The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

General guidelines for use of wild mammal species are updated from the 1998 version approved by the American Society of Mammalogists (ASM) and expanded to include additional resources. Included are details on marking, housing, trapping, and collecting mammals. These guidelines cover current professional techniques and regulations involving mammals used in research. Institutional animal care and use committees, regulatory agencies, and investigators should review and approve procedures concerning use of vertebrates at any particular institution. These guidelines were prepared and approved by the ASM, whose collective expertise provides a broad and comprehensive understanding of the biology of nondomesticated mammals in their natural environments.

/pdf/guidelines-of-the-american-society-of-mammalogists-for-the-2g7v778e1f.pdf

Guidelines of the american society of mammalogists for the use of wild mammals in research

The past two decades have seen an increasing number of virulent infectious diseases in natural populations and managed landscapes. In both animals and plants, an unprecedented number of fungal and fungal-like diseases have recently caused some of the most severe die-offs and extinctions ever witnessed in wild species, and are jeopardizing food security. Human activity is intensifying fungal disease dispersal by modifying natural environments and thus creating new opportunities for evolution. We argue that nascent fungal infections will cause increasing attrition of biodiversity, with wider implications for human and ecosystem health, unless steps are taken to tighten biosecurity worldwide.

/pdf/emerging-fungal-threats-to-animal-plant-and-ecosystem-health-2dipzrtz7g.pdf

Emerging fungal threats to animal, plant and ecosystem health.

Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals.

http://media.longnow.org/files/2/REVIVE/nature05634.pdf

The delayed rise of present-day mammals

Guidelines for use of wild mammal species in research are updated from [Sikes et al. (2011)][1]. These guidelines cover current professional techniques and regulations involving the use of mammals in research and teaching; they also incorporate new resources, procedural summaries, and reporting requirements. Included are details on capturing, marking, housing, and humanely killing wild mammals. It is recommended that Institutional Animal Care and Use Committees (IACUCs), regulatory agencies, and investigators use these guidelines as a resource for protocols involving wild mammals, whether studied in the field or in captivity. These guidelines were prepared and approved by the American Society of Mammalogists (ASM), in consultation with professional veterinarians experienced in wildlife research and IACUCs, whose collective expertise provides a broad and comprehensive understanding of the biology of nondomesticated mammals. The current version of these guidelines and any subsequent modifications are available online on the Animal Care and Use Committee page of the ASM website ( ). Additional resources pertaining to the use of wild animals in research are available at: .

Resumen Los lineamientos para el uso de especies de mamiferos de vida silvestre en la investigacion con base en [Sikes et al. (2011)][1] se actualizaron. Dichos lineamientos cubren tecnicas y regulaciones profesionales actuales que involucran el uso de mamiferos en la investigacion y ensenanza; tambien incorporan recursos nuevos, resumenes de procedimientos y requisitos para reportes. Se incluyen detalles acerca de captura, marcaje, manutencion en cautiverio y eutanasia de mamiferos de vida silvestre. Se recomienda que los comites institucionales de uso y cuidado animal (cifras en ingles: IACUCs), las agencias reguladoras y los investigadores se adhieran a dichos lineamientos como fuente base de protocolos que involucren mamiferos de vida silvestre, ya sea investigaciones de campo o en cautiverio. Dichos lineamientos fueron preparados y aprobados por la ASM, en consulta con profesionales veterinarios experimentados en investigaciones de vida silvestre y IACUCS, de quienes cuya experiencia colectiva provee un entendimiento amplio y exhaustivo de la biologia de mamiferos no-domesticados. La presente version de los lineamientos y modificaciones posteriores estan disponibles en linea en la pagina web de la ASM, bajo Cuidado Animal y Comite de Uso: ( ). Recursos adicionales relacionados con el uso de animales de vida silvestre para la investigacion se encuentran disponibles en ( ).

 [1]: #ref-69

/pdf/2016-guidelines-of-the-american-society-of-mammalogists-for-3an7mvie1s.pdf

2016 Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education.

Several house bat specimens superficially resembling the white-bellied house bat Scotophilus leucogaster (Cretzschmar, 1830), were recently captured in southwestern Ethiopia and southern South Sudan. These S . cf. leucogaster differed from typical S. leucogaster by their slightly smaller size and ventral coloration, conforming instead with the original description of S . altilis Allen, 1914. Scotophilus altilis is an overlooked taxon known from the Blue Nile region in Sudan that is currently considered a junior synonym of S . leucogaster . Phylogenetic analysis of mitochondrial cytochrome b gene ( cytb ) sequences revealed S . cf. leucogaster as a sister clade to S . leucogaster with a genetic distance of ca. 10%. Comparative specimens of questionable S . nigritellus de Winton, 1899 from northwestern Ethiopia and a wing biopsy sample of another S . cf. leucogaster from western Kenya also fell within this clade. Sequence data from two nuclear markers ( zfy and fgb7 ) corroborated the distinction of S . cf. leucogaster from S . leucogaster . Likewise, morphometric analysis of cranial data largely supported this distinction, as well as taxonomic affiliation with S . altilis based on comparison with the only available paratype specimen. The position of this paratype specimen within the new Scotophilus clade, inferred from analysis of a short fragment of cytb , confirmed its taxonomic identity. Based on the presented evidence, the overlooked East African taxon S. altilis should be resurrected as a full species within the genus Scotophilus .

DeeAnn M. Reeder

Papers

Resurrection of an East African house bat species Scotophilus altilis Allen, 1914 (Chiroptera: Vespertilionidae)

CETAF-DiSSCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary

Misconceptions and misinformation about bats and viruses.

SARS-CoV-2 Compatible ACE2 Receptors in Little Brown Bats ( Myotis lucifugus)

Interdisciplinary Insights from the Plague of Cyprian: Pathology, Epidemiology, Ecology and History