人类对于自然的认识来源于命名自然界物质的能力，这也是我们组织生物知识的能力的核心。无论是涉及物种分类，还是基因组中的基因及其编码的蛋白质，准确和精确的术语对于理解生物化学、细胞和生理途径以及推断生态学和进化的基本过程都至关重要。
Human understanding of nature derives from the ability to name the substances in the nature, which is central to our ability to organize biological knowledge. Whether it concerns species classification or the genes in a genome and the proteins they encode, accurate and precise terms are essential for understanding biochemical, cellular and physiological pathways and for inferring the fundamental processes of ecology and evolution.
随着测序技术的发展以及基因数据的累计，识别、鉴定微型真核生物物种的方法也越来越成熟。事实上，随着对共生物种的关注，珊瑚-虫黄藻共生类研究已经取得较大的突破。这些突破目前主要来源于珊瑚-虫黄藻的基于系统发育、种群遗传、生态学的一致性以及形态学类研究。这些研究也为建立正式的珊瑚共生虫黄藻的分类以及物种名称提供了理论基础。2018年，Todd LaJeunesse教授对于虫黄藻分类的系统性修订研究使得科学界对虫黄藻多样性及其与动物宿主的各种生态相互作用和进化历史的研究得到复兴(LaJeunesse et al., 2018)。虽然目前虫黄藻已经有11个属，并且更多未知的属还在计数，但目前还没有统一完备的虫黄藻物种分类法来帮助区分不同虫黄藻物种，阻碍了对虫黄藻的进一步研究，特别是关于珊瑚-甲藻共生体系应对海洋变暖的研究。
With the development of sequencing technologies and the accumulation of genetic data, methods to identify micro-eukaryotic species are becoming more sophisticated. In fact, with the focus on symbiotic species, breakthroughs have been made in the study of coral-zooxanthella symbiont. These breakthroughs are now mainly derived from the studies of phylogenetic features, population genetic features, ecological congruence, and morphological features of coral-zooxanthella symbiont. These studies have also provided the theoretical basis for the establishment of a formal taxonomy of coral-zooxanthella symbiont as well as the species’ name. In 2018, Professor Todd LaJeunesse’s systematic study of the taxonomy of zooxanthella led to a revival of scientific research on its diversity, its various ecological interactions with host animals and its evolutionary history (LaJeunesse et al, 2018). Although there are currently 11 genera of zooxanthellae and more unknown genera are still being counted, there is no uniform and complete taxonomy of zooxanthellae to help distinguish between different zooxanthella species, hindering further research on zooxanthellae, especially on coral-dinoflagellate symbiotic systems in response to marine warming.
与几十年前相比，通过获取信息丰富的遗传数据，现在识别物种的模糊性要小得多。直到最近，自然历史学家还缺乏这些事实所提供的洞察力。DNA序列的使用使分类学和系统学的过程更加客观和可验证。此外，引入遗传信息能够帮助鉴定在形态学上分类困难的生物，特别是对于微生物的鉴定和研究方面尤为重要。虫黄藻作为在许多无脊椎动物和原生生物宿主中发现的微小的黄棕色光合共生细胞也属于在形态学中难以区分的情况，它们曾经被认为是单一物种。目前，科学家对虫黄藻多年来的研究已经获得了大量的遗传信息，同时发表了数十篇研究论文；然而，由于学界没有就虫黄藻正式的分类达成一致，对珊瑚-虫黄藻共生生态和进化的研究中共生现象的描述差异很大，阻碍了科学进步。因此目前虫黄藻研究重点再次转向分类学研究。
With access to rich genetic data, there is now much less ambiguity in identifying species than there was decades ago. Until recently, natural historians lack the insight provided by these facts. The use of DNA sequences has made the process of taxonomy and systematics more objective and verifiable. In addition, the introduction of genetic information can aid the identification of organisms that are morphologically difficult to classify and can be particularly important in the identification and study of microorganisms. The zooxanthella, as tiny yellow-brown photosynthetic symbiotic cells found in many invertebrate and protist hosts, also falls into the morphologically indistinguishable category, and they were once considered to be a single species. Scientists, having studied the zooxanthella for many years, have obtained a wealth of genetic information and have published dozens of research papers; however, scientific progress has been hampered by the lack of agreement in the academic community on a formal taxonomy for the zooxanthella and the wide variation in the description of symbiotic phenomenon in studies of the ecology and evolution of coral-zooxanthella symbiosis. As a result, the focus of current research on zooxanthella has shifted once again to taxonomy.
