PeerJ

There is a reproducibility crisis in scientific studies. Some of these crises arise from incorrect application of statistical tests to data that follow inappropriate distributions, have inconsistent equivariance, or have very small sample sizes. As determining which test is most appropriate for all data in a multicategorical study (such as comparing taxa between sites in microbiome studies), we present statsSuma, an interactive Python notebook (which can be run from any desktop computer using the Google Colaboratory web service) and does not require a user to have any programming experience. This software assesses underlying data structures in a given dataset to advise what pairwise or listwise statistical procedure would be best suited for all data. As some users may be interested in further mining specific trends, statSuma performs 5 different two-tailed pairwise tests (Students t-test, Welchs t-test, Mann-Whitney U-test, Brunner-Munzel test, and a pairwise Kruskal-Wallis H-test) and advises the best test for each comparison. This software also advises whether ANOVA or a multicategorical Kruskal-Wallis H-test is most appropriate for a given dataset and performs both procedures. A data distribution-vs-Gaussian distribution plot is produced for each taxon at each site and a variance plot between all combinations of 2 taxa at each site are produced so Gaussian tests and variance tests can be visually confirmed alongside associated statistical determinants.

Wildlife may be attracted or repelled by anthropogenic stimuli - by understanding these responses we gain powerful tools to modify their behavior. Anthropogenic lighting is ubiquitous but little is known about how it influences carnivores. We focused on pumas (Puma concolor) living around Los Angeles, California for which vehicular collision is an important source of mortality. We used GPS collars to track their movement around roads and combined this with ground-level and remotely sensed data of human generated nighttime light to see how that influenced activity around roads. There are multiple landscape level scales, and metrics of light relevant at each scale, that influence the perceptual landscape of wildlife and thus these different scales must be considered. We found that, at a broad spatial scale, pumas crossed roads more frequently in areas with low levels of anthropogenic light (controlling for distance to urbanization). However, while pumas crossed roads in darker parts of the landscape at a broad-landscape scale, we did not find a statistically significant relationship between puma eye-level light intensity and predicted road crossing locations. Regarding pumas and nighttime light, it appears that having dark swaths of land, at a broad spatial scale, is important. This is important for puma conservation and road design as little is currently known about wildlife movement response to nighttime light and the ideal placement for mitigation structures. Ultimately, anthropogenic light at night is a landscape aspect that needs to be better understood and integrated into conservation as the human footprint increases.

There are increasing findings of the bivalve transmissible neoplasia derived from the Pacific mussel Mytilus trossulus (MtrBTN) in populations of different Mytilus species worldwide. The Subarctic is an area where this disease has not yet been sought despite the fact that Mytilus spp. are widespread there, and M. trossulus itself is a boreal species. We used cytological and histological techniques to diagnose disseminated neoplasia in a sample of M. trossulus from Magadan in the subarctic Sea of Okhotsk. Neoplasia was identified in 11 of 214 mussels studied. Using mtDNA COI sequencing, we revealed genotypes identical or nearly identical to known MtrBTN ones in the hemolymph of most of the diseased mussels. Both MtrBTN evolutionary lineages have been identified, the widespread MtrBTN2, and MtrBTN1, so far only known from M. trossulus in British Columbia on the other side of the Pacific from Magadan. In addition, MtrBTN2 was represented by two common diverged mtDNA haplolineages. These conclusions have been confirmed for selected cancerous mussels by molecular cloning of COI and additional nuclear and mtDNA genes. On the background of high genetic diversity, different cancers were similar in terms of ploidy (range 4.0 - 5.8n) and nuclear to cell ratio. Our study provides the first description of neoplasia and MtrBTN in mussels from the Sea of Okhotsk and from the Subarctic, of both MtrBTN1 and MtrBTN2 in the same mussel population, and the first direct comparison between these transmissible cancers.

This physio-ecological study investigated the physiology and distribution of Lamellodysidea sp. in Moorea, French Polynesia. Specifically, its distribution was described across three reef types--fringing, mid-barrier, and barrier reefs--as well as across sites between Cooks Bay and Opunohu Bay. Additionally, filtration experiments were conducted to test how temperature impacts filtration efficiency. This is informative when predicting how future ocean temperatures are going to affect sponges success and distribution. Sponge abundance was found to decrease from the fringing reef out to the barrier reef, with the highest number of sponges in the fringing reef, less in the mid-barrier reef, and none found in the barrier reef. Sponges were also unevenly distributed across sites, with sponge abundance clearly increasing as you move away from Cooks Bay. Together, these data show that sponges demonstrate habitat preference that is related to their physiological tolerances. Filtration data showed that over a 3-hour period sponges increase their physiological output when introduced to environments 3-6 degrees Celsius above normal. This suggests that as ocean temperatures warm, sponges are likely to increase their filtration efficiency, thus increasing their ecological role as filter feeders, or struggle to survive at this new level of physiological function.

