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Scholarly Works (5 results)

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Frontiers of Biogeography, Volume 11, Issue 1 (2019)

Recent climatic models suggest the late Pleistocene was colder and had different precipitation regimes from the present. If this climatic shift occurred more rapidly than species could adapt, species likely shifted their ranges as populations moved in concert with suitable environmental conditions. We examined changes in altitudinal and horizontal distribution in response to past climate change of amphibian species from different elevational zones and habitat requirements in the Eastern Cordillera of the Colombian Andes. We used environmental information and species occurrence data to model the distribution of 14 amphibian species (seven highland and seven lowland) which we projected to the Last Glacial Maximum (LGM) using two past climatic reconstructions. For these 14 species, we studied the predicted elevational and areal shifts. In agreement with palynological-derived models for Andean flora, we predicted that the elevation of montane amphibians shifted downwards increasing their total altitudinal range. We did not detect any evidence of compression related to drier lowlands. In some cases, the wider distribution areas of high-elevation amphibians during the LGM overlapped with contemporary distributions implying that these areas are present-day refugia for some species. Lowland species showed little or no elevational changes across time, but their areal distributions changed depending on habitat requirements. Four lowland frog species occurring in present-day xeric environments showed substantial range expansion across the lowlands during the LGM, while two species occurring in humid habitats likely expanded their ranges since the LGM. Since the LGM ended, ranges of mid‐ to high-elevation species shrank and shifted to higher elevation. Lowland species in xeric or open habitats have also experienced shrinking ranges, with some evidence that they have been moving upwards. Thus, low- and high-elevation species may be at risk under predicted anthropogenic climate change. Our results generate spatial hypotheses about amphibian responses to climate change that can be tested with phylogeographic data.

 

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Cover page: Testing effects of Pleistocene climate change on the altitudinal and horizontal distributions of frogs from the Colombian Andes: a species distribution modeling approachCreative Commons 'BY' version 4.0 license
  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2021)

Background

Limiting the incidence of opioid-naïve patients who transition to long-term opioid use (i.e., continual use for > 90 days) is a key strategy for reducing opioid-related harms.

Objective

To identify variables constructed from data routinely collected by prescription drug monitoring programs that are associated with opioid-naïve patients' likelihood of transitioning to long-term use after an initial opioid prescription.

Design

Statewide cohort study using prescription drug monitoring program data PARTICIPANTS: All opioid-naïve patients in California (no opioid prescriptions within the prior 2 years) age ≥ 12 years prescribed an initial oral opioid analgesic from 2010 to 2017.

Methods and main measures

Multiple logistic regression models using variables constructed from prescription drug monitoring program data through the day of each patient's initial opioid prescription, and, alternatively, data available up to 30 and 60 days after the initial prescription were constructed to identify probability of transition to long-term use. Model fit was determined by the area under the receiver operating characteristic curve (C-statistic).

Key results

Among 30,569,125 episodes of patients receiving new opioid prescriptions, 1,809,750 (5.9%) resulted in long-term use. Variables with the highest adjusted odds ratios included concurrent benzodiazepine use, ≥ 2 unique prescribers, and receipt of non-pill, non-liquid formulations. C-statistics for the day 0, day 30, and day 60 models were 0.81, 0.88, and 0.94, respectively. Models assessing opioid dose using the number of pills prescribed had greater discriminative capacity than those using milligram morphine equivalents.

Conclusions

Data routinely collected by prescription drug monitoring programs can be used to identify patients who are likely to develop long-term use. Guidelines for new opioid prescriptions based on pill counts may be simpler and more clinically useful than guidelines based on days' supply or milligram morphine equivalents.
    Cover page: Using Prescription Drug Monitoring Program Data to Assess Likelihood of Incident Long-Term Opioid Use: a Statewide Cohort Study.
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2022)
    A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
      Cover page: Standards recommendations for the Earth BioGenome Project
      • Article
      • Peer Reviewed
      UC Santa Cruz Previously Published Works (2021)
      High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
        Cover page: Towards complete and error-free genome assemblies of all vertebrate species
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2022)
        Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
          Cover page: Global urban environmental change drives adaptation in white cloverCreative Commons 'BY-NC-ND' version 4.0 license
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