitidae (1 sp), Hemisotidae (1 sp), and Microhylidae (1 sp). Museum and locality information for all specimens is provided in Supplementary Table  S1  available on Dryad at http://dx. doi. org/10. 5061/dryad. 1740n0h. Sequence capture data and alignments. -The full details of transcriptome sequencing, probe design, library preparation, sequence captures, and bioinformatics pipelines are described in  Portik et al.
Transcriptomes, target sequences, and probe designs are available on Dryad  (Portik et al. 2016c). Genomic DNA was extracted using a high-salt extraction method  (Aljanabi and Martinez 1997)  and individual genomic libraries were prepared following  Meyer and Kircher (2010)  with modifications described in  Portik et al. (2016b). Samples were pooled for capture reactions based on phylogenetic relatedness, and the combined postcapture libraries were sequenced on 3 lanes of an Illumina HiSeq2500 with 100 bp paired-end reads. Raw sequence data were cleaned following  Singhal (2013)  and  Bi et al. (2012) , and the cleaned reads of each sample were de novo assembled, filtered, and mapped as described in  Portik et al. (2016b). The final filtered assemblies were aligned using MAFFT  (Katoh et al.
2002 (Katoh et al. , 2005;; Katoh and Standley 2013)  and trimmed using trimAl  (Capella-Gutierrez et al. 2009 ). We enforced additional postprocessing filters for alignments, including a minimum length of 90 bp and a maximum of 30% total missing data across an alignment, resulting in 1047 exon alignments totaling 561,180 bp. Raw sequencing reads are deposited in the NCBI Sequence Read Archive (BioProject: PRJNA521610), newly generated sequences for the 5 captured nuclear loci are deposited in GenBank (Accession numbers: MK497946-MK499204), and all sequence capture alignments are available at https://osf. io/ykthm/. Species tree estimation. -We used the sequence capture data set to estimate a species tree for Hyperoliidae using ASTRAL-III  (Mirarab et al. 2014; Mirarab and Warnow 2015; Zhang et al.
The set of 1047 gene trees was used to infer a species tree with ASTRAL-III, and node support was assessed with (i) quartet support values, or local posterior probabilities computed from gene tree quartet frequencies, which also allows the calculation of branch lengths in coalescent units  (Sayyari and Mirarab 2016) , and (ii) 200 replicates of multilocus bootstrapping, where each of the 200 RAxML bootstrap trees per locus are used to infer a species tree and a greedy consensus tree is created from the 200 species trees to calculate percent support across nodes  (Seo 2008). Evolutionary Relationships of Afrobatrachian Frogs DNA barcoding. -We obtained sequence data from the mitochondrial marker 16S ribosomal RNA (16S) for all samples included in the sequence capture experiment and for additional species that we were unable to include in our sequence capture experiment due to insufficient DNA yield.
Polymerase chain reactions (PCRs) were carried out in 12. 5 L volumes consisting of: 1. 25 L Roche 10× (500 mM Tris/HCl, 100 mM KCl, 50 mM (NH 4 ) 2 SO 4 , 20 mM MgCl 2 , pH = 8. 3), 0. 75 L 25 mM MgCl 2 , 0. 75 L 2 mM dNTPs, 0. 25 L 10. 0 M forward primer, 0. 25 L 10. 0 M reverse primer, 8. 40 L H 2 O, 0. 10 L Taq, and 0. 75 L DNA. Amplification involved initial denaturation at 94 • C for 4 min, followed by 35 cycles of 95 • C for 60 s, 51 • C for 60 s, 72 • C for 90 s, and a final extension at 72 • C for 7 min, using the primer pairs 16SA and 16SB  (Palumbi et al. 1991). The PCR amplifications were visualized on an agarose gel, cleaned using ExoSAP-IT, and sequenced using BigDye v3. 1 on an ABI3730 sequencer (Applied Biosystems). Newly generated 16S sequence data are deposited in GenBank (Accession numbers: MK509481-MK509743).
GenBank data. -To expand our taxonomic sampling, we included all available published sequence data of afrobatrachian frogs. We built a molecular data matrix using the 5 nuclear loci included in our captures (FICD, KIAA2013, POMC, TYR, and RAG-1) and the mtDNA marker 16S. This resulted in the inclusion of 30 additional hyperoliids and 130 arthroleptid, brevicipitid, and hemisotid species, though many are represented solely by 16S mtDNA data. Nuclear loci were aligned using MUSCLE  (Edgar 2004) , and 16S sequences were aligned using MAFFT with the E-INS-i algorithm  (Katoh et al. 2002 (Katoh et al. , 2005)). The final concatenated alignment of the expanded taxonomic data set consisted of 283 taxa and 3991 bp, with 36% total missing data.
