dataesr/scientific-paragraphs-categorization huggingface dataset:
Results and discussion Tenebrio molitor chromosome-scale genome assembly The T. molitor genome size was estimated around 310 Mb with a heterozygosity rate of 1. 43% (Figure  S1 , Extended data). By combining long, short reads and Hi-C data, we obtained a final genome assembly of 287. 9 Mb (Table  1 ) representing a single haplotype of the T. molitor diploid genome (2n=20)  40  with a BUSCO  41  (BUSCO, RRID:SCR_015008) completeness of 99. 5% (using version 5. 0. 0 with Insecta database odb10) (Figure  S1 , Extended data). The assembly presents a N50 of 21. 9Mb, which is higher than T. castaneum's one  42  and much higher than the previously published T. molitor genome N50 (24. 1kb). In our assembly, the largest 16 scaffolds represent 90% of the total assembly, leading to a chromosome-scale assembly which provides high-quality support for gene annotation.
The longest form covers approximately 89% of the satellite (126-129bp), with average identity score 77%, while the shorter one, which is more abundant, covers about 44% of satellite (62-66bp) with mean sequence similarity of 85% (Figure  S5 , Extended data). The mitochondrial genome was detected in two scaffolds. More precisely, the genbank mitochondrial genome of T. molitor (15,785 bp) was aligned to our assembly using Minimap2  45  and detected three times in scaffold 94 with a nucleotide identity of 85-89% (Figure  S6 , Extended data) but also in several other regions of the same scaffold with a lower nucleotide identity (53-73%) (Table  S5 , Extended data). The high copy number of mitochondrial DNA (mtDNA) per cell leads to relatively high depth of coverage, which causes misassemblies.
NECAT constructed initially one single contig presenting three supplicated mitochondrial genomes. To resolve this misassembly, we re-assembled long reads that aligned to scaffold 94, using Flye version 2. 9 (Flye, RRID:SCR_017016) with genome size parameter set to 15k. Subsequently, the mitogenome was polished using Racon and Hapo-G with short reads (with the same methods used for the whole genome assembly) and obtained one single contig of 15,724 bp. The latter aligns with 98. 39% identity to the T. molitor genbank mitogenome (15,785 bp) (Figure  S8 ). Mitochondrial DNA was also detected in scaffold 65 (Figure  S7 , Extended data). However, due to its low ANI (50-75%) and the small fraction it occupies in the scaffold, we considered this alignment as a probable insertion of mtDNA in the nuclear genome.
Tenebrio molitor genome annotation By combining RNA-seq and Coleoptera proteomes, we predicted a total of 21,435 genes which is higher than the number observed in T. castaneum. Beside this difference, other metrics are very comparable (Table  2 ). Quality of the gene prediction was assessed using BUSCO version 5. 0. 0 with Insecta database odb10 which contains 1,367 genes and showed a gene completeness of 96. 5%. The published gene prediction based on the T. castaneum genome has fewer genes but a higher BUSCO score, which reflects the completeness of the gene prediction while the BUSCO score on the genome assembly reflects the completeness of the genome assembly. The tools and resources (transcriptomes, proteomes) used for gene prediction are different for the two beetles, so we can expect different gene completion between the two predictions.
BUSCO with Insecta database (N = 1,367) Complete 1,319 (96. 5%) 1,361 (99. 6%) Duplicated 8 (0. 6%) 339 (24. 8%) Fragmented 12 (0. 9%) 3 (0. 2%) Missing 36 (2. 6%) 3 (0. 2%).
The deuterostome branch is short and has low support compared to the protostome branch The different topologies relating Chordata, Xenambulacraria, and Protostomia seen in recently published animal phylogenies suggest that the support for monophyletic deuterostomes (Fig. 1A ) may be weak. This contrasts with consistent, strong support for the monophyly of the protostomes. To study the support for the deuterostome clade in the context of the well-supported protostome clade, we use five recent, independently generated, phylogenomic datasets covering the diversity of animal phyla [i. e. ,  (2) (3) (4) (5) (6) ]. We investigate the support for different topologies relating the Chordata, Xenambulacraria, Ecdysozoa, and Lophotrochozoa. We first asked whether the branches leading to protostomes and deuterostomes are of similar length, under the assumption that both are monophyletic.