Shrews in the genus Episoriculus are among the least known mammals in China. It occurs mainly in the Himalayas and the Hengduan Mountains. We report the sequencing and analyses of one mitochondrial gene (Cyt b) and three nuclear genes (Apob, Brca1, and Rag2) for 77 specimens, and analyses of morphological measurements for 56 specimens. Phylogenetic and morphological studies answer three longstanding questions. First, Episoriculus sacratus and E. umbrinus are valid species, and not subspecies of E. caudatus. Second, Pseudosoriculus fumidus is a valid taxon that does not belong to the genus Episoriculus. Third, the genus Episoriculus has eight valid species: E. baileyi, E. caudatus, E. leucops, E. macrurus, E. sacratus, E. soluensis, Episoriculus sp., and E. umbrinus. Ultimately, we erected subgenus Longacauda subgen. nov. for morphologically distinct E. macrurus, which leaves the nominate subgenus Episoriculus with the remaining seven congeners.

It is postulated that tumor tissue microbiome is one of the enabling characteristics that either promote or suppress cancer cells and tumors to acquire certain hallmarks (functional traits) of cancers, which highlights their critical importance to carcinogenesis, cancer progression and therapy responses. However, characterizing the tumor microbiomes is extremely challenging because of their low biomass and severe difficulties in controlling laboratory-borne contaminants, which is further aggravated by lack of comprehensively effective computational approaches to identify unique or enriched microbial species associated with cancers. Here we take advantages of two recent computational advances, one by Poore et al (2020, Nature) that computationally generated the microbiome datasets of 33 cancer types [of 10481 patients, including primary tumor (PT), solid normal tissue (NT), and blood samples] from whole-genome and whole-transcriptome data deposited in "The Cancer Genome Atlas" (TCGA), another termed "specificity diversity framework" (SDF) developed recently by Ma (2023). By reanalyzing Poores datasets with the SDF framework, further augmented with complex network analysis, we produced the following catalogues of microbial species (archaea, bacteria and viruses) with statistical rigor including unique species (USs) and enriched species (ESs) in PT, NT, or blood tissues. We further reconstructed species specificity network (SSN) and cancer microbiome heterogeneity network (CHN) to identify core/periphery network structures, from which we gain insights on the codependency of microbial species distribution on landscape of cancer types, which seems to suggest that the codependency appears to be universal across all cancer types.

Chemical analysis of archeological objects can provide important clues about their purpose and function. In this study, we used scanning electron microscopy (SEM) and chemical spectroscopy (SEM-EDS and XRD) to identify a white residue present on cylindrical rhizoliths from a component at an archaeological site (CA-SNI-25) on San Nicolas Island, California, dated ca. AD 1300 to 1700. The residue was found to consist of biogenic calcite and aragonite particles, different in composition and morphology from the CaCO3 particles in the rhizoliths, but identical to marine shell material. These results, together with observations of surface micro-wear patterning on fishhooks and rhizoliths, replicative experiments, in situ spatial analysis, and other archaeological evidence, show that rhizoliths were used as files in a larger tool kit for crafting shell fishhooks. Our findings shed new light on the technological innovations devised by Native Americans to exploit the rich marine resources surrounding the Channel Islands, and provide the first analytical evidence for the use of rhizoliths as a production tool.

West African chimpanzees (Pan troglodytes verus) are critically endangered, therefore knowing their ecological needs is necessary to implement proper conservation measures, especially in the face of climatic change. We report here the consumption of soil by wild chimpanzees living in Comoe National Park, Ivory Coast. We confirmed through camera-trap recording that chimpanzees of all ages and both sexes consumed it for several years at least in one community and more occasionally in a second one, aided by leaf-sponge tools. Our results suggest that these chimpanzees living in a savanna-forest mosaic may need minerals supplement, including sodium or/and clay to aid digestion, mainly during the dry season.

