dataesr/scientific-paragraphs-categorization huggingface dataset:
A table of counts was built with the featureCounts software (R version 3. 4. 0). Only genes with at least 10 reads in both regions in either condition were kept for further analysis. In total, 4,208 genes passed all these steps and were used for subsequent analysis. The differential analysis between the UV+ and UVÀ conditions was done using two independent biological replicates per condition. For each gene, the fold regulation of the downstream region (that is the ratio of normalized read counts between conditions) was compared with the fold regulation of the upstream region using a Wald test implemented in DESeq2  (Love et al, 2014). Gene ontology (GO) analysis of genes was carried out by the functional enrichment analysis tool DAVID.
Acknowledgements We thank the  Institut Curie Next Generation Sequencing platform (Sylvain Baulande ) for high-throughput sequencing. Research was funded by grants from  Equipe labellis ee Ligue Nationale Contre le Cancer (LNCC) ,  Institut Curie, Gustave Roussy , and  Centre National de la Recherche Scientifique (CNRS). R. S. was successively supported by a predoctoral fellowship from the  Minist ere de l'Enseignement Sup erieur et de la Recherche (MESR)  and the  Association pour la Recherche sur le Cancer (ARC).
Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardized sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus Cirripectes. Recent studies discovered several Cirripectes species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, to evaluate the diversity and distribution of Cirripectes species in the Mascarene Archipelago, a little-studied region but an important biodiversity hotspot, complete mitochondrial genomes, and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analyzed to integrate these specimens within the largest dataset of publicly available sequences.
Currently, 14 species are recorded with COI DNA sequences in the BOLD database  (Ratnasingham & Hebert, 2007) , plus three genetically divergent groups that possibly represent not yet described new species. Most Cirripectes species are smaller than 100 mm. They are herbivorous and/or detrivorous cryptobenthic teleosts that primarily inhabit rocky or coral substrates in shallow (<5 m depth) high-surge fore reef habitats  (Williams, 1988). However, individuals of Cirripectes matatakaro and Cirripectes castaneus may be encountered deeper (more than 20 m and over 32 m depth, respectively;  Williams, 1988 , Hoban & Williams, 2020). Species show considerable variation in geographic range sizes, from small area endemism (e. g. , Cirripectes heemstraorum endemic to the East coast of South Africa at Cape Vidal;  Williams, 2010)  to Indo-Pacific-wide distributions (e.
Affixed to the seabed, they are left to be colonized by a diversity of marine species, then collected and dismantled to study the associated biota (see  Zimmerman & Martin, 2004  for more details). To evaluate the diversity and distribution of Cirripectes species in the Mascarene Archipelago, a little-studied region with high endemism and source of type material for this genus, we reconstructed the phylogeographic relationships within Cirripectes collected using ARMS. We conducted a multi-marker approach by sequencing mitochondrial and nuclear genes and integrated newly collected specimens within the largest dataset of publicly available sequences. We sequenced complete mitochondrial ge-.
| Sequences processing and public sequences retrieval Reads were processed with Geneious Prime 2019. 2. 3. Paired-end reads were merged, the primers were used as barcodes to recover the fragment ends and the merged reads were de novo assembled. The resulting contigs were checked in BOLD and Genbank databases before being used as references for elongation through TA B L E 1 Cirripectes species reported from the Mascarene Archipelago with their ecological and geographical distributions. Note: The types of polymorphism were indicated as 'S' for sexual and 'G' for geographical. Species with more than one sympatric sexual color pattern are indicated by *. Information was synthetized from  Williams (1988) ,  Letourneur et al. (2004), and Allen et al. (2013). repeated mapping of reads with a maximum of 1% mismatch and three bases gap allowed.
Mapping was repeated until no further reads could be mapped. Complete linear mitochondrial consensuses were transformed into circular sequences and overlapping sections were manually inspected and adjusted. Last, reads were mapped back against the obtained circular sequences to check coverage and final assembly. The mitogenome sequences were annotated using online MitoFish  (Iwasaki et al. , 2013). Sanger sequences were assembled and checked in Geneious Prime. 2. 3 (2019). To increase taxonomic and spatiotemporal coverage, our datasets were extended with publicly available sequences from BOLD and/or GenBank (Figure  1 ; ESM 1). In some instances, sequences were renamed according to the conclusions of the papers in which they were published, even if the names were not corrected in the database: sequences within BOLD BIN:AAU0601 were renamed from C.
