Combining species delimitation, species trees, and tests for gene flow illuminates complex speciation in scrub-jays

Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating i...复杂物种形成过程涉及快速分化与多轮分化后基因流事件，常会混淆系统发育关系与物种界定。在北美，复杂物种形成的案例十分常见，这至少部分归因于该大陆周期性的更新世冰川活动历史。丛鸦属（Aphelocoma）灌丛鸦是研究复杂物种形成的理想案例类群：它们在北美的分布范围受多重系统地理屏障分隔，且存在多例分化支系间二次接触的情形。本研究证实，尽管存在复杂物种形成过程，整合物种界定、物种树重建、种群历史模型检验以及基因流检测等方法的基因组水平演化历史重建综合策略，仍可厘清物种的演化历程。我们在所有统计分析框架下均获得了一致的证据，证实墨西哥南部特有支系（A. w. sumichrasti）的分化独立性，相关研究结果最终……