We note that although many sexually dichromatic species also exhibit variation in male color phase (e. g. , adult males in the population display Phase J and Phase F), the females of these dichromatic species consistently display one color phase (Phase F). A summary of the sexual dichromatism data is provided in Supplementary Table  S2  available on Dryad. We reconstructed the evolution of sexual dichromatism on the time-calibrated phylogeny of Afrobatrachia using Bayesian ancestral state reconstruction in BEAST  (Drummond et al. 2012)  and with HiSSE analyses using the R package HiSSE (Beaulieu and O'Meara 2016) (described below). We VOL. 68 performed Bayesian ancestral state reconstructions using several combinations of clock and character models in BEAST v1. 8. 1  (Drummond et al. 2012)  following  King and Lee (2015).
We performed HiSSE analyses using the R package HiSSE  (Beaulieu and O'Meara 2016)  to identify if sexual dichromatism in afrobatrachian frogs is associated with increased diversification rates, and to reconstruct ancestral states while accounting for transition rate and diversification rate heterogeneity. The HiSSE model builds upon the popular binary-state speciation and extinction (BiSSE) model  (Maddison et al. 2007 ) by incorporating "hidden states" representing unmeasured traits that could impact the diversification rates estimated for states of the observed trait. The HiSSE model is therefore able to account for diversification rate heterogeneity that is not linked to the observed trait, while still identifying trait-dependent processes. The HiSSE framework also includes a set of null models that explicitly assume the diversification process is independent from the observed trait, without constraining diversification rates to be homogenous across the tree.
One concern raised by  Beaulieu and O'Meara (2016)  is that neutrally evolving traits simulated on trees generated from a complex heterogenous rate branching process can lead to false signals of trait-dependent diversification, signifying the HiSSE framework may be sensitive to particular types of tree shapes. To evaluate the performance of these methods given our empirical tree topology, we simulated neutrally evolving traits on the afrobatrachian frog phylogeny and tested for trait-dependent diversification using both the BiSSE and HiSSE frameworks. We conducted independent simulations of a binary trait with the "sim. history" function in R package PHYTOOLS (Revell 2012) using the unequal rates q-matrices obtained from our empirical data and enforcing a root state of trait absence. We required a minimum of 10% of taxa to exhibit the derived state and conducted simulations until we obtained 1500 replicates meeting this criterion.
We used ML to fit a BiSSE model and the typical "null" model with equal speciation and extinction rates to each simulated trait using the R package DIVERSITREE  (Maddison et al. 2007; FitzJohn et al. 2009; FitzJohn 2012). We performed likelihood ratio tests and calculated AIC scores to determine if the constraint model could be rejected with confidence ( AIC > 2 or P-value < 0. 05), and summarized the number of instances each of the 2 models was favored across the simulations. We analyzed the simulated data in the HiSSE framework as with our empirical data, but with a reduced set of 5 models representing each major category of model. This reduced model set included 2 BiSSE-like models that differed only in the constraint of , a CID-2 and CID-4 model, and a HiSSE model with 2 hidden states, 3 transition rates, equal ε, and distinct.
Phylogenetic Relationships The sequence capture data set consisting of 1047 loci and 561,180 bp produced a well-resolved species tree with a normalized quartet score of 0. 877 and only 8 of 150 nodes (5%) with quartet scores below 0. 9 (Supplementary Fig. S1  available on Dryad). The multilocus bootstrapping analysis produced similar results with low support for only 7 nodes, 6 of which also received low support in the species tree analyses (Supplementary Fig. S1  available on Dryad). The higherlevel relationships recovered in the species tree are largely congruent with those recovered by  Portik and Blackburn (2016) , though we found strong support for a different placement of the genus Acanthixalus as sister to the clade containing Semnodactylus, Paracassina, Phlyctimantis, and Kassina, which together are sister to all other hyperoliids.