castaneus to C. randalli  (Hoban & Williams, 2020) , and MH932003 to MH932007 were renamed from C. alboapicalis to C. patuki sensu  Delrieu-Trottin et al. , 2018 (Delrieu-Trottin et al. , 2018). Two sequences, GBMNB4802-20 and KX223895. 1, respectively from BOLD and Genbank, probably belong to a different genus and were removed from the analyses.
| Molecular and phylogenetic analyses All analyses were performed on three datasets: (i) mitochondrial Sequences of each marker were aligned separately via Muscle 3. 8. 425 (Edgar, 2004) , implemented in Geneious Prime 2019. 2. 3 using default parameters, and manually trimmed to maximize the shared length among the sequences (COI = 506 bp, Rho = 737 bp). For the mt dataset, complete mitogenomes were aligned and translated into protein to check the codon position for the coding genes. The two tRNA and 13 CDS were kept according to coding position and overlapping CDS portions were trimmed at the end to prevent a shift in the translation frame. ModelFinder 1. 6. 8 (Kalyaanamoorthy et al. , 2017)  in PhyloSuite  (Zhang et al. , 2020)  was used to select the evolutionary model with the best Akaike Information Criterion (AIC; Akaike, 1974) for each dataset.
Maximum-likelihood (ML) and Bayesian inference (BI) analyses were conducted. ML tree searching was conducted in W-IQ-TREE  (Trifinopoulos et al. , 2016)  for 1000 ultrafast bootstraps  (Hoang et al. , 2018). Multiple independent Bayesian inference searches used strict or uncorrelated log-normal relaxed molecular clock models with a Yule or birth rate ratio tree prior in BEAST2 2. 1. 2 (Bouckaert et al. , 2014). Codon partitions gene and chains were run for 10 million generations, using  Tracer (Rambaut et al. , 2018)  to confirm stationarity and mixing. Maximum Clade Credibility (MCC) tree was obtained through TreeAnnotator 1. 10. 4 and the generations before reaching stability were discarded as burn-in. For the mt dataset, TreeAnnotator did not allow to recover an MCC tree, which is consistent with the lack of convergence observed in Tracer.
Therefore Bayesian inference was computed with MrBayes 3. 2. 6  (Ronquist & Huelsenbeck, 2003)  in PhyloSuite  (Zhang et al. , 2020). The reconstruction was visualized in R 4. 1 (R Core Team, 2021). Three molecular delineation approaches were run separately on the COI, rhodopsin, and mitochondrial concatenated datasets: (i) Assemble Species by Automatic Partitioning (ASAP;  Puillandre et al. , 2021) , (ii) the multi-rate Poisson Tree Processes (mPTP) method  (Zhang et al. , 2013) , and (iii) a single threshold General Mixed Yule-Coalescent (GMYC) approach  (Fujisawa & Barraclough, 2013)  implemented with the R 4. 1 package "splits"  (Ezart et al. , 2009; R Core Team, 2021). Additionally, Refined Single Linkage (RESL) analysis was performed on the COI dataset. RESL is used for the barcode identification numbers (BINs) system implemented in BOLD.
| Phylogenic reconstruction of Cirripectes For the COI dataset, the nucleotide substitution model with codon partition had less good fit than the single model; hence, the GTR + F + I + G4 model was selected for the analysis (Appendix S4). For the mitochondrial concatenated dataset sequences, the bestfit partitioning scheme was GTR + I + G4. For rhodopsin, different partition models were used. While TVM + F + G was the best-fit partitioning scheme for the first codon position, this scheme was unfortunately not implemented in BEAST. However, it was equivalent to the GTR + F + I + G4 model with fixed AG rate parameters (1. 0; Bagley, 2018). For the second and third codon positions, F81 + F + G4 and GTR + F + G4 were respectively selected. Maximum-likelihood and BI-based phylogenetic reconstructions for COI resulted in tree topologies with marked similarities (Figure  2 ).
