Most downloaded biology preprints, all time
in category zoology
852 results found. For more information, click each entry to expand.
7,813 downloads bioRxiv zoology
The number of dogs in the UK is on the rise, as are canine sports involving the use of a harness to allow the dog to pull against an interface in the same way as a husky might pull a sled. Service dogs and those involved in essential work commonly wear a harness throughout their working lives, yet little is understood regarding the biomechanical impact of their use. This systematic review was conducted to review reported evidence of the biomechanical effects of harness and head collar (Halti) use in dogs. Searches were applied covering 1910 to 2018 on the following databases: PubMed, Web of Science and Writtle Discovery. Three publications were identified as suitable which were then critically evaluated using predefined criteria and ARRIVE based guidelines for bias assessment. Only one was considered to provide the most reliable data regarding the influence of harnesses on gait, whilst the remainder were considered to suffer a variety of issues including poor sample size, repeatability and study execution. The most appropriate study found that wearing a chest strap harness reduced shoulder extension in both walk and trot by up to 8 0 of movement, whilst a Y-shaped harness commonly marketed as non-restrictive reduced shoulder extension by up to 10 0 of movement, suggesting that the use of harness type restraints can affect canine gait, whereas no studies were found relating to the biomechanical effects of head-collar usage
4,545 downloads bioRxiv zoology
Like the Dodo and Passenger Pigeon before it, the predatory marsupial Thylacine (Thylacinus cynocephalus), or 'Tasmanian tiger', has become an iconic symbol of human-caused extinction. The last captive animal died in 1936, but even today reports of the Thylacine's possible ongoing survival in remote regions of Tasmania are newsworthy and capture the public's imagination. Extirpated from mainland Australia in the mid-Holocene, the large island of Tasmania became the species' final stronghold. Following European settlement in the 1800s, the Thylacine was heavily persecuted and pushed to the margins of its range, although many sightings were reported thereafter, even well beyond the 1930s. To gain a new depth of insight into the extinction of the Thylacine, we assembled an exhaustive database of 1,237 observational records from Tasmania (from 1910 onwards), quantified their uncertainty, and charted the patterns these revealed. We also developed a new method to visualize the species' 20th-century spatio-temporal dynamics, to map potential post-bounty refugia and pinpoint the most-likely location of the final persisting subpopulation. A direct reading of the high-quality records (confirmed kills and captures, in combination with sightings by past Thylacine hunters and trappers, wildlife professionals and experienced bushmen) implies a most-likely extinction date within four decades following the last capture (i.e., 1940s to 1970s). However, uncertainty modelling of the entire sighting record, where each observation is assigned a probability and the whole dataset is then subject to a sensitivity analysis, suggests that extinction might have been as recent as the late 1980s to early 2000s, with a small chance of persistence in the remote south-western wilderness areas. Beyond the intrinsically fascinating problem of reconstructing the final fate of the Thylacine, the new spatio-temporal mapping of extirpation developed herein would also be useful for conservation prioritization and search efforts for other rare taxa of uncertain status.
3,754 downloads bioRxiv zoology
Feathers are one of the defining characteristics of birds and serve a critical role in thermal insulation and physical protection against the environment. Feather structure is known to vary among individuals, and it has been suggested that populations exposed to different environmental conditions may exhibit different patterns in feather structure. We examined both down and contour feathers from two populations of male Torrent Ducks (Merganetta armata) from Lima, Peru, including one high-altitude population from the Chancay-Huaral River at approximately 3500 meters (m) elevation and one low-altitude population from the Chillón River at approximately 1500 m. Down feather structure differed significantly between the two populations. Ducks from the high-altitude population had longer, denser down compared with low-altitude individuals. Contour feather structure varied greatly among individuals but showed no significant difference between populations. These results suggest that the innermost, insulative layer of plumage (the down), may have developed in response to lower ambient temperatures at high elevations. The lack of observable differences in the contour feathers may be due to the general constraints of the waterproofing capability of this outer plumage layer.
