Subspecies is used to designate taxa below species but above geographical populations. What patterns of genomic variation are expected if taxa are designated as subspecies? In this study, we carry out such a survey on the mangrove tree Avicennia marina (Forssk.) Vierh. of the Indo-West Pacific coasts. This species has three subspecies, distinguished by morphological traits and geographical distribution. We collected samples from 16 populations (577 individuals) covering all three subspecies and sequenced 94 nuclear genes. We reveal comprehensive genetic divergence among subspecies, generally higher than among geographical populations within subspecies. The level of genetic diversity differs among the three subspecies, possibly hinting at a degree of separation among their gene pools. We observed that divergence varies from locus to locus across the genome. A small portion of the genome is most informative about subspecies delineation, whereas the rest is undifferentiated or slightly differentiated, hinting at uneven gene flow and incomplete isolation. The three subspecies likely split simultaneously with gene flow among lineages. This reticulate evolution results in some discordance between morphology and genetics in areas of population contact. In short, A. marina subspecies show species-like patterns in some respects and population-like patterns in others. We propose that the subspecies designated in A. marina are informative in predicting genetic divergences and useful in making conservation decisions.

中文翻译：

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由表型标准定义的亚种基因组变异模式：红树林物种复合体分析，Avicennia marina

亚种用于指定低于物种但高于地理种群的分类群。如果分类群被指定为亚种，预计会有哪些基因组变异模式？在这项研究中，我们对红树林Avicennia marina进行了这样的调查。（福斯克）维尔。印度-西太平洋沿岸。该物种具有三个亚种，以形态特征和地理分布为特征。我们从涵盖所有三个亚种的 16 个种群（577 个个体）中收集了样本，并对 94 个核基因进行了测序。我们揭示了亚种之间的全面遗传差异，通常高于亚种内地理种群之间的差异。三个亚种的遗传多样性水平不同，可能暗示它们的基因库之间存在一定程度的分离。我们观察到，基因组中不同位点的差异有所不同。基因组的一小部分对亚种的描述信息最多，而其余部分未分化或略有分化，暗示基因流动不均匀和不完全隔离。这三个亚种可能随着谱系间的基因流动同时分裂。这种网状进化导致种群接触区域的形态学和遗传学之间存在一些不一致。简而言之，A. marina亚种在某些方面表现出类似物种的模式，在其他方面表现出类似种群的模式。我们建议A. marina中指定的亚种在预测遗传分歧方面提供信息，并有助于做出保护决策。