Dataset Information

The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).

ABSTRACT: Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male golden eagle (Aquila chrysaetos) captured in western North America. We constructed genomic libraries that were sequenced using Illumina technology and assembled the high-quality data to a depth of ?40x coverage. The genome assembly includes 2,552 scaffolds >10 Kb and 415 scaffolds >1.2 Mb. We annotated 16,571 genes that are involved in myriad biological processes, including such disparate traits as beak formation and color vision. We also identified repetitive regions spanning 92 Mb (?6% of the assembly), including LINES, SINES, LTR-RTs and DNA transposons. The mitochondrial genome encompasses 17,332 bp and is ?91% identical to the Mountain Hawk-Eagle (Nisaetus nipalensis). Finally, the data reveal that several anonymous microsatellites commonly used for population studies are embedded within protein-coding genes and thus may not have evolved in a neutral fashion. Because the genome sequence includes ?800,000 novel polymorphisms, markers can now be chosen based on their proximity to functional genes involved in migration, carnivory, and other biological processes.

SUBMITTER: Doyle JM

PROVIDER: S-EPMC3997482 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).

Doyle Jacqueline M JM Katzner Todd E TE Bloom Peter H PH Ji Yanzhu Y Wijayawardena Bhagya K BK DeWoody J Andrew JA

PloS one 20140423 4

Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male golden eagle (Aquila chrysaetos) captured in western North America. We constructed genomic libraries that were sequenced using Illumin ...[more]

PMID: 24759626

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Project description:Different forms of outdoor recreation have different spatiotemporal activity patterns that may have interactive or cumulative effects on wildlife through human disturbance, physical habitat change, or both. In western North America, shrub-steppe habitats near urban areas are popular sites for motorized recreation and nonmotorized recreation and can provide important habitat for protected species, including golden eagles. Our objective was to determine whether recreation use (i.e., number of recreationists) or recreation features (e.g., trails or campsites) predicted golden eagle territory occupancy, egg-laying, or the probability a breeding attempt resulted in ?1 offspring (nest survival). We monitored egg-laying, hatching and fledging success, eagle behavior, and recreation activity within 23 eagle territories near Boise, Idaho, USA. Territories with more off-road vehicle (ORV) use were less likely to be occupied than territories with less ORV use (? = -1.6, 85% CI: -2.8 to -0.8). At occupied territories, early season pedestrian use (? = -1.6, 85% CI: -3.8 to -0.2) and other nonmotorized use (? = -3.6, 85% CI: -10.7 to -0.3) reduced the probability of egg-laying. At territories where eagles laid eggs, short, interval-specific peaks in ORV use were associated with decreased nest survival (? = -0.5, 85% CI: -0.8 to -0.2). Pedestrians, who often arrived near eagle nests via motorized vehicles, were associated with reduced nest attendance (? = -11.9, 85% CI: -19.2 to -4.5), an important predictor of nest survival. Multiple forms of recreation may have cumulative effects on local populations by reducing occupancy at otherwise suitable territories, decreasing breeding attempts, and causing nesting failure. Seasonal no-stopping zones for motorized vehicles may be an alternative to trail closures for managing disturbance. This study demonstrates the importance of considering human disturbance across different parts of the annual cycle, particularly where multiple forms of recreation have varying spatiotemporal use patterns that create human-wildlife interactions.

Project description:Wind power is a major candidate in the search for clean, renewable energy. Beyond the technical and economic challenges of wind energy development are environmental issues that may restrict its growth. Avian fatalities due to collisions with rotating turbine blades are a leading concern and there is considerable uncertainty surrounding avian collision risk at wind facilities. This uncertainty is not reflected in many models currently used to predict the avian fatalities that would result from proposed wind developments. We introduce a method to predict fatalities at wind facilities, based on pre-construction monitoring. Our method can directly incorporate uncertainty into the estimates of avian fatalities and can be updated if information on the true number of fatalities becomes available from post-construction carcass monitoring. Our model considers only three parameters: hazardous footprint, bird exposure to turbines and collision probability. By using a Bayesian analytical framework we account for uncertainties in these values, which are then reflected in our predictions and can be reduced through subsequent data collection. The simplicity of our approach makes it accessible to ecologists concerned with the impact of wind development, as well as to managers, policy makers and industry interested in its implementation in real-world decision contexts. We demonstrate the utility of our method by predicting golden eagle (Aquila chrysaetos) fatalities at a wind installation in the United States. Using pre-construction data, we predicted 7.48 eagle fatalities year-1 (95% CI: (1.1, 19.81)). The U.S. Fish and Wildlife Service uses the 80th quantile (11.0 eagle fatalities year-1) in their permitting process to ensure there is only a 20% chance a wind facility exceeds the authorized fatalities. Once data were available from two-years of post-construction monitoring, we updated the fatality estimate to 4.8 eagle fatalities year-1 (95% CI: (1.76, 9.4); 80th quantile, 6.3). In this case, the increased precision in the fatality prediction lowered the level of authorized take, and thus lowered the required amount of compensatory mitigation.

Dataset Information

The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).

Publications

The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).

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