3,513 downloads bioRxiv zoology
Wan-Ting He, Xin Hou, Jin Zhao, Jiumeng Sun, Haijian He, Wei Si, Jing Wang, Zhiwen Jiang, Ziqing Yan, Gang Xing, Meng Lu, Marc A Suchard, Xiang Ji, Wenjie Gong, Biao He, Jun Li, Philippe Lemey, Deyin Guo, Changchun Tu, Edward C. Holmes, Mang Shi, Shuo Su
Game animals are wildlife species often traded and consumed as exotic food, and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1725 game animals, representing 16 species and five mammalian orders, sampled across China. From this we identified 71 mammalian viruses, with 45 described for the first time. Eighteen viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high risk viruses. We identified the transmission of Bat coronavirus HKU8 from a bat to a civet, as well as cross-species jumps of coronaviruses from bats to hedgehogs and from birds to porcupines. We similarly identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.
3,473 downloads bioRxiv zoology
Susan L Bartlett, Diego G. Diel, Leyi Wang, Stephanie Zec, Melissa Laverack, Mathias Martins, Leonardo Cardia Caserta, Mary Lea Killian, Karen Terio, Colleen Olmstead, Martha A Delaney, Tracy Stokol, Marina Ivančić, Melinda Jenkins-Moore, Karen Ingerman, Taryn Teegan, Colleen McCann, Patrick Thomas, Denise McAloose, John M Sykes, Paul P Calle
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged as the cause of a global pandemic in 2019-2020. In March 2020 New York City became the USA epicenter for the pandemic. On March 27, 2020 a Malayan tiger (Panthera tigris jacksoni) at the Bronx Zoo in New York City developed a cough and wheezing with subsequent inappetence. Over the next week, an additional Malayan tiger and two Amur tigers (P. t. altaica) in the same building and three lions (Panthera leo krugeri) in a separate building also became ill. The index case was immobilized, and physical examination and bloodwork results were unremarkable. Thoracic radiography and ultrasonography revealed peribronchial cuffing with bronchiectasis, and mild lung consolidation with alveolar-interstitial syndrome, respectively. SARS-CoV-2 RNA was identified by real-time, reverse transcriptase PCR (rRT-PCR) on oropharyngeal and nasal swabs and tracheal wash fluid. Cytologic examination of tracheal wash fluid revealed necrosis, and viral RNA was detected in necrotic cells by in situ hybridization, confirming virus-associated tissue damage. SARS-CoV-2 was isolated from the tracheal wash fluid of the index case, as well as the feces from one Amur tiger and one lion. Fecal viral RNA shedding was confirmed in all seven clinical cases and an asymptomatic Amur tiger. Respiratory signs abated within 1-5 days for most animals, though persisted intermittently for 16 days in the index case. Fecal RNA shedding persisted for as long as 35 days beyond cessation of respiratory signs. This case series describes the clinical presentation, diagnostic evaluation, and management of tigers and lions infected with SARS-CoV-2, and describes the duration of viral RNA fecal shedding in these cases. This report documents the first known natural transmission of SARS-CoV-2 from humans to animals in the USA, and is the first report of SARS-CoV-2 in non-domestic felids. ### Competing Interest Statement The authors have declared no competing interest.
3,313 downloads bioRxiv zoology
We challenge the oft-repeated claim that the beetles (Coleoptera) are the most species-rich order of animals. Instead, we assert that another order of insects, the Hymenoptera, are more speciose, due in large part to the massively diverse but relatively poorly known parasitoid wasps. The idea that the beetles have more species than other orders is primarily based on their respective collection histories and the relative availability of taxonomic resources, which both disfavor parasitoid wasps. Though it is unreasonable to directly compare numbers of described species in each order, the ecology of parasitic wasps - specifically, their intimate interactions with their hosts - allows for estimation of relative richness. We present a simple logical model that shows how the specialization of many parasitic wasps on their hosts suggests few scenarios in which there would be more beetle species than parasitic wasp species. We couple this model with an accounting of what we call the "genus-specific parasitoid-host ratio" from four well-studied genera of insect hosts, a metric by which to generate extremely conservative estimates of the average number of parasitic wasp species attacking a given beetle or other insect host species. Synthesis of our model with data from real host systems suggests that the Hymenoptera may have 2.5 - 3.2x more species than the Coleoptera. While there are more described species of beetles than all other animals, the Hymenoptera are almost certainly the larger order.
