skip to main content

Search for: All records

Creators/Authors contains: "Scott, J."

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Free, publicly-accessible full text available April 1, 2023
  2. Free, publicly-accessible full text available March 1, 2023
  3. Ge, Deyan (Ed.)
    Abstract Biologists have long pondered the extreme limits of life on Earth, including the maximum elevation at which species can live and reproduce. Here we review evidence of a self-sustaining population of mice at an elevation that exceeds that of all previously reported for mammals. Five expeditions over 10 years to Volcán Llullaillaco on the Argentina/Chile border observed and collected mice at elevations ranging from 5,070 m at the mountain’s base to the summit at 6,739 m (22,110 feet). Previously unreported evidence includes observations and photographs of live animals and mummified remains, environmental DNA, and a soil microbial community reflectingmore »animal activity that are evaluated in combination with previously reported video recordings and capture of live mice. All of the evidence identifies the mouse as the leaf-eared mouse Phyllotis vaccarum, and it robustly places the population within a haplotype group containing individuals from the Chilean Atacama Desert and nearby regions of Argentina. A critical review of the literature affirms that this population is not only an elevational record for mammals but for all terrestrial vertebrates to date, and we further find that many extreme elevations previously reported for mammals are based on scant or dubious evidence.« less
    Free, publicly-accessible full text available April 5, 2023
  4. Free, publicly-accessible full text available November 1, 2022
  5. Abstract Background The Aedes aegypti mosquito is a threat to human health across the globe. The A. aegypti genome was recently re-sequenced and re-assembled. Due to a combination of long-read PacBio and Hi-C sequencing, the AaegL5 assembly is chromosome complete and significantly improves the assembly in key areas such as the M/m sex-determining locus. Release of the updated genome assembly has precipitated the need to reprocess historical functional genomic data sets, including cis -regulatory element (CRE) maps that had previously been generated for A. aegypti. Results We re-processed and re-analyzed the A. aegypti whole embryo FAIRE seq data to createmore »an updated embryonic CRE map for the AaegL5 genome. We validated that the new CRE map recapitulates key features of the original AaegL3 CRE map. Further, we built on the improved assembly in the M/m locus to analyze overlaps of open chromatin regions with genes. To support the validation, we created a new method (PeakMatcher) for matching peaks from the same experimental data set across genome assemblies. Conclusion Use of PeakMatcher software, which is available publicly under an open-source license, facilitated the release of an updated and validated CRE map, which is available through the NIH GEO. These findings demonstrate that PeakMatcher software will be a useful resource for validation and transferring of previous annotations to updated genome assemblies.« less
    Free, publicly-accessible full text available December 1, 2022
  6. Mendoza-Lera, Clara (Ed.)
    Hyporheic exchange is now widely acknowledged as a key driver of ecosystem processes in many streams. Yet stream ecologists have been slow to adopt nuanced hydrologic frameworks developed and applied by engineers and hydrologists to describe the relationship between water storage, water age, and water balance in finite hydrosystems such as hyporheic zones. Here, in the context of hyporheic hydrology, we summarize a well-established mathematical framework useful for describing hyporheic hydrology, while also applying the framework heuristically to visualize the relationships between water age, rates of hyporheic exchange, and water volume within hyporheic zones. Building on this heuristic application, wemore »discuss how improved accuracy in the conceptualization of hyporheic exchange can yield a deeper understanding of the role of the hyporheic zone in stream ecosystems. Although the equations presented here have been well-described for decades, our aim is to make the mathematical basis as accessible as possible and to encourage broader understanding among aquatic ecologists of the implications of tailed age distributions commonly observed in water discharged from and stored within hyporheic zones. Our quantitative description of “hyporheic hydraulic geometry,” associated visualizations, and discussion offer a nuanced and realistic understanding of hyporheic hydrology to aid in considering hyporheic exchange in the context of river and stream ecosystem science and management.« less
    Free, publicly-accessible full text available January 14, 2023
  7. Free, publicly-accessible full text available November 1, 2022
  8. Free, publicly-accessible full text available November 1, 2022
  9. The increasing study of emerging wildlife pathogens and a lack of policy or legislation regulating their translocation and use has heightened concerns about laboratory escape, species spillover, and subsequent epizootics among animal populations. Responsible self-regulation by research laboratories, in conjunction with institutional-level safeguards, has an important role in mitigating pathogen transmission and spillover, as well as potential interspecies pathogenesis. A model system in disease ecology that highlights these concerns and related amelioration efforts is research focused on amphibian emerging infectious diseases. Whereas laboratory escape of amphibian pathogens has not been reported and may be rare compared with introduction events frommore »trade or human globalization, the threat that novel disease outbreaks with mass mortality effects pose to wild populations warrants thorough biosecurity measures to ensure containment and prevent spillover. Here, we present a case study of the laboratory biosecurity concerns for the emerging amphibian fungal pathogen Batrachochytrium salamandrivorans . We conclude that proactive biosecurity strategies are needed to integrate researcher and institutional oversight of aquatic wildlife pathogens generally, and we call for increased national and international policy and legislative enforcement. Furthermore, taking professional responsibility beyond current regulations is needed as development of legal guidance can be slow at national and international levels. We outline the need for annual laboratory risk assessments, comprehensive training for all laboratory personnel, and appropriate safeguards specific to pathogens under study. These strategies are critical for upholding the integrity and credibility of the scientific community and maintaining public support for research on wildlife diseases.« less
    Free, publicly-accessible full text available December 16, 2022
  10. Free, publicly-accessible full text available April 21, 2023