Our improved sampling provides the first comprehensive assessment of evolutionary relationships within the speciose genera Afrixalus and Hyperolius. The monophyly of Hyperolius is supported, however Afrixalus is paraphyletic, and we found a sister relationship between the Ethiopian-endemic Afrixalus enseticola and the Malagasy-Seychelles species of Heterixalus and Tachycnemis, which are in turn sister to all remaining Afrixalus (Supplementary Fig. S1  available on Dryad). We found strong support for the southern African species Hyperolius semidiscus as sister to all other lineages in the genus, and furthermore recovered Hyperolius parkeri, Hyperolius lupiroensis, and VOL. 68 FIGURE 2. Ancestral state reconstruction of sexual dichromatism in afrobatrachian frogs from HiSSE using model averaging to account for uncertainty in both models and reconstructions.
Circles at tips and nodes are colored by state with node pie charts indicating probability of a state assignment. Branches are colored using a gradient from the model-averaged net diversification rate, with black representing the slowest rate. The arrow highlights the node identified as displaying an unambiguous transition from monochromatism to sexual dichromatism. the Hyperolius nasutus complex as sister to 2 larger subclades of Hyperolius (Clades 1 and 2; Fig. 2 , Supplementary Fig. S1  available on Dryad). In an effort to distinguish the main division within Hyperoliidae, we recognize the subfamilies Kassininae Laurent, 1972 and Hyperoliinae Laurent, 1943 and define the content within each on the basis of our species tree analysis as follows: (i) Kassininae: Acanthixalus, Kassina, Paracassina, Phlyctimantis, and Semnodactylus; (ii) Hyperoliinae: Afrixalus, Cryptothylax, Heterixalus, Hyperolius, Morerella, and Opisthothylax (Fig.
Evolution of Sexual Dichromatism and State-Dependent Diversification We determined sexual dichromatism occurs in 60 of the 173 (34%) hyperoliid frog species included in our analyses. The greatest number of dichromatic species occurs in Hyperolius Clade 1 (35 of 39 species, 89%), followed by Hyperolius Clade 2 (18 of 50 species, 36%) and the genus Heterixalus (4 of 11 species, 36%) (Figs. 2  and 5 ). The Bayesian ancestral state reconstructions using 4 model combinations produced different patterns of character reconstructions and rates of trait evolution (Supplementary Fig. S3  available on Dryad). Overall, we found models with asymmetric character transition rates (Mk2) outperformed those with symmetric rates (Mk1), regardless of the clock model used (log-transformed Bayes factor range: 3.
40-10. 39; Table  2 ). The analysis with the highest log-marginal likelihood incorporated the relaxed local clock Mk2 model, though it was not a significantly better fit than the simpler SC Mk2 model (log-transformed Bayes factor of 0. 10) indicating there is low variation in lineage-specific evolutionary rates for this trait. The ancestral character reconstructions of the SC Mk2 model indicated a median of 2 transitions from monochromatism to dichromatism. However, the character reconstructions revealed that this estimate is due to low posterior probability estimates for 2 critical nodes within Hyperoliinae (Supplementary Fig. S3  available on Dryad). The presence of dichromatism at one or both of these nodes results in a single origin of sexual dichromatism. In contrast, the SC Mk2 model demonstrated approximately 27 independent losses of sexual dichromatism within hyperoliids, including losses in entire groups (Afrixalus, H.
nasutus complex) and numerous reversals within Heterixalus and Hyperolius (notably in Clade 2) (Supplementary Fig. S4  available on Dryad). Our HiSSE analyses revealed that a HiSSE model with 4 net turnover rates, equal extinction fraction rates, and 3 distinct transition rates was the bestfit model (Model 19, Table  1 ). The second and third ranked models ( AIC of 1. 0, 2. 5) were also HiSSE models that varied in the number of extinction fraction rates or the number of transition rates. Together these 3 HiSSE models accounted for 84. 1% of the model weight (Table  1 ) and support a signal of state-dependent diversification in which sexual dichromatism and a hidden state are associated with diversification rates. The net diversification rates inferred using the best-fit model were nearly twice as high in sexually dichromatic lineages (0.