3,203 downloads bioRxiv zoology
Abstract: The ascidian tunicate Corella inflata is relatively transparent compared to other solitary tunicates and the circulatory system can be visualized by injecting high molecular weight fluorescein labeled dextran into the beating heart or the large vessels at the ends of the heart. In addition, after staining with neutral red the movement of blood cells can be followed to further define and characterize the circulatory system. The heart is a gently curved tube with a constriction in the middle and extends across the width of the animal. As in other tunicates, pumping is peristaltic and periodically reverses direction. During the abvisceral directional phase blood leaves the anterior end of the heart in two asymmetric vessels that connect to the two sides of the branchial basket (or pharynx), in contrast to the direct connection between the heart and the endostyle seen in the commonly studied tunicate Ciona intestinalis. In Corella inflata blood then flows in both transverse directions through a complex system of ducts in the branchial basket into large ventral and dorsal vessels and then to the visceral organs in the posterior of the animal. During the advisceral phase blood leaves the posterior end of the heart in vessels that repeatedly bifurcate to fan into the stomach and gonads. Blood speed, determined by following individual cells, is high and pulsatory near the heart, but decreases and becomes more constant in peripheral regions. Estimated blood flow volume during one directional phase is greater than the total volume of the animal. Circulating blood cells are confined to vessels or ducts in the visible parts of the animal and retention of high molecular weight dextran in the vessels is comparable to that seen in vertebrates. These flow patterns are consistent with a closed circulatory network. Additional key words: heart, pharynx, branchial basket, blood circulation, blood velocity
3,083 downloads bioRxiv zoology
Invertebrate biodiversity remains poorly explored although it comprises much of the terrestrial animal biomass, more than 90% of the species-level diversity, and supplies many ecosystem services. The main obstacle is specimen- and species-rich samples. Traditional sorting techniques require manual handling and are slow while molecular techniques based on metabarcoding struggle with obtaining reliable abundance information. Here we present a fully automated sorting robot which detects each specimen, images and measures it before moving it from a mixed invertebrate sample to the well of a 96-well microplate in preparation for DNA barcoding. The images are used by a newly trained convolutional neural network (CNN) to assign the specimens to 14 particularly common classes of insects (N=14) in Malaise trap samples. The average assignment precision for the classes is 91.4 % (75-100 %). In order to obtain biomass information, the specimen images are also used to measure specimen length and estimate body volume. We outline how the DiversityScanner robot can be a key component for tackling and monitoring invertebrate diversity. The robot generates large numbers of images that become training sets for CNNs once the images are labelled with identifications based on DNA barcodes. In addition, the robot allows for taxon-specific subsampling of large invertebrate samples by only removing the specimens that belong to one of the 14 classes. We conclude that a combination of automation, machine learning, and DNA barcoding has the potential to tackle invertebrate diversity at an unprecedented scale.
2,891 downloads bioRxiv zoology
Sarah A Hamer, Alex Pauvolid-Correa, Italo B Zecca, Edward Davila, Lisa D Auckland, Christopher M. Roundy, Wendy Tang, Mia K Torchetti, Mary Lea Killian, Melinda Jenkins-Moore, Katie Mozingo, Yao Akpalu, Ria R Ghai, Jessica R Spengler, Casey Barton Behravesh, Rebecca Fischer, Gabriel L. Hamer
The natural infections and epidemiological roles of household pets in SARS-CoV-2 transmission are not understood. We conducted a longitudinal study of dogs and cats living with at least one SARS-CoV-2 infected human in Texas and found 47.1% of 17 cats and 15.3% of 59 dogs from 25.6% of 39 households were positive for SARS-CoV-2 via RT-PCR and genome sequencing or neutralizing antibodies. Virus was isolated from one cat. The majority (82.4%) of infected pets were asymptomatic. Re-sampling of one infected cat showed persistence of viral RNA at least 32 d-post human diagnosis (25 d-post initial test). Across 15 antibody-positive animals, titers increased (33.3%), decreased (33.3%) or were stable (33.3%) over time. A One Health approach is informative for prevention and control of SARS-CoV-2 transmission.