For the 17 species in the dataset, the COI trees recovered well-supported clades within the genus. However, the branching order of these clades presented differences among methods. Clades 6 and 7 were sister species in the BI analysis, while clade 6 was closer to clade 8 within the ML approach. These incongruent results were probably related to the short branch lengths at the base of clades 1-8. Cirripectes appear to be a monophyletic genus relative to outgroups (Figure  2 ). Cirripectes collected in the Mascarenes were present in three clusters within two separate larger clades of the trees (Figure  2 ). For the mitochondrial dataset, both ML and BI trees strongly supported the grouping of our specimens in three clades (Appendix S5). For the rhodopsin dataset, both BI and ML trees had poorly supported clades (not shown) probably because of the low variability of sequences (1.
| Molecular species delimitation Based on the COI dataset, the ASAP molecular species delimitation approach divided the sequences into 16 groups, while the GMYC and BIN subdivided the COI dataset into 17 groups, and mPTP subdivided into 19 groups (Figure  2 ; ESM 1). For the sequences from specimens identified as C. filamentosus and Cirripectes chelomatus, GMYC, BIN, and mPTP methods divided sequences according to geographic origin (the western Indian and western Pacific oceans, respectively) and distinct morphological characters  (Williams, 1988). The mPTP method was the only one that subdivided specimens identified as Cirripectes matakaro into two groups, as was the case for those identified as Cirripectus variolosus. These two subdivisions were not supported by the other methods and they will not be considered further here.
| Molecular delimitation of Cirripectes The number of clusters recovered by molecular species delineation approaches using the COI gene depends on the method used. In our case, the number of recovered clusters varied from 16 to 19. The ASAP delimitation approach generated less clusters than the treebased methods GMYC and mPTP, which is consistent with the literature  (Dvořák et al. , 2022; Kekkonen & Hebert, 2014; Puillandre et al. , 2021). These results highlight the importance of performing multiple molecular approaches to determine the congruent clusters. However, using multiple molecular markers (ideally from mitochondrial and nuclear DNA) combined with geographically wide sampling is needed to resolve remaining uncertainties. In addition, independent evidence, such as ecological data or morphological characters must be examined on all the specimens for integrative taxonomy and validation of the molecular species hypothesis  (Puillandre et al.
| Cirripectes in the Mascarene Islands The type localities of two Cirripectes species are in the Mascarene Islands. The holotype of Salarias castaneus Valenciennes in Cuvier and Valenciennes (  1836 ) was collected at Isle de France (Mauritius). This species was later assigned to Cirripectes and, according to  Williams (1988) , several times erroneously synonymized with C. variolosus (e. g. ,  Smith, 1959)   et al. , 2009; Letourneur et al. , 2004). Heemstra et al. (2004)  provided a preliminary fish list for Rodrigues and referred to the earlier studies of Gunther (  1879 ), de Baissac (1968) and  Fricke (1999)  as problematic, due to misidentifications and undocumented sight records  (Heemstra et al. , 2004). The Cirripectes sequences found in public databases were produced by studies not focused on Cirripectes but on taxonomically broad barcoding efforts of Indo-Pacific coral-reef fishes  (Hubert et al.
| Extending and using DNA databases for specimen identification It is of utmost importance to share molecular datasets that can be cross-checked and used openly for taxonomic or identification purposes. Private datasets limit error detection and correction, and the comparability of many current metabarcoding studies is limited because of the inaccessibility of the datasets used for taxon assignment. The newly added sequences expand the reference   Williams, 2020). The presence and problem of misidentified specimens in reference databases are well documented, even for Indo-Pacific fishes  (Leis, 2015; Pentinsaari et al. , 2020). In fact, even when authors are aware of this problem, the wrong assignation may occur. Indeed, if a specimen is assigned to a BOLD BIN that contains specimens assigned to different species with no obvious errors about the geographic distribution, deciding which name is correct is problematic.
The genome areas targeted by COI and Teleo primers had a divergence >3% and thus allow automated species identification using the commonly used threshold for discriminating potential species. However, for the 12S targeted by the Teleo primers, only one sequence was available as a reference for this genus before our study, therefore, only the COI barcodes could truly be used for species identification. In the future, primer limitations for eDNA surveys will be overcome with the development of shotgun sequencing for the eDNA, by direct sequencing of total eDNA and bypassing the PCR limitations associated with metabarcoding to provide insights into community composition  (Taberlet et al. , 2012; Tringe & Rubin, 2005). Currently, this approach is still limited by the completeness of the reference databases, in terms of species diversity (as barcoding) and in terms of reference genomes coverage (e.
