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Open Access Publications from the University of California

Scholarly Works (14 results)

  • Article
Research Reports (2020)

Recent studies have highlighted alarming rates of declines in bird populations across the country. The State of California is home to over 650 resident and migrant avian species. Legislation for protecting these species has existed for over a century now, yet tools for identifying populations and understanding seasonal movement remain limited. Recently, genetic and genomic tools have provided a method for understanding population structure, allowing for more informed delineation of management units. The goal of this project was to create a genetic toolkit for identifying breeding populations and assigning individuals to those populations. Ultimately, such tools could be used to assess population-level impacts when there are conflicts with birds at infrastructure construction sites. As a test case, we sequenced entire genomes for 40 individual Anna’s hummingbirds (Calypte anna) from across the state. Based on this initial data, we found low levels of differentiation between sampled locations, suggesting that C. anna in California are not subdivided into different population units. However, there was a weak signal of geography suggesting there may be localized genetic differences in a small proportion of the genome. Follow-up work will focus on a broader sampling across the state of California to clarify any possible population subdivision or geographical patterns of differentiation.

View the NCST Project Webpage

    Cover page: Genetic Toolkit for Assessment and Prediction of Population-Level Impacts of Bridge Construction on Birds
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2020)
    Hummingbirds are essential pollinators in many ecosystems, making their conservation critical. As is the case with many species, hummingbirds are now facing a variety of challenges resulting from anthropogenic changes. As populations shift and species interactions change, disease is likely to pose a significant threat. There is a basic understanding of which pathogens currently affect a variety of hummingbird species, however there is a paucity of information about their immune systems capacity to kill pathogens and what specific factors may affect immunity. The objective of this study was to gain a basic understanding of the effect of age, sex, and molt on the constitutive innate immunity of hummingbirds. An in vitro assay was used to assess the microbiocidal capacity of the whole blood of Annas Hummingbirds (Calypte anna) against three different microbes: Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Candida albicans (C. albicans). The effect of age, sex and molt on anti-microbial capacity varied based on the microbe type. After-hatch-year birds tended to have better anti-microbial capacity compared to hatch-year birds. Male birds had higher anti-microbial activity than female birds, although this was not observed against C. albicans. Molting birds had a weaker antimicrobial activity against E. coli and S. aureus than birds that were not molting. These results represent an important first step towards defining the parameters of constitutive innate immunity of Annas Hummingbirds as well as providing important knowledge about factors that should be considered when evaluating the health of wild populations.
      Cover page: Anti-microbial activity of whole blood and plasma collected from Annas Hummingbirds (Calypte anna) against three different microbes.Creative Commons 'BY' version 4.0 license
      • Article
      Policy Briefs (2020)

      Recent research suggests that bird populations are declining at alarming rates across the United States. Over the last century, local, national, and international efforts to limit declines in bird populations have resulted in state and federal laws that now protect most of California’s 650 bird species. To comply with these protections, transportation infrastructure projects often face strict mitigation requirements, which can be expensive and cause delays. Understanding a project’s effects on specific bird populations can refine mitigation requirements and optimize infrastructure planning.

      The tools for identifying separate populations within species and understanding protected birds’ seasonal movement have been limited until recently. New genetic and genomic tools now provide a method for understanding population differentiation, which is vital to a wide array of conservation goals including estimating population declines, identifying potential for adaptation to stressors, measuring connectivity between populations, and estimating inbreeding. Because infrastructure projects can directly impact genetic diversity and connectivity, a toolkit to assess population structure and the distribution of genetic variation could aid in predicting and mitigating the impacts of such projects. As a test case, researchers at the University of California, Davis, sequenced entire genomes for 40 individual Anna’s hummingbirds (Calypte anna) from across California to identify breeding populations and develop a genetic toolkit to assign individuals to those populations. The presence of this species at bridge construction sites has resulted in construction delays in part because little information exists on the status of different populations within the species.

