Data from: ALG11 – a new variable DNA marker for sponge phylogeny: comparison of phylogenetic performances with the 18S rDNA and the COI gene

Phylogenetic relationships within sponge classes are highly debated. The
low phylogenetic signal observed with some current molecular data can be
attributed to the use of few markers, usually slowly-evolving, such as the
nuclear rDNA genes and the mitochondrial COI gene. In this study, we
conducted a bioinformatics search for a new molecular marker. We sought a
marker that (1) is likely to have no paralogs; (2) evolves under a fast
evolutionary rate; (3) is part of a continuous exonic region; and (4) is
flanked by conserved regions. Our search suggested the nuclear ALG11 as a
potential suitable marker. We next demonstrated that this marker can
indeed be used for solving phylogenetic relationships within sponges.
Specifically, we successfully amplified the ALG11 gene from DNA samples of
representatives from all four sponge classes as well as from several
cnidarian classes. We also amplified the 18S rDNA and the COI gene for
these species. Finally, we analyzed the phylogenetic performance of ALG11
to solve sponge relationships compared to and in combination with the
nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker
seems to be superior to the widely-used COI marker. Our work thus
indicates that the ALG11 marker is a relevant marker which can complement
and corroborate the phylogenetic inferences observed with nuclear
ribosomal genes. This marker is also expected to contribute to resolving
evolutionary relationships of other apparently slow-evolving animal phyla,
such as cnidarians.

海绵纲内的系统发育关系存在广泛争议。
目前部分分子数据呈现的低系统发育信号，可归因于所用标记物数量有限——通常为核rDNA基因、线粒体COI基因等进化速率缓慢的标记。
本研究通过生物信息学方法筛选新型分子标记，目标标记需满足以下条件：（1）无旁系同源物（paralogs）可能性高；（2）进化速率较快；（3）属于连续外显子区域（exonic region）；（4）两侧为保守区域（conserved regions）。
搜索结果显示，核基因ALG11是潜在的合适标记。
随后，我们验证了该标记确实可用于解析海绵类群的系统发育关系：具体而言，成功从四大海绵纲代表物种及若干刺胞动物纲物种的DNA样本中扩增出ALG11基因，同时也对这些物种的18S rDNA与COI基因进行了扩增。
最后，我们分析了ALG11标记单独使用、以及与核18S rDNA和线粒体COI基因组合使用时，在解析海绵系统发育关系中的表现。
值得注意的是，ALG11标记的表现似乎优于广泛应用的COI标记。
综上，本研究表明ALG11标记是一种具有重要价值的分子标记，可补充并验证核核糖体基因所推导的系统发育结论；此外，该标记有望助力解析刺胞动物门等其他进化速率明显较慢的动物类群的系统发育关系。