The nut-cracking behaviour of the chimpanzees of Bossou Forest has been long documented and studied in order to understand ultimate drivers for this form of durophagy by these apes. At sites in which they break open the nuts of the oil palm (Elaeis guineaeensis) on stone anvils with stone hammers, fragments of the tools as well as remnants of the nuts may be deposited into local sediments; however, they may become less visible at the macroscopic level as these sites are no longer used (become dormant). We build upon work that has been done to document this unique cultural heritage in West African chimpanzees by interpreting phytolith assemblages in sediments at active nut-cracking sites (used within the last two months). We compare these assemblages with those found in sediments of sites that have been dormant for ~10 years and sites where chimpanzees have not been observed to access and crack open oil palm nuts with stone tools. We predicted that larger assemblages of spheroid echinates, a phytolith associated with palms, would be found at active nut-cracking sites, however we found no statistical difference between total spheroid echinates (measured as total number found per gram of dry sediment) assemblages produced across active nut-cracking, dormant, or non-nut-cracking sites. This may have been due to small sample size (N[≤]6 sediment samples for each of the three sites) and so further sample collection and analyses are needed for inter-site comparisons. We also measured 2D area (m2), perimeter and maximum diameter of spheroid echinates found in nut endocarps (shells) and leaflets from an oil palm frond. Intra-specific differences from all three measurements were found with these phytoliths being larger in the nut endocarp than the leaflet. This has implications for (re)interpreting the assemblages of spheroid echinate phytoliths at the three sites to determine if there is a greater productivity larger-sized spheroid echinates that fall within the size range of those measured for the nut endocarp (mean maximum diameter of 14.9 m versus 7.8 m for those found in oil palm leaflet). Finally, we argue for the importance of initialising and continuing the interpretation of phytolith assemblages in local sediments that are located near sites where directed plant input by non-human taxa has occurred, in this case, chimpanzees cracking open oil palm nuts using stone tools. This is important to refine our interpretation of phytolith assemblages where human and non-human taxa who use complex foraging strategies share ecological spaces.

ContextAs the COVID-19 pandemic persists around the world, the scientific community continues to produce and circulate knowledge on the deadly disease at an unprecedented rate. During the early stage of the pandemic, preprints represented nearly 40% of all English-language COVID-19 scientific corpus (6, 000+ preprints | 16, 000+ articles). As of mid-August 2020, that proportion dropped to around 28% (13, 000+ preprints | 49, 000+ articles). Nevertheless, preprint servers remain a key engine in the efficient dissemination of scientific work on this infectious disease. But, giving the uncertified nature of the scientific manuscripts curated on preprint repositories, their integration to the global ecosystem of scientific communication is not without creating serious tensions. This is especially the case for biomedical knowledge since the dissemination of bad science can have widespread societal consequences. ScopeIn this paper, I propose a robust method that will allow the repeated monitoring and measuring of COVID-19 preprints publication rate. I also introduce a new API called Upload-or-Perish. It is a micro-API service that enables a client to query a specific preprint manuscripts publication status and associated meta-data using a unique ID. This tool is in active development. DataI use Covid-19 Open Research Dataset (CORD-19) to calculate COVID-19 preprint corpus conversion rate to peer-reviewed articles. CORD-19 dataset includes preprints from arXiv, bioRxiv, and medRxiv. MethodsI utilize conditional fuzzy logic on article titles to determine if a preprint has a published counterpart version in the database. My approach is an important departure from previous studies that rely exclusively on bioRxiv API to ascertain preprints publication status. This is problematic since the level of false positives in bioRxiv metadata could be as high as 37%. FindingsMy analysis reveals that around 15% of COVID-19 preprint manuscripts in CORD-19 dataset that were uploaded on from arXiv, bioRxiv, and medRxiv between January and early August 2020 were published in a peer-reviewed venue. When compared to the most recent measure available, this represents a two-fold increase in a period of two months. My discussion review and theorize on the potential explanations for COVID-19 preprints low conversion rate.