We note that, while the classic phylogeny suggests that protostomes and deuterostomes originated at the same point (Urbilateria), there is no expectation that the branches leading to the common ancestors of Protostomia and Deuterostomia should be of the same length. The point of the comparison is to see whether there is a strong contrast in branch length between the well-supported Protostomia and the less wellsupported Deuterostomia. Using a fixed topology taken from the original publications for each dataset (modified when necessary to enforce monophyly of deuterostomes), we optimized branch lengths using the site-homogeneous LG + F + G model. While the overall amount of change in branches leading from the bilaterian common ancestor to both protostomes and deuterostomes differs between datasets, in all cases, the branch leading to the protostomes is approximately twice the length of the branch leading to the deuterostomes (Fig.
1B. ). Under more realistic site heterogeneous models, the protostome branch is almost six times longer. This difference is reinforced when we look at the change in log likelihood (∆lnL) between a fully resolved tree compared with 2 of 10 trees in which either the protostome or deuterostome branch is collapsed into a polytomy. The ∆lnL observed on collapsing the branch leading to protostomes is considerably greater for all five datasets than the ∆lnL when collapsing the deuterostome branch (Fig. 1C ). We repeated these measures of branch lengths and ∆lnL using all individual genes from all five datasets (Fig. 1, D  and E ). For the great majority of genes across all datasets, as for the concatenated datasets, there is a longer branch leading to the protostomes than to the deuterostomes (protostomes longer in 70% of genes) and consistently stronger support (larger ∆lnL) for protostomes than for deuterostomes (∆lnL protostomes larger for 68.
2 ). For the protostome trees, most genes have a strong preference for a single topology (77. 31% on average across datasets with the LG + F + G model); the majority of genes support the monophyly of protostomes (58. 94% versus 9. 71% and 8. 66% for PM, P1, and P2, respectively; table  S1 ). For the deuterostomes, the results are more equivocal; fewer genes have strong preference for a single topology (66. 99% on average), and there is only a small excess in the number of genes strongly supporting monophyletic deuterostomes over the other two topologies (28. 65% versus 19. 17% and 19. 17% for DM, D1, and D2, respectively; table  S1 ). To address potential questions regarding the monophyly of the Xenambulacraria, these individual gene analyses were repeated using datasets from which the Xenacoelomorph Xenoturbella had been removed.
The removal of this taxon resulted in subtle changes to the results but did not change any conclusions (see fig. S1 ). For all five datasets, the gene alignments strongly supporting the monophyletic protostomes topology were longer and had higher monophyly scores (a measure of their ability to support known clades) compared with the gene alignments that supported either of the two alternative topologies (fig. S2 ). For the deuterostomes, there was minimal evidence of a significant difference of alignment length between genes supporting DM versus either paraphyletic alternative (fig. S2 ), and there were no significant differences in monophyly scores between genes supporting DM versus either paraphyletic alternatives (table  S3 ). Monophyletic Protostomia, but not monophyletic Deuterostomia, is strongly preferred across five independent datasets by a clear majority of individual genes that are, on average, longer with a stronger phylogenetic signal.
DM is correlated with conditions that may lead to systematic error Whatever the true topology relating Xenambulacraria, Chordata, and Protostomia, we have shown that the branch separating them is short and might therefore be especially sensitive to systematic errors. Systematic errors can result from heterogeneities in the process of substitution that are not accommodated by the models used and can be exacerbated in faster evolving datasets. In the context of unequal rates of evolution among taxa, this may lead to a longbranch attraction (LBA) artifact  (7). The Bilateria consists of two branches: Protostomia (red, Lophotrochozoa and Ecdysozoa) and Deuterostomia (blue, Chordata and Xenambulacraria). (B) Comparison of branch lengths from the bilaterian common ancestor to the deuterostome common ancestor (blue) and to the protostome common ancestor (red).
In five datasets, the protostome branch is twice as long as the deuterostome branch. (C) Comparison of decrease in lnLikelihood of a tree in which the protostome or deuterostome branch has been collapsed (∆lnL). In five datasets, collapsing the protostome branch reduces lnL considerably more than collapsing the deuterostome branch. (D) Comparison of estimated protostome and deuterostome branch lengths for individual genes. Genes from all five datasets are ordered by the difference in length between protostome and deuterostome branches. In 3376 out of 4826 genes (69. 9%), the protostome branch is longer. (E) Comparison of protostome and deuterostome ∆lnL for individual genes. Genes from all five datasets are ordered by the difference in ∆lnL between proto stomes and deuterostomes. In 3312 out of 4826 genes (68.