      This research brief summarizes findings and implications from the project.

      View the NCST Project Webpage

        Cover page: Using Genetic Tools to Identify Populations Within Species Could Ease Infrastructure Mitigation
        • Article
        • Peer Reviewed
        LBL Publications (2019)
        This report examines how deploying fuel-saving technologies for new heavy-duty vehicles (HDVs) with gross vehicle weights (GVWs) of 3.5 to 12 tonnes in India could reduce petroleum consumption and carbon dioxide (CO2) emissions. Such HDVs play a vital role in India’s economic growth, but they also consume substantial fuel and produce major environmental impacts. Analyzing the efficiency improvement potential for this category of vehicles helps clarify the potential impacts of fuel efficiency and emission standards for all HDVs in India, the home of 18 of the world’s 100 worst pollution-affected cities (WHO, 2018). This report builds on a previous analysis of Indian heavy-duty vehicles over 12 tonnes.
          Cover page: Improving fuel efficiency for heavy-duty vehicles of 3.5–12 tonnes in India: Benefits, costs, and environmental impacts
          • Article
          • Peer Reviewed
          LBL Publications (2017)
          The main objectives of this analysis are to examine the benefits and costs of fuel-saving technologies for new heavy-duty vehicles (HDVs) in India over the next 10 years and, to explore how various scenarios for the deployment of vehicles with these technologies will impact petroleum consumption and carbon dioxide (CO2) emissions over the next three decades. The study team developed simulation models for three representative HDV types—a 40-tonne tractor-trailer, 25-tonne rigid truck, and 16-tonne transit bus—based on top-selling vehicle models in the Indian market. The baseline technology profiles for all three vehicles were developed using India-specific engine data and vehicle specification information from manufacturer literature and input from industry experts. For each of the three vehicles we developed a comprehensive set of seven efficiency technology packages drawing from five major areas: engine, transmission and driveline, tires, aerodynamics, and weight reduction. Our analysis finds that India has substantial opportunity to improve HDV fuel efficiency levels using cost-effective technologies. Results from our simulation modeling of three representative HDV types—a tractor-trailer, rigid truck, and transit bus—reveal that per-vehicle fuel consumption reductions between roughly 20% and 35% are possible with technologies that provide a return on the initial capital investment within 1 to 2 years. Though most of these technologies are currently unavailable in India, experiences in other more advanced markets such as the US and EU suggest that with sufficient incentives and robust regulatory design, significant progress can be made in developing and deploying efficiency technologies that can provide real-world fuel savings for new commercial vehicles in India over the next 10 years. Bringing HDVs in India up to world-class technology levels will yield substantial petroleum and GHG reductions. By 2030, the fuel and CO2 reductions of the scenarios range from 10% to 34%, and at the end of 2050, these reductions grow to 13% and 41%. If we constrain the analysis to select the most efficient technology package that provides the fleets with payback times of 3 years or less, there are annual fleet-wide savings of roughly 11 MTOE of diesel and 34 MMT of CO2 in 2030, and this grows to 31 MTOE and 97 MMT by 2050.
            Cover page: Improved heavy-duty vehicle fuel efficiency in India, benefits, costs and environmental impacts
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2020)
            BACKGROUND: Avian pox is a viral disease documented in a wide range of bird species. Disease-related detrimental effects can cause dyspnea and dysphagia, and birds with high metabolic requirements, such as hummingbirds, are thus especially vulnerable to the pathogen. Hummingbirds have a strong presence in California, especially in urban environments. However, little is understood regarding the impact of pox virus on hummingbird populations. Currently, diagnosing a pox infection relies on obtaining a tissue biopsy, which poses significant risks to birds and challenges in the field. Understanding the ecology of hummingbird pox viral infections could be advanced by a minimally invasive ante-mortem diagnostic method. Our aim was to address whether pox infections can be diagnosed using integumentary system samples besides tissue biopsies. To meet this goal, we tested multiple integumentary sample types using a quantitative real-time PCR assay. A secondary study goal was to determine which sample types (ranging from minimally to highly invasive sampling) were optimal for identifying infected birds. METHODOLOGY AND PRINCIPAL FINDINGS: Pox-like lesion tissue, pectoral muscle, feathers, toenail clippings, blood, and swabs (both pox-like lesion tissue and non pox-like lesion tissue) were taken from live birds and carcasses of two species of hummingbirds found in California. To maximize successful diagnosis, especially for samples with low viral load, a real-time quantitative PCR assay was developed for detecting the hummingbird-specific Avipoxvirus 4b core protein gene. Avipoxvirus DNA was successfully amplified from all sample types obtained from 27 individuals. These results were compared to those of conventional PCR and comparisons were also made among sample types, utilizing lesion tissue samples as the gold standard. CONCLUSIONS AND SIGNIFICANCE: Hummingbird avian pox can be diagnosed without relying on tissue biopsies. We identify that feather samples, of which contour feathers yielded the best results, can be used for diagnosing infected birds, thus reducing sampling risk. In sum, the real-time PCR assay detected viral DNA in various integumentary system sample types and will be useful in future studies of hummingbird disease ecology.
              Cover page: TaqMan quantitative real-time PCR for detecting Avipoxvirus DNA in various sample types from hummingbirds.Creative Commons 'BY' version 4.0 license
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2020)

