Data from: Genomic insights into isolation of the threatened Florida crested caracara (Caracara plancus)
Data files
Oct 10, 2023 version files 92.35 GB
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caracara_plancus_ddrad_seqs_part1.tar.gz
44.18 GB
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caracara_plancus_ddrad_seqs_part2.tar.gz
48.11 GB
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caracara_sample_information.csv
17.49 KB
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crca-all-lib-popmap.txt
3.19 KB
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populations.snps.vcf
57.87 MB
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README.md
1.52 KB
Abstract
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.
README: Genomic Insights into Isolation of the Threatened Florida Crested Caracara (Caracara plancus)
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.