New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)

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. 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.

背景：物种管理需要对物种间及物种内的遗传变异拥有充分认知，但目前多数物种仍缺乏此类数据。例如，尽管针对游隼（Falco peregrinus）已开展多项种群遗传学研究，但对其近缘物种草原隼（F. mexicanus）却暂无同类研究，且尚不明确该物种分布范围内存在多少遗传变异与种群结构。此外，草原隼与其他隼类的系统发育关系仍存在争议。本研究采用基因组学策略（即先进行基因组测序与组装，再开展单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因分型），以快速填补这些认知空白。
结果：本研究对一只雌性草原隼的基因组进行测序，获得了1.17 Gb（gigabases，吉碱基）的草图基因组组装结果。利用完整线粒体基因组与核蛋白编码基因，我们构建了最大似然法系统发育树。该分析结果表明，草原隼为包含游隼及隼亚属（Hierofalco）类群的演化支的外类群。我们对核基因组注释了超过16000个基因与近60万个高质量单核苷酸多态性（SNP）位点，为设计包含140余个基因关联标记及1个分子性别鉴定标记的SNP检测体系提供了原始数据。随后，我们对来自美国加利福尼亚州（涵盖旧金山东湾地区、尖顶国家公园与莫哈韦沙漠）以及爱达荷州（斯内克河猛禽国家保护区）的约100个个体进行了基因分型。我们对种群结构进行检测后发现，加利福尼亚州与爱达荷州的采样个体属于同一个随机交配种群。
结论：本研究展示了基因组学资源如何快速阐明研究不足物种的遗传变异特征并厘清其系统发育关系。此外，本研究证实采样范围内的草原隼为单一随机交配种群。草原隼具有极强的移动能力，偶发的长距离扩散事件可能促进其整个分布范围内的基因交流。因此，加利福尼亚州的草原隼可作为单一种群进行管理，这意味着为保护该物种而开展的本地管理措施，有望对整个物种种群产生积极影响。