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This short paper aims to present synthetically the genus Sylvilagus of the family Leporidae, order Lagomorpha. The genus Sylvilagus comprises a diverse group of small to medium-sized rabbits, commonly known as cottontails, distributed across North and South America. These adaptable mammals are characterized by a compact build, prominent hind legs, and a distinctive fluffy white tail resembling a cotton ball. Sylvilagus species play vital roles in ecosystem dynamics as herbivores, exhibiting crepuscular behavior and contributing to the balance of various habitats through their feeding habits.

Nesolagus netscheri , a Sumatran striped rabbit, is one of the rarest rabbits in the Leporidae family, and its genetic information is still limited. This study provides the first mitochondrial genome and molecular systematic characterization of the Sumatran striped rabbit, Nesolagus netscheri , Indonesia’s rarest rabbit. It consists of a circular double-stranded DNA of 16,709 bp. It showed that the mitochondrial genome structure of N. netscheri is similar to that of N. timminsi . The mitochondrial genome of N. netscheri contained 22 transfer RNA (tRNA) genes, and all tRNA except for trnS1 showed a characteristic cloverleaf secondary structure. Evidence was found that the atp8 gene of N. netscheri is under positive selection pressure. The phylogenetic analysis shows Leporidae was monophyletic, with Nesolagus at the basal. The study indicates a split between N. netscheri and N. timminsi in the Late Pleistocene around 0.43 million years ago. This research is a fundamental reference for the conservation of the rarest lagomorph species and provides important information for future evolutionary studies in the Leporidae family.

Anthropogenic activities since the European colonization of the North American Great Plains have drastically altered landscape composition and configuration, subsequently affecting native biodiversity. These contemporary human-modified landscapes may affect mammal species’ distributions, diel activity patterns, habitat use, and interspecific interactions, though a better understanding of these effects on mammals occurring in remaining prairie landscapes is needed. To fill this gap, we surveyed 381 randomly selected sites in 2018, 2019, and 2020 using motion-sensing camera traps across the western part of the US state of Kansas (7,160,077 ha). Sites were separated by ≥2 km (x = 8.16 km, SD = 3.61), and cameras were secured to a metal post 40 cm above ground and randomly oriented toward the north or south. We placed an olfactory attractant (mixture of skunk essence and petroleum jelly) on a wooden stake 3 m in front of each camera. Cameras were in place at each site for 28 consecutive days for each year. We manually identified all mammal species detected at each site, collating these data into a database that included taxonomic information for 14 families of mammals (Antilocapridae, Bovidae, Canidae, Cervidae, Cricetidae, Dasypodidae, Didelphidae, Erethizontidae, Felidae, Heteromyidae, Leporidae, Mephitidae, Mustelidae, Procyonidae, Sciuridae, and Muridae) comprising 28 total species. We recorded 31,178 mammal photographs (nonindependent events) over 27,954 camera trap nights during 2018 (n = 10,351), 2019 (n = 9478), and 2020 (n = 8125). Additionally, we included the time and date of each photocapture. Moreover, we gathered survey-specific data useful for modeling species-specific detection along with site-level habitat composition data taken at each site each year. These data will be useful for examining habitat use, species distributions, diel activity patterns, and spatiotemporal interactions between species and across guilds of mammals occurring in a rapidly changing agro-prairie ecosystem. There are no copyright restrictions, but we ask researchers to cite this paper when using these data for publication.

Short Interspersed Elements (SINEs) are eukaryotic non-autonomous retrotransposons that rely on RNA polymerase III (pol III) for transcription. A subset of mammalian SINEs—designated T+ SINEs—harbors a canonical polyadenylation signal (AATAAA), a pol III terminator, and an A-rich tail at their 3′ end, thereby acquiring the unusual ability to undergo AAUAAA-dependent polyadenylation. Here, we delineate the genomic architecture, evolutionary history, and polyadenylation behavior of the C SINE family in Lagomorpha. Comprehensive bioinformatics searches identified 1.2–1.6 million C copies distributed across Leporidae (hares and rabbits) and Ochotonidae (pikas) genomes. Phylogenetic reconstruction resolved two diverged leporid subfamilies, C1 and C2, with C1 predating C2 and comprising five-fold more copies. Only C1 qualifies as a T+ SINE, retaining functional or rudimentary AATAAA motifs and pol III terminators. In contrast, C2 is absent from pika genomes, yet remains retrotranspositionally competent in hares and rabbits. Lineage-specific analyses further reveal episodic activity of certain C1 variants throughout the last 10 million years of pika evolution. Functional assays in transfected HeLa cells demonstrate that AATAAA and an upstream polypyrimidine tract constitute the minimal cis-determinant for efficient C1 transcript polyadenylation. Finally, transcriptome profiling of pre-implantation rabbit embryos indicates that pol III-driven SINE C transcription is activated at the 16-cell stage.

