Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans.
Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans.
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DOI：
10.1371/journal.pone.0148847
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Ishitani Y
中科院分区：
文献类型：
--
作者：
Ujiié Y;Ishitani Y
对环境变化的生态适应是进化的强大驱动力，使远洋浮游生物能够在不存在基因流动的有效物理障碍的情况下形成物种。热带海洋环境在塑造海洋生物多样性方面发挥着重要作用，自上新世以来，热带海洋环境发生了剧烈而频繁的变化。然而，人们对热带中上层浮游生物的进化历史知之甚少，因为系统发育地理学研究仍处于发展阶段，古生物学方法不足以从深海沉积物中获得连续记录。浮游有孔虫 Pulleniatina obliquiloculata 广泛分布于世界各大洋的热带地区，其系统发育地理学十分成熟。因此，它是研究过去的环境变化如何改变热带浮游生物的空间分布并影响其多样化的最佳候选者之一。这样的检查需要浮游有孔虫的分化历史，但以前用于系统发育地理学研究的基因标记（部分小亚基（SSU）rDNA）不足以实现估计分化时间的高精度。本研究的重点是通过增加基因数量以及用于分子钟估计的核苷酸碱基数量来提高浮游有孔虫兄弟物种（遗传类型）之间分裂的分歧时间估计的精度。我们首次扩增了斜叶螟3个遗传类型和两个密切相关物种的两个核糖体RNA基因（SSU rDNA和大亚基（LSU）rDNA）的整个编码区，并将其应用于贝叶斯松弛时钟方法。由部分 SSU rDNA、完整 SSU rDNA、LSU rDNA 或两个基因组合 (SSU+LSU) 序列组成的四个数据集的可信区间的比较清楚地表明，双基因数据集提高了分歧时间估计的准确性。 P. obliquiloculata 谱系分裂了两次，第一次是在上新世末期（3.1Ma），第二次是在更新世中期（1.4Ma）。这两个时间点都与环境变化同时发生，这间接涉及了人口的地理分离。在稳定的温暖时期，P. obliquiloculata 的栖息地向高纬度地区扩展，随后在全球变冷后置于陡峭的环境梯度上。稳定的暖热带和不稳定的高纬度地区的不同环境条件可能引发了种群之间的生态分化，导致适应性分化并最终形成物种。对分歧时间估计与系统发育地理学的综合分析使我们能够揭示中上层浮游生物的进化历史，并发现可能改变其生物地理学和生态学的潜在古环境事件。
Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world’s oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology.