The contraction-expansion model (CEM) describes the dynamics of species that survived in refugia during the last glacial maximum (LGM) and expanded their range when environmental conditions slowly improved from the Late Glacial through to the Holocene. The CEM has been proposed to describe the dynamics of reef species in response to sea-level fluctuations from a range of disciplines, but genetic inferences rather suggest stable population sizes since the last glacial period. Here, we address this paradox by providing a new model of modern reef development, by assessing the effect of LGM bottlenecks using genetic simulations, and by using a survey of the literature on reef species to compile both estimates of times to expansion and applied rates of molecular evolution. Using previously published radiocarbon dates of core data, we propose a synthetic model for the dynamics of modern coral reefs in the Indo-Pacific region. This model describes both an initiation at 9.9 ka and subsequent development that confirms a strong influence of sea-level fluctuations on reef dynamics. Simulations based on mtDNA datasets showed that pre-LGM genetic signatures of expansion are lost. Recent literature shows that, although genetic expansions of tropical marine species are frequent (>95%), the onset of these expansions is old (median ~110 ka), which indicates that most populations have remained stable since before the LGM. These pre-LGM expansions are explained by the low mutation rates (1.66% changes/site/Myr) known to be inadequate to calibrate time at population level. Specific calibrations should help solve the paradox and generalise the CEM for reef species.

中文翻译：

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珊瑚礁物种对海平面变化的收缩-膨胀动力学

收缩-扩展模型（CEM）描述了在最后一次冰期最大值（LGM）期间在避难所中幸存的物种的动态，并且当环境条件从晚冰川期到全新世逐渐改善时，它们的范围扩大了。已经提出了CEM来描述各种学科对海平面波动的响应，礁石物种的动态，但是遗传推论反而表明自上个冰期以来种群数量稳定。在这里，我们通过提供一种新的现代珊瑚礁发展模型，通过使用遗传模拟评估LGM瓶颈的影响以及使用有关珊瑚礁物种的文献调查来编制该物种的扩张时间和应用率的估计，来解决这一矛盾。分子进化。使用以前发布的核心数据的放射性碳数据，我们为印度太平洋地区现代珊瑚礁的动力学提出了一个综合模型。该模型描述了在9.9 ka时的开始和随后的发展，证实了海平面涨落对礁石动力学的强烈影响。基于mtDNA数据集的模拟显示，LGM之前的遗传遗传签名已丢失。最近的文献表明，尽管热带海洋物种的遗传扩展很频繁（> 95％），但这些扩展的发生时间较早（中值约为110 ka），这表明自LGM以来，大多数种群一直保持稳定。这些LGM前的扩增是由低突变率（每个位点/ Myr的变化为1.66％）解释的，该突变率不足以在人群水平上校准时间。特定的校准应有助于解决这一矛盾，并使珊瑚礁物种的CEM普遍化。