Data from: Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens.

Speciation can be described as a reduction, and the eventual cessation, in the ability to interbreed. Thus, determining how gene flow differs within and between nascent species can illuminate the relative stage the taxa have attained in the speciation process. Aquilegia formosa and A. pubescens are fully intercompatible yet occur in different habitats and have flowers specialized for pollination by hummingbirds and hawkmoths respectively. Using 79 SNP loci we genotyped nearly 1,000 individuals from populations of both species in close proximity to each other and from putative hybrid zones. The species shared all but one SNP polymorphism and on average, allele frequencies differed by only 0.14. However, the species were clearly differentiated using Structure and admixed individuals were primarily identified at putative hybrid zones. PopGraph identified a highly integrated network among all populations but populations of each species and hybrid zones occupied distinct regions in the network. Using either conditional graph distance (cGD) or Fst/(1-Fst) we found significant isolation by distance (IBD) among populations. Within species, IBD was strong, indicating high historic gene flow. IBD extended approximately 100 km in A. pubescens and 30 km in A. formosa. However, IBD between the species was very weak and extended only a few km beyond hybrid zones, suggesting little recent gene flow. The extensive sharing of SNP polymorphisms between these species suggests that they are very early in the speciation process while the low signal of IBD suggests that they have largely ceased gene exchange.

物种形成（Speciation）可被定义为类群间杂交繁殖能力的逐步衰减乃至最终完全丧失。因此，解析基因流在新生物种内部及物种间的差异模式，可揭示这些类群在物种形成进程中所处的相对阶段。华丽耧斗菜（Aquilegia formosa）与毛耧斗菜（A. pubescens）虽具备完全互交兼容性，但二者栖息生境截然不同，且花部特征特化，分别适配蜂鸟与天蛾的传粉需求。本研究利用79个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，对两个物种的近缘种群及推定杂交带的近1000个个体开展了基因分型工作。两个物种共享除1个之外的全部SNP多态性位点，平均等位基因频率差异仅为0.14。然而，借助Structure群体结构分析软件可清晰区分两个物种，且杂交个体主要在推定杂交带中被鉴定出来。PopGraph网络分析软件则显示，所有种群间构建出高度整合的遗传网络，但两个物种种群与杂交带各自占据网络中的独特空间区域。无论是采用条件图距离（conditional graph distance, cGD）还是Fst/(1-Fst)指标，均检测到种群间存在显著的距离隔离（Isolation by Distance, IBD）信号。在物种内部，IBD信号较强，表明历史基因流水平较高。其中，毛耧斗菜的IBD信号覆盖范围约为100 km，华丽耧斗菜则约为30 km。但两物种间的IBD信号极弱，仅在杂交带外数公里范围内可被检测到，暗示近期二者的基因交流极少。两物种间广泛的SNP多态性共享现象表明它们尚处于物种形成的极早期阶段，而微弱的IBD信号则说明二者已基本停止了基因交换。