A Resource of Genome-Wide Single Nucleotide Polymorphisms (SNPs) for the Conservation and Management of Golden Eagles
Elucidating the genetic structure and ascertaining the natal origin of Golden Eagles (Aquila chrysaetos) are challenging for a number of reasons, including the lack of highly reproducible, variant genetic loci. Here, we developed a new high-quality Golden Eagle genome reference to serve as a computational atlas for future genetic investigations. We then generated unique genetic resources for the Golden Eagle by performing low-coverage genomic sequencing for 32 individuals ranging from Alaska to southern New Mexico and California to Nebraska. By aligning the reads from these 32 individuals to our Golden Eagle reference genome, we detected approximately 900,000 population variants in the form of Single Nucleotide Polymorphisms (SNPs). Using linkage disequilibrium and other quality filters, we next derived a set of 30,006 SNPs that were used to cluster our samples into three genetic groups. Although additional work is needed to fully characterize these loci, we provide a high-quality Golden Eagle genome reference and a comprehensive set of genetic markers for the conservation and management of Golden Eagles. Additionally, with a more comprehensive Golden Eagle genome assembly and associated transcriptomes, it is now possible to target specific genes or other biologically relevant regions for evaluating the effects of many anthropogenic stressors on Golden Eagle survival. Dilucidar la estructura genética y determinar el origen natal de Aquila chrysaetos representa un desafío por numerosas razones, incluyendo la falta de loci genéticos variables altamente reproducibles. Desarrollamos un nuevo genoma de referencia de elevada calidad para A. chrysaetos para que sirva como un atlas computacional para futuras investigaciones genéticas. A continuación, generamos fuentes genéticas únicas para esta especie realizando secuenciaciones genómicas de baja cobertura para 32 individuos distribuidos entre Alaska y el sur de Nuevo México y entre California y Nebraska. Al alinear las lecturas de estos 32 individuos con nuestro genoma de referencia para A. chrysaetos, detectamos aproximadamente 900,000 variantes poblacionales en la forma de Polimorfismos de Nucleótidos Individuales (PNI). Utilizamos el desequilibrio de ligamiento y otros filtros de calidad y luego derivamos un conjunto de 30,006 PNI que fueron utilizados para agrupar nuestras muestras en tres grupos genéticos. Aunque se necesita trabajo adicional para caracterizar completamente estos loci, proporcionamos un genoma de referencia y un detallado conjunto de marcadores para la conservación y la gestión de A. chrysaetos. Adicionalmente, con un ensamble genómico y transcriptomas asociados más detallados, es posible ahora identificar genes específicos u otras regiones biológicamente relevantes para evaluar los efectos de las diversas presiones antrópicas sobre la supervivencia de A. chrysaetos. [Traducción del equipo editorial]Abstract
Resumen
Results from STRUCTURE analysis showing the three genetically defined groups of Golden Eagles based on our analysis of 30,006 Single Nucleotide Polymorphisms and 32 individuals. Individual histograms represent the percentage of each individual's genome that was assigned to each of the three genetic units. The Alaska-British Columbia group is colored gray, California-Oregon-Idaho group is white, and the Arizona-Colorado-Nebraska-New Mexico-Oklahoma-Wyoming group is black.
Spatially explicit population structure of our sample of 32 Golden Eagles. The colors in the pie charts reflects the relative posterior probability of membership of the individual's genome belonging to each of the three genetic groups identified by STRUCTURE with the Alaska-British Columbia, California-Oregon-Idaho, and Arizona-Colorado-Nebraska-New Mexico-Oklahoma-Wyoming groups represented by gray, white, and black, respectively.
Contributor Notes
Associate Editor: Christopher W. Briggs