BackgroundThe relationships between tumor and its microbiome are still puzzling, with possible bidirectional interactions. Tumor microbiomes may suppress or stimulate tumor growth on the one hand; on the other hand, tumor growth may exert selection pressure on its microbiomes. There is not any consensus on the mode and/or extension of the bidirectional interactions. The objective of this study is to estimate the selection pressure from the primary tumors on tumor microbiomes by comparing with the selection pressure from the solid normal tissues on their corresponding tissue microbiomes across 20+ cancer types. MethodsWe apply Sloan near neutral theory and big datasets of tumor tissue microbiomes from the TCGA (The Cancer Genome Atlas) databases to achieve the above objective. The near neutral theory model can determine the proportions of above-neutral, neutral and below-neutral species in microbial communities, corresponding with positive, neutral and negative selection pressures from host tissues. By comparing the proportions between the primary tumors and solid normal tissues, we can infer the selection pressure of tumor growth on tissue microbiomes. ResultsWe find that approximately 65% of species in solid normal tissue microbiomes are neutral, and the proportion is only 40% in the primary tumor microbiomes. In contrast, the proportion of positively selected species exceeds 60% in the primary tumor microbiomes. Furthermore, simulations with neutral theory model reveal that most abundant species are mostly neutral, while non-neutral species are in the long tail of the species abundance distributions. ConclusionsTumor growth exerts strong positive selection on resident microbiomes, driving the abundances of certain species above the levels expected by the neutral process. Nevertheless, neutral species are still among the most abundant species, suggesting the necessity to pay close attention to the low-abundance or rare species because they are likely to play a critical role in oncogenesis.

We classify Nepenthes species into 12 functional pitcher types, based on combinations of traits that appear to comprise different syndromes for capturing nutrients, usually from animals. For nine of these types the trapping syndromes are already documented, six targeting live animals (hence carnivorous), and three targeting other nutrient sources (non-carnivorous). Yet, for three pitcher types here is no previous documentation of the syndrome and we do not yet know what sources of nutrients are being targeted. Mapping all these pitcher types on the latest, near comprehensive species-level phylogenomic tree of Nepenthes (Murphy et al. 2019) shows that apart from the ancestral pitcher type 1, most of the remaining pitcher types have evolved independently, in different parts of the phylogenetic tree, usually in several different places. Each of the 12 pitcher types is characterised morphologically and illustrated, its trapping syndrome discussed, and example species are given. An identification key to the 12 pitcher types is presented. The possibility of additional pitcher types being present is discussed. O_FIG O_LINKSMALLFIG WIDTH=96 HEIGHT=200 SRC="FIGDIR/small/852137v1_fig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@bbfa57org.highwire.dtl.DTLVardef@13084e7org.highwire.dtl.DTLVardef@658770org.highwire.dtl.DTLVardef@19eca44_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOType 1 (Fig. 1).C_FLOATNO Ancestral (N. mirabilis) These species have upper pitchers which are more-or-less ovoid-cylindric in shape. The basal, ovoid part, often but not always a little wider than the upper part, is usually separated from the upper, usually cylindrical part by a "hip" or raised ridge that girdles the circumference of the pitcher on the exterior (also present in the six species of pitcher types 7, 8 and 10). Examination of the inner surface shows that the "hip" divides the glossy, broad, basal, fluid-containing, digestive, part (referred to as the "detentive" zone by Macfarlane (1908) because prey are detained here) from the upper opaque, dull, off-white to slightly purple, waxy or "pruinose" zone. This waxy zone is referred to as the "conductive" zone by Macfarlane because it helps conducts the insects downwards to the detentive zone with the digestive fluid. Such type 1 pitchers are shown in Fig. 1, exemplified by the upper pitchers of Nepenthes mirabilis (Lour.) Druce. The waxy zone is so-called because its surface is made up of numerous minute platelets of wax, each platelet like a roof-tile and held on a fragile stalk from the underlying surface. Juniper et al. (1989) documented how the waxy zone functions to prevent animals, usually insects, from leaving the pitchers once they have fallen in. Pressure from a foot placed on a wax "tile" will result in the stalk breaking, so that the insect loses its foothold and may fall back into the pitcher. C_FIG O_FIG O_LINKSMALLFIG WIDTH=111 HEIGHT=200 SRC="FIGDIR/small/852137v1_fig12.gif" ALT="Figure 12"> View larger version (39K): org.highwire.dtl.DTLVardef@1f13b4borg.highwire.dtl.DTLVardef@6bc534org.highwire.dtl.DTLVardef@1600959org.highwire.dtl.DTLVardef@5ee42_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOPitcher type 12. (Fig. 12).C_FLOATNO Flat lip (N. jacquelineae Nepenthes jacquelineae (Sumatra, Sect. Montanae) and N. platychila Ch.C.Lee (Borneo, Sect C.Clarke et al.).. Regiae, Lee 2002) both have all the features of type 3 pitchers: widely funnel-shaped to cup-shaped, non-waxy upper parts of pitchers draining into a more slender cylindrical lower part with viscous liquid. Both species however differ from all type 3 species in their very large, flat, dark red peristomes which can be up to 3.5 cm wide in N. jacquelineae. These peristomes have been speculated to act as a landing platform for large flying insects such as blattid cockroaches and moths, which might act with the contrasting lighter, green pitcher body as a light trap for such prey. It is also possible that such prey are lured into a precarious place above the mouth by the copious nectar produced from the lower surface of the lid from large nectar glands 1.5 mm diam. (Clarke 2001). The morphological convergence between the pitchers of these two species is remarkable. Further investigation of the prey trapped in the wild would be desirable for both species. Nepenthes echinostoma Hook.f. is a species closely related to N. mirabilis but with a remarkably flat and extended peristome which resembles type 3, although it has a different pitcher shape and inner surface C_FIG