Todd LaJeunesse教授课题组最近在ISME J上发表的新的研究论文。在二十年的研究中，收集了跨越印度洋和太平洋的 Pocillopora 属分支珊瑚的样本集。使用这些样本，描述了Cladocopium pacificum 和 Cladocopium latusorum两种珊瑚共生藻类（图1）。它们海洋中地理分布上始终与不同的 Pocillopora 物种相关联。这种特殊性对珊瑚保护工作以及研究珊瑚-虫黄藻应对气候持续变暖具有重大意义(Turnham et al., 2021)。
A new research paper by Prof. Todd LaJeunesse’s team has recently published in ISME J. A sample set of branching corals of the genus Pocillopora has been collected across the Indian and Pacific Oceans over the past two decades to describe Cladocopium pacificum and Cladocopium latusorum. They are consistently associated with different Pocillopora species in their geographic distribution in the ocean, which is a specificity that has significant implications for coral conservation efforts and for the study of coral-zooxanthella responses to continued climate warming (Turnham et al., 2021).
微生物极少有化石记录，因此很难准确推断它们的进化历史和进程。科学家可以通过生物的地理位置，结合历史中相应的地质事件来校准DNA序列变化的速率。基于该方法，Turnham等研究了两个滨珊瑚属的兄弟物种的进化历程，它们可能在巴拿马地峡形成大约 3-500 万年后开始从一个共同的祖先分化，自此其中一个在东太平洋进化，另一个在加勒比海进化。同时它们的Cladocopium共生体也具有遗传上紧密的联系。 基于这些信息计算了大约 2-3 Mya 的 C. pacificum 和 C. latusorum的遗传分歧时间，并通过Porites共生体校准。结果表明，这个时间对应于Pocillopora在多样化和新物种形成的时间，表明了宿主和共生物种的进化可能同时发生。重要的一点是，该研究表明尽管已知更新世的全球温度发生了重大波动，但珊瑚共生（包括Pocillopora和Porites）已经进化，并且在地质时间尺度上保持了特定的伙伴关系(Turnham et al., 2021)。
Microorganisms are rarely recorded in the form of fossil, making it difficult to accurately infer their evolutionary history and processes. Scientists can calibrate the rate of DNA sequence change by the geographic location of organisms in conjunction with corresponding geological events in history. Based on this approach, Turnham and other researchers study the evolutionary history of two sibling species of Porites which probably began to diverge from a common ancestor about 3-5 million years after the formation of the Isthmus of Panama, and since then one of them evolved in the eastern Pacific Ocean and the other in the Caribbean. And their Cladocopium symbionts are genetically closely related. Based on this information, the time of genetic divergence between C. pacificum and C. latusorum was calculated for approximately 2-3 Mya and was calibrated by Porites symbiosis. The results suggest that this time corresponds to the time of Pocillopora in diversification and new species formation, indicating that the evolution of host and symbiotic species may have occurred simultaneously. Importantly, this study shows that coral symbioses (both Pocillopora and Porites) have evolved and maintained specific partnerships on geological time scales despite major fluctuations in global temperature during the known Pleistocene (Turnham et al., 2021).
目前尚还有数百种未表征的共生甲藻（虫黄藻），每种都有自己独特的进化历史、地理分布以及生理特点和生态功能。它们作为内共生体的重要性是无可争议的，但由于目前的研究尚缺乏对这类物种的充分表征和命名，科学家对它们的理解仍然模糊不清。在接下来的几年里，随着测序技术的发展和分类学的进一步利用，这些共生关系将进一步被科学家揭示。
There are still hundreds of unidentified symbiotic dinoflagellates (zooxanthellae), and each has its own unique evolutionary history, geographic distribution and physiological characteristics and ecological functions. Their importance as endosymbionts is undisputed, but scientists’ understanding of such species remains ambiguous due to the lack of adequate characterization and naming of such species in current studies. In the next few years, these symbiotic relationships will be further revealed by scientists with the development of sequencing technologies and the further use of taxonomy.
参考文献
LaJeunesse, T. C., Parkinson, J. E., Gabrielson, P. W., Jeong, H. J., Reimer, J. D., Voolstra, C. R., & Santos, S. R. (2018). Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts. Current Biology: CB, 28(16), 2570–2580.e6. https://doi.org/10.1016/j.cub.2018.07.008
Turnham, K. E., Wham, D. C., Sampayo, E., & LaJeunesse, T. C. (2021). Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development. The ISME Journal. https://doi.org/10.1038/s41396-021-01007-8
公众号