Genetic Toolkit for Assessment and Prediction of Population-Level Impacts of Bridge Construction on Birds

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 Webpag

Genetic Toolkit for Assessment and Prediction of Population-Level Impacts of Bridge Construction on Birds

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 Webpag

Using Genetic Tools to Identify Populations Within Species Could Ease Infrastructure Mitigation

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 Webpag

TaqMan quantitative real-time PCR for detecting Avipoxvirus DNA in various sample types from hummingbirds.

BackgroundAvian 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 findingsPox-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 significanceHummingbird 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

Acarbose and Postprandial Hypotension

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

Quantifying phenology and migratory behaviours of hummingbirds using single-site dynamics and mark-detection analyses.

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