This study examines the morphological variations within and between regional populations via geometric morphometrics of larger samples of three-dimensional data of J[o]mon human crania (N = 363, including 146 females, 215 males and two unknown-sex individuals) from 97 sites to investigate the population interactions in the period, which Japanese anthropologists and archaeologists have extensively discussed. The results show that morphological variations are more pronounced within individual populations especially in the principal component one, relating to the facial width, degree of prognathism, and location of occipital areas, in contrast to the relatively smaller variations observed between different phases and geographical regions. This observation is consistent with the possibility that the population interactions of the J[o]mon people had been widespread and continuous, and which has an important implication for their resilience against severe climate changes at that time: The relative stability of the J[o]mon society might be sustained by their frequent interactions with various populations, as suggested by insights from relevant archaeological, ethnographic, and genetic research.

Several metrics exists to evaluate the impact of publications and researchers, but most are based on citation counts, which usually fail to capture the temporal aspect of citations. Time to first citation represents a useful metric for research evaluation, and informs the speed at which scientific knowledge is disseminated through the scientific community. Understanding which factors affect such metrics is important as they impact resource allocation and career progression, besides influencing knowledge promotion across disciplines. Many ecological works rely on species identity, which is the coin of taxonomy. Despite its importance, taxonomy is a discipline in crisis lacking staff, funds and prestige, which ultimately may affect the evaluation and dissemination of taxonomic works. We used a time-to-event analysis to investigate whether taxonomic, socioeconomic, and scientometric factors influence first citation speed across hundreds of ecological and taxonomic articles. Time to first citation differed greatly between these areas. Ecological studies were first cited much faster than taxonomic studies. Multitaxa articles received first citations earlier than studies focused on single major taxonomic groups. Article length and h-index among authors were negatively correlated with time to first citation, while the number of authors, number of countries, and Gross Domestic Product was unimportant. Knowledge dissemination is faster for lengthy, multitaxa, and ecological articles relative to their respective counterparts, as well as for articles with highly prolific authors. We stress that using several unrelated metrics is desirable when evaluating research from different-and even related-disciplines, particularly in the context of professional progression and grant allocation.

Triple-negative breast cancer (TNBC) remains one of the most aggressive breast cancer subtypes and lacks durable targeted therapies. Dysregulation of cell-cycle control, particularly through CDK4/6 signaling, is a defining feature of TNBC biology (Garrido-Castro et al., 2019). Extracts of Moringa oleifera have repeatedly been shown to induce G1-phase arrest in breast cancer models, yet the molecular basis of this phenotype remains unclear (Al-Asmari et al., 2015) (Gaffar et al., 2019). Emerging work on cross-kingdom regulation has raised the possibility that plant-derived microRNAs may, under specific conditions, interact with mammalian transcripts (Zhang et al., 2012) (Chin et al., 2016). Sequence shuffling for the negative control was performed with set.seed(42) to ensure reproducibility. Additional visualisations (nucleotide alignment and thermodynamic analyses) were generated using Python 3 (matplotlib v3.7). Here, we performed a high-stringency computational screen of conserved Moringa microRNAs against 30 genes implicated in TNBC pathogenesis using local sequence alignment. We identify a predicted high-affinity interaction between mol-miR156 and the human CDK4 3' untranslated region (3'UTR), characterized by an uninterrupted 12-nucleotide complementary motif that exceeds canonical mammalian microRNA seed requirements. These findings support the hypothesis that conserved plant microRNAs may exhibit latent structural compatibility with oncogenic human transcripts. While physiological delivery and functional repression are not demonstrated here, this work establishes a molecular framework for future experimental investigation into cross-kingdom RNA interactions relevant to cancer cell-cycle regulation. Impact StatementA high-stringency computational screen identifies latent molecular compatibility between a conserved plant microRNA and the human CDK4 oncogene, establishing a testable framework for cross-kingdom RNA interference in triple-negative breast cancer.

