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.

Nuclear and Mitochondrial DNA Analyses of Golden Eagles (Aquila chrysaetos canadensis) from Three Areas in Western North America; Initial Results and Conservation Implications

“…Thus, it may be possible to distinguish eagles from different breeding grounds by analyzing additional loci as was demonstrated in Doyle et al [14]. The recent completion of a genome sequence for golden eagles [53] and the identification of neutral and adaptive SNPs [14] will facilitate future analyses.…”

“…Similar to Doyle et al [14], we recommend extensive field sampling to assess genetic structure at the scale of eagle management units. The ecology and management of NA golden eagles [27,31] will benefit from building on recent genetic results [14,17] and the new genome sequence [53], and by continuing to use archived tissue samples, gathering and analyzing additional localized, seasonal samples, and by genetic monitoring [35,82]. …”

Population structure and dispersal patterns in Scottish Golden Eagles Aquila chrysaetos revealed by molecular genetic analysis of territorial birds

“…); indeed, the North American Golden Eagle genome has now been sequenced (Doyle et al . ), providing comparative data and additional resources for applied management of this species. This wealth of scientific literature has helped raise the Golden Eagle towards the status of a model species in raptor conservation.…”

Relevance of individual and environmental drivers of movement of Golden Eagles

“…Upon capture, each bird was aged using moult patterns (Jollie 1947, Bloom & Clark 2001 as sub-adult (nestling and first-year to 4 years) or adult (> 4 years). Sex of the birds was determined based on morphology (Bortolotti 1984, Edwards & Kochert 1986, Watson 2010) and, for a subset, verified by genetic testing (n = 38; Doyle et al 2014). Eagles were outfitted with 80-95 g solarpowered GPS/GSM transmitters produced by Cellular Tracking Technologies (Rio Grande, NJ, USA) attached as backpacks using non-abrasive Teflon ribbon harness (Bally Ribbon Mills, Bally, PA, USA; Dunstan 1972, Kenward 1985.…”