              Background

              Avian pox is a viral disease documented in a wide range of bird species. Disease-related detrimental effects can cause dyspnea and dysphagia, and birds with high metabolic requirements, such as hummingbirds, are thus especially vulnerable to the pathogen. Hummingbirds have a strong presence in California, especially in urban environments. However, little is understood regarding the impact of pox virus on hummingbird populations. Currently, diagnosing a pox infection relies on obtaining a tissue biopsy, which poses significant risks to birds and challenges in the field. Understanding the ecology of hummingbird pox viral infections could be advanced by a minimally invasive ante-mortem diagnostic method. Our aim was to address whether pox infections can be diagnosed using integumentary system samples besides tissue biopsies. To meet this goal, we tested multiple integumentary sample types using a quantitative real-time PCR assay. A secondary study goal was to determine which sample types (ranging from minimally to highly invasive sampling) were optimal for identifying infected birds.

              Methodology and principal findings

              Pox-like lesion tissue, pectoral muscle, feathers, toenail clippings, blood, and swabs (both pox-like lesion tissue and non pox-like lesion tissue) were taken from live birds and carcasses of two species of hummingbirds found in California. To maximize successful diagnosis, especially for samples with low viral load, a real-time quantitative PCR assay was developed for detecting the hummingbird-specific Avipoxvirus 4b core protein gene. Avipoxvirus DNA was successfully amplified from all sample types obtained from 27 individuals. These results were compared to those of conventional PCR and comparisons were also made among sample types, utilizing lesion tissue samples as the gold standard.