nomes as part of the current effort to complete the inventory of teleosts in French territories led by the Muséum national d'Histoire naturelle (MNHN). Having available complete mitogenomes enables the construction of more robust phylogenies, but the current paucity of mitogenomes in public databases makes such analyses premature. Finally, we explored the nucleotide divergences between Cirripectes species found in the Mascarene Islands to assess the performance of current mini-barcodes used to detect teleosts species in eDNA studies. Specimen collection Specimens were collected from 54 ARMS deployed between September 2014 and August 2021 at two islands of the Mascarene Archipelago (South-West Indian Ocean): along the western and south-western coasts of Reunion Island (10 sites) and along the North coast of Rodrigues (3 sites).
cytochrome oxidase I (further called COI dataset; N = 296; ESM 1), (ii) nuclear rhodopsin (further called Rho dataset; ESM 2) for which 53 sequences were used corresponding to 17 homozygotes and 2 × 18 heterozygotes (NGS reads were checked for gene versions); for haplotype analyses, 70 sequences were used corresponding to 35 specimens with two alleles, and (iii) a dataset consisting of the concatenated two rRNA (12S and 16S) and 13 coding DNA sequence (CDS: ND1, ND2, COI, COII, ATPase 8, ATPase 6, COIII, ND3, ND4L, ND4, ND5, ND6, and Cyt b) from the complete F I G U R E 1 Cirripectes species distribution inferred from the COI dataset based on molecular delimitation analyses. AUS, Australia; CAL, New Caledonia; FIJ, Fiji; FPA, French Polynesia, Austral Islands; FPL, French Polynesia, Leeward Islands; FPM, French Polynesia, Marquesas and Society Islands; FPT, French Polynesia, Tuamotu-Gambier; HAW, Hawaii; JAP, Japan; KIR, Kiribati; MAR, Marshall Islands; NZE, New Zealand; RAP, Rapa Nui; REU, Reunion; ROD, Rodrigues; SAF, South Africa; SAU, Saudi Arabia; SEY, Seychelles; TAI, Taiwan; TON, Tonga; WAF, Wallis and Futuna.
The size of pie charts is proportional to the number of samples. mitogenome (henceforth called mt dataset; N = 24). Based on the Blenniidae phylogeny of Lin and Hastings (2013), we selected sequences from multiple outgroup species (COI: N = 5; Rho: N = 4; mt: N = 4) from the recognized tribes Ophioblennius macclurei, Omobranchus elegans, Omobranchus obliquus, Petroscirtes breviceps, Salarias fasciatus, and Ecsenius bicolor (Appendix S3).
under collection numbers MNHN-IC-2023-0216 to MNHN-IC-2023-0254. The sequences produced in this study were deposited in the BOLD dataset "Cryptic fishes from IO ARMS" (IOACT) and in Genbank under accession numbers presented in Appendix S2; the specimens were deposited in the collections of the MNHN. We generated 34 complete COI sequences representing 22 haplotypes. Including public sequences from BOLD and GenBank databases, the COI dataset was composed of 296 sequences of 506 bp from 15 species names and two undescribed groups, including 15 public BOLD BINs and 18 localities (Figure1).
grouping and high levels of genetic structure, with Fst = 0. 94 (p <. 001) for COI. Moreover, a high percentage variation (94. 59%) was observed for COI among species while a low percentage variation (5. 41%) occurred within species (Appendix S7). Population pairwise tests also revealed that COI haplotypes were significantly genetically different in 113 of 136 comparisons (p <. 05; Appendices S8 and S9). Most non-significant values were obtained for comparison with Cirripectes obscurus due to the insufficient number of sequences (N = 1; Table2). For rhodopsin, the AMOVA results also supported the above species grouping (for species present in the dataset: Fst = 0. 86; p <. 001;Appendix S7). The haplotype networks based on COI sequences were computed for each of the 17 species from the molecular delineation analyses (Figure2).
