Dimond James L, Gamblewood Sanoosh K, Roberts Steven B
School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA.
Shannon Point Marine Center, Western Washington University, Anacortes, WA, USA.
Mol Ecol. 2017 Oct;26(19):5031-5042. doi: 10.1111/mec.14252. Epub 2017 Aug 12.
Incongruence between conventional and molecular systematics has left the delineation of many species unresolved. Reef-building corals are no exception, with phenotypic plasticity among the most plausible explanations for alternative morphospecies. As potential molecular signatures of phenotypic plasticity, epigenetic processes may contribute to our understanding of morphospecies. We compared genetic and epigenetic variation in Caribbean branching Porites spp., testing the hypothesis that epigenetics-specifically, differential patterns of DNA methylation-play a role in alternative morphotypes of a group whose taxonomic status has been questioned. We used reduced representation genome sequencing to analyse over 1,000 single nucleotide polymorphisms and CpG sites in 27 samples of Porites spp. exhibiting a range of morphotypes from a variety of habitats in Belize. We found stronger evidence for genetic rather than epigenetic structuring, identifying three well-defined genetic groups. One of these groups exhibited significantly thicker branches, and branch thickness was a better predictor of genetic groups than depth, habitat or symbiont type. In contrast, no clear epigenetic patterns emerged with respect to phenotypic or habitat variables. While there was a weak positive correlation between pairwise genetic and epigenetic distance, two pairs of putative clones exhibited substantial epigenetic differences, suggesting a strong environmental effect. We speculate that epigenetic patterns are a complex mosaic reflecting diverse environmental histories superimposed over a relatively small heritable component. Given the role of genetics in branching Porites spp. morphospecies we were able to detect with genomewide sequencing, use of such techniques throughout the geographic range of these corals may help settle their phylogeny.
传统分类学与分子系统学之间的不一致使得许多物种的界定尚未解决。造礁珊瑚也不例外，表型可塑性是对不同形态物种最合理的解释之一。作为表型可塑性的潜在分子特征，表观遗传过程可能有助于我们理解形态物种。我们比较了加勒比地区分支鹿角珊瑚属物种的遗传和表观遗传变异，检验了这样一个假设：表观遗传学——具体来说，DNA甲基化的差异模式——在一个分类地位受到质疑的群体的不同形态类型中发挥作用。我们使用简化基因组测序分析了来自伯利兹各种栖息地、呈现一系列形态类型的27个鹿角珊瑚属样本中的1000多个单核苷酸多态性和CpG位点。我们发现了更强的遗传结构而非表观遗传结构的证据，确定了三个明确的遗传群体。其中一个群体的分支明显更粗，分支粗细比深度、栖息地或共生体类型更能预测遗传群体。相比之下，在表型或栖息地变量方面没有出现明显的表观遗传模式。虽然成对的遗传距离和表观遗传距离之间存在微弱的正相关，但两对假定的克隆显示出显著的表观遗传差异，表明环境影响很大。我们推测表观遗传模式是一个复杂的镶嵌体，反映了叠加在相对较小的可遗传成分上的多样环境历史。鉴于遗传学在我们通过全基因组测序能够检测到的分支鹿角珊瑚属形态物种中的作用，在这些珊瑚的整个地理范围内使用此类技术可能有助于确定它们的系统发育。