Lagomorpha (lagomorphs), the order of mammals including pikas, hares, and rabbits, is distributed on all continents. The order currently is hypothesized to comprise 12 genera and 108 species, split into two families: Ochotonidae (pikas) and Leporidae (rabbits and hares). Molecular and morphological attempts have been undertaken to resolve the phylogeny of lagomorphs, although chronological relationships are still to be established. The aim of this research was to unravel lagomorph phylogeny using ultraconserved elements. We focused on Romerolagus , in light of its largely unknown phylogenetic relationships and sparse fossil record, to assess times of divergence for the genus. We obtained samples from at least one species in each of 11 genera (except Caprolagus ) comprising the order and captured and sequenced ultraconserved elements (UCEs). A Maximum-Likelihood phylogenetic analysis was carried out on the 4,195 loci captured, resulting in 59,112 informative sites. We further used BEAST2 v2.6.3 on the CIPRES computing cluster to estimate the timing of cladogenesis in lagomorph evolution. Our results confirm that lagomorphs and rodents split about 65 million years ago. The former further split into its constituent families, Leporidae and Ochotonidae, about 60 million years ago. Pronolagus rupestris and Nesolagus timminsi were retrieved as basal sister taxa; the most recent common ancestor of that clade and remaining leporids was estimated to have existed about 47 million years ago. Romerolagus diazi is sister to remaining Leporidae excluding Pronolagus and Nesolagus , a topology that generally matches previously published phylogenies, although our results suggest a most recent common ancestor of Romerolagus and remaining ingroup leporids at ca. 4.8 Ma (95% highest posterior density [HPD] interval: 5.9 – 3.8 Ma), with an internal diversification in the Middle to Late Pleistocene (0.9 Ma; 95% HPD 1.8 – 0.2 Ma). Our final results yielded a robust phylogeny with high support values for every clade of the order Lagomorpha and unraveled previously unresolved phylogenetic relationships. In addition, we further conclude that the method we used, UCEs, may serve to complete the entire phylogeny of mammals by using existing museum specimens.

Directly comparable data on the environmental and socio-economic impacts of alien species informs the effective prioritisation of their management. We used two frameworks, the Environmental Impact Classification for Alien Taxa (EICAT) and Socio-Economic Impact Classification for Alien Taxa (SEICAT), to create a unified dataset on the severity and type of impacts caused by alien leporids (rabbits and hares). Literature was reviewed to collate impact data, which was categorised following EICAT and SEICAT guidelines. We aimed to use these data to identify: (1) alien leporid species with severe impacts, (2) their impact mechanisms, (3) the native species and local communities vulnerable to impacts and (4) knowledge gaps. Native species from a range of taxonomic groups were affected by environmental impacts which tended to be more damaging than socio-economic impacts. Indirect environmental impacts were particularly damaging and underreported. No impact data were found for several alien leporid species.

Analyzing predator scats for the presence of prey is a common noninvasive approach to understanding trophic interactions. Morphological analysis of prey remains has been the prevailing method of diet analysis, but molecular methods are becoming more widely used. Previous analyses suggest molecular methods detect target prey species more frequently than morphological methods. We compared these methods by analyzing coyote (Canis latrans) scats—collected in Tooele County, Utah, USA, in the winter of 2014—for leporids, a taxonomic group for which a molecular species identification test has been developed. We included 25 scats in which leporids were detected and 25 scats in which leporids were not detected by morphological methods. Additionally, because few studies have explored the effect of fecal sampling protocols on prey DNA detection, we analyzed subsamples taken from 5 locations on each scat to compare prey detection frequencies. We found that molecular analysis detected leporid prey in scats at a rate similar to or greater than morphological analysis, depending on the number of fecal sampling locations considered. Of the single samples, the homogenized (46%) and side (44%) samples provided the greatest rates of leporid prey DNA detection, followed by the ends (mean across both ends = 35%) and center (38%) of scats. When multiple sampling locations were considered, the homogenized-side combination (70%) had a detection rate similar to when all sampling locations were considered (76%). Our results indicate that molecular analysis detected prey more frequently than morphological analysis, but that prey detection was not equitable among fecal sampling locations and multiple sampling locations may be required.

