Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets.

To explore complex biological questions, it is often necessary to access various data types from public data repositories. As the volume and complexity of biological sequence data grow, public repositories face significant challenges in ensuring that the data is easily discoverable and usable by the biological research community. To address these challenges, the National Center for Biotechnology Information (NCBI) has created NCBI Datasets.

Are rabid raccoons () ready for the rapture? Determining the geographic origin of rabies virus-infected raccoons using RADcapture and microhaplotypes.

North America is recognized for the exceptional richness of rabies virus (RV) wildlife reservoir species. Management of RV is accomplished through vaccination targeting mesocarnivore reservoir populations, such as the raccoon () in Eastern North America. Raccoons are a common generalist species, and populations may reach high densities in developed areas, which can result in contact with humans and pets with potential exposures to the raccoon variant of RV throughout the eastern United States.

Old specimens for old branches: Assessing effects of sample age in resolving a rapid Neotropical radiation of squirrels.

Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear.

Comparative Analysis of Annotation Pipelines Using the First Japanese White-Eye (Zosterops japonicus) Genome.

Introduced into Hawaii in the early 1900s, the Japanese white-eye or warbling white-eye (Zosterops japonicus) is now the most abundant land bird in the archipelago. Here, we present the first Z. japonicus genome, sequenced from an individual in its invasive range.

Whole-Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (Potos flavus) and Northern Raccoon (Procyon lotor).

Here, we present the initial comparison of the nuclear genomes of the North American raccoon (Procyon lotor) and the kinkajou (Potos flavus) based on draft assemblies. These two species encompass almost 21 Myr of evolutionary history within Procyonidae. Because assemblies greatly impact downstream results, such as gene prediction and annotation, we tested three de novo assembly strategies (implemented in ALLPATHS-LG, MaSuRCA, and Platanus), some of which are optimized for highly heterozygous genomes.

Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul.

Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology.

First Genome Sequence of the Gunnison's Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague.

Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America's grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators.

Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys, Nannosciurinae).

The plain long-nosed squirrels, genus Dremomys, are high elevation species in East and Southeast Asia. Here we present a complete molecular phylogeny for the genus based on nuclear and mitochondrial DNA sequences. Concatenated mitochondrial and nuclear gene trees were constructed to determine the tree topology, and date the tree.

In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA.

Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X.

Taxonomic revision of the olingos (Bassaricyon), with description of a new species, the Olinguito.

We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), lowland species with eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes.