Data from: Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds

Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of communities often results from dynamic processes linked to numerous population histories among co-distributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification. We employed a genome reduction technique, double digest restriction-site associated DNA sequencing, and obtained 4,407–7,186 genome-wide SNPs. We estimated demographic history in each taxon pair and inferred that all pairs had the same best-fit demographic model: isolation with asymmetric gene flow from the Tumbes into the Marañón Valley, suggesting a common diversification mode. Overall, we also observed congruence in effective population size (Ne) patterns where ancestral Ne were 2.9–11.0x larger than present-day Marañón Valley populations and 0.3–2.0x larger than Tumbesian populations. Present-day Marañón Valley Ne was smaller than Tumbes. In contrast, we found simultaneous population isolation due to a single event to be unlikely as taxon pairs diverged over an extended period of time (0.1–2.9 Ma) with multiple non-overlapping divergence periods. Our results show that even when populations of co-distributed species asynchronously diverge, the mode of their differentiation can remain conserved over millions of years. Divergence by allopatric isolation due to barrier formation does not explain the mode of differentiation between these two bird assemblages; rather, migration of individuals occurred before and after geographical isolation.

南美洲西北部的干旱森林鸟类群落常被穿插其间的山脉与雨林碎片化，由此形成了极高的地方特有性（local endemism）。群落的历史组装过程通常由与多个共分布物种的种群历史相关联的动态演化进程所塑造。然而，倘若景观与环境特征，抑或是物种的生态特性能够以相似的方式塑造种群结构，那么不同物种仍可能在时间尺度上遵循一致的多样化路径。本研究针对分布于南美洲西北部坦贝斯（Tumbes）与马拉尼翁河谷（Marañón Valley）干旱森林中的6组共分布类群对，检验其是否呈现出一致的多样化格局与分化模式。我们采用了基因组简化技术——双酶切限制性位点关联DNA测序（double digest restriction-site associated DNA sequencing），共获得4407~7186个全基因组范围的单核苷酸多态性位点（single nucleotide polymorphisms, SNPs）。我们对每一组类群对的种群历史进行了推断，结果显示所有类群对均适配同一最优种群历史模型：带有从坦贝斯向马拉尼翁河谷方向不对称基因流的隔离模式，这暗示了共通的多样化途径。总体而言，我们还观察到有效种群大小（effective population size, Ne）的变化格局具有一致性：祖先有效种群大小为现今马拉尼翁河谷种群的2.9~11.0倍，是坦贝斯种群的0.3~2.0倍；且现今马拉尼翁河谷种群的有效种群大小小于坦贝斯种群。与之相反，我们发现单一事件同步导致种群隔离的可能性极低，因为各分类群对的分化发生在一段延展的时间范围内（0.1~2.9 Ma），且分化时期互不重叠。本研究结果表明，即便共分布物种的种群异步分化，其分化模式仍可在数百万年的时间尺度上保持保守。由地理屏障形成引发的异域隔离分化，无法解释这两类鸟类群落间的分化模式；相反，在地理隔离形成的前后均存在个体迁移事件。