Data_Sheet_4_Evidence for Introgression Among Three Species of the Anastrepha fraterculus Group, a Radiating Species Complex of Fruit Flies.XLS

Introgression should no longer be considered as rare a phenomenon as once thought, since several studies have recently documented gene flow between closely related and radiating species. Here, we investigated evolutionary relationships among three closely related species of fruit flies of the Anastrepha fraterculus group (Anastrepha fraterculus, A. obliqua and A. sororcula). We sequenced a set of 20 genes and implemented a combined populational and phylogenetic inference with a model selection approach by an ABC framework in order to elucidate the demographic history of these species. The phylogenetic histories inferred from most genes showed a great deal of discordance and substantial shared polymorphic variation. The analysis of several population and speciation models reveal that this shared variation is better explained by introgression rather than convergence by parallel mutation or incomplete lineage sorting. Our results consistently showed these species evolving under an isolation with migration model experiencing a continuous and asymmetrical pattern of gene flow involving all species pairs, even though still showed a more closely related relationship between A. fraterculus and A. sororcula when compared with A. obliqua. This suggests that these species have been exchanging genes since they split from their common ancestor ∼2.6 MYA ago. We also found strong evidence for recent population expansion that appears to be consequence of anthropic activities affecting host crops of fruit flies. These findings point that the introgression here found may have been driven by genetic drift and not necessary by selection, which has implications for tracking and managing fruit flies.

基因渗入现象已不再如昔日那般被视为罕见，鉴于近期多项研究已记录了密切相关及辐射物种间的基因流动。本研究旨在探究Anastrepha fraterculus群（Anastrepha fraterculus、A. obliqua及A. sororcula）三种密切相关的果蝇物种之间的进化关系。我们对20个基因进行了测序，并采用ABC框架结合种群和系统发育推断方法，辅以模型选择策略，以阐明这些物种的种群历史。从大多数基因推断出的系统发育历史显示出显著的分歧和大量的共享多态性变异。对多种种群和物种形成模型的解析表明，这种共享变异更宜用基因渗入而非平行突变或谱系排序不完整所导致的趋同来解释。我们的结果一致表明，这些物种在经历着隔离与迁移模型的连续且不对称的基因流动模式中进化，尽管与A. obliqua相比，A. fraterculus和A. sororcula之间仍显示出更密切的亲缘关系。这表明，自约2.6百万年前它们从共同祖先分离以来，这些物种便开始交换基因。我们还发现了近期种群扩张的强烈证据，这看似是人类活动影响果蝇宿主作物的结果。这些发现指出，此处发现的基因渗入可能是由遗传漂变而非选择所驱动，这对于追踪和管理果蝇具有重要意义。