157) as compared with monochromatic lineages (0. 091) in the absence of the hidden state (Fig. 3 ), and the combination of the hidden state and dichromatism or monochromatism resulted in much lower net diversification rate estimates (0. 02 and <0. 001, respectively). The trait reconstructions for all 4 state combinations indicated that the dichromatism plus hidden state combination occurs in the MRCA of 2 species-poor or monotypic genera (Cryptothylax, Morerella) (Supplementary Fig. S5  available on Dryad), and is associated with a markedly lower diversification rate (Fig. 3 ). The model-averaged ancestral state reconstructions demonstrated strong support for a single origin of sexual dichromatism and 25 independent reversals to monochromatism within Hyperoliinae, with reversal patterns similar to the Mk2 analyses (Fig.
2  and Supplementary Fig. S5  available on Dryad). Simulated traits and state-dependent diversification. -Analyzed in the BiSSE framework, we found that many of the trait simulations on the phylogeny of Afrobatrachia resulted in the rejection of the "null" model of equal diversification rates across character  states. Based on the significance of likelihood ratio tests, we rejected the "null" model in favor of traitdependent diversification for 565 (37. 6%) of our 1500 comparisons. We recovered similar results using a delta AIC cutoff value of 2, for which we found support for trait-dependent diversification in 546 (36. 4%) of the simulations (Fig. 4 ). In many of these cases, we found unexpectedly strong support for the BiSSE model, and 160 (10. 6%) of the comparisons resulted in delta AIC values ranging from 10 to 40.
Here, we have produced the most comprehensive hyperoliid species tree to date and found support for an Eocene origin of 2 subfamilies representing a major division within Hyperoliidae: Kassininae (26 species) and Hyperoliinae (∼200 species). Within Hyperoliinae, we clarified relationships within the hyperdiverse genus Hyperolius (∼150 species), which consists of 2 major clades (Fig. 2 , Supplementary Figs. S1 and S2 available on Dryad). These clades represent parallel radiations with species distributed across a variety of habitats and altitudes throughout sub-Saharan Africa, which showcases Hyperoliidae as a rich comparative framework for future biogeographic research. Although both Kassininae and Hyperoliinae include colorful species, sexual dichromatism only occurs within Hyperoliinae where it is present in the genera Tachycnemis, Cryptothylax, and Morerella, several species of Heterixalus, and more than half of the Hyperolius species we sampled (Fig.
2 , Supplementary Table  S2  available on Dryad). A previous study hypothesized that sexual dichromatism evolved multiple times within Hyperoliidae  (Veith et al. 2009 ); however, we found overwhelming support for a single origin of sexual dichromatism (Fig. 2 , Supplementary Fig. S3  available on Dryad) and over 20 independent reversals to monochromatism that range from early transitions that characterize entire genera (e. g. , Afrixalus) to recent reversals within Heterixalus and Hyperolius (Fig. 2 , Supplementary Fig. S4  available on Dryad). This transition bias from dichromatism to monochromatism also occurs in birds  (Price and Birch 1996; Omland 1997; Burns 1998; Kimball et al. 2001; Hofmann et al. 2008; Dunn et al. 2015; Shultz and Burns 2017) , in which secondary monochromatism can evolve as the result of a color change in either sex  (Kimball and Ligon 1999; Johnson et al.
Conversely, the effects of testosterone appear to differ across species  (Richards 1982; Hayes and Menendez 1999) , suggesting that evolutionary transitions from dichromatism to monochromatism result directly from differences in hormone sensitivities among species. Reversals to monochromatism are especially prominent in Hyperolius Clade 2 (12 independent events; Fig. 2 , Supplementary Fig. S4  available on Dryad), highlighting the potential for future research in this group to identify the physiological basis and molecular underpinnings of these transitions. For example, 3 monochromatic species of the Hyperolius cinnamomeoventris complex that are endemic to the islands of São Tomé and Príncipe (Hyperolius drewesi, Hyperolius molleri, Hyperolius thomensis; both sexes with Phase F coloration) are derived from a mainland clade containing a mix of sexually dichromatic species (Hyperolius cinnamomeoventris, Hyperolius olivaceus; females Phase F, males Phase J) and monochromatic species (Hyperolius veithi; both sexes Phase J) (Fig.
The shift to the sexual dichromatism plus hidden state character combination occurred only once in the common ancestor of 2 genera (Cryptothylax, Morerella; Supplementary Fig. S5  available on Dryad) and is actually associated with lower diversification rates (Fig. 3 ). Together, our results demonstrate that diversification rate heterogeneity occurs within Afrobatrachia, and that the origin and persistence of sexual dichromatism in hyperoliid frogs is linked to their rapid diversification across sub-Saharan Africa.
