Data from: Recent chapters of Neotropical history overlooked in phylogeography: shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins

Establishing links between phenotypic and genotypic variation is a central goal of evolutionary biology, as they might provide important insights into evolutionary processes shaping genetic and species diversity in nature. One of the more intriguing possibilities is when no genetic divergence is found to be associated with conspicuous phenotypic divergence. In that case, speciation theory predicts that phenotypic divergence may still occur in the presence of significant gene flow—thereby resulting in little genomic divergence—when genetic loci underpinning phenotypes are under strong divergent selection. However, a finding of phenotypic distinctiveness with weak or no population genetic structure may simply result from low statistical power to detect shallow genetic divergences when small datasets are used. Here, we used a subgenomic dataset of 2386 ultraconserved elements to explore genome-wide divergence between two species of Antilophia manakins, which are phenotypically distinct yet evidently lack strong genetic differentiation according to previous studies based on a limited number of loci. Our results revealed clear population structure that matches the two phenotypes, supporting the idea that smaller datasets lacked the power to detect this recent divergence event (likely < 100 k ya). Indeed, we found little or no introgression between the species, as well as evidence of genome-wide divergence. One implication of our study is that the Araripe plateau may be a hotspot of cryptic-diverging forest Cerrado populations. Besides their use in biogeography, subgenomic datasets may help redefine local conservation programs by revealing cryptic population structure that may be key to population management.阐明表型变异与基因型变异之间的关联，是进化生物学的核心研究目标之一，此类关联可为解析自然界中驱动遗传多样性与物种多样性形成的进化进程提供关键视角。其中一类颇具研究价值的情形是：当观测到显著的表型分化时，却未发现与之相关的遗传分化。在此情形下，物种形成理论预测：若支撑表型的遗传位点受到强烈的定向选择压力，那么即便存在显著的基因流，表型分化仍可发生，进而仅伴随极低水平的基因组分化。不过，若仅采用小型数据集开展研究，即便观测到表型分化却未检测到显著的种群遗传结构，该结果也可能仅仅是由于统计效力不足，无法检出微弱的遗传分化所致。本研究利用包含2386个超保守元件（ultraconserved elements）的亚基因组数据集，探究盔侏儒鸟属（Antilophia）两个物种间的全基因组分化模式。此前基于有限遗传位点的研究显示，这两个物种虽表型分化显著，但遗传分化程度极低。本研究结果显示，存在与两种表型完全匹配的清晰种群结构，印证了小型数据集统计效力不足、无法检出此次近期分化事件（距今或不足10万年）的观点。进一步分析表明，两物种间几乎不存在基因渐渗（introgression），同时也存在全基因组分化的证据。本研究的一项启示是，阿拉里皮高原（Araripe Plateau）可能是塞拉多（Cerrado）森林种群隐秘分化的热点区域。除在生物地理学领域的应用价值外，亚基因组数据集还可通过揭示隐秘的种群结构（此类结构对种群管理至关重要），助力重新制定区域保护方案。