DOI: 10.5061/dryad.8b0s04t
title: Data from: New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)

description: Background: Management requires a robust understanding of between- and
 within-species genetic variability, however such data are still lacking in
 many species. For example, although multiple population genetics studies
 of the peregrine falcon (Falco peregrinus) have been conducted, no similar
 studies have been done of the closely-related prairie falcon (F.
 mexicanus) and it is unclear how much genetic variation and population
 structure exists across the species’ range. Furthermore, the phylogenetic
 relationship of F. mexicanus relative to other falcon species is
 contested. We utilized a genomics approach (i.e., genome sequencing and
 assembly followed by single nucleotide polymorphism genotyping) to rapidly
 address these gaps in knowledge. Results: We sequenced the genome of a
 single female prairie falcon and generated a 1.17 Gb (gigabases) draft
 genome assembly. We generated maximum likelihood phylogenetic trees using
 complete mitochondrial genomes as well as nuclear protein-coding genes.
 This process provided evidence that F. mexicanus is an outgroup to the
 clade that includes the peregrine falcon and members of the subgenus
 Hierofalco. We annotated &gt; 16,000 genes and almost 600,000
 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome,
 providing the raw material for a SNP assay design featuring &gt; 140
 gene-associated markers and a molecular-sexing marker. We subsequently
 genotyped ~ 100 individuals from California (including the San Francisco
 East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho
 (Snake River Birds of Prey National Conservation Area). We tested for
 population structure and found evidence that individuals sampled in
 California and Idaho represent a single panmictic population. Conclusions:
 Our study illustrates how genomic resources can rapidly shed light on
 genetic variability in understudied species and resolve phylogenetic
 relationships. Furthermore, we found evidence of a single, randomly mating
 population of prairie falcons across our sampling locations. Prairie
 falcons are highly mobile and relatively rare long-distance dispersal
 events may promote gene flow throughout the range. As such, California’s
 prairie falcons might be managed as a single population, indicating that
 management actions undertaken to benefit the species at the local level
 have the potential to influence the species as a whole.
description: Falco mexicanus SNP
 genotypes103 Prairie falcons were
 genotyped at 143 SNPs. Sampling locations included the San Francisco East
 Bay Area, Pinnacles National Park, the Mojave Desert, Northern California
 and the Snake River Birds of Prey National Conservation Area in Idaho.
 SNPs are coded as follows: Adenine=1, Cytosine=2, Guanine=3, Thymine=4,
 missing data = 0.SNP_genotypes.xlsxFalco mexicanus genome annotation16,320 genes were annotated in the Falco mexicanus genome, this is the .gff file associated with the annotations.genome.all.gffFalco mexicanus mitochondrial genome assemblyThe F. mexicanus mitochondrial genome was assembled using MITObim vs. 1.6. The genome assembly is 17,117 bp in length and characterized by 13 protein-coding genes, two ribosomal subunit genes (rRNA), 22 transfer RNA genes and a control region.complete_PRFA_mito_30March2017_307.fastaFalco mexicanus genome annotation - protein sequences16,320 genes were annotated in the Falco mexicanus genome, this is the .fasta file with predicted protein sequences.AbySS_min10000_falcon2015_.proteins.fastaFalco mexicanus genome assembly scaffoldsThe Falco mexicanus draft genome was generated from paired-end, mate-paired and long reads using ABySS vs. 1.5.2 and SPAdes 3.1.1. This file includes the scaffolds greater than 10 kb in length.AbySS_min10000.fasta