Data available from the Dryad Digital Repository: http://dx. doi. org/10. 5061/dryad. 1740n0h. FUNDING Molecular data collection by DMP was funded by a National Science Foundation Doctoral Dissertation Improvement Grant (DEB: 1311006), an Ecological, Evolutionary, and Conservation Genomics Research Award presented to DMP by the American Genetic Association, a National Science Foundation grant (DEB: 1202609) awarded to DCB, a UC Berkeley President's Postdoctoral Fellowship awarded to RCB, and by the Museum of Vertebrate Zoology.
ACKNOWLEDGMENTS We thank the following institutions for accessioning field collections and for facilitating loan access:  California Academy of Sciences, Cornell University Museum of Vertebrates, Institut National de Recherche en Sciences Exactes et Naturelles, Museum für Naturkunde, Berlin, Museìum National d'Histoire Naturelle, Museum of Comparative Zoology, Museum of Vertebrate Zoology, National Museum Prague, Natural History Museum London, North Carolina Museum of Natural Sciences, Port Elizabeth Museum, Senckenberg Natural History Collections Dresden, South African Institute for Aquatic Biodiversity, South African VOL. 68 National Biodiversity Institute, The Field Museum, Trento Museum of Science, University of Texas at El Paso Biodiversity Collections , and the  Zoological Natural History Museum, Addis Ababa University.
DATA ACCESSIBILITY Raw sequencing reads are deposited in the NCBI Sequence Read Archive (BioProject: PRJNA521610), newly generated sequences for the 5 captured nuclear loci and 16S are deposited in GenBank (Accession numbers: MK497946-MK499204; MK509481-MK509743), and the sequence capture alignments are available at https://osf. io/ykthm/. We developed a project page (https://osf. io/yeu38) using the Open Science Framework that includes all data, scripts, and instructions required to replicate our analyses. We include all relevant material for the species tree analyses (https://osf. io/295qp/), phylogenetic reconstructions using constraint trees (https://osf. io/vhup5/), divergence dating in BEAST using a fixed starting tree topology (https://osf. io/7y59t/), Bayesian ancestral state reconstructions using BEAST (https://osf.
io/dybu3/), trait-dependent diversification analyses of empirical data using HiSSE (https://osf. io/akcpb/), and trait-dependent diversification analyses of simulated trait data using both BiSSE and HiSSE (https://osf. io/pvq7x/). The alignment files for the sequence capture data and the GenBank data are also available here (https://osf. io/ykthm/). The R scripts required to run the empirical HiSSE analyses are also available on github (https://github. com/ dportik/HiSSE_for_Afrobatrachia). The concatenated GenBank alignment and resulting time-calibrated phylogeny are also available on TreeBase (http://purl. org/phylo/treebase/phylows/study/TB2:S23981).
We recovered an Eocene age for the time to most recent common ancestor (TMRCA) of the families Hyperoliidae, Arthroleptidae, and Brevicipitidae, of approximately 42. 4 Ma (95% highest posterior density region [HPD]: 39. 1-51. 6 Ma), 45. 4 Ma (95% HPD: 35. 5-48. 7 Ma), and 41. 8 Ma (95% HPD: 33. 9-49. 8 Ma) (Supplementary Fig. S2 available on Dryad). These dates are younger than previous estimates (Roelants et al. 2007; Loader et al. 2014) but are consistent with more recent multilocus phylogenetic analyses (Portik and Blackburn 2016; Feng et al. 2017). We found diversification events began within Hyperoliinae approximately 35. 8 Ma (95% HPD: 30. 1-41. 6 Ma) and within Kassininae approximately 38. 3 Ma (95% HPD: 30. 9-45. 6 Ma). The majority of speciation events within Hyperolius occurred from the late Miocene to the Plio-Pleistocene (Supplementary Fig.
The core requirements are: ability to collect logistics data in real-time from multiple heterogeneous sensors, social media, and business processes; ability to process data efficiently in real-time or batch-style; a model for analyzing data for predicting the delay; and a model which produces an optimal routing plan to prevent the predicted delay. However, since data is the key element of analysis, efficient processing of data to produce quality dataset is a sine qua non. In this paper, we focus on developing a hybrid solution which enables efficient processing of data in realtime and batch style. It is worth noting that this paper is an extension of our previous work  [3]  where we developed batch style data processing. In this paper, we added functionalities that enable real-time processing of data.