6%), the protostome ∆lnL is larger. All analyses used the LG + F + G model. S C I E N C E A D V A N C E S | R E S E A R C H A R T I C L E 3 of 10 For each dataset, we measured the average branch lengths within the protostome, chordate, and xenambulacrarian clades (average distance from the bilaterian common ancestor to each taxon within each clade) and the average distance from each outgroup taxon to the bilaterian common ancestor. The branches leading to the outgroups and to the protostomes are always longer than the branch leading to the chordate and xenambulacrarian clades (Fig. 3A ). Under LBA, the long-branched protostomes and outgroup might be expected to be mutually attracted, resulting in clustering of shortbranched Chordata and Xenambulacraria. The three datasets that supported monophyletic deuterostomes (2, 3, 6) had taxon samples that resulted in the three largest rate inequalities with the longest average protostome and outgroup branch lengths relative to chordate and xenambulacrarian branches (Fig.
3A ). The three datasets that support monophyletic Deuterostomia are also the fastest evolving (expected substitutions per site measured across a tree containing the eight taxa that all five datasets have in common: Philippe, 1. 971; Marletaz, 2. 2082; Cannon, 2. 537; Laumer, 2. 6578; and Rouse, 2. 8741). Last, while two datasets support paraphyletic deuterostomes under complex site heterogeneous models  (4, 5) , which account for across-site amino acid preference variability  (8) , all five datasets support monophyletic deuterostomes when using simpler and less well-fitting site homogeneous models. Unequal rates, faster-evolving loci, and inadequate site homogeneous models are all known to promote LBA artifacts, especially in the context of short internal nodes  (1, 7, 9). All these problem-causing conditions correlate with support for Deuterostomia.
Less well-fitting models produce conditions that may bias toward monophyletic deuterostomes We further examined the possible effect of model misspecification by comparing branch lengths estimated using different models. We used the Laumer et al. dataset  (3) , which has the clearest branch length heterogeneity (Fig. 3A ). We estimated the lengths of the branches leading to the deuterostomes, the protostomes, and the outgroup. We see that as we use models that fit the data increasingly well, the estimated length of the branch leading to the deuterostomes decreases, and the lengths of the branches leading to the protostomes and outgroup increase (Fig. 3B ). Using inadequate models will underestimate the likelihood of convergence between Protostomia and outgroup, possibly resulting in an LBA between protostomes and outgroups.
Simulations show that the monophyletic deuterostome topology is favored under conditions producing systematic errors We next followed a data simulation approach to ask whether any of the three topologies relating the Protostomia, Chordata, and Xenambulacraria (Fig. 4A ) could gain artifactual support as a result of systematic error. Using 50,000 positions and 36 taxa from the Laumer dataset, we estimated parameters using the three alternative   (10). For each topology, we simulated 100 datasets using these estimated parameters. For data simulated according to the DM topology, we are able to reconstruct monophyletic deuterostomes (DM) correctly in 100% of replicates under both correct (site heterogeneous) and model violating (site homogeneous models) (Fig. 4B ). In contrast, for data simulated under the two topologies with paraphyletic deuterostomes, recovering the true relationships was more challenging.
As predicted by the consistency of probabilistic models, under the correct, site heterogeneous model, the correct paraphyletic topology was always recovered. Under the model-violating site homogeneous model (expected to exacerbate LBA artifacts), the true tree was recovered in 60 and 88% of the datasets simulated under the D1 and D2 hypotheses, respectively (Fig. 4B ). In both cases, the remaining 40% (D1) and 12% (D2) of the datasets incorrectly recovered monophyletic deuterostomes (the DM topology). These analyses were repeated using a dataset from which the Xenacoelomorph Xenoturbella had been removed. The removal of this taxon resulted in subtle changes to the results that do not affect the conclusions drawn (see table  S4 ).
