The meadow jumping mouse genome and transcriptome suggest mechanisms of hibernation [preprint]

Hibernating mammals exhibit medically relevant phenotypes, but the genetic basis of hibernation remains poorly understood. Using the meadow jumping mouse (Zapus hudsonius), we investigated the genetic underpinnings of hibernation by uniting experimental and comparative genomic approaches. We assembled a Z. hudsonius genome and identified widespread expression changes during hibernation in genes important for circadian rhythm, membrane fluidity, and cell cycle arrest. Tissue-specific gene expression changes during torpor encompassed Wnt signaling in the brain and structural and transport functions in the kidney brush border. Using genomes from the closely related Zapus oregonus (previously classified as Z. princeps) and leveraging a panel of hibernating and non-hibernating rodents, we found selective pressure on genes involved in feeding behavior, metabolism, and cell biological processes potentially important for function at low body temperature. Leptin stands out with elevated conservation in hibernating rodents, implying a role for this metabolic hormone in triggering fattening and hibernation. These findings illustrate that mammalian hibernation requires adaptation at all levels of organismal form and function and lay the groundwork for future study of hibernation phenotypes

Mammal collections of the Western Hemisphere: A survey and directory of collections

As a periodic assessment of the mammal collection resource, the Systematic Collections Committee (SCC) of the American Society of Mammalogists undertakes decadal surveys of the collections held in the Western Hemisphere. The SCC surveyed 429 collections and compiled a directory of 395 active collections containing 5,275,155 catalogued specimens. Over the past decade, 43 collections have been lost or transferred and 38 new or unsurveyed collections were added. Growth in number of total specimens, expansion of genomic resource collections, and substantial gains in digitization and web accessibility were documented, as well as slight shifts in proportional representation of taxonomic groups owing to increasingly balanced geographic representation of collections relative to previous surveys. While we find the overall health of Western Hemisphere collections to be adequate in some areas, gaps in spatial and temporal coverage and clear threats to long-term growth and vitality of these resources have also been identified. Major expansion of the collective mammal collection resource along with a recommitment to appropriate levels of funding will be required to meet the challenges ahead for mammalogists and other users, and to ensure samples are broad and varied enough that unanticipated future needs can be powerfully addressed. © 2018 The Author(s)

Imaging biomarker roadmap for cancer studies.

Imaging biomarkers (IBs) are integral to the routine management of patients with cancer. IBs used daily in oncology include clinical TNM stage, objective response and left ventricular ejection fraction. Other CT, MRI, PET and ultrasonography biomarkers are used extensively in cancer research and drug development. New IBs need to be established either as useful tools for testing research hypotheses in clinical trials and research studies, or as clinical decision-making tools for use in healthcare, by crossing 'translational gaps' through validation and qualification. Important differences exist between IBs and biospecimen-derived biomarkers and, therefore, the development of IBs requires a tailored 'roadmap'. Recognizing this need, Cancer Research UK (CRUK) and the European Organisation for Research and Treatment of Cancer (EORTC) assembled experts to review, debate and summarize the challenges of IB validation and qualification. This consensus group has produced 14 key recommendations for accelerating the clinical translation of IBs, which highlight the role of parallel (rather than sequential) tracks of technical (assay) validation, biological/clinical validation and assessment of cost-effectiveness; the need for IB standardization and accreditation systems; the need to continually revisit IB precision; an alternative framework for biological/clinical validation of IBs; and the essential requirements for multicentre studies to qualify IBs for clinical use.Development of this roadmap received support from Cancer Research UK and the Engineering and Physical Sciences Research Council (grant references A/15267, A/16463, A/16464, A/16465, A/16466 and A/18097), the EORTC Cancer Research Fund, and the Innovative Medicines Initiative Joint Undertaking (grant agreement number 115151), resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and European Federation of Pharmaceutical Industries and Associations (EFPIA) companies' in kind contribution

Collection of Scientific Specimens:Benefits for Biodiversity Sciences and Limited Impacts on Communities of Small Mammals

Despite increasing use of specimens from natural-history collections, continued field sampling has met with growing resistance attributable to changing societal values. Widespread perception persists that the removal of individuals from wild populations will affect the integrity of natural communities. Ecological studies often document the resilience of wildlife to sustainable removal and the negligible contributions to mortality of scientific collecting compared with those of other natural or anthropogenic-induced causes. Nevertheless, few studies have directly assessed the consequences of specimen removal on populations or communities. We present long-term ecological research data that suggest removal trapping has negligible impacts on the species richness, diversity, or abundance of small mammals. The maintenance and future growth of natural-history archives for integrated biodiversity sciences may hinge on increased dedication to specimen vouchering across ecological and evolutionary disciplines and wider acceptance by regulatory authorities and funding agencies. The effects of low-intensity collecting should be investigated for other taxa and across biomes. community ecology, long-term research, museum voucher, natural-history collections, removal trappingacceptedVersio

Data from: Using biogeographic history to inform conservation: the case of Preble’s meadow jumping mouse

The last Pleistocene deglaciation shaped temperate and boreal communities in North America. Rapid northward expansion into high latitudes created distinctive spatial genetic patterns within species that include closely related groups of populations that are now widely spread across latitudes, while longitudinally adjacent populations, especially those near the southern periphery, often are distinctive due to long-term disjunction. Across a spatial expanse that includes both recently colonized and long-occupied regions, we analyzed molecular variation in zapodid rodents to explore how past climate shifts influenced diversification in this group. By combining molecular analyses with species distribution modeling and tests of ecological interchangeability, we show that the lineage including the Preble's meadow jumping mouse (Zapus hudsonius preblei), a US federally listed taxon of conservation concern, is not restricted to the southern Rocky Mountains. Rather, populations along the Front Range are part of a single lineage that is ecologically indistinct and extends to the far north. Of the 21 lineages identified, this Northern lineage has the largest geographic range and low measures of intra-lineage genetic differentiation, consistent with recent northward expansion. Comprehensive sampling combined with coalescent-based analyses and niche modeling lead to a radically different view of geographic structure within jumping mice and indicates the need to re-evaluate their taxonomy and management. This analysis highlights a premise in conservation biology, that biogeographic history should play a central role in establishing conservation priorities

SDM_records

High-quality, natural history museum-based samples obtained from MANIS (Jan-2011) and down-sampled (aka thinned) to 10km radius to offset sampling bias. Taxa are lineage-based assignments for each species used in niche modeling

Cytb alignment by group (sets)

Nexus file of 762 samples of DNA sequence data for the cytochrome b gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies). Also includes a taxon set conforming to the 21 jumping mice lineages and 4 species

BRCA alignment

Ninety-two samples of sequence data from the BRCA gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies)