Genetics and Genomics of Golden Eagles With Contrasting Demographic Histories

Most species are constrained by geographic barriers to dispersal and geneflow, and such limitations have demographic and genetic consequences. We tested whether a highly vagile bird of prey, the golden eagle (GOEA; Aquila chrysaetos), exhibits disparate genetic signatures among island (Channel Islan...

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Main Author: Fernandez, Nadia B
Other Authors: DeWoody, James A.
Format: Text
Language:English
Published: Purdue University 2018
Subjects:
Online Access:https://docs.lib.purdue.edu/dissertations/AAI10845248
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spelling ftpurdueuniv:oai:docs.lib.purdue.edu:dissertations-21460 2023-07-02T03:33:59+02:00 Genetics and Genomics of Golden Eagles With Contrasting Demographic Histories Fernandez, Nadia B DeWoody, James A. 2018-01-01T08:00:00Z https://docs.lib.purdue.edu/dissertations/AAI10845248 ENG eng Purdue University https://docs.lib.purdue.edu/dissertations/AAI10845248 Theses and Dissertations Available from ProQuest Molecular biology|Genetics|Conservation biology text 2018 ftpurdueuniv 2023-06-12T21:15:38Z Most species are constrained by geographic barriers to dispersal and geneflow, and such limitations have demographic and genetic consequences. We tested whether a highly vagile bird of prey, the golden eagle (GOEA; Aquila chrysaetos), exhibits disparate genetic signatures among island (Channel Islands, California, USA), peninsular (Baja California Peninsular region, USA) and mainland (California, USA) regions given the contrasting demography and phylogeography among regions. We utilized a SNP assay to estimate heterozygosity, inbreeding coefficients, and the effective population sizes (Ne) of GOEAs. In addition, we sequenced six GOEA genomes to obtain comprehensive measures of homozygosity (i.e., runs of homozygosity, ROHs) burden as well as estimates of nucleotide diversity. Our samples from the Channel Islands were clearly differentiated from both the peninsular and mainland samples, but there was no genetic differentiation between the peninsular and mainland samples. We found that the island samples exhibited signatures of a founder effect, including lower heterozygosity, reduced N e, and a higher ROH burden than the mainland or peninsular samples. Overall, the genetic markers and the whole-genome sequence data indicate that the Channel Islands samples are genetically distinct from the mainland and peninsular samples, likely as a result of a relatively recent demographic bottleneck followed by bouts of genetic drift and inbreeding. We also found that, unlike smaller and less mobile vertebrates (e.g., rodents, passerines, and lizards), the GOEA gene pool near Baja California is relatively homogenous across distinct phylogeographic domains separated by the San Andreas fault. The genetic isolation exhibited by the island GOEAs almost certainly results from their recent colonization (due to bald eagle extirpation associated with DDT exposure) and subsequent anthropogenic removal (due to predation on an endangered island fox). Text Aquila chrysaetos golden eagle Purdue University: e-Pubs Andreas ENVELOPE(-60.729,-60.729,-64.008,-64.008) Baja
institution Open Polar
collection Purdue University: e-Pubs
op_collection_id ftpurdueuniv
language English
topic Molecular biology|Genetics|Conservation biology
spellingShingle Molecular biology|Genetics|Conservation biology
Fernandez, Nadia B
Genetics and Genomics of Golden Eagles With Contrasting Demographic Histories
topic_facet Molecular biology|Genetics|Conservation biology
description Most species are constrained by geographic barriers to dispersal and geneflow, and such limitations have demographic and genetic consequences. We tested whether a highly vagile bird of prey, the golden eagle (GOEA; Aquila chrysaetos), exhibits disparate genetic signatures among island (Channel Islands, California, USA), peninsular (Baja California Peninsular region, USA) and mainland (California, USA) regions given the contrasting demography and phylogeography among regions. We utilized a SNP assay to estimate heterozygosity, inbreeding coefficients, and the effective population sizes (Ne) of GOEAs. In addition, we sequenced six GOEA genomes to obtain comprehensive measures of homozygosity (i.e., runs of homozygosity, ROHs) burden as well as estimates of nucleotide diversity. Our samples from the Channel Islands were clearly differentiated from both the peninsular and mainland samples, but there was no genetic differentiation between the peninsular and mainland samples. We found that the island samples exhibited signatures of a founder effect, including lower heterozygosity, reduced N e, and a higher ROH burden than the mainland or peninsular samples. Overall, the genetic markers and the whole-genome sequence data indicate that the Channel Islands samples are genetically distinct from the mainland and peninsular samples, likely as a result of a relatively recent demographic bottleneck followed by bouts of genetic drift and inbreeding. We also found that, unlike smaller and less mobile vertebrates (e.g., rodents, passerines, and lizards), the GOEA gene pool near Baja California is relatively homogenous across distinct phylogeographic domains separated by the San Andreas fault. The genetic isolation exhibited by the island GOEAs almost certainly results from their recent colonization (due to bald eagle extirpation associated with DDT exposure) and subsequent anthropogenic removal (due to predation on an endangered island fox).
author2 DeWoody, James A.
format Text
author Fernandez, Nadia B
author_facet Fernandez, Nadia B
author_sort Fernandez, Nadia B
title Genetics and Genomics of Golden Eagles With Contrasting Demographic Histories
title_short Genetics and Genomics of Golden Eagles With Contrasting Demographic Histories
title_full Genetics and Genomics of Golden Eagles With Contrasting Demographic Histories
title_fullStr Genetics and Genomics of Golden Eagles With Contrasting Demographic Histories
title_full_unstemmed Genetics and Genomics of Golden Eagles With Contrasting Demographic Histories
title_sort genetics and genomics of golden eagles with contrasting demographic histories
publisher Purdue University
publishDate 2018
url https://docs.lib.purdue.edu/dissertations/AAI10845248
long_lat ENVELOPE(-60.729,-60.729,-64.008,-64.008)
geographic Andreas
Baja
geographic_facet Andreas
Baja
genre Aquila chrysaetos
golden eagle
genre_facet Aquila chrysaetos
golden eagle
op_source Theses and Dissertations Available from ProQuest
op_relation https://docs.lib.purdue.edu/dissertations/AAI10845248
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