Branch length heterogeneity is correlated with support for monophyletic deuterostomes To explore the hypothesis of unequal rates of evolution lending exaggerated support to the monophyletic Deuterostomia topology, we reinferred trees using the same simulated data after first removing the 13 longest branched taxa of protostome and outgroup clades  (11, 12). We reinferred the trees using the site homogeneous LG + F + G model, which had resulted in some incorrect topologies with the full dataset. Regardless of the topology under which the  data were simulated, removing these long branches resulted in recovering the correct topology in 100% of cases (Fig. 4B ). We contrast this with an equivalent experiment designed to exaggerate artifacts caused by rate heterogeneity. We removed the 13 shortest protostome and outgroup taxa from the simulated data and again reinferred the tree topologies under the site homogeneous LG + F + G model.
Regardless of the topology under which the data were simulated, we recovered monophyly of the deuterostomes (DM topology) in 100% of replicates (Fig. 4B ). Our results show that if deuterostomes are paraphyletic (either paraphyletic topology), then conditions we have shown to affect real datasets could easily result in artifactual support for monophyletic deuterostomes (Fig. 4C  and table  S4 ).
Implications of difficulties resolving relationships between Protostomia, Chordata, and Xenambulacraria We have shown that the branch leading to monophyletic Deuterostomia, if it exists, is short and weakly supported; for comparison, we demonstrate unequivocal strong support for Protostomia especially S C I E N C E A D V A N C E S | R E S E A R C H A R T I C L E 6 of 10 from higher-quality gene alignments. Comparisons of rates and relative branch lengths between datasets and the effects of model misspecification show that given some support for monophyletic Deuterostomia correlates with conditions expected to enhance systematic error. The contention that monophyletic Deuterostomia could result from systematic error is given some support by our simulation experiments. Systematic error is especially likely to affect our ability to reconstruct relationships between taxa separated by the very short branches we have described.
Nevertheless, recent analyses using large datasets and the best available models give weak support to a sister group relationship between the Chordata and Protostomia to the exclusion of the Xenambulacraria. To facilitate future studies of this problem, we propose the name "Centroneuralia" for a potential Chordata and Protostomia clade, recognizing their shared characteristic of a centralized nervous system. We propose the name "Orthozoa" for a potential Xenambulacraria and Prostostomia clade, recognizing the shared character of having an orthodox dorsoventral orientation when compared with the axis-inverted Chordata.
Datasets used All analyses were based on five recently published phylogenomic datasets (2-6) covering all major clades of the animal phylogeny. For convenience, we will refer to each dataset by the name of the first author of each study (i. e. , "Marletaz," "Philippe," "Laumer," "Cannon," and "Rouse"). In all our analyses, we kept the full set of taxa apart from the fast-evolving Acoelomorpha species that have been shown to be prone to phylogenetic inference errors (4). In our analyses, the Cannon dataset consisted of 67 taxa and 881 genes ("proteinortho. phy" in the original study), the Laumer dataset consisted of 422 genes and 152 taxa (167 taxa in dataset M in the original study), the Marletaz dataset consisted of 70 species and 1174 genes (alignments provided in the original study after the HMMClean and BMGE filtering), the Philippe dataset consisted of 51 taxa and 1173 genes (trimmed alignments provided in the original study), and, last, the Rouse dataset consisted of 26 taxa and 1178 partitions ("70.
Measuring lengths of branches leading to deuterostomes and protostomes The protostomes and the deuterostomes are traditionally treated as two equally strongly supported clades. To assess whether molecular phylogenetics supports this perception of bilaterian evolution, we compared the branch lengths of the two clades across the Downloaded from https://www. science. org at Universite Pierre Et Marie Curie -Paris 6 (Upmc) on November 15, 2021 five concatenated datasets as well as for each gene of each dataset individually. For each dataset, we assumed the tree topology as reported in the original studies, specifically, for Cannon, Laumer, Marletaz, and Rouse the trees we used relate to Fig. 2 , Fig. 2A , Fig. 2 , and Fig. 3  from their respective publications, while for the Philippe data, we assumed the relationships as in the "PHILIPPE-ALL-SPP-NOACOEL-CATGTR-100JP.
tre" from the original publication. For the Cannon, Laumer, and Rouse data, Xenoturbella are considered to be sister to Ambulacraria rather than Nephrozoa. This position for Xenoturbella in the absence of the long-branched Acoelomorpha is supported by these datasets. For the Philippe and Marletaz data, we altered the tree only to enforce DM, as this was not supported in the published phylogenies. For the analyses performed per gene, we cropped the original trees using newick-tools  (33) , such that only the taxa present in the relevant gene alignment were present. Given the fixed topology, the branch lengths were estimated with IQ-TREE  (34)  under the state frequency homogeneous model LG + F + G. We used the optimized topologies to measure the length of the branch leading from the common ancestor of Bilateria (protostomes and deuterostomes) to the common ancestors, respectively, of deuterostomes and protostomes.