Caledonia and one by Reunion and Australia; Figure 2). The C. randalli network displayed one haplotype common to both Mascarene localities (only one specimen for Rodrigues) and one C. stigmaticus haplotype was shared among Indo-South Pacific localities (Reunion, Rodrigues, Fiji, Wallis & Futuna, and Tonga). Compared to other species included in the dataset, only C. castaneus and C. stigmaticus contained specimens from Indo-Pacific localities. The haplotype network computed on the rhodopsin F I G U R E 2 Ultrametric BEAST Bayesian Inference (left) and Maximum-Likelihood (right) trees of COI mitochondrial dataset, with a graphical representation of the results of the ASAP, GMYC, and mPTP molecular species delimitation analyses, BIN clustering from BOLD (RESL), and the resulting consensus clusters (Cons.
castaneus (Accession number OP749996) with that of C. stigmaticus (OP575312) was 16,485 bp long and contained 1162 variable characters. The uncorrected pairwise distance overall between this pair of taxa was 7. 1% (p-distance; Srivathsan & Meier, 2012). The alignment of the complete mitogenome of C. stigmaticus with that of C. randalli (OP749983) was 16,489 bp long and contained 1795 variable characters corresponding to an uncorrected pairwise distance of 10. 9% (p-distance). The divergence between species was calculated specifically for four fragments amplified by several commonly used primers pairs (Table3). The PCR in silico failed for the MiFish primers pair (Miya et al. , 2015)  as no binding site was found for the F I G U R E 3 Sliding window analyses of the alignment between C. castaneus and C.
New Caledonia and one by Reunion and Australia; Figure 2). The C. randalli network displayed one haplotype common to both Mascarene localities (only one specimen for Rodrigues) and one C. stigmaticus haplotype was shared among Indo-South Pacific localities (Reunion, Rodrigues, Fiji, Wallis & Futuna, and Tonga). Compared to other species included in the dataset, only C. castaneus and C. stigmaticus contained specimens from Indo-Pacific localities. The haplotype network computed on the rhodopsin F I G U R E 2 Ultrametric BEAST Bayesian Inference (left) and Maximum-Likelihood (right) trees of COI mitochondrial dataset, with a graphical representation of the results of the ASAP, GMYC, and mPTP molecular species delimitation analyses, BIN clustering from BOLD (RESL), and the resulting consensus clusters (Cons.
20457758, 2023, 3, Downloaded from https://onlinelibrary. wiley. com/doi/10. 1002/ece3. 9850 by Ifremer -Centre Atlantique, Wiley Online Library on [17/03/2023]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License dataset generated similar but less detailed information in terms of haplotype diversity, due to the lack of representation by available sequences (Appendix S10). No haplotypes were shared by species among the specimens studied.
For this reason, we can confirm with certitude the presence of C. castaneus, C. stigmaticus, and C. randalli in Reunion and Rodrigues. In the same way the COI marker is highly useful for Cirripectes identification, the mitochondrial dataset provided here should allow the detection of the three 'missing' species with an eDNA metabarcoding study and resolve the uncertainty about their occurrence in the Mascarene. among studies. Moreover, C. cas- taneus collected with ARMS had smaller sizes (median of 37 mm) than rotenone-collected specimens from shallow reef flats (median of 71 mm; JHB, pers. comm. ), suggesting that ARMS provide habitat for juvenile individuals following recruitment. Molecular studies are not limited by morphological identifica- tion and allow reliable identification of specimens and matching.
20457758, 2023, 3, Downloaded from https://onlinelibrary. wiley. com/doi/10. 1002/ece3. 9850 by Ifremer -Centre Atlantique, Wiley Online Library on [17/03/2023]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License COUËDEL et al. | 13 of 17 public DNA database of Cirripectes to 85 individual sequences. The new sequences are all attached to a specimen deposited in a regis- tered collection and correspond therefore to genseq-3 (collection- vouchered non-types) according to the nomenclature of Chakrabarty et al. (2013). Of these, 24 represent the first mitogenome sequences for the genus and these three species. These additions will support future studies using mitochondrial markers other than COI for speci- men identification or phylogenetic reconstruction.
Available com- plete mitogenomes enable the selection of the most appropriate marker to respond to the objectives of such studies. Likewise, we deposited the first Cirripectes sequences from Rodrigues for three species and added 23 sequences to the 14 Cirripectes sequences from Reunion. Finally, this study added 45 new sequences for the rhodopsin gene (27 specimens with 18 heterozygotes) to the existing 12 public sequences (8 specimens with 3 heterozygotes). There are still very few Cirripectes sequences for nuclear markers, and the rho- dopsin gene was one of the most represented with eight sequences. Sequences previously deposited in the BOLD and GenBank databases and previous studies allowed us to assign the speci- mens we collected to two taxonomic names. Further analyses re- vealed the existence of misidentified specimens in these databases.