DOI: 10.5061/dryad.h44j0zprq
title: Dataset for: Utilizing high-resolution genetic markers to track population-level exposure of migratory birds to renewable energy development

description: With new motivation to increase the proportion of energy demands met by
 zero-carbon sources, there is a greater focus on efforts to assess and
 mitigate the impacts of renewable energy development on sensitive
 ecosystems and wildlife, of which birds are of particular interest. One
 challenge for researchers, due in part to a lack of appropriate tools, has
 been estimating the effects from such development on individual breeding
 populations of migratory birds. To help address this, we utilize a newly
 developed, high-resolution genetic tagging method to rapidly identify the
 breeding population of origin of carcasses recovered from renewable energy
 facilities and combine them with maps of genetic variation across
 geographic space (called ‘genoscapes’) for five species of migratory birds
 known to be exposed to energy development, to assess the extent of
 population-level effects on migratory birds. We demonstrate that most
 avian remains collected were from the largest populations of a given
 species. In contrast, those remains from smaller, declining populations
 made up a smaller percentage of the total number of birds assayed. Results
 suggest that application of this genetic tagging method can successfully
 define population-level exposure to renewable energy development and may
 be a powerful tool to inform future siting and mitigation activities
 associated with renewable energy programs.
description: For 5 migratory bird species, we used targeted SNP-genotyping of
 breeding reference birds and carcasses of birds sampled at alternative
 energy sites. We then assigned the birds recovered from renewable energy
 facilities (lebeled "solar") back to breeding population of
 origin. This repository includes data files for the 5 species and an R
 markdown file that can be used to replicate the assignment analyses in
 rubias, as well as final assignments to species as reported in the
 associated manuscript.  
description: R RUBIAS
description: # Dataset for: Utilizing high-resolution genetic markers to track
 population-level exposure of migratory birds to renewable energy
 development --- For 5 migratory bird species, we used targeted
 SNP-genotyping of breeding reference birds and carcasses of birds sampled
 at alternative energy sites. We then assigned the "solar" birds
 back to breeding population of origin. This repository includes data files
 for the 5 species and a R markdown that can be used to replicate the
 assignment analyses in rubias. ## Description of the data and file
 structure 1. AMKE_genotypes_rubias.xlsx - Consisting of two tabs: a)
 AMKE.186SNPgenotypes.breeders - This tab includes genotype of 186 SNP-type
 assays for 597 American Kestrel (AMKE) breeding individuals. These are the
 reference individuals used in the rubias analysis. Missing genotypes are
 categorized as NA. Genotypes are labeled as: 1=A, 2=C, 3=G, 4=T, and b)
 AMKE.solar.rubias.input - This tab includes 186 genotypes for 190 birds
 collected at alternative energy sites. These "solar" birds are
 assigned back to breeding unites defined on the first tab:
 AMKE.186SNPgenotypes.breeders. Genotypes are labeled as: 1=A, 2=C, 3=G,
 4=T. 2. COLO_genotypes_rubias.xlsx - Consisting of two tabs: a)
 COLO.158SNPgenotypes.breeders - This tab includes genotype of 158 SNP-type
 assays for 301 Common Loon (COLO) breeding individuals. These are the
 reference individuals used in the rubias analysis. Missing genotypes are
 categorized as NA. Genotypes are labeled as: 1=A, 2=C, 3=G, 4=T, and b)
 COLO.solar.rubias.input - This tab includes 158 genotypes for 15 birds
 collected at alternative energy sites. These "solar" birds are
 assigned back to breeding unites defined on the first tab:
 COLO.158SNPgenotypes.breeders. Genotypes are labeled as: 1=A, 2=C, 3=G,
 4=T. 3. COYE_genotypes_rubias.xlsx - Consisting of two tabs: a)
 COYE.96SNPgenotypes.breeders - This tab includes genotype of 96 SNP-type
 assays for 235 Common Yellowthroat (COYE) breeding individuals. These are
 the reference individuals used in the rubias analysis. Missing genotypes
 are categorized as NA. Genotypes are labeled as: 1=A, 2=C, 3=G, 4=T, and
 b) COYE.solar.rubias.input - This tab includes 96 genotypes for 25 birds
 collected at alternative energy sites. These "solar" birds are
 assigned back to breeding unites defined on the first tab:
 COYE.96SNPgenotypes.breeders. Genotypes are labeled as: 1=A, 2=C, 3=G,
 4=T. 4. WIWA_genotypes_rubias.xlsx - Consisting of two tabs: a)
 WEWA.96SNPgenotypes.breeders - This tab includes genotype of 96 SNP-type
 assays for 407 Wilson's Warbler (WIWA) breeding individuals. These
 are the reference individuals used in the rubias analysis. Missing
 genotypes are categorized as NA. Genotypes are labeled as: 1=A, 2=C, 3=G,
 4=T, and b) WIWA.solar.rubias.input - This tab includes 96 genotypes for
 216 birds collected at alternative energy sites. These "solar"
 birds are assigned back to breeding unites defined on the first tab:
 WEWA.96SNPgenotypes.breeders. Genotypes are labeled as: 1=A, 2=C, 3=G,
 4=T. 5. YEWA_genotypes_rubias.xlsx - Consisting of two tabs: a)
 YEWA.96snpgenotypes.breeders - This tab includes genotype of 96 SNP-type
 assays for 418 Yellow Warbler (YEWA) breeding individuals. These are the
 reference individuals used in the rubias analysis. Missing genotypes are
 categorized as NA. Genotypes are labeled as: 1=A, 2=C, 3=G, 4=T, and b)
 YEWA.solar.rubias.input - This tab includes 96 genotypes for 288 birds
 collected at alternative energy sites. These "solar" birds are
 assigned back to breeding unites defined on the first tab:
 YEWA.96SNPgenotypes.breeders. Genotypes are labeled as: 1=A, 2=C, 3=G,
 4=T. 6. Final.assignment.to.species.xlsx: This excel sheet holds the meta
 data for each individual genotyped for 5 species. The data includes Sample
 name, State, Alternative energy site, Day, Month and Year the sample was
 collected, Latitude and Longitude, as well as the assignment results of
 rubias in the form of the probability of assignment of each bird to each
 population-specific breeding unit. Describe relationships between data
 files, missing data codes, other abbreviations used. Be as descriptive as
 possible. ## Sharing/Access information Links to other publicly accessible
 locations of the data: *
 ## Code/Software 1. Solar_Indiv_PopAssignment.Rmd: This is a R markdown script that will assign solar birds back to a distinct breeding unit defined in the breeding bird input file using the rubias software program.