2,834 downloads bioRxiv zoology
The free-living marine flatworm Macrostomum lignano is a powerful model organism to study mechanisms of regeneration and stem cell regulation due to its convenient combination of biological and experimental properties, including the availability of transgenesis methods, which is unique among flatworm models. However, due to its relatively recent introduction in research, there are still many biological aspects of the animal that are not known. One of such questions is the influence of the culturing temperature on Macrostomum biology. Here we systematically investigated how different culturing temperatures affect the development time, reproduction rate, regeneration, heat shock response, and gene knockdown efficiency by RNA interference in M. lignano. We used marker transgenic lines of the flatworm to accurately measure the regeneration endpoint and to establish the stress response threshold for temperature shock. We found that compared to the culturing temperature of 20°C commonly used for M. lignano, elevated temperatures of 25°C-30°C substantially speed-up the development and regeneration time and increase reproduction rate without detectable negative consequences for the animal, while temperatures above 30°C elicit a heat shock response. We show that altering the temperature conditions can be used to shorten the time required to establish M. lignano cultures, store important lines and optimize the microinjection procedures for transgenesis. Our findings will help to optimize the design of experiments in M. lignano and thus facilitate future research in this model organism.
2,792 downloads bioRxiv zoology
A new endemic subspecies of gray wolf from the island of Sicily (Italy) is described. While usually considered extinct before 1940, there's some evidence it may have survived up to 1970. This wolf was widespread throughout the island and characterized by a smaller size and a paler coloration than the Apennine wolf (Canis lupus italicus) from Central-Southern Italy. This subspecies is described from a mounted specimen (the holotype) including also a separate skull stored at the Museo di Storia Naturale "La Specola", Universita di Firenze, Italy. The three paratypes are: a) a mounted specimen stored at the "Museo Regionale Interdisciplinare di Terrasini" in Terrasini (PA), Italy, b) a mounted specimen stored at the Museo di Zoologia "Pietro Doderlein", Universita di Palermo, Palermo, Italy, c) a mounted specimen stored at the "Museo Civico Baldassarre Romano" in Termini Imerese (PA), Italy. This new subspecies is described as Canis lupus cristaldii subsp. nov. We suggest "Sicilian wolf" as common name for this new taxon.
2,560 downloads bioRxiv zoology
The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria (=Planulozoa), also seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that the support for Planulozoa can be assigned to this source of systematic error. In interpreting this placozoan-cnidarian clade, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.
2,410 downloads bioRxiv zoology
Accurate species delimitation and description are necessary to guide effective conservation management of imperiled species. The Eastern Indigo Snake (Drymarchon couperi) is a large species in North America that is federally-protected as Threatened under the Endangered Species Act. Recently, two associated studies hypothesized that Drymarchon couperi is two species. Here, we use diverse approaches to test the two-species hypothesis for D. couperi. Our analyses reveal that (1) phylogenetic reconstruction in Krysko et al. (2016a) was based entirely on analysis of mitochondrial DNA sequence data, (2) microsatellite data demonstrate significant nuclear gene flow between mitochondrial lineages and a clear isolation-by-distance pattern across the species entire range, and (3) morphological analyses recover a single diagnosable species. Our results reject recent conclusions of Krysko et al. (2016a,b) regarding species delimitation and taxonomy of D. couperi, and we formally place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA may be driven by high dispersal of males relative to females. We caution against species delimitation exercises when one or few loci are used without evaluation of contemporary gene flow, particularly species with strong sex-biased dispersal (e.g., squamates) and/or when results have implications for ongoing conservation efforts.