Measuring lnLikelihood support for the branches leading to deuterostomes and protostomes We performed a second analysis where we measured the difference in the likelihood score between the fully resolved phylogeny and for the topology after collapsing either the protostome or the deuterostome branch into a polytomy. Collapsed Protostomia branch = (Lophotrochozoa, Ecdysozoa, (Ambulacraria, Chordata)) Collapsed Deuterostomia branch = ((Lophotrochozoa, Ecdysozoa), Ambulacraria, Chordata) For calculating the lnLikelihoods, we used the LG + F + G model. We measured the difference in lnLikelihood in both the five full concatenated alignments and for each gene from each dataset individually.
Measuring difference in lnLikelihood per gene for topologies with monophyletic and paraphyletic deuterostomes and protostomes We measured the proportion of genes in each dataset that strongly support the monophyly of the deuterostome clade DM over the two alternative paraphyletic topologies. Specifically, we compared the lnLikelihood of the topologies, assuming monophyletic deuterostomes DM and two possible paraphyletic alternatives. Deuterostome paraphyly "D1": (Chordata, (Xenambulacraria, (Lophotrochozoa, Ecdysozoa))) Deuterostome paraphyly "D2": (Xenambulacraria, (Chordata, (Lophotrochozoa, Ecdysozoa))) We performed the equivalent analyses for the protostomes; specifically, we compared the lnLikelihood of the topologies assuming monophyletic protostomes PM and the two possible paraphyletic alternatives.
By scaling the three likelihoods in the range [0,1] such that lnLn1 + lnL2 + lnL3 = 1 (the relevant python script "likelihood_transform. py" is available at https://github. com/MaxTelford/MonoDeutData), we could use their transformed values as coordinates in a ternary plot, whose corners represent the three topologies. We considered a gene to support a particular topology if the corresponding scaled likelihood was larger than two-thirds (and the likelihoods for the other two topologies were therefore smaller than one-third). We divided the triangle into compartments to reflect these cutoffs and plotted the points using the R package "ggtern" (36) (the relevant R script "plot_triangles. R" is available at https://github. com/MaxTelford/ MonoDeutData). Identical steps were taken when repeating these analyses with datasets from which the Xenacoelomorpha had been excluded.
Comparing the phylogenetic informativeness of genes supporting topologies with monophyletic and paraphyletic protostomes and deuterostomes To identify potential reasons for individual genes supporting alternative topologies for both the deuterostome and the protostome clades, we evaluated two parameters known to be related to errors in phylogenetic inference. For each gene alignment from each dataset, we first measured the alignment length. Subsequently, we inferred the maximum likelihood phylogeny for each gene with IQ-TREE under the LG + F + G model and measured the monophyly score of the tree [this is a measure of a dataset's ability to reconstruct known monophyletic groups and is described in  (36) ]. We used Welch's t test to determine whether the difference in these scores between the sets of genes supporting different topologies was significant (table  S3 ).
Measuring branch lengths of different clades across datasets We assessed how the average branch lengths of the two clades Protostomia and Deuterostomia and of the outgroup clan differ across the five datasets. Using the complete alignments, we estimated the branch lengths under the LG + F + G model, assuming the DM topology with IQ-TREE. To measure the average tip-to-stem branch length in each clade or clan, we used the "pynt. py" script (available at https://github. com/MaxTelford/XenoCtenoSims). We additionally measured the tree length (sum of all branch lengths) for the five datasets after reducing each of them to the eight species they all had in common (i. e. , Amphimedon queenslandica, Nematostella vectensis, Strongylocentrotus purpuratus, Ciona intestinalis, Peripatopsis capensis, Priapulus caudatus, Capitella teleta, and Lottia gigantea).