              Conclusions and significance

              Hummingbird avian pox can be diagnosed without relying on tissue biopsies. We identify that feather samples, of which contour feathers yielded the best results, can be used for diagnosing infected birds, thus reducing sampling risk. In sum, the real-time PCR assay detected viral DNA in various integumentary system sample types and will be useful in future studies of hummingbird disease ecology.
                Cover page: TaqMan quantitative real-time PCR for detecting Avipoxvirus DNA in various sample types from hummingbirds
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2019)
                OBJECTIVE:To estimate the prevalence of ocular disease and obtain normative ocular data for free-living hummingbirds. ANIMALS STUDIED:Two hundred and sixty-three free-living, adult Hummingbirds from coastal and inland central California were studied, including Anna's (Calypte anna, n = 186) and Black-chinned (Archilochus alexandri; n = 77) hummingbirds. PROCEDURES:Slit lamp biomicroscopy and indirect ophthalmoscopy were performed on all individuals. Rebound tonometry, measurement of horizontal palpebral fissure length, and streak retinoscopy were performed on select individuals. Five conscious Anna's Hummingbirds underwent ocular imaging including fundus photography, digital slit lamp photography, and anterior segment and retinal optical coherence tomography. RESULTS:The prevalence of ocular disease in this population was 2.28%. Ocular imaging revealed a thin cornea, shallow anterior chamber, large lens, and a single central, deep convexiclivate fovea. Mean ± SD intraocular pressure was 11.21 ± 2.23 mm Hg. Mean ± SD eyelid length was 2.59 ± 0.19 mm. All eyes were emmetropic or mildly hyperopic with a mean (range) ± SD refractive error of +0.32 (-0.25 to +1) ± 0.33 diopters. CONCLUSIONS:Consistent with previous reports, these data suggest that hummingbirds have visual characteristics found in predatory and prey species, as well as a low prevalence of spontaneous ocular disease. This work provides a set of reference values and clinical findings that can be used in the future research on hummingbird vision and ocular disease. It also provides representative diagnostic images of normal birds and demonstrates that advanced ocular imaging can be performed on manually restrained hummingbirds without pharmacologic dilation.
                  Cover page: Clinical findings and normative ocular data for free‐living Anna's (Calypte anna) and Black‐chinned (Archilochus alexandri) Hummingbirds
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2020)
                  Hummingbirds are essential pollinators in many ecosystems, making their conservation critical. As is the case with many species, hummingbirds are now facing a variety of challenges resulting from anthropogenic changes. As populations shift and species interactions change, disease is likely to pose a significant threat. There is a basic understanding of which pathogens currently affect a variety of hummingbird species, however there is a paucity of information about their immune systems capacity to kill pathogens and what specific factors may affect immunity. The objective of this study was to gain a basic understanding of the effect of age, sex, and molt on the constitutive innate immunity of hummingbirds. An in vitro assay was used to assess the microbiocidal capacity of the whole blood of Anna's Hummingbirds (Calypte anna) against three different microbes: Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Candida albicans (C. albicans). The effect of age, sex and molt on anti-microbial capacity varied based on the microbe type. After-hatch-year birds tended to have better anti-microbial capacity compared to hatch-year birds. Male birds had higher anti-microbial activity than female birds, although this was not observed against C. albicans. Molting birds had a weaker antimicrobial activity against E. coli and S. aureus than birds that were not molting. These results represent an important first step towards defining the parameters of constitutive innate immunity of Anna's Hummingbirds as well as providing important knowledge about factors that should be considered when evaluating the health of wild populations.
                    Cover page: Anti-microbial activity of whole blood and plasma collected from Anna’s Hummingbirds (Calypte anna) against three different microbes
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2022)
                    Nuanced understanding of seasonal movements of partially migratory birds is paramount to species and habitat conservation. Using nascent statistical methods, we identified migratory strategies of birds outfitted with radio-frequency identification (RFID) tags detected at RFID feeders in two sites in California, USA. We quantified proportions of migrants and residents and the seasonal phenology for each movement strategy in Allen's and Anna's hummingbirds; we also validated our methodology by fitting our model to obligate migratory black-chinned hummingbirds. Allen's and Anna's hummingbirds exhibited characteristics of facultative migratory behaviour. We also quantified apparent annual survival for each migratory strategy and found that residents had significantly higher probabilities of apparent survival. Low survival estimates for migrants suggest that a high proportion of birds in the migrant group permanently emigrated from our study sites. Considered together, our analyses suggest that hummingbirds in both northern and southern California sites partake in diverse and highly plastic migratory behaviours. Our assessment elucidates the dynamics underlying idiosyncratic migratory behaviours of two species of hummingbirds, in addition to describing a framework for similar assessments of migratory behaviours using the multi-state open robust design with state uncertainty model and single-site dynamics.
                      Cover page: Quantifying phenology and migratory behaviours of hummingbirds using single-site dynamics and mark-detection analyses.
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