2,327 downloads bioRxiv zoology
The Portuguese man of war, Physalia physalis , is a siphonophore that uses a gas-filled float as a sail to catch the wind. It is one of the most conspicuous, but poorly understood members of the pleuston, a community of organisms that occupy a habitat at the sea-air interface. The development, morphology, and colony organization of P. physalis is very different from all other siphonophores. Here, we propose a framework for homologizing the axes with other siphonophores, and also suggest that the tentacle bearing zooids should be called tentacular palpons. We also look at live and fixed larval and non-reproductively mature juvenile specimens, and use optical projection tomography to build on existing knowledge about the morphology and development of this species. Previous descriptions of P. physalis larvae, especially descriptions of budding order, were often framed with the mature colony in mind. However, we use the simpler organization of larvae and the juvenile specimens to inform our understanding of the morphology, budding order, and colony organization in the mature specimen. Finally, we review what is known about the ecology and lifecyle of P. physalis .
2,285 downloads bioRxiv zoology
A taxonomic revision of the cichlid fish genus Petrochromis endemic to Lake Tanganyika. All recognized taxa are herein described, one subspecies is given species status and five new species, viz. P. calliris, P. daidali, P. heffalumpus, P. lisachisme and P. paucispinis, are presented. P. calliris is described from 6 specimens from Cape Mpimbwe, and distinguished primarily by having a high number of both gill rakers on the lower limb of the first gill arch and vertebrae. P. daidali is described from 18 specimens from Cape Mpimbwe, Kansombo and Nkwazi point, and distinguished primarily by males having a labyrinth-like pattern on the head. P. heffalumpus is described from 7 specimens from Cape Mpimbwe, and distinguished primarily by its great size. P. lisachisme is described from 12 specimens from Cape Mpimbwe and Lyamembe, and distinguished primarily by having a high number of dorsal spines. P. paucispinis is described from 4 specimens from Halembe, and distinguished primarily by having a low number of dorsal spines. A revised key to Petrochromis is included. A phylogenetic tree hypothesis of the genus, based on molecular (mitochondrial cytochrome b and d-loop) and morphological results show that jaw position and number of vertebrae are important diagnostic characters. Analyses suggest that the "ancestral Petrochromis" might have looked something like P. orthognathus.
2,278 downloads bioRxiv zoology
Background: Most species of owls (Strigidae) represent cryptic species and their taxonomic study is in flux. In recent years, two new species of owls of the genus Strix have been described from the Arabian peninsula by different research teams. It has been suggested that one of these species, S. omanensis, is not a valid species but taxonomic comparisons have been hampered by the lack of specimens of S. omanensis, and the poor state of the holotype of S. butleri. Methods: Here we use new DNA sequence data to clarify the taxonomy and nomenclature of the S. butleri complex. We also report the capture of a single S. butleri in Mashhad, Iran. Results: A cytochrome b sequence of S. omanensis was found to be identical to that of the holotype of S. butleri, indicating that the name S. omanensis is best regarded as a junior synonym of S. butleri. The identity of the S. butleri captured in Mashhad, Iran, was confirmed using DNA sequence data. This represents a major (1,400 km) range extension of this species. Conclusions: The population discovered in Oman in 2013 and originally named ‘S. omanensis’ actually represents the rediscovery of S. butleri, which was known from a single specimen and had not been recorded since 1878. The range of S. butleri extends into northeast Iran. Our study augments the body of evidence for the recognition of S. butleri and S. hadorami as separate species and highlights the importance of using multiple evidence to study cryptic owl species.
