Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thus it is often unclear how many species coexist in sympatry, what are their phylogenetic relationships and their demographic history. We answer these questions using morphologically similar species of the genus Mugil that are sympatric in the largest coastal Marine Protected Area in the Tropical Southwestern Atlantic marine province. Using a sub-representation of the genome, we show that individuals are assigned to five highly differentiated genetic clusters that are coincident with five mitochondrial lineages, but discordant with morphological information, supporting the existence of five species with conserved morphology in this region. A lack of admixed individuals is consistent with strong genetic isolation between sympatric species, but the most likely species tree suggests that in one case speciation has occurred in the presence of interspecific gene flow. Patterns of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions since species formation. Together, our results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.

人类对自然资源的过度开发使保护和管理成为现代社会最紧迫的挑战之一，特别是在高度脆弱的海洋生态系统方面。在这种情况下，神秘物种的保护尤其具有挑战性，因为它们很难仅根据形态来区分，因此通常不清楚有多少物种共存，它们的系统发育关系和人口历史是什么。我们使用形态相似的鲻鱼属物种来回答这些问题，这些物种同域于热带西南大西洋海洋省最大的沿海海洋保护区。使用基因组的子表示，我们表明个体被分配到五个高度分化的遗传簇，这些遗传簇与五个线粒体谱系一致，但与形态信息不一致，支持该区域存在五个具有保守形态的物种。缺乏混合个体与同域物种之间的强烈遗传隔离是一致的，但最可能的物种树表明，在一种情况下，物种形成是在存在种间基因流的情况下发生的。物种内遗传多样性的模式表明，有效种群规模差异高达两倍，这可能反映了自物种形成以来种群扩张幅度的差异。总之，我们的结果表明，海洋环境中强烈的形态保守性可能导致难以在形态上区分的物种，但其特征是独立的进化历史，因此值得采取针对物种的管理策略。