New Insights Into the Phylogenetics and Population Structure of the Prairie Falcon (Falco Mexicanus) Jacqueline M
Doyle et al. BMC Genomics (2018) 19:233 https://doi.org/10.1186/s12864-018-4615-z RESEARCH ARTICLE Open Access New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus) Jacqueline M. Doyle1,2*, Douglas A. Bell3,4, Peter H. Bloom5, Gavin Emmons6, Amy Fesnock7, Todd E. Katzner8, Larry LaPré9, Kolbe Leonard10, Phillip SanMiguel11, Rick Westerman11 and J. Andrew DeWoody2,12 Abstract 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 > 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 > 140 gene-associated markers and a molecular-sexing marker.
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