Background The density of questing ticks infected with tick-borne pathogens is an important parameter that determines tick-borne disease risk. An important factor determining this density is the availability of different wildlife species as hosts for ticks and their pathogens. Here, we investigated how wildlife communities contribute to tick-borne disease risk. The density of Ixodes ricinus nymphs infected with Borrelia burgdorferi ( sensu lato ), Borrelia miyamotoi , Neoehrlichia mikurensis and Anaplasma phagocytophilum among 19 forest sites were correlated to the encounter probability of different vertebrate hosts, determined by encounter rates as measured by (camera) trapping and mathematical modeling. Result We found that the density of any tick life stage was proportional to the encounter probability of ungulates. Moreover, the density of nymphs decreased with the encounter probability of hare, rabbit and red fox. The density of nymphs infected with the transovarially-transmitted B. miyamotoi increased with the density of questing nymphs and the encounter probability of bank vole. The density of nymphs infected with all other pathogens increased with the encounter probability of competent hosts: bank vole for Borrelia afzelii and N. mikurensis , ungulates for A. phagocytophilum and blackbird for Borrelia garinii and Borrelia valaisiana . The negative relationship we found was a decrease in the density of nymphs infected with B. garinii and B. valaisiana with the encounter probability of wood mouse. Conclusions Only a few animal species drive the densities of infected nymphs in forested areas. There, foxes and leporids have negative effects on tick abundance, and consequently on the density of infected nymphs. The abundance of competent hosts generally drives the abundances of their tick-borne pathogen. A dilution effect was only observed for bird-associated Lyme spirochetes.

New variants in the SARS‐CoV‐2 pandemic are more contagious (Alpha/Delta), evade neutralizing antibodies (Beta), or both (Omicron). This poses a challenge in vaccine development according to WHO. We designed a more universal SARS‐CoV‐2 DNA vaccine containing receptor‐binding domain loops from the huCoV‐19/WH01, the Alpha, and the Beta variants, combined with the membrane and nucleoproteins. The vaccine induced spike antibodies crossreactive between huCoV‐19/WH01, Beta, and Delta spike proteins that neutralized huCoV‐19/WH01, Beta, Delta, and Omicron virus in vitro . The vaccine primed nucleoprotein‐specific T cells, unlike spike‐specific T cells, recognized Bat‐CoV sequences. The vaccine protected mice carrying the human ACE2 receptor against lethal infection with the SARS‐CoV‐2 Beta variant. Interestingly, priming of cross‐reactive nucleoprotein‐specific T cells alone was 60% protective, verifying observations from humans that T cells protect against lethal disease. This SARS‐CoV vaccine induces a uniquely broad and functional immunity that adds to currently used vaccines. Synopsis This work describes the design and evaluation of a new type of genetic COVID‐19 vaccine, containing three binding domains from three SARS‐CoV‐2 variants combined with the M and the N proteins. The DNA vaccine induces high levels of broadly cross‐reactive and neutralizing antibodies to multiple SARS‐CoV‐2 variants. The vaccine primes broadly cross‐reactive T cells that even recognize Bat SARS‐COV sequences. The vaccine completely protects K18 mice from lethal disease caused by a challenge with the SARS‐CoV‐2 Beta variant. The data supports clinical data of this completely new DNA vaccine design. Graphical Abstract This work describes the design and evaluation of a new type of genetic COVID‐19 vaccine, containing three binding domains from three SARS‐CoV‐2 variants combined with the M and the N proteins.

Australia has multiple lagoviruses with differing pathogenicity. The circulation of these viruses was traditionally determined through opportunistic sampling events. In the lead up to the nationwide release of RHDVa-K5 (GI.1aP-GI.1a) in 2017, an existing citizen science program, RabbitScan, was augmented to allow members of the public to submit samples collected from dead leporids for lagovirus testing. This study describes the information obtained from the increased number of leporid samples received between 2015 and 2022 and focuses on the recent epidemiological interactions and evolutionary trajectory of circulating lagoviruses in Australia between October 2020 and December 2022. A total of 2771 samples were tested from January 2015 to December 2022, of which 1643 were lagovirus-positive. Notable changes in the distribution of lagovirus variants were observed, predominantly in Western Australia, where RHDV2-4c (GI.4cP-GI.2) was detected again in 2021 after initially being reported to be present in 2018. Interestingly, we found evidence that the deliberately released RHDVa-K5 was able to establish and circulate in wild rabbit populations in WA. Overall, the incorporation of citizen science approaches proved to be a cost-efficient method to increase the sampling area and enable an in-depth analysis of lagovirus distribution, genetic diversity, and interactions. The maintenance of such programs is essential to enable continued investigations of the critical parameters affecting the biocontrol of feral rabbit populations in Australia, as well as to enable the detection of any potential future incursions.