Data from: Climate niche differentiation between two passerines despite ongoing gene flow

Niche evolution underpins the generation and maintenance of biological diversity, but niche conservatism, in which niches remain little changed over time in closely related taxa and the role of ecology in niche evolution are continually debated. To test whether climate niches are conserved in two closely related passerines in East Asia – the vinous-throated (Paradoxornis webbianus) and ashy-throated (P. alphonsianus) parrotbills – we established their potential allopatric and sympatric regions using ecological niche models and compared differences in their climate niches using niche overlap indices in background tests and multivariate statistical analyses. We also used polymorphism data on 44 nuclear genes to infer their divergence demography. We found that these two parrotbills occupy different climate niches, in both their allopatric and potential sympatric regions. Because the potential sympatric region is the area predicted to be suitable for both parrotbills based on the ecological niche models, it can serve as a natural common garden. Therefore, their observed niche differences in this potential sympatry were not simply rendered by phenotypic plasticity, and probably had a genetic basis. Our genetic analyses revealed that the two parrotbills are not evolutionarily independent for the most recent part of their divergence history. The two parrotbills diverged c. 856,000 years ago, and have had substantial gene flow since a presumed secondary contact c. 290,000 years ago. This study provides an empirical case demonstrating that climate niches may not be homogenized in nascent species in spite of substantial, ongoing gene flow, which in turn suggests a role for ecology in promoting and maintaining diversification among incipient species.生态位演化是生物多样性产生与维持的基础，但生态位保守性（niche conservatism）——即近缘类群的生态位随演化时间几乎无显著变化——以及生态学在生态位演化中的作用，始终是学界持续争论的议题。为验证东亚地区两种近缘雀形目鸟类：酒喉鸦雀（Paradoxornis webbianus）与灰喉鸦雀（P. alphonsianus）的气候生态位是否保守，我们借助生态位模型（ecological niche models）划定了二者的潜在异域分布区与同域分布区，并通过背景检验中的生态位重叠指数（niche overlap indices）与多变量统计分析，比较了二者气候生态位的差异。我们还利用44个核基因（nuclear genes）的多态性数据，推断了它们的种群分化历史（divergence demography）。研究发现，无论是在潜在异域分布区还是潜在同域分布区，这两种鸦雀（parrotbills）均占据了不同的气候生态位。鉴于潜在同域分布区是基于生态位模型预测的、可同时适宜两种鸦雀生存的区域，该区域可作为天然的共同花园（common garden）实验场。因此，二者在该潜在同域分布区中观测到的生态位差异并非仅由表型可塑性（phenotypic plasticity）导致，大概率具有遗传基础。我们的遗传分析显示，这两种鸦雀在其分化历史的近期阶段并未形成进化上独立的类群。二者的分化时间约为85.6万年前，且自约29万年前推测的二次接触以来，便持续存在大规模的基因流（gene flow）。本研究提供了一则实证案例，表明即便存在持续且大规模的基因流，初期物种（incipient species）间的气候生态位也未必会趋于同质化；这一结果反过来暗示，生态学在促进并维持初期物种的分化过程中发挥着关键作用。