Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD, 21212, USA.
Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN, 47907, USA.
BMC Genomics. 2018 Apr 4;19(1):233. doi: 10.1186/s12864-018-4615-z.
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.
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.
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.
物种间和种内遗传变异的管理需要深入了解，但许多物种仍缺乏此类数据。例如，尽管已经对游隼（Falco peregrinus）进行了多项群体遗传学研究，但对亲缘关系密切的草原隼（F. mexicanus）却没有类似的研究，也不清楚该物种的遗传变异和种群结构在其分布范围内有多大。此外，F. mexicanus 与其他隼类物种的系统发育关系存在争议。我们利用基因组学方法（即基因组测序和组装，然后进行单核苷酸多态性基因分型）来快速填补这些知识空白。
我们对一只雌性草原隼进行了基因组测序，并生成了 1.17Gb 的基因组草图。我们利用完整的线粒体基因组和核蛋白编码基因构建了最大似然系统发育树。这一过程为 F. mexicanus 是游隼和 Hierofalco 亚属成员所在分支的外群提供了证据。我们注释了核基因组中 >16000 个基因和近 60 万个高质量单核苷酸多态性（SNP），为设计 SNP 检测提供了材料，其中包括 140 多个与基因相关的标记和一个分子性别标记。随后，我们对加利福尼亚州（包括旧金山湾区、皮纳克尔兹国家公园和莫哈韦沙漠）和爱达荷州（蛇河鸟类保护区）的约 100 只个体进行了基因分型。我们检测了种群结构，发现加利福尼亚州和爱达荷州采样的个体代表了一个单一的混合群体。
我们的研究表明，基因组资源如何快速揭示研究较少的物种的遗传变异，并解决系统发育关系。此外，我们发现证据表明，在我们的采样地点，草原隼是一个单一的、随机交配的种群。草原隼是高度迁徙的，相对较少的长距离扩散事件可能会促进整个范围内的基因流动。因此，加利福尼亚州的草原隼可以作为一个单一的种群进行管理，这表明为当地物种利益而采取的管理行动有可能对整个物种产生影响。