2,089 downloads bioRxiv zoology
Crustaceans are a morphologically, physiologically and ecologically highly diverse animal group and correspondingly diverse are their reproductive characteristics. They have evolved structural specialities with respect to penis construction, sperm form, sperm storage, fertilization and brood care. Unique in the animal kingdom are safety lines that safeguard hatching and first molting. Further curiosities are dwarf males in parasitic and sessile taxa and bacteria-induced gigantism and infectious feminization in crustacean hosts. Record-breaking features in animals are relative penis length, clutch size, sperm size, chromosome number, viability of resting eggs, and fossil ages of penis, sperm and brooded embryos. These reproductive peculiarities are reviewed and their implication for basic and applied biology is discussed, including the early evolution and diversification of brood care in arthropods, sperm competition and assurance of paternity, posthumous paternity and sustainable male-based fishery, and ecotype changes by man-made pollution.
2,047 downloads bioRxiv zoology
Linnaean taxonomy is a cornerstone of Western biology in which organisms are given a two-part name (a genus and species), creating biological units that help us order and manage our knowledge of the living world. In this system, the names of species themselves take on additional functions, such as describing features of the organism or honoring individuals (known as eponyms). Here, we interrogate how power and authority over the natural world are claimed through Western scientific naming practices to evaluate the legacies of imperialism, dispossession, and exclusion in these practices. We compile and analyze a dataset of all bird species descriptions from 1950 to present, asking: who has access and power to name species, and who is honored in species names? We show that 95% of newly described species are described from the global South, but the majority of species and eponyms are described by authors, and named after individuals, from the global North. We find an increase through time in authors from the global South, which is associated with a rise in eponyms that honor individuals from global South countries. However, this formal inclusion of global South authors has not translated into increases in first authorship (a primary form of credit and authority in Western science). We contextualize these disparities in naming and authorship within broader global structures of access and power put in place through centuries of European and U.S. imperialism, but a historical perspective alone ignores institutional and individual agency and incentives in present-day actions. As we increasingly reflect on the social foundations and impacts of our science, these findings show how research and labor in the global South continue to be disproportionately translated into power and authority in the global North, upholding and re-enacting imperial structures of domination.
1,996 downloads bioRxiv zoology
Artificial insemination is routinely used in commercial pig breeding, for which the use of high quality semen samples is imperative. Currently, semen quality is determined manually by morphological assessment. This method leads to high inter-operator variability due to its subjective nature. The development of a semi-automated software-based approach to assess sperm morphology would enable faster identification of morphological defects and permit identification of subtle differences that may affect fertilisation success. Here we have used a novel method to comprehensively analyse pig sperm nuclear morphology in greater detail than was previously possible. Semen samples from 50 fertile and 50 sub-fertile samples that had been previously manually categorised as fertile or sub-fertile were analysed using this new method, with at least 200 fixed and DAPI (4',6-diamidino-2-phenylindole) stained sperm heads imaged per sample. Differences in sperm nuclear morphology were observed between fertile and sub-fertile samples; specifically, fertile samples were associated with higher mean nuclear area, a consequence of a greater head width and a lower variability between sperm heads. This novel, unbiased and fast analysis method demonstrates a significant difference in sperm head morphology between fertile and sub-fertile animals, and has the potential to be further developed and used as a tool for sperm morphology assessment in the pig breeding industry.
1,771 downloads bioRxiv zoology
A small, juvenile rorqual live-stranded on Qeshm Island, Iran, in the northern Strait of Hormuz (Persian Gulf) in September 2007. Cause of stranding remains unknown but the whale (QE22.09.2007) showed no severe traumatic injuries nor was emaciated. Based on at least seven morphological features, considered diagnostic in combination, allowed a positive identification as Omura's whale Balaenoptera omurai. Features included diminutive body size (397 cm), a large number of ventral grooves (n=82) extending caudad of the umbilicus, a strongly falcate dorsal fin, asymmetric colouration of the head (especially lower jaws) reminiscent of fin whale, including three unilateral dark stripes, faint/incomplete lateral rostral ridges, record low number of short, broad baleen plates (204 in right jaw). The likelihood for the existence of a local B. omurai population in the eastern Persian Gulf or northern Arabian Sea seems higher than the wandering of a very young animal or mother/calf pair from any of the known distant distribution areas in the eastern Indian Ocean or SW Indian Ocean (Madagascar). This is the first record of B. omurai in the NW Indian Ocean.
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