High-efficiency 18S microalgae barcoding by coalescent,distance and character-based approaches: a test in Chlorella and Scenedesmus

The relatively conserved 18S is often used in the phylogenetic analysis of microalgae. However, whether it can really help in barcoding microalgae needs to be evaluated. In this study the multiple approaches of coalescent, distance and character-based barcoding are first employed in C hlorella and Scenedesmus to test the efficiency of 18S sequences for barcoding green microalgae. We show that most Chlorella and Scenedesmus species, including the cryptic species, can be distinguished by 18S sequences with all coalescent General Mixed Yule-coalescent(GMYC), poisson tree process(PTP), and P ID, distance(ABGD) and character-based approaches. Both GMYC and PTP analyses produce more genetic groups. The P ID and ABGD analyses only cluster some species. All species(apart from a few of lineages) can be separated in character-based barcoding analysis with more than three character attributes. In comparison with previous barcoding results with r bcL, tufA, ITS and 16 S, 18S produces good resolution in identifying Chlorella and Scenedesmus. Our results reveal that 18S is highly efficient in identifying taxa of green microalgae at species level, based on a combination of multiple barcoding approaches. Combining 18S with other gene markers may be useful in barcoding microalgae.

基于DNA条形码的物种界定算法比较研究——以北京周边地区舟蛾科为例

[目的]为了探究3种常用物种界定方法(jMOTU、ABGD、GMYC)的界定效果。[方法]本研究以中国北京周边地区10个采样点483个舟蛾科样品为例,利用线粒体细胞色素C氧化酶Ⅰ亚基基因(Cytochrome c oxidase subunitⅠgene,COⅠ或COX1,约650 bp)的部分序列,进行3种物种界定算法(jMOTU、ABGD、GMYC)的实例比较研究。[结果]3种物种界定方法的鉴定效力存在差异,与形态学结果相比较,ABGD方法划分物种的准确率为100%,基于BEAST的GMYC模型结果与形态学结果一致,产生的置信区间(64~68)覆盖了形态学的结果(67)。然而,基于d8tree/MPLtree的GMYC方法倾向于高估MOTUs,jMOTU方法倾向于低估物种数目。[结论]结果显示,ABGD方法和基于BEAST的GMYC模型方法对于本文研究对象舟蛾科能够较好地划分,可以对基于形态学的物种界定进行有效补充。

太平洋西部鳓鱼隐蔽种的界定及系统发育关系重建

鳓鱼(Ilisha elongata)属于鲱形目(Clupeiformes),是锯腹鳓科的鱼类之一,鳓鱼目前在世界上主要分布在太平洋西部和沙捞越爪哇海海域。本研究报道了来自丹东和烟台的鳓鱼完整的线粒体基因组序列。线粒体基因组长度为16809 bp,包括13个蛋白编码基因、22个tRNA、2个rRNA、12S rRNA、16S rRNA和控制区D-loop基因。本研究还对上述2个地点的6尾鳓鱼,利用完整的线粒体基因组以及非洲鳓作为外群重建了系统发育关系。结果显示,来自丹东和烟台的鳓鱼群体分成两个姊妹关系的单系群。用物种界定的方法(基于BEAST的GMYC模型)对丹东鳓鱼群体有较好的划分,研究显示丹东鳓鱼群体是太平洋西部的隐蔽种。由此推断,丹东鳓鱼群体隐蔽种的形成很可能是更新世冰期海平面下降产生了地理隔离以及后续长时间的基因交流障碍的结果。