Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans
Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans
复制标题
序列捕获和 ddRAD 方法在解析六珊瑚动物物种和种群方面的比较
DOI：
10.1016/j.ympev.2021.107233
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发表时间：
2021
影响因子：
4.1
通讯作者：
Daly, Marymegan
中科院分区：
文献类型：
--
作者：
Glon, Heather;Quattrini, Andrea;Rodríguez, Estefanía;Titus, Benjamin M.;Daly, Marymegan
基因组水平的测序是了解珊瑚虫(软珊瑚、海葵、石珊瑚及其近亲)物种水平关系的下一步，因为形态和聚合酶链式反应(单基因座)测序方法往往不能区分物种。海葵属(Metridium)是一种常见的北方温带海葵，仅凭形态很难区分其种类。在这里，我们以绿僵菌为例，证实了猕猴桃属常见的6个基因座在物种分化方面的低水平信息，并探索和比较了ddRAD和序列捕获方法在物种水平系统学和生物地理学研究中的有效性。我们从串联的数据集生成系统发育树，并使用SNP数据进行DAPC和结构分析。传统的6个基因座不能一致地区分Metridium内的物种。序列捕获数据集对当前物种和地理区域之间的关系都有很高的支持和分辨率。DdRAD数据集在物种之间表现出模糊性，主要地理分组之间的支持率没有序列捕获数据集那么高。序列捕获数据所产生的分辨率和支持水平，再加上随着时间的推移增加更多的个体和扩展到Metridia属之外的能力，强调了序列捕获方法在珊瑚虫内的系统学和未来的生物地理研究中的实用性。根据我们的发现，我们讨论了基因组方法的优点和缺点，并根据我们的采样提出了对Metridium生物地理学的潜在影响。
Genome-level sequencing is the next step in understanding species-level relationships within Anthozoa (soft corals, anemones, stony corals, and their kin) as morphological and PCR-directed (single-locus) sequencing methods often fall short of differentiating species. The sea anemone genusMetridiumis a common northern temperate sea anemone whose species are difficult to differentiate using morphology alone. Here we useMetridiumas a case study to confirm the low level of information available in six loci for species differentiation commonly sequenced for Actiniaria and explore and compare the efficacy of ddRAD and sequence-capture methods in species-level systematics and biogeographic studies. We produce phylogenetic trees from concatenated datasets and perform DAPC and STRUCTURE analyses using SNP data. The six conventional loci are not able to consistently differentiate species withinMetridium. The sequence-capture dataset resulted in high support and resolution for both current species and relationships between geographic areas. The ddRAD datasets displayed ambiguity among species, and support between major geographic groupings was not as high as the sequence-capture datasets. The level of resolution and support resulting from the sequence-capture data, combined with the ability to add additional individuals and expand beyond the genusMetridiumover time, emphasizes the utility of sequence-capture methods for both systematics and future biogeographic studies within anthozoans. We discuss the strengths and weaknesses of the genomic approaches in light of our findings and suggest potential implications for the biogeography ofMetridiumbased on our sampling.