Table_1_Population Genomics of the “Arcanum” Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages.XLSX

Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the “Arcanum” group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological “selfing syndrome.” Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species’ geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as “var. marañón” has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.

鉴于野生番茄（Solanum section Lycopersicon）具有多样的交配系统与新近分化的演化历程，其已成为研究生态分化、生殖屏障形成，以及自交不亲和性（self-incompatibility）崩溃的成因与后果的理想模式系统。本研究聚焦于鲜少被深入探究的“Arcanum组”类群，该类群包含正式分类物种：Solanum arcanum、Solanum chmielewskii与Solanum neorickii。后两个分类单元（taxa）为自交亲和类群，且因各自呈现出独特的形态学“自交综合征（selfing syndrome）”特征，被认为以不同速率进行自花授粉。
本研究针对覆盖各物种地理分布范围的39份独立种质居群对应的39个不同基因型，开展了杂交实验与转录组测序（transcriptome sequencing），为S. arcanum内部存在深度谱系分化提供了强有力证据：仅被称为“var. marañón”的自交不亲和谱系，与这两个自交亲和物种存在紧密的谱系亲缘关系。此外，多种谱系推断方法均支持：S. arcanum var. marañón的不同地理亚群，分别与S. chmielewskii和S. neorickii亲缘关系最近。
为全面表征这些新近发生的交配系统转变及其伴随的物种形成事件所带来的群体基因组学效应，本研究拟合了种群动态模型（demographic models），结果显示有效种群规模（effective population size）出现显著下降，这与两个独立起源的自交亲和物种中核苷酸多样性（nucleotide diversity）与S位点（S-locus）多样性的降低结果一致。