The wintering phase of the Western Burrowing Owl (Athene cunicularia hypugaea) life cycle has received little attention in the literature. Small numbers of Burrowing Owls have been observed and recorded since 2008 in the winter season in Cesar Chavez Park, a 36-ha peninsula that forms part of the waterfront of the City of Berkeley. The relative ease of observation in this setting allows study of their arrival and departure dates, selection of micro-habitats, tolerance of human presence, behavior in inclement weather, and response to avian and canine predator threats. Viewed over a decade, fewer owls arrived, arrived later, left earlier, and spent less time in residence. Most owls settled in shoreline rip-rap or in tall vegetation; only one fourth settled in short grass. Owls chose exposure to rain for as long as two days. Owls varied widely in tolerance to human proximity. Owls successfully dealt with avian predators, but displayed stress and in some cases became casualties of loose Canis lupus familiaris. Recommendations for habitat management follow.

1Freshwater fishes from northern Colombia are reported from the Sincelejo and Ware formations, of Pliocene age. A total of ten taxa have been identified comprising two orders, five families, and nine genera. Characters from dental morphology, fin spines, and cranial bones are provided as taxonomic tools for the study of fossil fishes. All of the taxa are members of groups currently restricted to drainages east of the Andes, suggesting that physical drainage connection was still present by the Pliocene between the Amazon-Orinoco and trans-Andean drainages such as the Magdalena-Cauca, or that these groups persisted in the trans-Andean region at least until Pliocene times. The genera Hemidoras, Serrasalmus, and Trachely-opterichthys are new records for the fossil fish fauna of South America. The genus Zungaro represents a new record for the trans-Andean region, whereas the genus Platysilurus is for the first time in Colombia. Most of these occurrences also represent the youngest occurrences in the fossil record. Literature records are reidentified as Pygocentrus from the La Venta fauna and the earily Oligocene in Peru. These assemblages suggest that the Sincelejo and Ware formations were deposited in rivers of large size that were part of a large drainage network connected to the Amazon-Orinoco despite being currently located west of the Andes. These findings suggest that the Cordillera Oriental and the Merida Andes were not dividing yet the drainage network in northern South America by the middle to late Miocene.

Corals should make excellent models for cross-kingdom regulation research because of their natural animal-photobiont holobiont composition, yet a lack of studies and experimental data restricts their use. Here we integrate new full-length transcriptomes and small RNAs of four common reef-building corals with the published Symbiodinium C1 genome to gain deeper insight into mutual gene regulation in coral-zooxanthella holobionts. We show that zooxanthellae secrete miRNA to downregulate rejection from host coral cells, and that a potential correlation exists between miRNA diversity and physiological activity. Convergence of these holobionts biological functions in different species is also revealed, which implies the low gene impact on bottom ecological niche organisms. This work provides evidence for the early origin of cross-kingdom regulation as a mechanism of self-defense autotrophs can use against heterotrophs, sheds more light on coral-zooxanthella holobionts, and contributes valuable data for further coral research.

In this short note I present a way to enhance GraftM performance and incorporate novel genome-based prokaryotic taxonomy to sequencing data classification.

Sequence transfer and genome remodeling are very frequent events in microorganisms, especially prokaryotes. This is due to the mosaic structure of the genomes, which calls into question the correct classification of genomes in terms of a single gene or a group of genes. We started here, as a first step, the inventory of bioinformatics tools applied to the detection of horizontal sequence transfers in microorganisms in the genomic era by applying bibliometric survey. Our bibliographic analysis allowed us to identify 17 main tools for the detection of chimeras. The first Bellerophon developed in 2004, followed by CCode and Pintail in 2005; Mallard in 2006; Mothur in 2009; Blackbox Chimera in 2010; Perseus, ChimeraSlayer, UCHIME 1 and UCHIME2, and ChimeraScan in 2011; Decipher in 2012; EBARDenovo and FunFrame in 2013; CATCh in 2015; Uchime 2 in 2016 and ChimeraMiner in April 2019. We then described each of these tools, highlighting their operating principles as well as the advantages and limitations of each (specificities, sensitivity, rapidity and frequent updates). The number of articles citing these tools has increased over the years especially for Mothur, Uchime, VSEARCH and ChimeraSlayer, thus demonstrating the interest of researchers in these tools and the need to decipher chimeras in genomic era.