DOI: 10.5061/dryad.0cfxpnw81
title: Data from: Genomic insights into isolation of the threatened Florida crested caracara (Caracara plancus)

description: We conducted a population genomic study of the crested caracara (Caracara
 plancus) using samples (n = 290) collected from individuals in Florida,
 Texas, and Arizona, USA. Crested caracaras are non-migratory raptors
 ranging from the southern tip of South America to the southern United
 States, including a federally protected relict population in Florida long
 thought to have been isolated since the last ice age. Our objectives were
 to evaluate genetic diversity and population structure of Florida’s
 apparently isolated population and to evaluate taxonomic relationships of
 crested caracaras at the northern edge of their range. Using DNA purified
 from blood samples, we conducted double-digest restriction site associated
 DNA sequencing and sequenced the mitochondrial ND2 gene. Analyses of
 population structure using over 9000 SNPs suggest that two major clusters
 are best supported, one cluster including only Florida individuals and the
 other cluster including Arizona and Texas individuals. Both SNPs and
 mitochondrial haplotypes reveal the Florida population to be highly
 differentiated genetically from Arizona and Texas populations, whereas
 Arizona and Texas populations are moderately differentiated from each
 other. The Florida population’s mitochondrial haplotypes form a separate
 monophyletic group, while Arizona and Texas populations share
 mitochondrial haplotypes. Results of this study provide substantial
 genetic evidence that Florida’s crested caracaras have experienced
 long-term isolation from caracaras in Arizona and Texas and, thus,
 represent a distinct evolutionary lineage possibly warranting distinction
 as an Evolutionarily Significant Unit (ESU) or subspecies. This study will
 inform conservation strategies focused on long-term survival of Florida’s
 distinct, panmictic population.
description: # Genomic Insights into Isolation of the Threatened Florida Crested
 Caracara (Caracara plancus)
 [https://doi.org/10.5061/dryad.0cfxpnw81](https://doi.org/10.5061/dryad.0cfxpnw81) ## Description of the data and file structure This dataset contains raw double-digest restriction-site-associated DNA paired-end sequencing reads from 209 crested caracaras (*Caracara plancus*) from Florida (n = 196), Arizona (n = 8), and Texas (n = 5). PCR duplicates were removed with the Stacks v. 2.60 *clone_filter* module, and these data were then demultiplexed, quality filtered with default settings, and filtered for missing restriction enzymes sites and adapter contamination using the Stacks *process_radtags* module (using options -c -q -r). The dataset contains four fastq (.fq) files for each individual, corresponding to paired reads (".1.fq.gz"/".2.fq.gz") and reads remaining after one read from the read pair was discarded (".rem.1.fq.gz"/".rem.2.fq.gz"). Files are named according to sample ID. The population map file necessary to process the fastq files with Stacks *denovo_map* is included. This dataset includes reads for 10 individuals later filtered due to missing data, as well as reads for two pairs of duplicated individuals. We removed one individual from each pair and reran Stacks *populations*, and the final SNP set is included here as a .vcf file. We have additionally included a .csv file including location information and mitochondrial haplotypes for each sample, for a total sample set of 290 caracaras.